# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln1.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln1.fa

LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGG-aaCAc-
LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGG-aaUA-U
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGG-aaUG-U
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<..>>>>>>>...<<.<<<<<<<...<<.<

LYC.ES-J      UGGGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCAaG
TRI.AE-B      uGGUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCCAaG
ARA.TH-E      UGGuUCGGgUCcaCGGGCC-GGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCCAaG
LYC.ES-E      UGGGCuGUcCCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAaG
LYC.ES-N      UGGGCuGUaCCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUCCAaG
#=GC SS_cons  <<<<<.<<.<<....<<<..<<<<<<<<...<<<.<.....<<<<<<<<.<<..<<<<.<

LYC.ES-J      CACAGAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAG-uGGG
TRI.AE-B      UUGGuAGU-gGgCUGGGuGGcUGGGGCgaaaGCUUCGcCUuCUCAGgC-CUuaAG-uGGC
ARA.TH-E      CUGUGAGU-AAGaCGUgUGuGUCAAGCgaagGCUUGGCuCAaACGgCUUCUaaAGuuGGA
LYC.ES-E      UACAGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAG-uGGG
LYC.ES-N      CUUAGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg-uGGG
#=GC SS_cons  <<<<<<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>>>><<..>>..<<<

LYC.ES-J      GCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAa
TRI.AE-B      AGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAACggUGGAA
ARA.TH-E      GGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUGGAC
LYC.ES-E      GUggacc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAa
LYC.ES-N      gCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAa
#=GC SS_cons  <<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.

LYC.ES-J      GGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCCUaaUGG-GuuGCU-cCAA-U
TRI.AE-B      GGauaaCAGGCCGcuG-cAgcAUGGGCCCgcuc-uGGGCCucCuA--CCcCGCcaU-AGC
ARA.TH-E      GGaucaCAGUUUAGcg-UCGcuCAGAACCacu--auGGCCUGcuGGuCCGAuC-uCAuaU
LYC.ES-E      GGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-GCuGUU-cUAGuU
LYC.ES-N      GGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCCugaUGG-GUuGCU-cCAAuU
#=GC SS_cons  >>....>>>>>>>>.>.>>>.>>>>>>>>........>>>....>>.>>.>>>..>>>.>

LYC.ES-J      AaaCAACCACcUUu-
TRI.AE-B      AgacCACCaUCUUu-
ARA.TH-E      GaaCCACCAUUUu--
LYC.ES-E      AaaCUACCACaUUuu
LYC.ES-N      AaaCCACCAUuUUu-
#=GC SS_cons  >..>>>>>>>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln2.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln2.fa

LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGG-aaUA-U
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGG-aaUG-U
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGG-aaUG-U
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>....<.<<<<.<<...<<.<

LYC.ES-O      UG-GGCuGUcCCAgauGGCu-GGGCUUGG-uGGGcUA-auuuCUGGcCUGcCCuaUCCAa
LYC.ES-N      UG-GGCuGUaCCAgauGGUu-GGGCUUGG-uGGGcUA-auuuCUGACUUGcCCuaUCCAa
ZEA.MA-H      aauugu-ggu-gcaugugccuGGGUCUA-guGCuacA-aacuGUGGacCAcCCaUUCCAa
CIN.HYB.      UGaGCUuGgcUUAGcuaguu-GGGUCUGu-aGACACc-gcacCUGGCUUGcCCgUUCCAA
LYC.ES-F      UG-GGUccauCUugauGGaU-GGGCUUGA-aGGGcUAauguuCUGGCCUGcCCugUCCAa
#=GC SS_cons  <<.<<<....<<.........<<<<<<<...<<<.<<.....<<<<.<<<.<<..<<<<.

LYC.ES-O      GCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAG-u
LYC.ES-N      GCUU-AGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg-u
ZEA.MA-H      GUUGcGUaGU-ggGUUucGGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAG-u
CIN.HYB.      GUCG-AGAGugGGUUCA-UGUUuCCUGAGCgaagGCUCGGGuGAUGUGAGCUUUagAAuc
LYC.ES-F      GCAC-AGAGUuGGGUCA-AGUGGuCUAUACgaaaGUAUAG-CCACUUGGCCUUUagAG-u
#=GC SS_cons  <<<<.<<<<<.<<<<<...<<<<.<<<.<<....>>.>>>.>>>>..>>>>><<..>>..

LYC.ES-O      GGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUG
LYC.ES-N      GGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUG
ZEA.MA-H      GGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcGCcACCAGCggUG
CIN.HYB.      GGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCUacCUCUCGACUgUG
LYC.ES-F      GGGAUggacugCGUgaggCUGguuucaCAGagcaACGacuaGUCCCcGCUCUGUGCagUG
#=GC SS_cons  <<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>

LYC.ES-O      GAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGGGCuGCUcCAAu
LYC.ES-N      GAaGGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCCugaUGGGUuGCUcCAAu
ZEA.MA-H      GAAGGauaaUGagUCGCUa-uGCuaUAGGCCCaau-------------------------
CIN.HYB.      GAAGGauuaCAAGCCGGaGUGUC-uUAGGCUC-auauaaccag-cCUGG-CuAGCcCAAc
LYC.ES-F      GAaGGaucaCGGGCUAGUGcUCU-UUGAGUCCuaacaaaAaCCugauAGguuGCC-UAAu
#=GC SS_cons  >>.>>....>>>.>>>>>>.>>>..>>>>>>>...............>>...>>>.>>>.

LYC.ES-O      UAaaCCACCACUUU-
LYC.ES-N      UAaaCCACCAUuUUu
ZEA.MA-H      ---------------
CIN.HYB.      AGgaCAcCCAUUU--
LYC.ES-F      UAaaCCAUCACuUUu
#=GC SS_cons  >>..>>.>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln3.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln3.fa

LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG--aaUG-
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG--aaUA-
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG--aaUG-
ORY.SA-B      GCCGAGCCAGguagcgUUGGCUUgucaCCCGagCGGGGGCaauAAGGUGGUGuuggaUGC
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG--aaUA-
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<....<<.

LYC.ES-I      UUG---GGCuGUaCCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUC
LYC.ES-K      UUG---GGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUC
LYC.ES-B      UUG---GGCuGUaCCAgauGGUu-GGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUC
ORY.SA-B      CugGucGuuuGCg-CUUGgGGUCuGcGCCuGugguUUGcac-uauGCGGCCCGcCCgUUC
LYC.ES-J      UUG---GGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUC
#=GC SS_cons  <<<...<<<..<.<<<...<<<..<<<<<<<<...<<<.<.....<<<<<<<<.<<..<<

LYC.ES-I      CAaGCUU-AGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACu-UGAUUCgUaaA
LYC.ES-K      CAaGCAC-AGAGUaGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUCCUaaA
LYC.ES-B      CAaGCUU-AGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACu-UGAUUCgUaaA
ORY.SA-B      CAaGUUGcGuAGCguGUGUGGGGCGCcUGGGCgaagGCUCGaGCGUCCcUGCAC-CUagA
LYC.ES-J      CAaGCAC-AGAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUCCUaaA
#=GC SS_cons  <<.<<<<.<<<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>..>>>>>>.<..>

LYC.ES-I      guGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCgg
LYC.ES-K      GcGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
LYC.ES-B      guGGGGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCgg
ORY.SA-B      GuGGCGGguauugCGUgaggCUGguuucaCAGagcaGCGaguaCCGCCcGCUuCCAACgg
LYC.ES-J      GuGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
#=GC SS_cons  ..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..

LYC.ES-I      UGGAaGGauaaCGAGUCGGUGuUCU--CUGAGUCC-ag-uaacGCCugaUGGGUuGCUcC
LYC.ES-K      UGGAaGGauaaUGGGUCGGuGuCUUA-UCAAGUUC-ag-uaacGCCUaaUGGGuuGCUcC
LYC.ES-B      UGGAaGGauaaCGAGUCGGUG-UUC-uCUGAGUCCagu--aauGCCugaUGGGCuGCUcU
ORY.SA-B      UGGAAGGauaaCGGGCCGCug-CAGc-cCuGGCcCgcuu-ccGGCC-CAAGuGCcuuCCa
LYC.ES-J      UGGAaGGauaaUGGGUCGGuGuCUUA-UCAAGUUC-ag-uaacGCCUaaUGGGuuGCUcC
#=GC SS_cons  >>>>.>>....>>>>>>>>.>.>>>..>>>>>>>>........>>>...>>>>..>>>.>

LYC.ES-I      AAuUAaaCCACCAUuUUu
LYC.ES-K      AA-UAaaCAACCACcUUu
LYC.ES-B      AAuUAaaCCACCACuUUu
ORY.SA-B      uGGCAgacCACCACCUUu
LYC.ES-J      AA-UAaaCAACCACcUUu
#=GC SS_cons  >>.>>..>>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln4.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln4.fa

ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
ZEA.MA-E      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUG-aaUA-U
ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaauAAGGUGGUGG-aaCAG-
ARA.TH-A      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAcU
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>....<<.<<<<<<....<...

ZEA.MA-H      aauugu-ggu--gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCA
ZEA.MA-E      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
LYC.ES-A      UG-GGCuuUa-CCAgaAGGUu-GGGCUUGGU--GGGcUuaguuCUGGCCUGcCCugUCCA
ARA.TH-D      uG-GuUCaAu-UCcuCGGGUC-GGAcCUGAugcuGAcaUauaucUGAGCUGcCCaGUCCA
ARA.TH-A      G--GUUcGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCA
#=GC SS_cons  .....<..<...<...<<.<..<<<<<<<.....<<........<<<<<<<.<<.<<<<<

ZEA.MA-H      aGUUGcGUaGU-ggGUUuc-GGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAG
ZEA.MA-E      aGUUG-GuAGU-GgCUGGc-GGAGGCUuuAGCggaaGCUuuGGUCUCUCCAGaCCUgaAG
LYC.ES-A      aGCAC-AGAGUuGGAUCu--cGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAG
ARA.TH-D      aGCUG-UGAGu-AAUCUG--UgUGGGUCAGGCgaagGCUUGACUCAgGCGGAUUCUaaAG
ARA.TH-A      aGCUG-UGAGU-AAUUaG-uguUGAGUUGAGCgaagGCUUGGCUCAugCaGGUUCUagAG
#=GC SS_cons  .<<<<.<<<<<.<.<<<.....<<<<<..<<<....>>>..>>>>>...>>>.><<..>>

ZEA.MA-H      -uGGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCC-GCCcGCcACCAGCg
ZEA.MA-E      -UGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCGGCUuCCAACg
LYC.ES-A      -uGGGGCGgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGC-UCCcGCUCUGUGCa
ARA.TH-D      ucGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCU-UCCcuCUUACAGCa
ARA.TH-A      ucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUACAGCa
#=GC SS_cons  ..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>>.

ZEA.MA-H      gUGGAAGGauaaUGagUCGCUauGCu-aUAGGCCCaau----------------------
ZEA.MA-E      gUGGGAGGauaaCGGGCCGcuGCACu-uCGAGCCCaacucaGGCCCAGAG--CC-UCaCu
LYC.ES-A      gUGGAaGGauaaUGGGUCGGuGUCUuAUCAAGUUCagu-aacGCCUaaUGG-GuuGCUcC
ARA.TH-D      gUGGAUGGaucaUAGUUCGaAgUCuc-UCAGaUCCacu-auGGCCCGcuGGuUcGAuCuC
ARA.TH-A      gUGGACGGaucaCGGUUUAGcgUCgc-UCAGAACCacu-auGGcCUGcuGG-UCcGAUcu
#=GC SS_cons  .>>>>>>>....>>>>>>>...>>....>>>>>>>.......>.>>...>..>..>....

ZEA.MA-H      -------------------
ZEA.MA-E      AA-GcAgacCACCAUCUUu
LYC.ES-A      AA--UAaaCAACCACcUUu
ARA.TH-D      uc-CUGgaCCACCACUUU-
ARA.TH-A      CAuaUGaaCCACCAUUUU-
#=GC SS_cons  .....>...>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln5.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln5.fa

CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUGaaCU-UU
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGGgaCAc-U
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUA-UU
HUM.LU-A      GCCGGuCUUAgcaacgUGGGcCUguaaCCCAagUGGGGGCauGuGGGAAAUGGgaCU-UU
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>....<.<<<<<<<..<<.<<

CIN.HYB.      GaGCUuGgcUUAGcuaguuGGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCAAGU
LYC.ES-B      G-GGCuGUaCCAgauGGUuGGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUCCAaGC
ARA.TH-F      G-GuUCGGuUCcuCGGaUCGGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCAaGC
LYC.ES-K      G-GGCuuUaCCAgaAGGUuGGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCAaGC
HUM.LU-A      G-GGUCAacCUAGUGGAuCGGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaGC
#=GC SS_cons  <.<<<.<..<<<...<...<<<<<<<<...<<<.<.....<<<<<<<<.<<..<<<<.<<

CIN.HYB.      CGAGAGugGGUUCA-UGUUuCCUGAGCgaagGCUCGGGuGAUGUGAGCUUUagAAu-cGG
LYC.ES-B      UUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg--uGG
ARA.TH-F      UGUGAGU-AAUUaguguUGAGUUGAGCgaagGCUUGGCUUGca--GGUUCUagAG-ucGG
LYC.ES-K      ACAGAGUaGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAG--cGG
HUM.LU-A      CGGGAGUuGGgcUG-aGUGACCUGGgCgaagGgCUGGGUUGCgCAcgUCCUagAG--uGG
#=GC SS_cons  <<<<<<<.<<<<<<..<<<<<<<<.<<....>>.>>>>>>>>.>>>>>><<..>>...<<

CIN.HYB.      GGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCUacCUCUCGACUgUGGA
LYC.ES-B      GGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggUGGA
ARA.TH-F      AGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUGGA
LYC.ES-K      GGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGA
HUM.LU-A      AGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGGA
#=GC SS_cons  <<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>

CIN.HYB.      AGGauuaCAAGCCGGaGUGUC--uUAGGCUC-auauaaccag-cCUGG--CuAGC-cCAA
LYC.ES-B      aGGauaaCGAGUCGGUG-UUC-uCUGAGUCCagu--aauGCCugaUGG-GCuGCU-cUAA
ARA.TH-F      CGGaucaCGGUUUAGcg-UCgc-UCAGAACCacu--auGGcCUGcuGGuCCGAuC-uCAu
LYC.ES-K      aGGauaaUGGGUCGGuGuCUUA-UCAAGUUC-ag-uaacGCCUaaUGG-GuuGCU-cCAA
HUM.LU-A      AGGauaaCGGGCCGGUG-CUAc-CUGGGUCCacc--auGcUUCACUAGgcUGACUcuUAA
#=GC SS_cons  .>>....>>>>>>>>.>.>>>..>>>>>>>>..........>...>>>..>.>>>..>>>

CIN.HYB.      cAGgaCAcCCAUUU--
LYC.ES-B      uUAaaCCACCACuUUu
ARA.TH-F      aUGaaCCACCAUUUU-
LYC.ES-K      -UAaaCAACCACcUUu
HUM.LU-A      uAGgaCCAUUUCUUuU
#=GC SS_cons  .>>..>>>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln6.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln6.fa

HUM.LU-B      ---GGcCUUAgcaacgUGGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaC-AU
HUM.JA-A      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAGAUGG-gacu-U
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGG-gaCG-U
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUg-aaU-AU
#=GC SS_cons  ...<<.<<<<......>>>>.>>....<<<<..>>>>.......<<<.<<.<....<..<

HUM.LU-B      UG-GGUCAGc-CCAGUGGauC-gGGuCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCA
HUM.JA-A      UG-GGUcaGc-cCAuUGGaUC-gGGUCCAGuguUAGcUGcuugCUGGUCUGcCCaUUCCA
ZEA.MA-B      uuGcGAuGGu--uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCA
ARA.TH-C      UG-GGUcGauCUcAUUGGGcC-GGgUUcGGguuGGGcUAuauucUGGCCCGcCCaUUCCA
LYC.ES-H      UG-GGCuGUa-CCAgauGGUu-GGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCCA
#=GC SS_cons  <<.<<<.<<....<.<<<..<..<<<<<<<...<<<.<<.....<<<<<<<.<<.<<<<<

HUM.LU-B      aGCCGGGAGUuGGGCUG-aGUGACCUGGGCgaagGCC-UGGGUUGCg-CAGCUCCUagAG
HUM.JA-A      aGCCGAGAGUuGGGCUG-UGUGAUCUgGGCgaagGCU-gGGGUCGCA-CAGCUCCUaaAG
ZEA.MA-B      aGUUGGuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacAG
ARA.TH-C      aGUUGGGAGUuGAGGCA-UGGGcUUCGAGCgaagGCU-CGGGuCUCA-UGUCUUCUagAG
LYC.ES-H      aGCuUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAa-UGGaCUACu-UGAUUCgUaaAg
#=GC SS_cons  .<<<<<<<<<.<<<<<<..<<<.<<<.<<<....>>>..>>>.>>>..>>>>>><<..>>

HUM.LU-B      uGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGacuaCC-UCCcGCUCCCGGCag
HUM.JA-A      aGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGaccaCC-UCCcGCUCUCGGCag
ZEA.MA-B      cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAACgg
ARA.TH-C      uGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCC-UCCcGCUCUUGACgg
LYC.ES-H      uGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGC-UCCcGCUCUGuGCag
#=GC SS_cons  .<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>>..

HUM.LU-B      UGGAAGGauaaCGGGCCGGUG-CUAcUUGGuCCa-cc--auGu-UCACUGGucCUGACUc
HUM.JA-A      UGGAAGGauaaCGGGUCGGUG-CUAcUUGGGCCa-cc--auGG-UCAcUGca-UgcACUc
ZEA.MA-B      UGGGAGGauaaCAAGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAGA---uCC-UCu-
ARA.TH-C      UGGAAGGauuaCGGGCCAuUG-CCU-UCcGAgCCcacu-auGaCCCAAUaAG--CcGCU-
LYC.ES-H      UGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG--GUuGCU-
#=GC SS_cons  >>>>>>>....>>>>>>>.>>.>>>.>>>>>>>........>..>>>.>....>>.>>>.

HUM.LU-B      uUAAUcGgaCCAUUUCCUuU
HUM.JA-A      uUAAucagaCCAUCUCUUuU
ZEA.MA-B      CuuAGCAaacCaCCAUCUUu
ARA.TH-C      cCGAuUGgaCCAUCaCUUU-
LYC.ES-H      cCAAUaAacaAcCacCUUUu
#=GC SS_cons  .>>>..>...>.>>.>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln7.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln7.fa

ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG--gaCAc
ORY.SA-B      GCCGAGCCAGguagcgUUGGCUUgucaCCCGagCGGGGGCaauAAGGUGGUGuuggaUGC
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGc-ggaUuC
ARA.TH-A      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG--gaCAc
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGG--aaUG-
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>...<<<<<<<<<.....<<.

ARA.TH-F      -UG---GuUCGGu-UCcuCGGaUC-GGUUCUGAugugGGcau-guuuCUGAGCUGcCCaG
ORY.SA-B      CugGucGuuuGCg--CUUGgGGUCuGcGCCuGugguUUGcac--uauGCGGCCCGcCCgU
ZEA.MA-D      UUuG--cGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCu-uuggcCGGCCUGcCCgU
ARA.TH-A      UG----GUUcGGu-UCcuCGGaUC-GGUUCUGAugugGGcau-guuuCUGAGCUGcCCaG
LYC.ES-F      UUG---GGUccau-CUugauGGaU-GGGCUUGA--aGGGcUAauguuCUGGCCUGcCCug
#=GC SS_cons  <<....<.<.<<...<..<.<.<<.<<<<<<<.....<<........<<<<<<<<.<<.<

ARA.TH-F      UCCAaGCUG-UGAGU-AAUUag-uguUGAGUUGAGCgaagGCUUGGCUUGca---GGUUC
ORY.SA-B      UCCAaGUUGcGuAGCguGUGUG--GGGCGCcUGGGCgaagGCUCGaGCGUCCcUGCAC-C
ZEA.MA-D      CCCAaGUUG-GuAGU-GgCUGGc-GGAGGCUuuAGCggaaGCUuuGGUCUCU-CCAGaCC
ARA.TH-A      UCCAaGCUG-UGAGU-AAUUaG-uguUGAGUUGAGCgaagGCUUGGCUCAug-CaGGUUC
LYC.ES-F      UCCAaGCAC-AGAGUuGGGUCA--AGUGGuCUAUACgaaaGUAUAG-CCACU-UGGCCUU
#=GC SS_cons  <<<<.<<<<.<.<<<.<<<<.<....<<<<<<<<<<....>>>>>>>>>>...>.>>>><

ARA.TH-F      UagAGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUA
ORY.SA-B      UagAG-uGGCGGguauugCGUgaggCUGguuucaCAGagcaGCGaguaCC-GCCcGCUuC
ZEA.MA-D      UgaAG-uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuC
ARA.TH-A      UagAGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUA
LYC.ES-F      UagAG-uGGGAUggacugCGUgaggCUGguuucaCAGagcaACGacuaGU-CCCcGCUCU
#=GC SS_cons  <..>>..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>

ARA.TH-F      CAGCagUGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcCUGcuGGuCC
ORY.SA-B      CAACggUGGAAGGauaaCGGGCCGCug-CAGccCuGGCcCgcuu-ccGGCC-CAAGu-GC
ZEA.MA-D      CAACggUGGGAGGauaaCAGGCCGcuG-CACuuCGAGCCCaacu-caGGCCCAGAG--CC
ARA.TH-A      CAGCagUGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcCUGcuGG-UC
LYC.ES-F      GUGCagUGGAaGGaucaCGGGCUAGUGcUCU-UUGAGUCCuaacaaaAaCCugauAG-gu
#=GC SS_cons  >>>>..>>>>>>>....>>>>>>>>...>>...>>>>>>>.......>>.>.>..>..>>

ARA.TH-F      GAuCuCAu-aUGaaCCACCAUUUU-
ORY.SA-B      cuuCCauG-GCAgacCACCACCUUu
ZEA.MA-D      -UCaCuAA-GcAgacCACCAUCUU-
ARA.TH-A      cGAUcuCAuaUGaaCCACCAUUUU-
LYC.ES-F      uGCC-UAA-uUAaaCCAUCACuUUu
#=GC SS_cons  .>.>..>>..>>...>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln8.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln8.fa

TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaCU-U
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>.....<.<<<<<<<...<<.<

TRI.AE-A      GuuGUA-Gcg-CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCAa
HUM.LU-C      UG-GGUCAacCCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCCAa
LYC.ES-J      UG-GGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCAa
LYC.ES-K      UG-GGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCAa
CIN.HYB.      UGaGCUuGgcUUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCAA
#=GC SS_cons  <<.<<<....<<<...<....<<<<<<<<...<<<.<.....<<<<<<<<.<<..<<<<.

TRI.AE-A      GUUGcGuAGU-gGACCGccUGGGGCUUAuGCgaaaGC-UGGGUCUCACGGUC-CAuaaUG
HUM.LU-C      GCCG-GGAGguGGGcUG--aGggaCcugGGCgaagGCUnnnGgngCgCA-CUCcU-agAc
LYC.ES-J      GCAC-AGAGUuGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCU-aaAG
LYC.ES-K      GCAC-AGAGUaGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCU-aaAG
CIN.HYB.      GUCG-AGAGugGGUUCA--UGUUuCCUGAGCgaagGCUCGGGuGAUGUGAGCUUU-agAA
#=GC SS_cons  <<<<.<<<<..<<<<<<...<<<.<<<<.<<....>>.>>>>.>>>.>>>>>><<...>>

TRI.AE-A      -uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcGCUuCCAACgg
HUM.LU-C      -uGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgCUCUCGGCag
LYC.ES-J      -uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
LYC.ES-K      -cGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
CIN.HYB.      ucGGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCUacCUCUCGACUg
#=GC SS_cons  ..<<<<<......<<<....<<<......>>>....>>>....>>>>>..>>>>>>>>..

TRI.AE-A      UGGAAGGauaaUGGGCCGcUG-CACuCCUAGGCCaau--uGGGCCuCGCAG---CcUAC-
HUM.LU-C      UGGAAGGauaaCGGgCcGGUG-CgccUUGagCCaaca--cuGuuC-aACUGGgcUGACUc
LYC.ES-J      UGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCC-UaaUGG-GuuGCU-
LYC.ES-K      UGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCC-UaaUGG-GuuGCU-
CIN.HYB.      UGGAAGGauuaCAAGCCGGaGUGUC-uUAGGCUC-auauaaccag--cCUGG--CuAGC-
#=GC SS_cons  >>>>.>>....>>>>>>>>.>.>>>.>>>>>>>>..........>....>>>....>>>.

TRI.AE-A      ucCAGCagacCAcC------
HUM.LU-C      uUAAuAGgaCCAUUUCUUuU
LYC.ES-J      cCAA-UAaaCAACCACcUUu
LYC.ES-K      cCAA-UAaaCAACCACcUUu
CIN.HYB.      cCAAcAGgaCAcCCAUUU--
#=GC SS_cons  .>>>.>>..>>>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln9.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln9.fa

LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACau-cAAAGugGuUg--aaU-
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaa-uaagguagugu-ggaug
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACau-uAAGAUGGUGG--gaCA
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACau-cAAaGUGGUUG--aaUA
ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>....<<.<..<.......<.

LYC.ES-H      AUUG----GGCuGUa-CCAgauGGUu-GGGCUUGG--UGGGcUAauuuCUGACUUGcCCu
ZEA.MA-H      ucaau---ugu-ggu--gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCa
ARA.TH-F      c-UG----GuUCGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCa
LYC.ES-K      -UUG----GGCuuUa-CCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCu
ORY.SA-A      uUUGgugUGGAuucuGAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCCg
#=GC SS_cons  ..<<....<.<.....<<....<.<..<<<<<<<....<<........<<<<<<<<.<<.

LYC.ES-H      aUCCAaGCuU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGGaCUACu-UGAUUC
ZEA.MA-H      UUCCAaGUUGcGUaGU-ggGUUuc-GGAUGcCuuGGCgaaaGCUuuG-CAUCC-cAACa-
ARA.TH-F      GUCCAaGCUG-UGAGU-AAUUag-uguUGAGUUGAGCgaagGCUUGGCUUGca---GGUU
LYC.ES-K      gUCCAaGCAC-AGAGUaGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUC
ORY.SA-A      UUCCAaGuUGcGuAGU-GGGccGG-aGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUCC
#=GC SS_cons  .<<<<.<<<<.<<<<<.<<<<.....<<<<.<...<<....>>...>.>>>>....>>>>

LYC.ES-H      ----gUaaAg-uGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcG
ZEA.MA-H      ----CUaaAG-uGGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcG
ARA.TH-F      ----CUagAGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcG
LYC.ES-K      ----CUaaAG-cGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcG
ORY.SA-A      ggccCUaaAG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcG
#=GC SS_cons  ....<<..>>..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>

LYC.ES-H      CUCUGuGCagUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUG
ZEA.MA-H      CcACCAGCggUGGAAGGauaaUGagUCGCUa-uGCuaUAGGCCCaau-------------
ARA.TH-F      CUUACAGCagUGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcCUGcuG
LYC.ES-K      CUCUGUGCagUGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCCUaaUG
ORY.SA-A      CUuCCAuCggUGGAAGGauaaCAGGCUGcuG-cACcuUGGgcccgcuu-cuGGCCCAGaG
#=GC SS_cons  >>>>>>>>..>>>>.>>....>>>>>>>>....>>..>>>>>>>........>.>....>

LYC.ES-H      G-GUuGCU-cCAAUaAacaAcCacCUUUu
ZEA.MA-H      -----------------------------
ARA.TH-F      GuCCGAuC-uCAuaUGaaCCACCAUUUU-
LYC.ES-K      G-GuuGCU-cCAA-UAaaCAACCACcUUu
ORY.SA-A      UC-ccUCUA-CAA-CAgaCcaCCAUCUUU
#=GC SS_cons  >....>.>..>>...>.....>..>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln10.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln10.fa

ZEA.MA-F      nCCGAGCUCUguagcgAGAGCUUguaaCCUaagcGGGGGcauuAAGGUGGUGuggaUGUU
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAc-
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUg-aaU-AU
TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGG-aaUG-U
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>....<<.<.<<<<....<<.<

ZEA.MA-F      UccUGAcGGa-UUCUGgGcCUGGGCUUGU-auGUGcCAcuggcCGGCCUGcCCgUUCCAa
ARA.TH-F      UG-GuUCGGuUCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCAa
LYC.ES-H      UG-GGCuGUaCCAgauGGUu-GGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCCAa
TRI.AE-A      GuuGUA-Gcg-CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCAa
LYC.ES-N      UG-GGCuGUaCCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUCCAa
#=GC SS_cons  <..<<<.<<..<<...<<<..<<<<<<<<...<<<.<<.....<<<<<<<.<<..<<<<.

ZEA.MA-F      GUUG-GuuGU-GgCUGGu--GGGG-CUCGGGCgaagGCCUGGGcCUCUUUAGaCCU-gaA
ARA.TH-F      GCUG-UGAGU-AAUUag--uguUGAGUUGAGCgaagGCUUGGCUUGca--GGUUCU-agA
LYC.ES-H      GCuU-AGAGUuGGAUCA---uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgU-aaA
TRI.AE-A      GUUGcGuAGU-gGACCGcc-UGGGGCUUAuGCgaaaGC-UGGGUCUCACGGUC-CAuaaU
LYC.ES-N      GCUU-AGAGUuGGAUCA---uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgU-aaA
#=GC SS_cons  <<<<.<.<<<.<<<<<<....<<<<.<<<.<<....>>.>>>.>>>>.>>>>>>.<...>

ZEA.MA-F      G-cGGCAGgcauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCuuCCAAC
ARA.TH-F      GucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUACAGC
LYC.ES-H      g-uGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGC-UCCcGCUCUGuGC
TRI.AE-A      G-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCU-GCCcGCUuCCAAC
LYC.ES-N      g-uGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG--UUUcGCUCUAAGC
#=GC SS_cons  ...<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>

ZEA.MA-F      ggUGGGAGGauaaCAGGCCGcUG-CAUuGCAAGCCCaacu-cGGuC--CAGAG--CC-UC
ARA.TH-F      agUGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcC-UGcuGGuCCGAu
LYC.ES-H      agUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCC-uaaUGG-GUuGC
TRI.AE-A      ggUGGAAGGauaaUGGGCCGcUG-CACuCCUAGGCCaau--uGGGCCuCGCAG---CcUA
LYC.ES-N      ggUGGAaGGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCC-ugaUGG-GUuGC
#=GC SS_cons  ..>>>>.>>....>>>>>>>.>>.>>>.>>>>>>>>........>>>....>>..>>.>>

ZEA.MA-F      AuuAAACAgacCACCAUCUUu
ARA.TH-F      CuCAuaUGaaCCACCAUUUU-
LYC.ES-H      UcCAAUaAacaAcCacCUUUu
TRI.AE-A      CucCAGCagacCAcC------
LYC.ES-N      UcCAAuUAaaCCACCAUuUUu
#=GC SS_cons  >..>>.>>...>>>>.>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln11.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln11.fa

LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGG-aaUA-U
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaCU-U
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
#=GC SS_cons  ..<<<<<<.<......>.>>>>>....<<<<..>>>>>......<<<<<<.<....<<.<

LYC.ES-O      UG-GGCuGUcCCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAa
HUM.LU-C      UG-GGUCAacCCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCCAa
TRI.AE-B      uG-GUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCCAa
ZEA.MA-B      uuGcGAuGGu-uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCAa
CIN.HYB.      UGaGCUuGgcUUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCAA
#=GC SS_cons  .<.<<<.<...<<<..<....<<<<<<<.....<<.<......<<<.<<<.<<.<<<<<.

LYC.ES-O      GCACAGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAa-UGGGCUACu-aGAUUCCUaaAG-
HUM.LU-C      GCCGGGAGguGGGcUG-aGggaCcugGGCgaagGCU-nnnGgngCg-CA-CUCcUagAc-
TRI.AE-B      GUUGGuAGU-gGgCUG-GGuGGcUGGGGCgaaaGCU-UCGcCUuCU-CAGgC-CUuaAG-
ZEA.MA-B      GUUGGuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacAG-
CIN.HYB.      GUCGAGAGugGGUUCA-UGUUuCCUGAGCgaagGCU-CGGGuGAUG-UGAGCUUUagAAu
#=GC SS_cons  <<<<<.<<..<<<<<...<.<.<<<.<<<....>>>..>>>.>.>...>>>>><<..>>.

LYC.ES-O      uGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaAC-UUCcGCUUUGUGCag
HUM.LU-C      uGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcgCUCUCGGCag
TRI.AE-B      uGGCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCU-GCC-GCUuCCAACgg
ZEA.MA-B      cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAACgg
CIN.HYB.      cGGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCC-UCUacCUCUCGACUg
#=GC SS_cons  .<<<<<......<<<....<<<......>>>....>>>....>>.>>>..>>.>>>>>..

LYC.ES-O      UGGAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG--GCuGCU-
HUM.LU-C      UGGAAGGauaaCGGgCcGGUG-CgccUUGagCCaaca--cuGuuCaACUGGg-cUGACUc
TRI.AE-B      UGGAAGGauaaCAGGCCGcuG-cAgcAUGGGCCCgcuc-uGGGCCucCuA---CCcCGCc
ZEA.MA-B      UGGGAGGauaaCAAGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAGA---uCC-UCu-
CIN.HYB.      UGGAAGGauuaCAAGCCGGaGUGUC-uUAGGCUC-auauaaccag-cCUGG---CuAGC-
#=GC SS_cons  >>>>>>>....>>>.>>>..>.>>...>>>>>>>..........>..>>>....>.>>>.

LYC.ES-O      cCAAuUAaaCCACCACUUU-
HUM.LU-C      uUAAuAGgaCCAUUUCUUuU
TRI.AE-B      aU-AGCAgacCACCaUCUUu
ZEA.MA-B      CuuAGCAaacCaCCAUCUUu
CIN.HYB.      cCAAcAGgaCAcCCAUUU--
#=GC SS_cons  .>.>.>>...>.>>>>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln12.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln12.fa

TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcau-uaaaguGaUGu-gaacG
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACau-cAAaGUGGUUG--aaUA
ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUau-caAAGUGGuUG--aaCU
ZEA.MA-G      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcau-uAAGGUGGUGc-ggaUu
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>......<.<<<<.<.....<<

TRI.AE-A      CUGuu---GUA-Gcg---CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCC
LYC.ES-K      -UUG----GGCuuUa--CCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCC
ORY.SA-A      uUUGgugUGGAuucu-GAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCC
CIN.HYB.      -UUGa---GCUuGgc--UUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCC
ZEA.MA-G      CUUuG---cGAuGGcu--UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCC
#=GC SS_cons  .<<.....<<<.......<<<.<<<<..<<<<<<<....<<<.<......<<<<<<<.<<

TRI.AE-A      gUUCCAaGUUGcGuAGU-gGACCGccUGGGGCUUAuGCgaaaGC-UGGGUCUCA-CGGUC
LYC.ES-K      ugUCCAaGCAC-AGAGUaGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUU
ORY.SA-A      gUUCCAaGuUGcGuAGU-GGGccGG-aGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUC
CIN.HYB.      gUUCCAAGUCG-AGAGugGGUUCA--UGUUuCCUGAGCgaagGCUCGGGuGAUG-UGAGC
ZEA.MA-G      gUCCCAaGUUG-GuAGU-GgCUGGc-GGAGGCUuuAGCggaaGCUuuGGUCUCU-CCAGa
#=GC SS_cons  .<<<<<.<<<<.<.<<<.<<<<<<...<<<<<<...<<....>>...>>>>>>..>>>>>

TRI.AE-A      -----CAuaaUG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCC
LYC.ES-K      C----CU-aaAG-cGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCC
ORY.SA-A      CggccCU-aaAG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCC
CIN.HYB.      U----UU-agAAucGGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCU
ZEA.MA-G      C----CU-gaAG-uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCC
#=GC SS_cons  >....<<...>>..<<<<<......<<<....<<<......>>>....>>>....>>>>>

TRI.AE-A      cGCUuCCAACggUGGAAGGauaaUGGGCCGcUG-CACuCCUAGGCCaau--uGGGCCuCG
LYC.ES-K      cGCUCUGUGCagUGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCC-Ua
ORY.SA-A      cGCUuCCAuCggUGGAAGGauaaCAGGCUGcuG-cACcuUGGgcccgcuu-cuGGCC-CA
CIN.HYB.      acCUCUCGACUgUGGAAGGauuaCAAGCCGGaGUGUC-uUAGGCUC-auauaaccag--c
ZEA.MA-G      cGCUuCCAACggUGGGAGGauaaCGGGCCGcuG-CACuuCGAGCCCaacu-caGGCC-CA
#=GC SS_cons  .>>>.>>>>>..>>>>>>>....>>>>>>>..>.>>>..>>>>>>>........>>>.>.

TRI.AE-A      CAG---CcUAC-ucCAGCagacCAcC------
LYC.ES-K      aUGG-GuuGCU-cCAA-UAaaCAACCACcUUu
ORY.SA-A      GaGUC-ccUCUA-CAA-CAgaCcaCCAUCUUU
CIN.HYB.      CUGG--CuAGC-cCAAcAGgaCAcCCAUUU--
ZEA.MA-G      GAG--CC-UCa-CuAAGcAgacCACCAUCUUu
#=GC SS_cons  >>>.....>>>...>>.>>...>.>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln13.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln13.fa

ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGG-gaCG-U
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGG-aaCAc-
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUg-aaU-AU
TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>....<.<.<<<<....<<.<

ARA.TH-C      UG-GGUcGauCUcAUUGGGcC-GGgUUcGGguuGGGcUAuauucUGGCCCGcCCaUUCCA
ARA.TH-E      UG-GuUCGGg-UCcaCGGGCC-GGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCCA
LYC.ES-H      UG-GGCuGUa-CCAgauGGUu-GGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCCA
TRI.AE-A      GuuGUA-Gcg--CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCA
LYC.ES-B      UG-GGCuGUa-CCAgauGGUu-GGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUCCA
#=GC SS_cons  <<.<<<.<...<<<...<<<..<<<<<<<<...<<<.<<.....<<<<<<<.<<..<<<<

ARA.TH-C      aGUUG-GGAGUuGAGGCA--UGGGcUUCGAGCgaagGCUCGGGuCUCAUGUCUUCU-agA
ARA.TH-E      aGCUG-UGAGU-AAGaCG--UgUGuGUCAAGCgaagGCUUGGCuCAaACGgCUUCU-aaA
LYC.ES-H      aGCuU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgU-aaA
TRI.AE-A      aGUUGcGuAGU-gGACCGccUGGGGCUUAuGCgaaaGC-UGGGUCUCACGGUC-CAuaaU
LYC.ES-B      aGCUU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgU-aaA
#=GC SS_cons  .<<<<.<<<<<.<<<<<<...<<<..<<<.<<....>>.>>>..>>>.>>>>>>.<...>

ARA.TH-C      G-uGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCCUCCcGCUCUUGACg
ARA.TH-E      GuuGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcGCUUACAGCa
LYC.ES-H      g-uGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCa
TRI.AE-A      G-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcGCUuCCAACg
LYC.ES-B      g-uGGGGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCg
#=GC SS_cons  ...<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>.

ARA.TH-C      gUGGAAGGauuaCGGGCCAuUG-CCU--UCcGAgCCcacu-auGaCC-CAAUaAG-CcGC
ARA.TH-E      gUGGACGGaucaCAGUUUAGcg-UCGc-uCAGAACCacu--auGGCC-UGcuGGuCCGAu
LYC.ES-H      gUGGAaGGauaaUGGGUCGGUGuCUUA-UCAAGUUC-ag-uaacGCC-uaaUGG-GUuGC
TRI.AE-A      gUGGAAGGauaaUGGGCCGcUG-CACu-CCUAGGCCaau--uGGGCCuCGCAG---CcUA
LYC.ES-B      gUGGAaGGauaaCGAGUCGGUG-UUC-uCUGAGUCCagu--aauGCC-ugaUGG-GCuGC
#=GC SS_cons  .>>>>.>>....>>>>>>>.>>.>>>..>>>>>>>>........>>>....>>>..>.>>

ARA.TH-C      UcCGAuUGgaCCAUCaCUUU-
ARA.TH-E      CuCAuaUGaaCCACCAUUUu-
LYC.ES-H      UcCAAUaAacaAcCacCUUUu
TRI.AE-A      CucCAGCagacCAcC------
LYC.ES-B      UcUAAuUAaaCCACCACuUUu
#=GC SS_cons  >.>>>.>>...>>>>.>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln14.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln14.fa

LYC.ES-M      -----------------------------CAagUGgggaugu-uAAGGUGGUgG--aaUA
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaa-uaagguagugu-ggaug
ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACau-cAAaGUGGUUG--aaUA
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCau-uAAuGUGGUGG--aaUG
#=GC SS_cons  .<<<.<<.<........>.>>.>....<<<<..>>>>>>.....<<.<<<<..<....<<

LYC.ES-M      -UUG----GGCuGUc-CCAgauGGCu-GGGCUUGG-UGGGcUAauuuCUGGCCUGcCCug
ZEA.MA-H      ucaau---ugu-ggu--gcaugugccuGGGUCUA-guGCuacAaacuGUGGacCAcCCaU
ORY.SA-A      uUUGgugUGGAuucuGAUcCUGGGCCccaugUUGu-uGUaaUc-uugcUGGCUUGcCCgU
LYC.ES-K      -UUG----GGCuuUa-CCAgaAGGUu-GGGCUUGG-UGGGcUuaguuCUGGCCUGcCCug
LYC.ES-G      -UUG----GGCuGUa-CCAgauGGUu-GGGCUUGG-uGGGcUAauuuCUGGcCUGcCCua
#=GC SS_cons  .<<<....<<<.....<<....<<<..<<<<<<<...<<..<.....<<<<.<<<.<<..

LYC.ES-M      UCCAaGCAC-AGAGUuGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUC--
ZEA.MA-H      UCCAaGUUGcGUaGU-ggGUUucGGAUGcCuuGGCgaaaGCUuuG-CAUCC-cAACa---
ORY.SA-A      UCCAaGuUGcGuAGU-GGGccGGaGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUCCgg
LYC.ES-K      UCCAaGCAC-AGAGUaGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUC--
LYC.ES-G      UCCAaGCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACu-aGAUUC--
#=GC SS_cons  <<<<.<<<<.<<<<<.<<<<<...<<<<<<...<<....>>...>>>>>>...>>>>>..

LYC.ES-M      --CUaaAGuGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUC
ZEA.MA-H      --CUaaAGuGGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcGCcA
ORY.SA-A      ccCUaaAGuGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcGCUu
LYC.ES-K      --CUaaAGcGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUC
LYC.ES-G      --CUaaAGuGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUU
#=GC SS_cons  ..<<..>>.<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>

LYC.ES-M      UGUGCagUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG-G
ZEA.MA-H      CCAGCggUGGAAGGauaaUGagUCGCUa-uGCuaUAGGCCCaau----------------
ORY.SA-A      CCAuCggUGGAAGGauaaCAGGCUGcuG-cACcuUGGgcccgcuu-cuGGCCCAGaGUC-
LYC.ES-K      UGUGCagUGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCCUaaUGG-G
LYC.ES-G      UGUGCagUGGAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-G
#=GC SS_cons  >>>>>..>>>>.>>....>>>.>>>>.>..>>..>>>>>>>........>>>....>>..

LYC.ES-M      UuGCU-cCAA-UAaaCaACCACCUUu
ZEA.MA-H      --------------------------
ORY.SA-A      ccUCUA-CAA-CAgaCcaCCAUCUUU
LYC.ES-K      uuGCU-cCAA-UAaaCAACCACcUUu
LYC.ES-G      CuGCU-cCAAuUAaaCCACCACuUUu
#=GC SS_cons  ..>>>..>>>.>>..>..>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln15.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln15.fa

LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUG-UU
HUM.JA-B      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGGgaCU-UU
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUA-UU
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGGaaCAc-U
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGGaaUG-UU
#=GC SS_cons  ...<<.<<.<......>.>>.>>....<<<<..>>>>.......<<<<<<<<<..<<.<<

LYC.ES-N      GGGCuGUaCCAgauGGUuGGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUCCAaGCU
HUM.JA-B      AGuUCGGccCAuUGGAUCGGaUCCAGuguUAGcUGcuugCUGGgCUGcCCaUUCCAaGCC
LYC.ES-M      GGGCuGUcCCAgauGGCuGGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUCCAaGCA
ARA.TH-E      GGuUCGGgUCcaCGGGCCGGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCCAaGCU
LYC.ES-C      GAACAugcCCAgaAGGUAGGGCUUGUG--UGAcaAuucuCUGGCcUGcCCugUCCAaGCA
#=GC SS_cons  <<.<.<<.<<<...<<<.<<<<<<<<...<<<..<....<<<<<<<<.<<..<<<<.<<<

LYC.ES-N      UAGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg-uGGGgC
HUM.JA-B      GAGAGUuGAGCUGugUGAGCCGGACgaagGUCUGGCUUGguCAGCUCCUaaAG-cGGAGG
LYC.ES-M      CAGAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAG-uGGGGC
ARA.TH-E      GUGAGU-AAGaCGUgUGuGUCAAGCgaagGCUUGGCuCAaACGgCUUCUaaAGuuGGAGG
LYC.ES-C      aAGAGUuGGGUCUuGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCUaaAG-uGGGGU
#=GC SS_cons  <<<<<<.<<<<<<..<<<.<<<.<<....>>.>>>.>>>..>>>>>><<..>>..<<<<<

LYC.ES-N      ggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGG
HUM.JA-B      gcaaugCGUgaggCUGguuucaCAGagcaGCGacaaCCUCCcGCUCUCGGCagUGGAAGG
LYC.ES-M      ggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGG
ARA.TH-E      guaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUGGACGG
LYC.ES-C      ggacugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCagUGGAaGG
#=GC SS_cons  ......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>

LYC.ES-N      auaaCGAGUCGGUGuUCU--CUGAGUCC-aguaacGCCugaUGG-GUuGCU-cCAAuUAa
HUM.JA-B      auaaCGGgCCGGUG-CUGc-UUGGAcCCacc-auGGUUCAcUGagCUGAcUcuUAAuAGg
LYC.ES-M      auaaUGGGUCGGUGuCUUA-UCAAGUUC-aguaacGCCuaaUGG-GUuGCU-cCAA-UAa
ARA.TH-E      aucaCAGUUUAGcg-UCGc-uCAGAACCacu-auGGCCUGcuGGuCCGAuC-uCAuaUGa
LYC.ES-C      auaaCGaGCCAGUg-UCA-UAUAAGUUCaacgaaUGUCUgaUGG-gcUGUU-cUAGuUAa
#=GC SS_cons  ....>>>>>>>>>..>>>..>>>>>>>>.......>>>...>>>.>>.>.>..>>>.>>.

LYC.ES-N      aCCACCAUuUUu
HUM.JA-B      aCCAUUUCUUuU
LYC.ES-M      aCaACCACCUUu
ARA.TH-E      aCCACCAUUUu-
LYC.ES-C      aCUACCACAUUu
#=GC SS_cons  .>>>>>>>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln16.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln16.fa

ZEA.MA-F      nCCGAGCUCUguagcgAGAGCUUguaaCCUaagcGGGGGcauuAAGGUGGUGuggaUGUU
ZEA.MA-A      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGugaaUGCU
ZEA.MA-C      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGuggaUGCU
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaCU-U
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGG-aaUG-U
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>....<<<<<<<<<....<<.<

ZEA.MA-F      UccUGAcGGa--UUCUGgGcCU-GGGCUUGU-auGUGcCAcuggcCGGCCUGcCCgUUCC
ZEA.MA-A      UuGcGAuGGcu-UUCUGGGCCcuGGGCUCGu--uGUGaCAcuggcCGGCUUGcCCaUCCC
ZEA.MA-C      UG--GUaccGu-GUCUuuGCCU-GGGUUCAUggugUGcCuu-uguUGGCCUGcCCgUUCC
HUM.LU-C      UG-GGUCAac-CCAGUgGunC--gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCC
LYC.ES-C      UG-AACAugc-CCAgaAGGUA--GGGCUUGUG--UGAcaAuucuCUGGCcUGcCCugUCC
#=GC SS_cons  <...<<......<<<<..<.<..<<<<<<<<....<<.<<.....<<<<<<<.<<.<<<<

ZEA.MA-F      AaGUUGGuuGU-GgCUGGuGGGG-CUCGGGCgaagGCC-UGGGcCUCU-UUAGaCCUgaA
ZEA.MA-A      AaGUUGGuAGU-GUCUGgUGGGGGCUCuAGCgaaaGCUuuGGGUCUCUG-CAGACCUggA
ZEA.MA-C      AaGUUGGUAGU-GgCCGuuGGAAGCUUGGGCguagGCCcUGGGCUUCC-uUGGaCCUauA
HUM.LU-C      AaGCCGGGAGguGGGcUG-aGggaCcugGGCgaagGCU-nnnGgngCg-CA-CUCcUagA
LYC.ES-C      AaGCAaAGAGUuGGGUCU-uGUGGgCCAAGCgaagGCU-UGGgCUGCu-GGGCUCCUaaA
#=GC SS_cons  <.<<<<<.<<<.<.<<<...<<<.<<<.<<<....>>>..>>>.>>>...>>>.><<..>

ZEA.MA-F      GcGGCAGgcauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCuuCCAACg
ZEA.MA-A      GCGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCU-GCCGACUcCCAACg
ZEA.MA-C      GUGGCAGgaacggCGUgaggCUGucuucaCAGagcaGCGaucaCU-GCCGGCUAUUAACg
HUM.LU-C      cuGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcgCUCUCGGCa
LYC.ES-C      GuGGGGUggacugCGUgaggCUGguuucaCAGagcaACGaauaGC-UCCcGCUCUgUGCa
#=GC SS_cons  >.<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>.

ZEA.MA-F      gUGGGAGGauaaCA-GGCCGcUGCAUu-GCAAGCCCaacu-cGGuC-CAGAG---CC-UC
ZEA.MA-A      gUGGGAGGauaaCGaAGCCGcUGCACu-uUGAGCCUaacu-caGGCUCAGAA---CC-UC
ZEA.MA-C      gUGGAAGGauaaCA-GGCCAcuGCAgc-AUGGGCUCgcuu-aAGGCcuAGAC--Uuc-AU
HUM.LU-C      gUGGAAGGauaaCG-GgCcGGUGCgcc-UUGagCCaaca--cuGuuCaACUGGg-cUGAC
LYC.ES-C      gUGGAaGGauaaCG-aGCCAGUgUCA-UAUAAGUUCaac-gaaUGUCUgaUGG--gcUGU
#=GC SS_cons  .>>>>>>>....>>.>>>>>.>>>>...>>>>>>>>.......>.>..>>>>......>>

ZEA.MA-F      A-uuAA-ACAgacCACCAUCUUu
ZEA.MA-A      a-CuAA-GCAaacCACCAUCUUu
ZEA.MA-C      a-cUAAaGCAgacCACCAUUUUu
HUM.LU-C      UcuUAA-uAGgaCCAUUUCUUuU
LYC.ES-C      U-cUAG-uUAaaCUACCACAUUu
#=GC SS_cons  ....>>..>>...>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln17.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln17.fa

CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
ARA.TH-G      GUCGAGCUaUguaacgAgAGCUUguaaCCCAagUGGGGACuauAAGAUGGUGG-aaCAc-
HUM.JA-A      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAGAUGG-gacu-U
#=GC SS_cons  .<<<<<<<.<......>.>>>>>....<<<<..>>>>>>.....<.<<<<.<<.......

CIN.HYB.      UGaGCUuGgcUUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCAA
ZEA.MA-H      aauugu-ggu-gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCAa
LYC.ES-B      UG-GGCuGUaCCAgauGGUu-GGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUCCAa
ARA.TH-G      UG-gauCGGcCCA-CGGGUC-GGAUUUGUuguUGGcauaggucUGGACUGcCCaaUCCAa
HUM.JA-A      UG-GGUcaGccCAuUGGaUC-gGGUCCAGuguUAGcUGcuugCUGGUCUGcCCaUUCCAa
#=GC SS_cons  <<.........<<........<<<<<<<....<<<.......<<<<<<<<.<<..<<<<.

CIN.HYB.      GUCG-AGAGugGGUUCA-UGUUuCCUGAGCgaagGCUCGGGuGAUGUGAGCUUUagAAu-
ZEA.MA-H      GUUGcGUaGU-ggGUUucGGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAG--
LYC.ES-B      GCUU-AGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg--
ARA.TH-G      GCUG-uGAGU-gAACCG-UAUGaAcCAAGCgaagGUUUGaUcCGUACGGUUgCUaaAG-g
HUM.JA-A      GCCG-AGAGUuGGGCUG-UGUGAUCUgGGCgaagGCUgGGGUCGCACAGCUCCUaaAG--
#=GC SS_cons  <<<<.<<<<<..<<<<<.<<<<..<<.<<<....>>>.>>..>>>>>>>>>.<<..>>..

CIN.HYB.      cGGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCUacCUCUCGACUgU
ZEA.MA-H      uGGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcGCcACCAGCggU
LYC.ES-B      uGGGGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggU
ARA.TH-G      uuGAGGguauugCGUuaggCUGgcuucaCAGagcaGCGacuaCCUCccGCUCuCAGCagU
HUM.JA-A      aGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGaccaCCUCCcGCUCUCGGCagU
#=GC SS_cons  .<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>

CIN.HYB.      GGAAGGauuaCAAGCCGGaGUGUC--uUAGGCUC-auauaaccag-cCUGG--CuAGC-c
ZEA.MA-H      GGAAGGauaaUGagUCGCUa-uGCu-aUAGGCCCaau-----------------------
LYC.ES-B      GGAaGGauaaCGAGUCGGUG-UUC-uCUGAGUCCagu--aauGCCugaUGG-GCuGCU-c
ARA.TH-G      GGAcGGacaaCGGUUCGacg-CCAc-ACAAAUCCacu--auGGUCCGcUGGcUCGuaacc
HUM.JA-A      GGAAGGauaaCGGGUCGGUG-CUAc-UUGGGCCa-cc--auGG-UCAcUGcaUgcACUcu
#=GC SS_cons  >>>.>>....>>>>>>>>...>>>...>>>>>>>..............>>..........

CIN.HYB.      CAAcAGgaCAcCCAUUU--
ZEA.MA-H      -------------------
LYC.ES-B      UAAuUAaaCCACCACuUUu
ARA.TH-G      CGcuUGaaCCACCAUUUU-
HUM.JA-A      UAAucagaCCAUCUCUUuU
#=GC SS_cons  >>......>>.>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln18.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln18.fa

ZEA.MA-E      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaCU-U
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGG-aaUG-U
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>....<<<<<<<<<....<..<

ZEA.MA-E      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
ZEA.MA-B      uuGcGAuGGu--uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCA
ZEA.MA-D      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
HUM.LU-C      UG-GGUCAac-CCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCCA
LYC.ES-C      UG-AACAugc-CCAgaAGGUA-GGGCUUGUG--UGAcaAuucuCUGGCcUGcCCugUCCA
#=GC SS_cons  <...<<.<....<<<<<<<.<.<<<<<<<....<<<.<......<<<<<<<.<<.<<<<<

ZEA.MA-E      aGUUGGuAGU-GgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUgaAG
ZEA.MA-B      aGUUGGuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacAG
ZEA.MA-D      aGUUGGuAGU-GgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUgaAG
HUM.LU-C      aGCCGGGAGguGGGcUG-aGggaCcugGGCgaagGCU-nnnGgngCg-CA-CUCcUagAc
LYC.ES-C      aGCAaAGAGUuGGGUCU-uGUGGgCCAAGCgaagGCU-UGGgCUGCu-GGGCUCCUaaAG
#=GC SS_cons  .<<<<<.<<<.<.<<<<..<<<.<<..<<<....>>>...>>.>>>..>>>>.><<..>>

ZEA.MA-E      UGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCGGCUuCCAACgg
ZEA.MA-B      cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAACgg
ZEA.MA-D      uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAACgg
HUM.LU-C      uGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcgCUCUCGGCag
LYC.ES-C      uGGGGUggacugCGUgaggCUGguuucaCAGagcaACGaauaGC-UCCcGCUCUgUGCag
#=GC SS_cons  .<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>..

ZEA.MA-E      UGGGAGGauaaCGGGCCGcuGCACu-uCGAGCCCaacu-caGGCCCAGAG---CC-UCa-
ZEA.MA-B      UGGGAGGauaaCAAGCCGcuGCACu-uUGAGCCCaaca-cAGaCCCAGA---uCC-UCu-
ZEA.MA-D      UGGGAGGauaaCAGGCCGcuGCACu-uCGAGCCCaacu-caGGCCCAGAG---CC-UCa-
HUM.LU-C      UGGAAGGauaaCGGgCcGGUGCgcc-UUGagCCaaca--cuGuuCaACUGGg-cUGACUc
LYC.ES-C      UGGAaGGauaaCGaGCCAGUgUCA-UAUAAGUUCaac-gaaUGUCUgaUGG--gcUGUU-
#=GC SS_cons  >>>>>>>....>>>>>>>..>>>>...>>>>>>>.......>.>>>>>>>....>.>>..

ZEA.MA-E      CuAAGcAgacCACCAUCUUu
ZEA.MA-B      CuuAGCAaacCaCCAUCUUu
ZEA.MA-D      CuAAGcAgacCACCAUCUU-
HUM.LU-C      uUAAuAGgaCCAUUUCUUuU
LYC.ES-C      cUAGuUAaaCUACCACAUUu
#=GC SS_cons  ..>>..>...>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln19.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln19.fa

LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGGaaUGUUG
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUAUUG
HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCauGuGGGAAAUGGgaCUUUG
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUGUUG
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGGaaUGUUG
#=GC SS_cons  <.<<<<<<<........>>>>>>....<<<<..>>>>>.>...<<.<<<<<<<..<<<<<

LYC.ES-C      AACAugcCCAgaAGGUAGGGCUUGUG--UGAcaA-uucuCUGGCcUGcCCugUCCAaGCA
LYC.ES-M      GGCuGUcCCAgauGGCuGGGCUUGG--UGGGcUA-auuuCUGGCCUGcCCugUCCAaGCA
HUM.LU-D      GGUCAacCUAGUGGAuCGGGUCCAGuguUAGcUG-cuuaCUGGUCUGcCCaUUCCAaGCC
LYC.ES-N      GGCuGUaCCAgauGGUuGGGCUUGG--uGGGcUA-auuuCUGACUUGcCCuaUCCAaGCU
LYC.ES-F      GGUccauCUugauGGaUGGGCUUGA--aGGGcUAauguuCUGGCCUGcCCugUCCAaGCA
#=GC SS_cons  <<<....<<<...<<..<<<<<<<<...<<<.<<.....<<<<<<<<.<<..<<<<.<<<

LYC.ES-C      aAGAGUuGGGUCUuGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCUaaAGuGGGGUg
LYC.ES-M      CAGAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCg
HUM.LU-D      GGGAGUuGGGCUGaGUGACCUgGGCgaagGCU-GGGUUGCgCAGCUCCUagAGuGGAGGg
LYC.ES-N      UAGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCg
LYC.ES-F      CAGAGUuGGGUCAAGUGGuCUAUACgaaaGUAUAG-CCACUUGGCCUUUagAGuGGGAUg
#=GC SS_cons  <<<<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>>>><<..>>.<<<<<.

LYC.ES-C      gacugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCagUGGAaGGa
LYC.ES-M      gaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGa
HUM.LU-D      caaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGGAAGGa
LYC.ES-N      gaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGa
LYC.ES-F      gacugCGUgaggCUGguuucaCAGagcaACGacuaGUCCCcGCUCUGUGCagUGGAaGGa
#=GC SS_cons  .....<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>.

LYC.ES-C      uaaCGaGCCAGUg-UCA-UAUAAGUUCaac-gaaUGUCUgaUGG-gcUGUU-cUAGuUAa
LYC.ES-M      uaaUGGGUCGGUGuCUUA-UCAAGUUC-ag-uaacGCCuaaUGG-GUuGCU-cCAA-UAa
HUM.LU-D      uaaCGGGCCGGUG-CUAc-CUGGAUCCacc--auGcUUCACUGGgcUGACUcuUAAuAGg
LYC.ES-N      uaaCGAGUCGGUGuUCU--CUGAGUCC-ag-uaacGCCugaUGG-GUuGCU-cCAAuUAa
LYC.ES-F      ucaCGGGCUAGUGcUCU--UUGAGUCCuaacaaaAaCCugauAG-guuGCC--UAAuUAa
#=GC SS_cons  ...>>>>>>>>>>.>>>..>>>>>>>>.........>>...>>>....>>>..>>>.>>.

LYC.ES-C      aCUACCACAUUu
LYC.ES-M      aCaACCACCUUu
HUM.LU-D      aCCAUUUCUUuU
LYC.ES-N      aCCACCAUuUUu
LYC.ES-F      aCCAUCACuUUu
#=GC SS_cons  .>>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln20.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln20.fa

LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGG-gaCG-U
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUG-aaUA-U
ZEA.MA-G      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGG-aaCAc-
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<...<<.<

LYC.ES-K      UG-GGCuuUa--CCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCC
ARA.TH-C      UG-GGUcGau-CUcAUUGGGcC-GGgUUcGGguuGGGcUAuauucUGGCCCGcCCaUUCC
LYC.ES-A      UG-GGCuuUa--CCAgaAGGUu-GGGCUUGGU--GGGcUuaguuCUGGCCUGcCCugUCC
ZEA.MA-G      UuGcGAuGGcu--UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCC
ARA.TH-E      UG-GuUCGGg--UCcaCGGGCC-GGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCC
#=GC SS_cons  <<.<<<..<...<<<..<<<<..<<<<<<<....<<<.<......<<<<<<<.<<..<<<

LYC.ES-K      AaGCACAGAGUaGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAG-
ARA.TH-C      AaGUUGGGAGUuGAGGCA-UGGGcUUCGAGCgaagGCUCGGGuCUCAUGUCUUCUagAG-
LYC.ES-A      AaGCACAGAGUuGGAUCu-cGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAG-
ZEA.MA-G      AaGUUGGuAGU-GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCUCCAGaCCUgaAG-
ARA.TH-E      AaGCUGUGAGU-AAGaCG-UgUGuGUCAAGCgaagGCUUGGCuCAaACGgCUUCUaaAGu
#=GC SS_cons  <.<<<<<<<<<.<<<<<<..<<<.<<<<.<<....>>.>>>>.>>>.>>>>>><<..>>.

LYC.ES-K      cGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagU
ARA.TH-C      uGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCCUCCcGCUCUUGACggU
LYC.ES-A      uGGGGCGgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagU
ZEA.MA-G      uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcGCUuCCAACggU
ARA.TH-E      uGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagU
#=GC SS_cons  .<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>

LYC.ES-K      GGAaGGauaaUGGGUCGGuGuCUUA-UCAAGUUC-ag-uaacGCCUaaUGG-GuuGCUcC
ARA.TH-C      GGAAGGauuaCGGGCCAuUG-CCU--UCcGAgCCcacu-auGaCCCAAUaAG-CcGCUcC
LYC.ES-A      GGAaGGauaaUGGGUCGGuG-UCUuAUCAAGUUCagu--aacGCCUaaUGG-GuuGCUcC
ZEA.MA-G      GGGAGGauaaCGGGCCGcuG-CACu-uCGAGCCCaacu-caGGCCCAGAG--CC-UCaCu
ARA.TH-E      GGACGGaucaCAGUUUAGcg-UCGc-uCAGAACCacu--auGGCCUGcuGGuCCGAuCuC
#=GC SS_cons  >>>.>>....>>>>>>>..>.>>>...>>>>>>>........>>>>..>>>.>..>>>.>

LYC.ES-K      AA-UAaaCAACCACcUUu
ARA.TH-C      GAuUGgaCCAUCaCUUU-
LYC.ES-A      AA-UAaaCAACCACcUUu
ZEA.MA-G      AAGcAgacCACCAUCUUu
ARA.TH-E      AuaUGaaCCACCAUUUu-
#=GC SS_cons  >>.>>..>>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln21.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln21.fa

ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCau-uAAuGUGGUGG--aaUG
TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcau-uaaaguGaUGu-gaacG
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCau-cAGUGUGGUGG--aaUG
HUM.LU-B      ---GGcCUUAgcaacgUGGGcCUguaaCCCAagUGGGggcau-GuGGGAAAUGG--aaC-
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>......<.<<<<<<<....<<

ORY.SA-A      uUUGgugUGGAuucuGAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCCg
LYC.ES-I      -UUG----GGCuGUa-CCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCCu
TRI.AE-A      CUGuu---GUA-Gcg--CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCg
LYC.ES-C      -UUG----AACAugc-CCAgaAGGUA-GGGCUUGUG--UGAcaAuucuCUGGCcUGcCCu
HUM.LU-B      AUUG----GGUCAGc-CCAGUGGauC-gGGuCCAGuguUAGcUGcuuaCUGGUCUGcCCa
#=GC SS_cons  .<<<....<<<.....<<<..<<<<<..<<.<<<<...<<<.<<.....<<<<<<<.<<.

ORY.SA-A      UUCCAaGuUGcGuAGU-GGGccGG-aGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUCC
LYC.ES-I      aUCCAaGCUU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGGaCUACu-UGAUUC
TRI.AE-A      UUCCAaGUUGcGuAGU-gGACCGccUGGGGCUUAuGCgaaaGC-UGGGUCUCA-CGGUC-
LYC.ES-C      gUCCAaGCAa-AGAGUuGGGUCU--uGUGGgCCAAGCgaagGCUUGGgCUGCu-GGGCUC
HUM.LU-B      UUCCAaGCCG-GGAGUuGGGCUG--aGUGACCUGGGCgaagGCCUGGGUUGCg-CAGCUC
#=GC SS_cons  .<<<<.<<<<.<.<<<.<<<<<<...<<<<.<<<.<<....>>.>>>.>>>>..>>>>>>

ORY.SA-A      ggccCU-aaAGuGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcG
LYC.ES-I      ----gU-aaAguGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcG
TRI.AE-A      ----CAuaaUGuGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcG
LYC.ES-C      ----CU-aaAGuGGGGUggacugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcG
HUM.LU-B      ----CU-agAGuGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGacuaCCUCCcG
#=GC SS_cons  ....<<...>>.<<<<<......<<<....<<<......>>>....>>>....>>>>>.>

ORY.SA-A      CUuCCAuCggUGGAAGGauaaCAGGCUGcuG-cACc-uUGGgcccgcuu-cuGGCC-CAG
LYC.ES-I      CUCUAAGCggUGGAaGGauaaCGAGUCGGUGuUCU--CUGAGUCC-ag-uaacGCC-uga
TRI.AE-A      CUuCCAACggUGGAAGGauaaUGGGCCGcUG-CACu-CCUAGGCCaau--uGGGCCuCGC
LYC.ES-C      CUCUgUGCagUGGAaGGauaaCGaGCCAGUg-UCA-UAUAAGUUCaac-gaaUGUC-Uga
HUM.LU-B      CUCCCGGCagUGGAAGGauaaCGGGCCGGUG-CUAc-UUGGuCCa-cc--auGu-U-CAC
#=GC SS_cons  >>.>>>>>..>>>>.>>....>>>>>>>.>>.>>>..>>>>.>>........>>>>.>..

ORY.SA-A      aGUC--ccUCUA--CAA-CAgaCcaCCAUCUUU
LYC.ES-I      UGG--GUuGCU--cCAAuUAaaCCACCAUuUUu
TRI.AE-A      AG----CcUAC--ucCAGCagacCAcC------
LYC.ES-C      UGG--gcUGUU--cUAGuUAaaCUACCACAUUu
HUM.LU-B      UGGucCUGACU-cuUAAUcGgaCCAUUUCCUuU
#=GC SS_cons  >>>.....>>>...>>>.>>..>>>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln22.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln22.fa

ARA.TH-A      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAcU
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgG-aaUA-U
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
#=GC SS_cons  .<<<<<<............>>>>....<<<<..>>>>>>.....<.<<<<..<...<<.<

ARA.TH-A      G--GUUcGGuUCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCAa
CIN.HYB.      UGaGCUuGgcUUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCAA
LYC.ES-J      UG-GGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCAa
LYC.ES-M      UG-GGCuGUcCCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUCCAa
ZEA.MA-H      aauugu-ggu-gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCAa
#=GC SS_cons  <..<<<....<<.........<<<<<<<....<<<.......<<<<<<<<.<<..<<<<.

ARA.TH-A      GCUG-UGAGU-AAUUaG-uguUGAGUUGAGCgaagGCUUGGCUCAugCaGGUUCUagAG-
CIN.HYB.      GUCG-AGAGugGGUUCA--UGUUuCCUGAGCgaagGCUCGGGuGAUGUGAGCUUUagAAu
LYC.ES-J      GCAC-AGAGUuGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAG-
LYC.ES-M      GCAC-AGAGUuGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAG-
ZEA.MA-H      GUUGcGUaGU-ggGUUuc-GGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAG-
#=GC SS_cons  <<<<.<<<<<.<<<<<<...<<<<<<<<.<<....>>.>>>>>>>>.>>>>>><<..>>.

ARA.TH-A      ucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAGCag
CIN.HYB.      -cGGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCUacCUCUCGACUg
LYC.ES-J      -uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
LYC.ES-M      -uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
ZEA.MA-H      -uGGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcGCcACCAGCgg
#=GC SS_cons  ..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..

ARA.TH-A      UGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcCUGcuGGUCcGAUcuC
CIN.HYB.      UGGAAGGauuaCAAGCCGGaGUGUC-uUAGGCUC-auauaaccag-cCUGG-CuAGCcCA
LYC.ES-J      UGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCCUaaUGGGuuGCUcCA
LYC.ES-M      UGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGGGUuGCUcCA
ZEA.MA-H      UGGAAGGauaaUGagUCGCUa-uGCuaUAGGCCCaau-----------------------
#=GC SS_cons  >>>>.>>....>>>>>>>>...>>>..>>>>>>>...............>>...>>>..>

ARA.TH-A      AuaUGaaCCACCAUUUU-
CIN.HYB.      A-cAGgaCAcCCAUUU--
LYC.ES-J      A--UAaaCAACCACcUUu
LYC.ES-M      A--UAaaCaACCACCUUu
ZEA.MA-H      ------------------
#=GC SS_cons  >..>>..>..>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln23.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln23.fa

HUM.LU-B      ---GGcCUUAgcaacgUGGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGGaaC-AUU
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUgaaU-AUU
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUGaaUA-UU
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGGaaCAc-U
#=GC SS_cons  <.<<<<<<<<......>>>>>>>....<<<<..>>>>>.>....<.<<<<<<<..<..<<

HUM.LU-B      GGGUCAGcCCAGUGGauCgGGuCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaGCC
LYC.ES-G      GGGCuGUaCCAgauGGUuGGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAaGCA
LYC.ES-H      GGGCuGUaCCAgauGGUuGGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCCAaGCu
LYC.ES-A      GGGCuuUaCCAgaAGGUuGGGCUUGGU--GGGcUuaguuCUGGCCUGcCCugUCCAaGCA
ARA.TH-E      GGuUCGGgUCcaCGGGCCGGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCCAaGCU
#=GC SS_cons  <<<<.<<.<<<...<<<.<<<<<<<<...<<<.<.....<<<<<<<<.<<..<<<<.<<<

HUM.LU-B      GGGAGUuGGGCUGaGUGACCUGGGCgaagGCCUGGGUUGCgCAGCUCCUagAG-uGGAGG
LYC.ES-G      CAGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAG-uGGGGU
LYC.ES-H      UAGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg-uGGGGC
LYC.ES-A      CAGAGUuGGAUCucGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAG-uGGGGC
ARA.TH-E      GUGAGU-AAGaCGUgUGuGUCAAGCgaagGCUUGGCuCAaACGgCUUCUaaAGuuGGAGG
#=GC SS_cons  <<<<<<.<<<<<..<<<<<<<<.<<....>>.>>>>>>>>..>>>>><<..>>..<<<<<

HUM.LU-B      gcaaugCGUgaggCUGguuucaCAGagcaGCGacuaCCUCCcGCUCCCGGCagUGGAAGG
LYC.ES-G      ggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGG
LYC.ES-H      ggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCagUGGAaGG
LYC.ES-A      GgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagUGGAaGG
ARA.TH-E      guaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUGGACGG
#=GC SS_cons  ......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>

HUM.LU-B      auaaCGGGCCGGUG-CUAc-UUGGuCCa-cc-auGu-UCACUGGucCUGACUcuUAAUcG
LYC.ES-G      auaaCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGG--GCuGCU-cCAAuUA
LYC.ES-H      auaaUGGGUCGGUGuCUUA-UCAAGUUC-aguaacGCCuaaUGG--GUuGCU-cCAAUaA
LYC.ES-A      auaaUGGGUCGGuG-UCUuAUCAAGUUCagu-aacGCCUaaUGG--GuuGCU-cCAA-UA
ARA.TH-E      aucaCAGUUUAGcg-UCGc-uCAGAACCacu-auGGCCUGcuGGu-CCGAuC-uCAuaUG
#=GC SS_cons  ....>>>>>>>>.>.>>>..>>>>>>>>.......>>>...>>>..>>.>>>..>>>..>

HUM.LU-B      gaCCAUUUCCUuU
LYC.ES-G      aaCCACCACuUUu
LYC.ES-H      acaAcCacCUUUu
LYC.ES-A      aaCAACCACcUUu
ARA.TH-E      aaCCACCAUUUu-
#=GC SS_cons  ..>>>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln24.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln24.fa

LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUG-aaUA-U
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAc-
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGG-aaUG-U
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGG-aaUG-U
ZEA.MA-A      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGugaaUGCU
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<...<<.<

LYC.ES-A      UG-GGCuuUa-CCAgaAGGUu--GGGCUUGGU--GGGcUu-aguuCUGGCCUGcCCugUC
ARA.TH-F      UG-GuUCGGu-UCcuCGGaUC--GGUUCUGAugugGGcau-guuuCUGAGCUGcCCaGUC
LYC.ES-F      UG-GGUccau-CUugauGGaU--GGGCUUGA--aGGGcUAauguuCUGGCCUGcCCugUC
LYC.ES-C      UG-AACAugc-CCAgaAGGUA--GGGCUUGUG--UGAcaA-uucuCUGGCcUGcCCugUC
ZEA.MA-A      UuGcGAuGGcu-UUCUGGGCCcuGGGCUCGu--uGUGaCA-cuggcCGGCUUGcCCaUCC
#=GC SS_cons  <<.<<<.....<<...<<<<<..<<<<<<<<...<<<........<<<<<<<<.<<..<<

LYC.ES-A      CAaGCACAGAGUuGGAUCu--cGAGGCCCAaAUgaaaAUa-UGGGCUUCu-uGAUUCCUa
ARA.TH-F      CAaGCUGUGAGU-AAUUag-uguUGAGUUGAGCgaagGCU-UGGCUUGca---GGUUCUa
LYC.ES-F      CAaGCACAGAGUuGGGUCA--AGUGGuCUAUACgaaaGUA-UAG-CCACU-UGGCCUUUa
LYC.ES-C      CAaGCAaAGAGUuGGGUCU--uGUGGgCCAAGCgaagGCU-UGGgCUGCu-GGGCUCCUa
ZEA.MA-A      CAaGUUGGuAGU-GUCUGgU-GGGGGCUCuAGCgaaaGCUuuGGGUCUCUG-CAGACCUg
#=GC SS_cons  <<.<<<<<<<<<.<<<<<....<<<<.<<<<<<....>>>.>>>.>>>>...>>>>><<.

LYC.ES-A      aAG-uGGGGCGgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUG
ARA.TH-F      gAGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAG
LYC.ES-F      gAG-uGGGAUggacugCGUgaggCUGguuucaCAGagcaACGacuaGUCCCcGCUCUGUG
LYC.ES-C      aAG-uGGGGUggacugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUG
ZEA.MA-A      gAG-CGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUGCCGACUcCCAA
#=GC SS_cons  .>>..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>

LYC.ES-A      CagUGGAaGGauaaUG-GGUCGGuG-UCUuAUCAAGUUCagu--aacGCCUaaUGG-Guu
ARA.TH-F      CagUGGACGGaucaCG-GUUUAGcg-UCgc-UCAGAACCacu--auGGcCUGcuGGuCCG
LYC.ES-F      CagUGGAaGGaucaCG-GGCUAGUGcUCU--UUGAGUCCuaacaaaAaCCugauAG-guu
LYC.ES-C      CagUGGAaGGauaaCG-aGCCAGUg-UCA-UAUAAGUUCaac-gaaUGUCUgaUGG-gcU
ZEA.MA-A      CggUGGGAGGauaaCGaAGCCGcUG-CACu-uUGAGCCUaacu-caGGCUCAGAA--CC-
#=GC SS_cons  >..>>>>.>>....>>.>>>>>>...>>>..>>>>>>>>.......>>>>>...>>....

LYC.ES-A      GCUcCAA-UAaaCAACCACcUUu
ARA.TH-F      AuCuCAuaUGaaCCACCAUUUU-
LYC.ES-F      GCC-UAAuUAaaCCAUCACuUUu
LYC.ES-C      GUUcUAGuUAaaCUACCACAUUu
ZEA.MA-A      UCaCuAAGCAaacCACCAUCUUu
#=GC SS_cons  >>>.>>>.>>..>>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln25.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln25.fa

LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUg-aaU-AU
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
HUM.LU-A      GCCGGuCUUAgcaacgUGGGcCUguaaCCCAagUGGGGGCauGuGGGAAAUGG-gaCU-U
TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>.....<.<.<<<<....<..<

LYC.ES-J      UG-GGCuuUa-CCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCA
LYC.ES-H      UG-GGCuGUa-CCAgauGGUu-GGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCCA
ZEA.MA-D      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
HUM.LU-A      UG-GGUCAac-CUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCA
TRI.AE-A      GuuGUA-Gcg--CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCA
#=GC SS_cons  <..<<<.<....<<..<<<<..<<<<<<<<...<<<.<......<<<<<<<.<<..<<<<

LYC.ES-J      aGCAC-AGAGUuGGAUCA--cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCU-aaA
LYC.ES-H      aGCuU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgU-aaA
ZEA.MA-D      aGUUG-GuAGU-GgCUGGc-GGAGGCUuuAGCggaaGCUuuGGUCUCUCCAGaCCU-gaA
HUM.LU-A      aGCCG-GGAGUuGGgcUG--aGUGACCUGGgCgaagGgCUGGGUUGCgCAcgUCCU-agA
TRI.AE-A      aGUUGcGuAGU-gGACCGccUGGGGCUUAuGCgaaaGC-UGGGUCUCACGGUC-CAuaaU
#=GC SS_cons  .<<<<.<.<<<.<<<<<<...<<<<<<<<.<<....>>.>>>>>>>>.>>>>>><<...>

LYC.ES-J      GuGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGC-UCCcGCUCUGUGCa
LYC.ES-H      guGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGC-UCCcGCUCUGuGCa
ZEA.MA-D      GuGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAACg
HUM.LU-A      GuGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcGCUCUCGGCa
TRI.AE-A      GuGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCU-GCCcGCUuCCAACg
#=GC SS_cons  >.<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>.

LYC.ES-J      gUGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCC-UaaUGG-GuuGCU
LYC.ES-H      gUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCC-uaaUGG-GUuGCU
ZEA.MA-D      gUGGGAGGauaaCAGGCCGcuG-CACuuCGAGCCCaacu-caGGCC-CAGAG--CC-UCa
HUM.LU-A      gUGGAAGGauaaCGGGCCGGUG-CUAcCUGGGUCCacc--auGcUU-CACUAGgcUGACU
TRI.AE-A      gUGGAAGGauaaUGGGCCGcUG-CACuCCUAGGCCaau--uGGGCCuCGCAG---CcUAC
#=GC SS_cons  .>>>>.>>....>>>>>>>..>.>>>.>>>>>>>>........>>>.>..>>...>.>>>

LYC.ES-J      -cCAA-UAaaCAACCACcUUu
LYC.ES-H      -cCAAUaAacaAcCacCUUUu
ZEA.MA-D      -CuAAGcAgacCACCAUCUU-
HUM.LU-A      cuUAAuAGgaCCAUUUCUUuU
TRI.AE-A      -ucCAGCagacCAcC------
#=GC SS_cons  ...>>..>...>>>>.>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln26.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln26.fa

ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGGgaCGUUG
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUAUUG
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGGaaCUUUG
LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGGaaUAUUG
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGGaaUGUUG
#=GC SS_cons  ...<<..<<........>>..>>....<<<<..>>>>......<<.<<<<<<<..<<<<<

ARA.TH-C      GGUcGauCUcAUUGGGcCGGgUUcGGguuGGGcUA-uauucUGGCCCGcCCaUUCCAaGU
LYC.ES-M      GGCuGUc-CCAgauGGCuGGGCUUGG--UGGGcUA-auuuCUGGCCUGcCCugUCCAaGC
HUM.LU-C      GGUCAac-CCAGUgGunCgGGncCAGugcuaGcUG-cuuaCCcGgCUGcCCaUUCCAaGC
LYC.ES-E      GGCuGUc-CCAgauGGCuGGGCUUGG--uGGGcUA-auuuCUGGcCUGcCCuaUCCAaGU
LYC.ES-F      GGUccau-CUugauGGaUGGGCUUGA--aGGGcUAauguuCUGGCCUGcCCugUCCAaGC
#=GC SS_cons  <<<.<...<<<...<<..<<<<<<<<...<<<.<<.....<<<<.<<<.<<..<<<<.<<

ARA.TH-C      UGGGAGUuGAGGCAUGGGcUUCGAGCgaagGCUCGGGuCUCAUGUCUUCUagAGuGGGGG
LYC.ES-M      ACAGAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGC
HUM.LU-C      CGGGAGguGGGcUGaGggaCcugGGCgaagGCUnnnGgngCgCA-CUCcUagAcuGGAGG
LYC.ES-E      ACAGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGU
LYC.ES-F      ACAGAGUuGGGUCAAGUGGuCUAUACgaaaGUAUAG-CCACUUGGCCUUUagAGuGGGAU
#=GC SS_cons  <<<<<<<.<<<<<<.<<<.<<<<.<<....>>.>>>>.>>>.>>>>>><<..>>.<<<<<

ARA.TH-C      agaccGCGUgaggCUGguuucaCAGagcaGCGUccaCCUCCcGCUCUUGACggUGGAAGG
LYC.ES-M      ggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGG
HUM.LU-C      gcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgCUCUCGGCagUGGAAGG
LYC.ES-E      ggacc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGG
LYC.ES-F      ggacugCGUgaggCUGguuucaCAGagcaACGacuaGUCCCcGCUCUGUGCagUGGAaGG
#=GC SS_cons  ......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>

ARA.TH-C      auuaCGGGCCAuUG-CCU-UCcGAgCCcacu-auGaCCCAAUaAG-CcGCU-cCGAuUGg
LYC.ES-M      auaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG-GUuGCU-cCAA-UAa
HUM.LU-C      auaaCGGgCcGGUG-CgccUUGagCCaaca--cuGuuCaACUGGgcUGACUcuUAAuAGg
LYC.ES-E      auaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-GCuGUU-cUAGuUAa
LYC.ES-F      aucaCGGGCUAGUGcUCU-UUGAGUCCuaacaaaAaCCugauAG-guuGCC--UAAuUAa
#=GC SS_cons  ....>>>.>>>>>>.>>>.>>>>>>>>.........>>...>>>..>.>>>..>>>.>>.

ARA.TH-C      aCCAUCaCUUU--
LYC.ES-M      aCaACCACCUUu-
HUM.LU-C      aCCAUUUCUUuU-
LYC.ES-E      aCUACCACaUUuu
LYC.ES-F      aCCAUCACuUUu-
#=GC SS_cons  .>>>>>>>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln27.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln27.fa

TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
ZEA.MA-A      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGugaaUGCU
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
HUM.JA-A      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAGAUGG-gacu-U
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaCU-U
#=GC SS_cons  ...<<.<<.<......>.>>.>>....<<<<..>>>>.......<<<<<<<<....<<.<

TRI.AE-B      uG-GUGcGGu--UuGuuGGCCU-GGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCC
ZEA.MA-A      UuGcGAuGGcu-UUCUGGGCCcuGGGCUCGu--uGUGaCAcuggcCGGCUUGcCCaUCCC
LYC.ES-K      UG-GGCuuUa-CCAgaAGGUu--GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCC
HUM.JA-A      UG-GGUcaGc-cCAuUGGaUC--gGGUCCAGuguUAGcUGcuugCUGGUCUGcCCaUUCC
HUM.LU-C      UG-GGUCAac-CCAGUgGunC--gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCC
#=GC SS_cons  <<.<<<..<...<<...<.<<...<<<<<<<....<<.<......<<<<<<<.<<.<<<<

TRI.AE-B      AaGUUGGuAGU-gGgCUG-GGuGGcUGGGGCgaaaGCU-UCGcCUuCU-CAGgC-CUuaA
ZEA.MA-A      AaGUUGGuAGU-GUCUGgUGGGGGCUCuAGCgaaaGCUuuGGGUCUCUG-CAGACCUggA
LYC.ES-K      AaGCACAGAGUaGGAUCA-cGAGGCCCAaAUgaaaAUa-UGGGCUUCu-UGAUUCCUaaA
HUM.JA-A      AaGCCGAGAGUuGGGCUG-UGUGAUCUgGGCgaagGCU-gGGGUCGCA-CAGCUCCUaaA
HUM.LU-C      AaGCCGGGAGguGGGcUG-aGggaCcugGGCgaagGCU-nnnGgngCg-CA-CUCcUagA
#=GC SS_cons  <.<<<<<.<<<.<<<<<<..<.<<<<<.<<<....>>>..>>>>>.>..>>>>>><<..>

TRI.AE-B      GuGGCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAACgg
ZEA.MA-A      GCGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUGCCGACUcCCAACgg
LYC.ES-K      GcGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCag
HUM.JA-A      GaGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGaccaCCUCCcGCUCUCGGCag
HUM.LU-C      cuGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgCUCUCGGCag
#=GC SS_cons  >.<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>.>>>>>..

TRI.AE-B      UGGAAGGauaaCA-GGCCGcuG-cAgcAUGGGCCCgcuc-uGGGCCucCuA--CCcCGCc
ZEA.MA-A      UGGGAGGauaaCGaAGCCGcUG-CACuuUGAGCCUaacu-caGGCUCAGAA--CC-UCa-
LYC.ES-K      UGGAaGGauaaUG-GGUCGGuGuCUUAUCAAGUUC-ag-uaacGCCUaaUGG-GuuGCU-
HUM.JA-A      UGGAAGGauaaCG-GGUCGGUG-CUAcUUGGGCCa-cc--auGG-UCAcUGcaUgcACUc
HUM.LU-C      UGGAAGGauaaCG-GgCcGGUG-CgccUUGagCCaaca--cuGuuCaACUGGgcUGACUc
#=GC SS_cons  >>>>>>>....>>.>>>>>..>.>>..>>>>>>>........>>.>...>>..>..>>>.

TRI.AE-B      aU-AGCAgacCACCaUCUUu
ZEA.MA-A      CuAAGCAaacCACCAUCUUu
LYC.ES-K      cCAA-UAaaCAACCACcUUu
HUM.JA-A      uUAAucagaCCAUCUCUUuU
HUM.LU-C      uUAAuAGgaCCAUUUCUUuU
#=GC SS_cons  .>>>.>>...>>>>>>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln28.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln28.fa

ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgG-aaUA-U
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ZEA.MA-C      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGuggaUGCU
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAc-
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>....<<<<<<<<<....<<.<

ZEA.MA-B      uuGcGAuGGu--uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCA
LYC.ES-M      UG-GGCuGUc-CCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUCCA
ZEA.MA-D      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
ZEA.MA-C      UG--GUaccGu-GUCUuuGCCUGGGUUCAUggugUGcCuu-uguUGGCCUGcCCgUUCCA
ARA.TH-F      UG-GuUCGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCA
#=GC SS_cons  <...<<.<<...<<.<.<<<<.<<<<<<<.....<<.<......<<<<<<<.<<.<<<<<

ZEA.MA-B      aGUUGGuAGU-GUCUGaC-GGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacA
LYC.ES-M      aGCACAGAGUuGGAUCA--cGAGGCCCAaAUgaaaAUa-UGGGCUUCu-UGAUUCCUaaA
ZEA.MA-D      aGUUGGuAGU-GgCUGGc-GGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUgaA
ZEA.MA-C      aGUUGGUAGU-GgCCGuu-GGAAGCUUGGGCguagGCCcUGGGCUUCC-uUGGaCCUauA
ARA.TH-F      aGCUGUGAGU-AAUUag-uguUGAGUUGAGCgaagGCU-UGGCUUGca---GGUUCUagA
#=GC SS_cons  .<<<<<.<<<.<.<<<....<<<<<<<.<<<....>>>..>>>>>>>...>>>.><<..>

ZEA.MA-B      G-cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAAC
LYC.ES-M      G-uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGC-UCCcGCUCUGUGC
ZEA.MA-D      G-uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAAC
ZEA.MA-C      G-UGGCAGgaacggCGUgaggCUGucuucaCAGagcaGCGaucaCU-GCCGGCUAUUAAC
ARA.TH-F      GucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUACAGC
#=GC SS_cons  >..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>

ZEA.MA-B      ggUGGGAGGauaaCAAGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAGA---uCC-UC
LYC.ES-M      agUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG--GUuGC
ZEA.MA-D      ggUGGGAGGauaaCAGGCCGcuG-CACuuCGAGCCCaacu-caGGCCCAGAG---CC-UC
ZEA.MA-C      ggUGGAAGGauaaCAGGCCAcuG-CAgcAUGGGCUCgcuu-aAGGCcuAGAC--Uuc-AU
ARA.TH-F      agUGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcCUGcuGGu-CCGAu
#=GC SS_cons  ..>>>>>>>....>>>>>>>..>.>>...>>>>>>>.......>>>>.>.>>...>>.>>

ZEA.MA-B      uCuuA-GCAaacCaCCAUCUUu
LYC.ES-M      UcCAA--UAaaCaACCACCUUu
ZEA.MA-D      aCuAA-GcAgacCACCAUCUU-
ZEA.MA-C      acUAAaGCAgacCACCAUUUUu
ARA.TH-F      CuCAu-aUGaaCCACCAUUUU-
#=GC SS_cons  ...>>..>>...>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln29.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln29.fa

HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCauGuGGGAAAUGG-gaCU-U
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgG-aaUA-U
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGG-aaUA-U
#=GC SS_cons  ..<<<<<.<<......>>.>>>>....<<<<..>>>>>......<.<<<<<.<...<<.<

HUM.LU-D      UG-GGUCAacCUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAa
ZEA.MA-H      aauugu-ggu-gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCAa
LYC.ES-M      UG-GGCuGUcCCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUCCAa
LYC.ES-K      UG-GGCuuUaCCAgaAGGUu-GGGCUUGG--UGGGcUuaguuCUGGCCUGcCCugUCCAa
LYC.ES-O      UG-GGCuGUcCCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAa
#=GC SS_cons  <<.<<<....<<<...<<...<<<<<<<<...<<<.<<....<<<<.<<<.<<..<<<<.

HUM.LU-D      GCCG-GGAGUuGGGCUG-aGUGACCUgGGCgaagGCU-GGGUUGCgCAGCUCCUagAGuG
ZEA.MA-H      GUUGcGUaGU-ggGUUucGGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAGuG
LYC.ES-M      GCAC-AGAGUuGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuG
LYC.ES-K      GCAC-AGAGUaGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGcG
LYC.ES-O      GCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuG
#=GC SS_cons  <<<<.<<<<<.<<<<<...<<<<<<<..<<....>>..>>>>>>>..>>>>><<..>>.<

HUM.LU-D      GAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGG
ZEA.MA-H      GCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcGCcACCAGCggUGG
LYC.ES-M      GGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGG
LYC.ES-K      GGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGG
LYC.ES-O      GGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGG
#=GC SS_cons  <<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>

HUM.LU-D      AAGGauaaCGGGCCGGUG-CUAcCUGGAUCCacc-auGcUUCACUGGgcUGACUcuUAAu
ZEA.MA-H      AAGGauaaUGagUCGCUa-uGCuaUAGGCCCaau--------------------------
LYC.ES-M      AaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-aguaacGCCuaaUGG-GUuGCU-cCAA-
LYC.ES-K      AaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-aguaacGCCUaaUGG-GuuGCU-cCAA-
LYC.ES-O      AaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGG-GCuGCU-cCAAu
#=GC SS_cons  >.>>....>>>.>>>>>>.>>>.>>>>>>>>........>>...>>>....>>>..>>>.

HUM.LU-D      AGgaCCAUUUCUUuU
ZEA.MA-H      ---------------
LYC.ES-M      UAaaCaACCACCUUu
LYC.ES-K      UAaaCAACCACcUUu
LYC.ES-O      UAaaCCACCACUUU-
#=GC SS_cons  >>..>.>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln30.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln30.fa

TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGu-ggaUGC
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG--aaUG-
TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGu-gaacGC
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG--aaCU-
ORY.SA-B      GCCGAGCCAGguagcgUUGGCUUgucaCCCGagCGGGGGCaauAAGGUGGUGuuggaUGC
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>.....<.<.<<<<.....<<.

TRI.AE-B      UuG---GUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUC
LYC.ES-G      UUG---GGCuGUaCCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUC
TRI.AE-A      UGuu--GUA-Gcg-CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUC
HUM.LU-C      UUG---GGUCAacCCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUC
ORY.SA-B      CugGucGuuuGCg-CUUGgGGUCuGcGCCuGugguUUGcac-uauGCGGCCCGcCCgUUC
#=GC SS_cons  <.....<<<.<...<<<..<<<<.<<<<<<<<....<<.<......<<<.<<<.<<.<<<

TRI.AE-B      CAaGUUG-GuAGU-gGgCUG--GGuGGcUGGGGCgaaaGCUUCGcCUuCU-CAGgC-CU-
LYC.ES-G      CAaGCAC-AGAGUuGGAUCa--uGUGGUCCAaUUgaaaGAaUGGGCUACu-aGAUUCCU-
TRI.AE-A      CAaGUUGcGuAGU-gGACCGccUGGGGCUUAuGCgaaaGC-UGGGUCUCA-CGGUC-CAu
HUM.LU-C      CAaGCCG-GGAGguGGGcUG--aGggaCcugGGCgaagGCUnnnGgngCg-CA-CUCcU-
ORY.SA-B      CAaGUUGcGuAGCguGUGUG--GGGCGCcUGGGCgaagGCUCGaGCGUCCcUGCAC-CU-
#=GC SS_cons  <<.<<<<.<.<<<..<<<<<...<.<<<.<<.<<....>>.>>.>>>.>..>>>>>.<<.

TRI.AE-B      uaAGuGGCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAA
LYC.ES-G      aaAGuGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUG
TRI.AE-A      aaUGuGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcGCUuCCAA
HUM.LU-C      agAcuGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgCUCUCGG
ORY.SA-B      agAGuGGCGGguauugCGUgaggCUGguuucaCAGagcaGCGaguaCCGCCcGCUuCCAA
#=GC SS_cons  ..>>.<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>.>>>>

TRI.AE-B      CggUGGAAGGauaaCAGGCCGcuG-cAgcAUGGGCCCgcuc-uGGGCC-ucCuA--CCcC
LYC.ES-G      CagUGGAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCC-ugaUGG-GCuG
TRI.AE-A      CggUGGAAGGauaaUGGGCCGcUG-CACuCCUAGGCCaau--uGGGCCuCGCAG---CcU
HUM.LU-C      CagUGGAAGGauaaCGGgCcGGUG-CgccUUGagCCaaca--cuGuuC-aACUGGgcUGA
ORY.SA-B      CggUGGAAGGauaaCGGGCCGCug-CAGccCuGGCcCgcuu-ccGGCC--CAAGu-GCcu
#=GC SS_cons  >..>>>>>>>....>>>.>>>..>.>>..>>>>>>>>.......>>>>...>>>...>.>

TRI.AE-B      GCcaU-AGCAgacCACCaUCUUu
LYC.ES-G      CU-cCAAuUAaaCCACCACuUUu
TRI.AE-A      AC-ucCAGCagacCAcC------
HUM.LU-C      CUcuUAAuAGgaCCAUUUCUUuU
ORY.SA-B      uC-CauGGCAgacCACCACCUUu
#=GC SS_cons  >>....>.>>...>>>>.>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln31.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln31.fa

HUM.LU-B      ---GGcCUUAgcaacgUGGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaC-AU
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgG-aaUA-U
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
#=GC SS_cons  ...<<.<.<<......>>.>.>>....<<<<..>>>>.......<.<<<<......<..<

HUM.LU-B      UG-GGUCAGcCCAGUGGauC-gGGuCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAa
LYC.ES-M      UG-GGCuGUcCCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUCCAa
ZEA.MA-H      aauugu-ggu-gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCAa
LYC.ES-G      UG-GGCuGUaCCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAa
ZEA.MA-B      uuGcGAuGGu-uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCAa
#=GC SS_cons  ....<<.<<...<...<....<<<<<<<....<<<.<<....<<<<.<<<.<<..<<<<.

HUM.LU-B      GCCG-GGAGUuGGGCUG-aGUGACCUGGGCgaagGCC-UGGGUUGCg-CAGCUCCUagAG
LYC.ES-M      GCAC-AGAGUuGGAUCA-cGAGGCCCAaAUgaaaAUa-UGGGCUUCu-UGAUUCCUaaAG
ZEA.MA-H      GUUGcGUaGU-ggGUUucGGAUGcCuuGGCgaaaGCU-uuG-CAUCC-cAACa-CUaaAG
LYC.ES-G      GCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAa-UGGGCUACu-aGAUUCCUaaAG
ZEA.MA-B      GUUG-GuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacAG
#=GC SS_cons  <<<<.<<<<<.<<<<<...<<<<<<<..<<....>>...>>>>>>>...>>>>><<..>>

HUM.LU-B      uGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGacuaCC-UCCcGCUCCCGGCag
LYC.ES-M      uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGC-UCCcGCUCUGUGCag
ZEA.MA-H      uGGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCC-GCCcGCcACCAGCgg
LYC.ES-G      uGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaAC-UUCcGCUUUGUGCag
ZEA.MA-B      cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAACgg
#=GC SS_cons  .<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>>..

HUM.LU-B      UGGAAGGauaaCGGGCCGGUG-CUAcUUGGuCCa-cc--auGu-UCACUGGucCUGACUc
LYC.ES-M      UGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG--GUuGCU-
ZEA.MA-H      UGGAAGGauaaUGagUCGCUa-uGCuaUAGGCCCaau-----------------------
LYC.ES-G      UGGAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG--GCuGCU-
ZEA.MA-B      UGGGAGGauaaCAAGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAGA---uCC-UCu-
#=GC SS_cons  >>>>.>>....>>>.>>>>>>.>>>..>>>>>>>..........>...>....>>.>>..

HUM.LU-B      uUAAUcGgaCCAUUUCCUuU
LYC.ES-M      cCAA-UAaaCaACCACCUUu
ZEA.MA-H      --------------------
LYC.ES-G      cCAAuUAaaCCACCACuUUu
ZEA.MA-B      CuuAGCAaacCaCCAUCUUu
#=GC SS_cons  ...>..>.....>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln32.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln32.fa

ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ZEA.MA-C      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGuggaUGCU
ZEA.MA-G      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaauAAGGUGGUGG-aaCAG-
ZEA.MA-F      nCCGAGCUCUguagcgAGAGCUUguaaCCUaagcGGGGGcauuAAGGUGGUGuggaUGUU
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>....<<<<<<<<<....<.<<

ZEA.MA-D      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
ZEA.MA-C      UG--GUaccGu-GUCUuuGCCUGGGUUCAUggugUGcCuu-uguUGGCCUGcCCgUUCCA
ZEA.MA-G      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
ARA.TH-D      uG-GuUCaAu-UCcuCGGGUC-GGAcCUGAugcuGAcaUauaucUGAGCUGcCCaGUCCA
ZEA.MA-F      UccUGAcGGa--UUCUGgGcCUGGGCUUGU-auGUGcCAcuggcCGGCCUGcCCgUUCCA
#=GC SS_cons  <...<<..<...<<<<<.<<<.<<<<<<<.....<<.<......<<<<<<<.<<.<<<<<

ZEA.MA-D      aGUUGGuAGUGgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCUCCAGaCCUgaAG-u
ZEA.MA-C      aGUUGGUAGUGgCCGuuGGAAGCUUGGGCguagGCCcUGGGCUUCCuUGGaCCUauAG-U
ZEA.MA-G      aGUUGGuAGUGgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCUCCAGaCCUgaAG-u
ARA.TH-D      aGCUGUGAGuAAUCUG-UgUGGGUCAGGCgaagGCU-UGACUCAgGCGGAUUCUaaAGuc
ZEA.MA-F      aGUUGGuuGUGgCUGGuGGGG-CUCGGGCgaagGCC-UGGGcCUCUUUAGaCCUgaAG-c
#=GC SS_cons  .<<<<<.<<<<.<<<<.<<<<<<<..<<<....>>>...>>>>>>>>>>>.><<..>>..

ZEA.MA-D      GGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAACggU
ZEA.MA-C      GGCAGgaacggCGUgaggCUGucuucaCAGagcaGCGaucaCU-GCCGGCUAUUAACggU
ZEA.MA-G      GGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCU-GCCcGCUuCCAACggU
ARA.TH-D      GGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCU-UCCcuCUUACAGCagU
ZEA.MA-F      GGCAGgcauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCuuCCAACggU
#=GC SS_cons  <<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>..>

ZEA.MA-D      GGGAGGauaaCAGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG---CC-UCaCuAA
ZEA.MA-C      GGAAGGauaaCAGGCCAcuGCAgcAUGGGCUCgcuuaAGGCcuAGAC--Uuc-AUacUAA
ZEA.MA-G      GGGAGGauaaCGGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG---CC-UCaCuAA
ARA.TH-D      GGAUGGaucaUAGUUCGaAgUCucUCAGaUCCacu-auGGCCCGcuGGu-UcGAuCuCuc
ZEA.MA-F      GGGAGGauaaCAGGCCGcUGCAUuGCAAGCCCaacucGGuC-CAGAG---CC-UCAuuAA
#=GC SS_cons  >>>>>>....>>>>>>>..>>>...>>>>>>>......>>>.>>>>>...>..>>...>>

ZEA.MA-D      -GcAgacCACCAUCUU-
ZEA.MA-C      aGCAgacCACCAUUUUu
ZEA.MA-G      -GcAgacCACCAUCUUu
ARA.TH-D      -CUGgaCCACCACUUU-
ZEA.MA-F      -ACAgacCACCAUCUUu
#=GC SS_cons  .>.>...>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln33.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln33.fa

ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGGgaCG-UU
ARA.TH-G      GUCGAGCUaUguaacgAgAGCUUguaaCCCAagUGGGGACuauAAGAUGGUGGaaCAc-U
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGGgaCAc-U
HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCauGuGGGAAAUGGgaCU-UU
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>...<<<<<<<<<<..<<..<

ARA.TH-C      GGGUcGauCUcAUUGGGcCGGgUUcGGguuGGGcUAuauucUGGCCCGcCCaUUCCAaGU
ARA.TH-G      GgauCGGc-CCA-CGGGUCGGAUUUGUuguUGGcauaggucUGGACUGcCCaaUCCAaGC
LYC.ES-I      GGGCuGUa-CCAgauGGUuGGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUCCAaGC
ARA.TH-F      GGuUCGGu-UCcuCGGaUCGGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCAaGC
HUM.LU-D      GGGUCAac-CUAGUGGAuCGGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaGC
#=GC SS_cons  <<.<.<...<<<.<<<<.<<<<<<<<<...<<<........<<<<<<<.<<..<<<<.<<

ARA.TH-C      UGGGAGUuGAGGCA-UGGGcUUCGAGCgaagGCUCGGGuCUCAUGUCUUCUagAG-uGGG
ARA.TH-G      UGuGAGU-gAACCG-UAUGaAcCAAGCgaagGUUUGaUcCGUACGGUUgCUaaAGguuGA
LYC.ES-I      UUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg-uGGG
ARA.TH-F      UGUGAGU-AAUUaguguUGAGUUGAGCgaagGCUUGGCUUGca--GGUUCUagAGucGGA
HUM.LU-D      CGGGAGUuGGGCUG-aGUGACCUgGGCgaagGCU-GGGUUGCgCAGCUCCUagAG-uGGA
#=GC SS_cons  <<<<<<<.<<<<<<..<<<.<<<<<<<....>>>>>>>.>>>.>>>>>><<..>>..<<<

ARA.TH-C      GGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCCUCCcGCUCUUGACggUGGAA
ARA.TH-G      GGguauugCGUuaggCUGgcuucaCAGagcaGCGacuaCCUCccGCUCuCAGCagUGGAc
LYC.ES-I      gCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAa
ARA.TH-F      GGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUGGAC
HUM.LU-D      GGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGGAA
#=GC SS_cons  <<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.

ARA.TH-C      GGauuaCGGGCCAuUG-CCU-UCcGAgCCcacu-auGaCCCAAUaAG-CcGCU-cCGAuU
ARA.TH-G      GGacaaCGGUUCGacg-CCAcACAAAUCCacu--auGGUCCGcUGGcUCGuaaccCGcuU
LYC.ES-I      GGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCCugaUGG-GUuGCU-cCAAuU
ARA.TH-F      GGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcCUGcuGGuCCGAuC-uCAuaU
HUM.LU-D      GGauaaCGGGCCGGUG-CUAcCUGGAUCCacc--auGcUUCACUGGgcUGACUcuUAAuA
#=GC SS_cons  >>....>>>>>>>....>>>.>>>>>>>>.......>.>>>>.>>>..>.>.>..>>..>

ARA.TH-C      GgaCCAUCaCUUU-
ARA.TH-G      GaaCCACCAUUUU-
LYC.ES-I      AaaCCACCAUuUUu
ARA.TH-F      GaaCCACCAUUUU-
HUM.LU-D      GgaCCAUUUCUUuU
#=GC SS_cons  >..>>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln34.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln34.fa

ARA.TH-A      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAcU
ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGG-gaCG-U
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>...<<<<<<<.<<...<<.<

ARA.TH-A      G--GUUcGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCA
ARA.TH-C      UG-GGUcGauCUcAUUGGGcC-GGgUUcGGguuGGGcUAuauucUGGCCCGcCCaUUCCA
CIN.HYB.      UGaGCUuGgc-UUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCA
ZEA.MA-B      uuGcGAuGGu--uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCA
LYC.ES-B      UG-GGCuGUa-CCAgauGGUu-GGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUCCA
#=GC SS_cons  <..<<<.<...<.<...<....<<<<<<<....<<<.<......<<<<<<<.<<.<<<<<

ARA.TH-A      aGCUGUGAGU-AAUUaG-uguUGAGUUGAGCgaagGCU-UGGCUCAug-CaGGUUCUagA
ARA.TH-C      aGUUGGGAGUuGAGGCA--UGGGcUUCGAGCgaagGCU-CGGGuCUCA-UGUCUUCUagA
CIN.HYB.      AGUCGAGAGugGGUUCA--UGUUuCCUGAGCgaagGCU-CGGGuGAUG-UGAGCUUUagA
ZEA.MA-B      aGUUGGuAGU-GUCUGaC-GGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacA
LYC.ES-B      aGCUUAGAGUuGGAUCA--uGUGGcCCAaUUgaagAAa-UGGaCUACu-UGAUUCgUaaA
#=GC SS_cons  .<<<<<<<<<.<<<<<<...<<<.<<<<<<<....>>>.>>>>.>>>..>>>>>><<..>

ARA.TH-A      G-ucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUACAG
ARA.TH-C      G--uGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCC-UCCcGCUCUUGA
CIN.HYB.      Au-cGGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCC-UCUacCUCUCGA
ZEA.MA-B      G--cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAA
LYC.ES-B      g--uGGGGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGU-UUCcGCUCUAAG
#=GC SS_cons  >...<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>

ARA.TH-A      CagUGGACGGaucaCGGUUUAGcg-UCgc-UCAGAACCacu--auGGcCUGcuGG--UCc
ARA.TH-C      CggUGGAAGGauuaCGGGCCAuUG-CCU--UCcGAgCCcacu-auGaCCCAAUaAG--Cc
CIN.HYB.      CUgUGGAAGGauuaCAAGCCGGaGUGUC--uUAGGCUC-auauaaccag-cCUGG---Cu
ZEA.MA-B      CggUGGGAGGauaaCAAGCCGcuG-CACu-uUGAGCCCaaca-cAGaCCCAGA---uCC-
LYC.ES-B      CggUGGAaGGauaaCGAGUCGGUG-UUC-uCUGAGUCCagu--aauGCCugaUGG--GCu
#=GC SS_cons  >..>>>>>>>....>>>>>>>..>.>>>...>>>>>>>..........>...>.>...>.

ARA.TH-A      GAUcuCAuaUGaaCCACCAUUUU-
ARA.TH-C      GCUcCGA-uUGgaCCAUCaCUUU-
CIN.HYB.      AGCcCAA-cAGgaCAcCCAUUU--
ZEA.MA-B      UCuCuuA-GCAaacCaCCAUCUUu
LYC.ES-B      GCUcUAA-uUAaaCCACCACuUUu
#=GC SS_cons  >>>..>>..>>..>>.>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln35.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln35.fa

LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCauGuGGGAAAUGG-gaCU-U
HUM.LU-A      GCCGGuCUUAgcaacgUGGGcCUguaaCCCAagUGGGGGCauGuGGGAAAUGG-gaCU-U
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>....<.<<<<<<<...<<.<

LYC.ES-I      UG-GGCuGUa-CCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUCCA
ZEA.MA-D      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
HUM.LU-D      UG-GGUCAac-CUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCA
HUM.LU-A      UG-GGUCAac-CUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCA
LYC.ES-G      UG-GGCuGUa-CCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCA
#=GC SS_cons  <<.<<<.<...<<<...<<...<<<<<<<<...<<<.<<....<<<<<<<<.<<..<<<<

LYC.ES-I      aGCUUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguG
ZEA.MA-D      aGUUGGuAGU-GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCUCCAGaCCUgaAGuG
HUM.LU-D      aGCCGGGAGUuGGGCUG-aGUGACCUgGGCgaagGCU-GGGUUGCgCAGCUCCUagAGuG
HUM.LU-A      aGCCGGGAGUuGGgcUG-aGUGACCUGGgCgaagGgCUGGGUUGCgCAcgUCCUagAGuG
LYC.ES-G      aGCACAGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuG
#=GC SS_cons  .<<<<<<<<<.<<<<<<..<<<<<<<..<<....>>..>>>>>>>.>>>>>><<..>>.<

LYC.ES-I      GGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG--UUUcGCUCUAAGCggUG
ZEA.MA-D      GCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAACggUG
HUM.LU-D      GAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcGCUCUCGGCagUG
HUM.LU-A      GAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcGCUCUCGGCagUG
LYC.ES-G      GGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaAC-UUCcGCUUUGUGCagUG
#=GC SS_cons  <<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>>..>>

LYC.ES-I      GAaGGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCCugaUGG-GUuGCU-cCA
ZEA.MA-D      GGAGGauaaCAGGCCGcuG-CACuuCGAGCCCaacu-caGGCCCAGAG--CC-UCa-CuA
HUM.LU-D      GAAGGauaaCGGGCCGGUG-CUAcCUGGAUCCacc--auGcUUCACUGGgcUGACUcuUA
HUM.LU-A      GAAGGauaaCGGGCCGGUG-CUAcCUGGGUCCacc--auGcUUCACUAGgcUGACUcuUA
LYC.ES-G      GAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-GCuGCU-cCA
#=GC SS_cons  >>.>>....>>>>>>>>>>.>>>.>>>>>>>>.........>>...>>>..>.>>>..>>

LYC.ES-I      AuUAaaCCACCAUuUUu
ZEA.MA-D      AGcAgacCACCAUCUU-
HUM.LU-D      AuAGgaCCAUUUCUUuU
HUM.LU-A      AuAGgaCCAUUUCUUuU
LYC.ES-G      AuUAaaCCACCACuUUu
#=GC SS_cons  >.>>..>>>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln36.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln36.fa

LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
ZEA.MA-A      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGugaaUGCU
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGG-gaCG-U
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>....<<.<<<<<<....<<.<

LYC.ES-B      UG-GGCuGUa--CCAgauGGUu--GGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUC
ZEA.MA-A      UuGcGAuGGcu--UUCUGGGCCcuGGGCUCGu--uGUGaCAcuggcCGGCUUGcCCaUCC
ZEA.MA-D      UuGcGAuGGcu--UUCUGGGCCc-GGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCC
ARA.TH-C      UG-GGUcGau-CUcAUUGGGcC--GGgUUcGGguuGGGcUAuauucUGGCCCGcCCaUUC
LYC.ES-I      UG-GGCuGUa--CCAgauGGUu--GGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUC
#=GC SS_cons  <...<<.<<....<<...<<<...<<<<<<<....<<<.<<.....<<<<<<<.<<..<<

LYC.ES-B      CAaGCUUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAa-UGGaCUACu-UGAUUCgUaa
ZEA.MA-A      CAaGUUGGuAGU-GUCUGgUGGGGGCUCuAGCgaaaGCUuuGGGUCUCUG-CAGACCUgg
ZEA.MA-D      CAaGUUGGuAGU-GgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUga
ARA.TH-C      CAaGUUGGGAGUuGAGGCA-UGGGcUUCGAGCgaagGCU-CGGGuCUCA-UGUCUUCUag
LYC.ES-I      CAaGCUUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAa-UGGaCUACu-UGAUUCgUaa
#=GC SS_cons  <<.<<<<<.<<<.<<<<<<..<<<<.<<..<<....>>...>>.>>>>..>>>>>>.<..

LYC.ES-B      AguGGGGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGU-UUCcGCUCUAAGC
ZEA.MA-A      AGCGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCU-GCCGACUcCCAAC
ZEA.MA-D      AGuGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAAC
ARA.TH-C      AGuGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCC-UCCcGCUCUUGAC
LYC.ES-I      AguGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG--UUUcGCUCUAAGC
#=GC SS_cons  >..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>

LYC.ES-B      ggUGGAaGGauaaCG-AGUCGGUG-UUC-uCUGAGUCCagu--aauGCCugaUGG-GCuG
ZEA.MA-A      ggUGGGAGGauaaCGaAGCCGcUG-CACu-uUGAGCCUaacu-caGGCUCAGAA--CC-U
ZEA.MA-D      ggUGGGAGGauaaCA-GGCCGcuG-CACu-uCGAGCCCaacu-caGGCCCAGAG--CC-U
ARA.TH-C      ggUGGAAGGauuaCG-GGCCAuUG-CCU--UCcGAgCCcacu-auGaCCCAAUaAG-CcG
LYC.ES-I      ggUGGAaGGauaaCG-AGUCGGUGuUCU--CUGAGUCC-ag-uaacGCCugaUGG-GUuG
#=GC SS_cons  ..>>>>.>>....>>.>>>>>.>>.>>>...>>>>>>>........>>>...>>..>>.>

LYC.ES-B      CUcUAAuUAaaCCACCACuUUu
ZEA.MA-A      CaCuAAGCAaacCACCAUCUUu
ZEA.MA-D      CaCuAAGcAgacCACCAUCUU-
ARA.TH-C      CUcCGAuUGgaCCAUCaCUUU-
LYC.ES-I      CUcCAAuUAaaCCACCAUuUUu
#=GC SS_cons  >...>>.>>...>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln37.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln37.fa

ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGG-aaCAc-
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
ZEA.MA-A      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGugaaUGCU
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUg-aaU-AU
#=GC SS_cons  .<<<<<<<.<......>.>>>>>....<<<<..>>>>>>....<<<<.<<.<....<<<<

ARA.TH-E      UG-GuUCGGg-UCcaCGGGCC--GGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCC
ZEA.MA-B      uuGcGAuGGu--uUCUGGGcCU-GGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCC
ZEA.MA-A      UuGcGAuGGcu-UUCUGGGCCcuGGGCUCGu--uGUGaCAcuggcCGGCUUGcCCaUCCC
TRI.AE-B      uG-GUGcGGu--UuGuuGGCCU-GGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCC
LYC.ES-H      UG-GGCuGUa-CCAgauGGUu--GGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCC
#=GC SS_cons  ....<<.<<...<....<<<<..<<<<<<<....<<<.<......<<<<<<<.<<.<<<<

ARA.TH-E      AaGCUGUGAGU-AAGaCG-UgUGuGUCAAGCgaagGCU-UGGCuCAaA-CGgCUUCUaaA
ZEA.MA-B      AaGUUGGuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacA
ZEA.MA-A      AaGUUGGuAGU-GUCUGgUGGGGGCUCuAGCgaaaGCUuuGGGUCUCUG-CAGACCUggA
TRI.AE-B      AaGUUGGuAGU-gGgCUG-GGuGGcUGGGGCgaaaGCU-UCGcCUuCU-CAGgC-CUuaA
LYC.ES-H      AaGCuUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAa-UGGaCUACu-UGAUUCgUaaA
#=GC SS_cons  <.<<<<<.<<<.<<<<<..<<<<..<<.<<<....>>>..>>..>>>>..>>>>><<..>

ARA.TH-E      GuuGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCU-UCCcGCUUACAGC
ZEA.MA-B      G-cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAAC
ZEA.MA-A      G-CGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCU-GCCGACUcCCAAC
TRI.AE-B      G-uGGCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCU-GCC-GCUuCCAAC
LYC.ES-H      g-uGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGC-UCCcGCUCUGuGC
#=GC SS_cons  >..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>

ARA.TH-E      agUGGACGGaucaCA-GUUUAGcg-UCGcuCAGAACCacu--auGGCCUGcuGGu-CCGA
ZEA.MA-B      ggUGGGAGGauaaCA-AGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAGA---uCC-U
ZEA.MA-A      ggUGGGAGGauaaCGaAGCCGcUG-CACuuUGAGCCUaacu-caGGCUCAGAA---CC-U
TRI.AE-B      ggUGGAAGGauaaCA-GGCCGcuG-cAgcAUGGGCCCgcuc-uGGGCCucCuA---CCcC
LYC.ES-H      agUGGAaGGauaaUG-GGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG--GUuG
#=GC SS_cons  ..>>>>>>>....>>.>>>>>..>.>>>..>>>>>>>.......>>>>....>...>>.>

ARA.TH-E      uC-uCAuaUGaaCCACCAUUUu-
ZEA.MA-B      Cu-CuuAGCAaacCaCCAUCUUu
ZEA.MA-A      Ca-CuAAGCAaacCACCAUCUUu
TRI.AE-B      GCcaU-AGCAgacCACCaUCUUu
LYC.ES-H      CU-cCAAUaAacaAcCacCUUUu
#=GC SS_cons  >.....>>>>...>.>>.>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln38.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln38.fa

ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaauAAGGUGGUGG--aaCAG
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGG--aaUA-
ORY.SA-B      GCCGAGCCAGguagcgUUGGCUUgucaCCCGagCGGGGGCaauAAGGUGGUGuuggaUGC
HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCauGuGGGAAAUGG--gaCU-
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgG--aaUA-
#=GC SS_cons  <.<<<<<<..........>>>>>....<<<<..>>>>>.>...<<<<<<<<<<....<<.

ARA.TH-D      -uG---GuUCaAuUCcuCGGGUC-GGAcCUGAugcuGAcaUauaucUGAGCUGcCCaGUC
LYC.ES-O      UUG---GGCuGUcCCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUC
ORY.SA-B      CugGucGuuuGCg-CUUGgGGUCuGcGCCuGugguUUGcac-uauGCGGCCCGcCCgUUC
HUM.LU-D      UUG---GGUCAacCUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUC
LYC.ES-M      UUG---GGCuGUcCCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUC
#=GC SS_cons  <.<...<.<.<<.<<<...<<<..<<<<<<<<...<<<..<....<<<<<<<<.<<..<<

ARA.TH-D      CAaGCUG-UGAGu-AAUCUGUgUGGGUCAGGCgaagGCUUGACUCAgG-CGGAUUCUaaA
LYC.ES-O      CAaGCAC-AGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACu-aGAUUCCUaaA
ORY.SA-B      CAaGUUGcGuAGCguGUGUGGGGCGCcUGGGCgaagGCUCGaGCGUCCcUGCAC-CUagA
HUM.LU-D      CAaGCCG-GGAGUuGGGCUGaGUGACCUgGGCgaagGCU-GGGUUGCg-CAGCUCCUagA
LYC.ES-M      CAaGCAC-AGAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUCCUaaA
#=GC SS_cons  <<.<<<<.<<<<<.<<<<<<.<<<<<<<<.<<....>>.>>>>>>>>..>>>>>><<..>

ARA.TH-D      GucGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcuCUUACAGCa
LYC.ES-O      G-uGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCa
ORY.SA-B      G-uGGCGGguauugCGUgaggCUGguuucaCAGagcaGCGaguaCCGCCcGCUuCCAACg
HUM.LU-D      G-uGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCa
LYC.ES-M      G-uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCa
#=GC SS_cons  >..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>.

ARA.TH-D      gUGGAUGGaucaUAGUUCGaAg-UCucUCAGaUCCacu--auGGCCCGcuGGuUcGAuC-
LYC.ES-O      gUGGAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-GCuGCU-
ORY.SA-B      gUGGAAGGauaaCGGGCCGCug-CAGccCuGGCcCgcuu-ccGGCC-CAAGu-GCcuuC-
HUM.LU-D      gUGGAAGGauaaCGGGCCGGUG-CUAcCUGGAUCCacc--auGcUUCACUGGgcUGACUc
LYC.ES-M      gUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG-GUuGCU-
#=GC SS_cons  .>>>>.>>....>>>>>>>>>..>>>.>>>>>>>>........>>>...>>>.>>.>.>.

ARA.TH-D      uCucCUGgaCCACCACUUU-
LYC.ES-O      cCAAuUAaaCCACCACUUU-
ORY.SA-B      CauGGCAgacCACCACCUUu
HUM.LU-D      uUAAuAGgaCCAUUUCUUuU
LYC.ES-M      cCAA-UAaaCaACCACCUUu
#=GC SS_cons  .>.>.>>..>>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln39.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln39.fa

LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
CIN.HYB.      ACCGGGCUuGguaacgCuAGUCUauaaCUCAagUGAGGGUaucaAAGUGGuUG-aaCU-U
ARA.TH-A      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAcU
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
#=GC SS_cons  <<<<<<<<..........>>>>>....<<<<..>>>>>>>...<<.<<<<<<<...<<.<

LYC.ES-B      UG-GGCuGUaCCAgauGGUu-GGGCUUGGu--GGGcUAauuuCUGACUUGcCCuaUCCAa
LYC.ES-G      UG-GGCuGUaCCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAa
CIN.HYB.      UGaGCUuGgcUUAGcuaguu-GGGUCUGu--aGACACcgcacCUGGCUUGcCCgUUCCAA
ARA.TH-A      G--GUUcGGuUCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCAa
TRI.AE-B      uG-GUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCCAa
#=GC SS_cons  <<.<<<.<<.<<....<.<..<<<<<<<<....<<.<.....<<<<<<<<.<<..<<<<.

LYC.ES-B      GCUUAGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg--u
LYC.ES-G      GCACAGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAG--u
CIN.HYB.      GUCGAGAGugGGUUCA-UGUUuCCUGAGCgaagGCUCGGGuGAUGUGAGCUUUagAAu-c
ARA.TH-A      GCUGUGAGU-AAUUaGuguUGAGUUGAGCgaagGCUUGGCUCAugCaGGUUCUagAG-uc
TRI.AE-B      GUUGGuAGU-gGgCUG-GGuGGcUGGGGCgaaaGCUUCGcCUuCUCAGgC-CUuaAG--u
#=GC SS_cons  <<<<<<<<<.<<<<<<..<<<<.<<<.<<....>>.>>>.>>>>.>>>>>><<..>>...

LYC.ES-B      GGGGCggaaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggUG
LYC.ES-G      GGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUG
CIN.HYB.      GGGGGgcaaugCGUuaggCUGguuucaCAGagcuGCGaaaaCCUCUacCUCUCGACUgUG
ARA.TH-A      GGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUG
TRI.AE-B      GGCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAACggUG
#=GC SS_cons  <<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>

LYC.ES-B      GAaGGauaaCGAGUCGGUG-UUC-uCUGAGUCCagu--aauGCCugaUGGGCuGCU-cUA
LYC.ES-G      GAaGGauaaCGGaCCGGUGcCUU--CCAAGUUCcau-uaauGCCugaUGGGCuGCU-cCA
CIN.HYB.      GAAGGauuaCAAGCCGGaGUGUC--uUAGGCUC-auauaaccag-cCUGG-CuAGC-cCA
ARA.TH-A      GACGGaucaCGGUUUAGcg-UCgc-UCAGAACCacu--auGGcCUGcuGGUCcGAU-cuC
TRI.AE-B      GAAGGauaaCAGGCCGcuG-cAgc-AUGGGCCCgcuc-uGGGCCucCuA-CCcCGCcaU-
#=GC SS_cons  >>.>>....>>>>>>>>.>.>>...>>>>>>>>........>.>....>>>>.>>>..>>

LYC.ES-B      A-uUAaaCCACCACuUUu
LYC.ES-G      A-uUAaaCCACCACuUUu
CIN.HYB.      A-cAGgaCAcCCAUUU--
ARA.TH-A      AuaUGaaCCACCAUUUU-
TRI.AE-B      A-GCAgacCACCaUCUUu
#=GC SS_cons  >..>>..>>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln40.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln40.fa

ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcau-uAAGGUGGcGc-ggaUG
ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaa-uAAGGUGGUGG--aaCA
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCau-uAAuGUGGUGG--aaUG
ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
ZEA.MA-C      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcau-uAAGGUGGUGu-ggaUG
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>.....<<<<<<<.<.....<<

ZEA.MA-B      CUuuG---cGAuGGu---uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCC
ARA.TH-D      G-uG----GuUCaAu--UCcuCGGGUC-GGAcCUGAugcuGAcaUauaucUGAGCUGcCC
LYC.ES-I      -UUG----GGCuGUa--CCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCC
ORY.SA-A      uUUGgugUGGAuucu-GAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCC
ZEA.MA-C      CUUG-----GUaccGu--GUCUuuGCCUGGGUUCAUggugUGcCuu-uguUGGCCUGcCC
#=GC SS_cons  .<.<.....<<.......<..<.<<<<.<<<.<<<.....<<.<......<<<<<<<.<<

ZEA.MA-B      aUCCCAaGUUG-GuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGA
ARA.TH-D      aGUCCAaGCUG-UGAGu-AAUCUG-UgUGGGUCAGGCgaagGCU-UGACUCAgG-CGGAU
LYC.ES-I      uaUCCAaGCUU-AGAGUuGGAUCA-uGUGGcCCAaUUgaagAAa-UGGaCUACu-UGAUU
ORY.SA-A      gUUCCAaGuUGcGuAGU-GGGccGGaGGGGCuuuGGCgaagGCC-uuuGCUUUgCUucUC
ZEA.MA-C      gUUCCAaGUUG-GUAGU-GgCCGuuGGAAGCUUGGGCguagGCCcUGGGCUUCC-uUGGa
#=GC SS_cons  .<<<<<.<<<<.<.<<<.<<<<<...<<<<<<<.<<<....>>>..>>>>>>>...>>>>

ZEA.MA-B      C----CUacAG-cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCC
ARA.TH-D      U----CUaaAGucGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCU-UCC
LYC.ES-I      C----gUaaAg-uGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG--UUU
ORY.SA-A      CggccCUaaAG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCU-GCC
ZEA.MA-C      C----CUauAG-UGGCAGgaacggCGUgaggCUGucuucaCAGagcaGCGaucaCU-GCC
#=GC SS_cons  >....<<..>>..<<<<<......<<<....<<<......>>>....>>>....>>.>>>

ZEA.MA-B      cACUuCCAACggUGGGAGGauaaCAAGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAG
ARA.TH-D      cuCUUACAGCagUGGAUGGaucaUAGUUCGaAg-UCucUCAGaUCCacu--auGGCCCGc
LYC.ES-I      cGCUCUAAGCggUGGAaGGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCCuga
ORY.SA-A      cGCUuCCAuCggUGGAAGGauaaCAGGCUGcuG-cACcuUGGgcccgcuu-cuGGCCCAG
ZEA.MA-C      GGCUAUUAACggUGGAAGGauaaCAGGCCAcuG-CAgcAUGGGCUCgcuu-aAGGCcuAG
#=GC SS_cons  .>>>.>>>>>..>>>>>>>....>>>>>>>..>.>>...>>>.>>>.......>>>>.>.

ZEA.MA-B      A---uCC-UCu-CuuA-GCAaacCaCCAUCUUu
ARA.TH-D      uGGu-UcGAuC-uCuc-CUGgaCCACCACUUU-
LYC.ES-I      UGG--GUuGCU-cCAA-uUAaaCCACCAUuUUu
ORY.SA-A      aGUC--ccUCUA-CAA--CAgaCcaCCAUCUUU
ZEA.MA-C      AC--Uuc-AUa-cUAAaGCAgacCACCAUUUUu
#=GC SS_cons  .>......>>...>.>..>>...>.>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln41.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln41.fa

ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUG-aaUA-U
LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGG-aaUA-U
ZEA.MA-E      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGG-aaCU-U
#=GC SS_cons  ..<<<<<<<<......>>>>>>>....<<<<..>>>>>......<.<<<<<<....<..<

ZEA.MA-H      aauugu-ggu--gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCA
LYC.ES-A      UG-GGCuuUa-CCAgaAGGUu-GGGCUUGGU--GGGcUuaguuCUGGCCUGcCCugUCCA
LYC.ES-E      UG-GGCuGUc-CCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCA
ZEA.MA-E      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
HUM.LU-C      UG-GGUCAac-CCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCCA
#=GC SS_cons  <...<<......<<...<....<<<<<<<....<<<.<.....<<<<.<<<.<<..<<<<

ZEA.MA-H      aGUUGcGUaGU-ggGUUucGGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAGu
LYC.ES-A      aGCAC-AGAGUuGGAUCu-cGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAGu
LYC.ES-E      aGUAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGu
ZEA.MA-E      aGUUG-GuAGU-GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCUCCAGaCCUgaAGU
HUM.LU-C      aGCCG-GGAGguGGGcUG-aGggaCcugGGCgaagGCUnnnGgngCgCA-CUCcUagAcu
#=GC SS_cons  .<<<<.<<<<<.<.<<<...<<<<<<...<<....>>...>>>>>>..>>>.><<..>>.

ZEA.MA-H      GGCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCC-GCCcGCcACCAGCggU
LYC.ES-A      GGGGCGgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGC-UCCcGCUCUGUGCagU
LYC.ES-E      GGGGUggacc-CGUgaggCUGguuucaCAGagcaACGaaaaAC-UUCcGCUUUGUGCagU
ZEA.MA-E      GGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCGGCUuCCAACggU
HUM.LU-C      GGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCcgCUCUCGGCagU
#=GC SS_cons  <<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>>..>

ZEA.MA-H      GGAAGGauaaUGagUCGCUa-uGCu-aUAGGCCCaau-----------------------
LYC.ES-A      GGAaGGauaaUGGGUCGGuG-UCUuAUCAAGUUCagu--aacGCCUaaUGG-GuuGCU-c
LYC.ES-E      GGAaGGauaaCGGaCCGGUGcCUU--CCAAGUUCcau-uaauGCCugaUGG-GCuGUU-c
ZEA.MA-E      GGGAGGauaaCGGGCCGcuG-CACu-uCGAGCCCaacu-caGGCCCAGAG--CC-UCa-C
HUM.LU-C      GGAAGGauaaCGGgCcGGUG-Cgcc-UUGagCCaaca--cuGuuCaACUGGgcUGACUcu
#=GC SS_cons  >>>.>>....>>>.>>>>.>.>>>...>>>>>>>..........>...>>.....>>...

ZEA.MA-H      --------------------
LYC.ES-A      CAA-UAaaCAACCACcUUu-
LYC.ES-E      UAGuUAaaCUACCACaUUuu
ZEA.MA-E      uAAGcAgacCACCAUCUUu-
HUM.LU-C      UAAuAGgaCCAUUUCUUuU-
#=GC SS_cons  .>>..>...>>>>>>.>...
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln42.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln42.fa

LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGGaaUA-UU
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGGaaUG-UU
LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGGaaUA-UU
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaauAAGGUGGUGGaaCAG-u
#=GC SS_cons  <<<<<<<<<........>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<..<<.<<

LYC.ES-O      GGGCuGUcCCAgauGGCuGGGCUUGG--uGGGcUA-auuuCUGGcCUGcCCuaUCCAaGC
LYC.ES-F      GGGUccauCUugauGGaUGGGCUUGA--aGGGcUAauguuCUGGCCUGcCCugUCCAaGC
LYC.ES-E      GGGCuGUcCCAgauGGCuGGGCUUGG--uGGGcUA-auuuCUGGcCUGcCCuaUCCAaGU
LYC.ES-I      GGGCuGUaCCAgauGGUuGGGCUUGG--uGGGcUA-auuuCUGACUUGcCCuaUCCAaGC
ARA.TH-D      GGuUCaAuUCcuCGGGUCGGAcCUGAugcuGAcaU-auaucUGAGCUGcCCaGUCCAaGC
#=GC SS_cons  <<<<..<.<<....<<<.<<<<<<<<...<<<.<<.....<<<<.<<<.<<..<<<<.<<

LYC.ES-O      ACAGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAG-uGGGG
LYC.ES-F      ACAGAGUuGGGUCAAGUGGuCUAUACgaaaGUAUAG-CCACUUGGCCUUUagAG-uGGGA
LYC.ES-E      ACAGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAG-uGGGG
LYC.ES-I      UUAGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAg-uGGGg
ARA.TH-D      UGUGAGu-AAUCUGUgUGGGUCAGGCgaagGCUUGACUCAgGCGGAUUCUaaAGucGGAG
#=GC SS_cons  <<<<<<<.<<<<<..<<<<.<<<.<<....>>.>>>.>>>>..>>>>><<..>>..<<<<

LYC.ES-O      UggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaG
LYC.ES-F      UggacugCGUgaggCUGguuucaCAGagcaACGacuaGUCCCcGCUCUGUGCagUGGAaG
LYC.ES-E      Uggacc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaG
LYC.ES-I      CggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaG
ARA.TH-D      GguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcuCUUACAGCagUGGAUG
#=GC SS_cons  <......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>

LYC.ES-O      GauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-GCuGCUcCAAuUAa
LYC.ES-F      GaucaCGGGCUAGUGcUCU-UUGAGUCCuaacaaaAaCCugauAG-guuGCC-UAAuUAa
LYC.ES-E      GauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG-GCuGUUcUAGuUAa
LYC.ES-I      GauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCCugaUGG-GUuGCUcCAAuUAa
ARA.TH-D      GaucaUAGUUCGaAg-UCucUCAGaUCCacu--auGGCCCGcuGGuUcGAuCuCucCUGg
#=GC SS_cons  >....>>>.>>>>>>.>>>.>>>>>>>>........>>>....>>.>..>>>.>>>.>>.

LYC.ES-O      aCCACCACUUU--
LYC.ES-F      aCCAUCACuUUu-
LYC.ES-E      aCUACCACaUUuu
LYC.ES-I      aCCACCAUuUUu-
ARA.TH-D      aCCACCACUUU--
#=GC SS_cons  .>>>>>>>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln43.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln43.fa

TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGG-aaUA-U
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAc-
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGG-aaUG-U
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>....<<.<.<<<<....<<.<

TRI.AE-A      GuuGUA-Gcg-CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCAa
LYC.ES-E      UG-GGCuGUcCCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCuaUCCAa
ARA.TH-F      UG-GuUCGGuUCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCAa
TRI.AE-B      uG-GUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCCAa
LYC.ES-C      UG-AACAugcCCAgaAGGUA-GGGCUUGUG--UGAcaAuucuCUGGCcUGcCCugUCCAa
#=GC SS_cons  <<.<<<.<...<....<<<<.<<<<<<<<....<<........<<<<<<<.<<..<<<<.

TRI.AE-A      GUUGcGuAGU-gGACCGcc-UGGGGCUUAuGCgaaaGC-UGGGUCUCACGGUC-CAuaaU
LYC.ES-E      GUAC-AGAGUuGGAUCa---uGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCU-aaA
ARA.TH-F      GCUG-UGAGU-AAUUag--uguUGAGUUGAGCgaagGCUUGGCUUGca--GGUUCU-agA
TRI.AE-B      GUUG-GuAGU-gGgCUG---GGuGGcUGGGGCgaaaGCUUCGcCUuCUCAGgC-CU-uaA
LYC.ES-C      GCAa-AGAGUuGGGUCU---uGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCU-aaA
#=GC SS_cons  <<<<.<.<<<..<<<<.....<<<<.<<<.<<....>>.>>>.>>>>..>>>>.<<...>

TRI.AE-A      G-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcGCUuCCAACg
LYC.ES-E      G-uGGGGUggacc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCa
ARA.TH-F      GucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAGCa
TRI.AE-B      G-uGGCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAACg
LYC.ES-C      G-uGGGGUggacugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCa
#=GC SS_cons  >..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>.>>>>>.

TRI.AE-A      gUGGAAGGauaaUGGGCCGcUG-CACu-CCUAGGCCaau--uGGGCCuCGCAG---CcUA
LYC.ES-E      gUGGAaGGauaaCGGaCCGGUGcCUU--CCAAGUUCcau-uaauGCC-ugaUGG-GCuGU
ARA.TH-F      gUGGACGGaucaCGGUUUAGcg-UCgc-UCAGAACCacu--auGGcC-UGcuGGuCCGAu
TRI.AE-B      gUGGAAGGauaaCAGGCCGcuG-cAgc-AUGGGCCCgcuc-uGGGCC-ucCuA--CCcCG
LYC.ES-C      gUGGAaGGauaaCGaGCCAGUg-UCA-UAUAAGUUCaac-gaaUGUC-UgaUGG-gcUGU
#=GC SS_cons  .>>>>.>>....>>>>>>>....>>...>>>>>>>>.......>>>>.....>...>.>>

TRI.AE-A      C-ucCAGCagacCAcC-------
LYC.ES-E      U-cUAGuUAaaCUACCACaUUuu
ARA.TH-F      C-uCAuaUGaaCCACCAUUUU--
TRI.AE-B      CcaU-AGCAgacCACCaUCUUu-
LYC.ES-C      U-cUAGuUAaaCUACCACAUUu-
#=GC SS_cons  >..>>>.>>...>>>>.>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln44.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln44.fa

TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAc-
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGG-aaUG-U
HUM.JA-B      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGG-gaCU-U
ZEA.MA-C      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGuggaUGCU
#=GC SS_cons  .<<<<<<<<........>>>>>>....<<<<..>>>>>>.....<.<<<<<<....<<.<

TRI.AE-A      GuuGUA-Gcg--CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCA
ARA.TH-F      UG-GuUCGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCA
LYC.ES-I      UG-GGCuGUa-CCAgauGGUu-GGGCUUGG--uGGGcUAauuuCUGACUUGcCCuaUCCA
HUM.JA-B      UA-GuUCGGc-cCAuUGGAUC-GGaUCCAGuguUAGcUGcuugCUGGgCUGcCCaUUCCA
ZEA.MA-C      UG--GUaccGu-GUCUuuGCCUGGGUUCAUggugUGcCuu-uguUGGCCUGcCCgUUCCA
#=GC SS_cons  <<.<.<.<....<<.<.<<<<.<<<<<<<<....<<.<......<<<<<<<.<<.<<<<<

TRI.AE-A      aGUUGcGuAGU-gGACCGcc-UGGGGCUUAuGCgaaaGC--UGGGUCUCACGGUC-CAua
ARA.TH-F      aGCUG-UGAGU-AAUUag--uguUGAGUUGAGCgaagGCU-UGGCUUGca--GGUUCU-a
LYC.ES-I      aGCUU-AGAGUuGGAUCA---uGUGGcCCAaUUgaagAAa-UGGaCUACuUGAUUCgU-a
HUM.JA-B      aGCCG-AGAGUuGAGCUG---ugUGAGCCGGACgaagGUC-UGGCUUGguCAGCUCCU-a
ZEA.MA-C      aGUUG-GUAGU-GgCCGuu--GGAAGCUUGGGCguagGCCcUGGGCUUCCuUGGaCCU-a
#=GC SS_cons  .<<<<.<<<<<.<<<<<......<<<<<<<.<<....>>..>>>>>>>...>>>>><<..

TRI.AE-A      aUG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcGCUuCCAA
ARA.TH-F      gAGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAG
LYC.ES-I      aAg-uGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAG
HUM.JA-B      aAG-cGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGacaaCCUCCcGCUCUCGG
ZEA.MA-C      uAG-UGGCAGgaacggCGUgaggCUGucuucaCAGagcaGCGaucaCUGCCGGCUAUUAA
#=GC SS_cons  .>>..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>

TRI.AE-A      CggUGGAAGGauaaUGGGCCGcUG-CACuCCUAGGCCaau--uGGGCCuCGCAG----Cc
ARA.TH-F      CagUGGACGGaucaCGGUUUAGcg-UCgcUCAGAACCacu--auGGcC-UGcuGGu-CCG
LYC.ES-I      CggUGGAaGGauaaCGAGUCGGUGuUCU-CUGAGUCC-ag-uaacGCC-ugaUGG--GUu
HUM.JA-B      CagUGGAAGGauaaCGGgCCGGUG-CUGcUUGGAcCCacc--auGGUU-CAcUGag-CUG
ZEA.MA-C      CggUGGAAGGauaaCAGGCCAcuG-CAgcAUGGGCUCgcuu-aAGGCc-uAGAC--Uuc-
#=GC SS_cons  >..>>>>>>>....>>>>>>>..>.>>..>>>>>>>>.......>>>>..>.>>....>.

TRI.AE-A      UAC-ucCA-GCagacCAcC------
ARA.TH-F      AuC-uCAu-aUGaaCCACCAUUUU-
LYC.ES-I      GCU-cCAA-uUAaaCCACCAUuUUu
HUM.JA-B      AcUcuUAA-uAGgaCCAUUUCUUuU
ZEA.MA-C      AUa-cUAAaGCAgacCACCAUUUUu
#=GC SS_cons  >.>..>>>..>>...>>>>>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln45.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln45.fa

ARA.TH-G      GUCGAGCUaUguaacgAgAGCUUguaaCCCAagUGGGGACuauAAGAUGGUGG-aaCAc-
ZEA.MA-H      nCCGAGCuCUguagcgAGuGCUUguaaCCCGagCGGGGGcaauaagguaguguggauguc
ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaauAAGGUGGUGG-aaCAG-
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGG-aaCAc-
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
#=GC SS_cons  .<<<<<<<..........>>>>>....<<<<..>>>>>>.....<<<.<<<<....<<..

ARA.TH-G      UG-gauCGGcCCA-CGGGUC-GGAUUUGUuguUGGcauaggucUGGACUGcCCaaUCCAa
ZEA.MA-H      aauugu-ggu-gcaugugccuGGGUCUA--guGCuacAaacuGUGGacCAcCCaUUCCAa
ARA.TH-D      uG-GuUCaAuUCcuCGGGUC-GGAcCUGAugcuGAcaUauaucUGAGCUGcCCaGUCCAa
ARA.TH-E      UG-GuUCGGgUCcaCGGGCC-GGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGUCCAa
TRI.AE-B      uG-GUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCCAa
#=GC SS_cons  .<......<..<....<<<<.<<<<<<<.....<.........<<<<<<<.<<.<<<<<.

ARA.TH-G      GCUG-uGAGUgAACCG-UAUGaAcCAAGCgaagGUUUGaUcCGUACGGUUgCUaaAGguu
ZEA.MA-H      GUUGcGUaGUggGUUucGGAUGcCuuGGCgaaaGCUuuG-CAUCCcAACa-CUaaAG-uG
ARA.TH-D      GCUG-UGAGuAAUCUG-UgUGGGUCAGGCgaagGCUUGACUCAgGCGGAUUCUaaAGucG
ARA.TH-E      GCUG-UGAGUAAGaCG-UgUGuGUCAAGCgaagGCUUGGCuCAaACGgCUUCUaaAGuuG
TRI.AE-B      GUUG-GuAGUgGgCUG-GGuGGcUGGGGCgaaaGCUUCGcCUuCUCAGgC-CUuaAG-uG
#=GC SS_cons  <<<<.<<<<<.<<<<<.<.<<..<<<<<<....>>>>>>..>>.>>>>>>.<<..>>..<

ARA.TH-G      GAGGguauugCGUuaggCUGgcuucaCAGagcaGCGacuaCCUCccGCUCuCAGCagUGG
ZEA.MA-H      GCGGacauugCGUgaggCUGgcuucaUAGagcaGCGaguaCCGCCcGCcACCAGCggUGG
ARA.TH-D      GAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcuCUUACAGCagUGG
ARA.TH-E      GAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcGCUUACAGCagUGG
TRI.AE-B      GCAGgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAACggUGG
#=GC SS_cons  <<<<......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>

ARA.TH-G      AcGGacaaCGGUUCGacgCCAcACAAAUCCacu-auGGUCCGcUGGcUCGuaaccCGcuU
ZEA.MA-H      AAGGauaaUGagUCGCUauGCuaUAGGCCCaau---------------------------
ARA.TH-D      AUGGaucaUAGUUCGaAgUCucUCAGaUCCacu-auGGCCCGcuGGuUcGAuC-uCucCU
ARA.TH-E      ACGGaucaCAGUUUAGcgUCGcuCAGAACCacu-auGGCCUGcuGGuCCGAuC-uCAuaU
TRI.AE-B      AAGGauaaCAGGCCGcuGcAgcAUGGGCCCgcucuGGGCCucCuA--CCcCGCcaU-AGC
#=GC SS_cons  >>>>....>>>>>>>....>...>>>>>>>......>>>>....>..>.......>...>

ARA.TH-G      GaaCCACCAUUUU-
ZEA.MA-H      --------------
ARA.TH-D      GgaCCACCACUUU-
ARA.TH-E      GaaCCACCAUUUu-
TRI.AE-B      AgacCACCaUCUUu
#=GC SS_cons  >...>>>>.>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln46.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln46.fa

ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGc-ggaUuC
ORY.SA-B      GCCGAGCCAGguagcgUUGGCUUgucaCCCGagCGGGGGCaauAAGGUGGUGuuggaUGC
ARA.TH-E      GUCGAGCUaAguaacaUgAGCUUguaaCCCAugUGGGGACauuuAGAUGGUGG--aaCAc
ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG--gaCAc
ZEA.MA-C      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGu-ggaUGC
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>....<<<<<<<<<.....<<.

ZEA.MA-D      UUuG--cGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUC
ORY.SA-B      CugGucGuuuGCg--CUUGgGGUCuGcGCCuGugguUUGcac-uauGCGGCCCGcCCgUU
ARA.TH-E      -UG---GuUCGGg-UCcaCGGGCC-GGUUCUGuuguUGGcauguuuCUGGGCUGcCCaGU
ARA.TH-F      -UG---GuUCGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGU
ZEA.MA-C      UUG----GUaccGu-GUCUuuGCCUGGGUUCAUggugUGcCuu-uguUGGCCUGcCCgUU
#=GC SS_cons  .<......<.<<...<..<.<<<<.<<<<<<<.....<<........<<<<<<<.<<.<<

ZEA.MA-D      CCAaGUUG-GuAGU-GgCUGGc-GGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCC
ORY.SA-B      CCAaGUUGcGuAGCguGUGUG--GGGCGCcUGGGCgaagGCU-CGaGCGUCCcUGCAC-C
ARA.TH-E      CCAaGCUG-UGAGU-AAGaCG--UgUGuGUCAAGCgaagGCU-UGGCuCAaA-CGgCUUC
ARA.TH-F      CCAaGCUG-UGAGU-AAUUag-uguUGAGUUGAGCgaagGCU-UGGCUUGca---GGUUC
ZEA.MA-C      CCAaGUUG-GUAGU-GgCCGuu-GGAAGCUUGGGCguagGCCcUGGGCUUCC-uUGGaCC
#=GC SS_cons  <<<.<<<<.<.<<<.<.<<<...<.<<<<<<<<<<....>>>.>>>>>>>.>..>>>.><

ZEA.MA-D      UgaAG-uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuC
ORY.SA-B      UagAG-uGGCGGguauugCGUgaggCUGguuucaCAGagcaGCGaguaCC-GCCcGCUuC
ARA.TH-E      UaaAGuuGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCU-UCCcGCUUA
ARA.TH-F      UagAGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCU-UCCcGCUUA
ZEA.MA-C      UauAG-UGGCAGgaacggCGUgaggCUGucuucaCAGagcaGCGaucaCU-GCCGGCUAU
#=GC SS_cons  <..>>..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>

ZEA.MA-D      CAACggUGGGAGGauaaCAGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG---CC-
ORY.SA-B      CAACggUGGAAGGauaaCGGGCCGCugCAGccCuGGCcCgcuuccGGCC-CAAGu--GCc
ARA.TH-E      CAGCagUGGACGGaucaCAGUUUAGcgUCGcuCAGAACCacu-auGGCCUGcuGGu-CCG
ARA.TH-F      CAGCagUGGACGGaucaCGGUUUAGcgUCgcUCAGAACCacu-auGGcCUGcuGGu-CCG
ZEA.MA-C      UAACggUGGAAGGauaaCAGGCCAcuGCAgcAUGGGCUCgcuuaAGGCcuAGAC--Uuc-
#=GC SS_cons  >>>>..>>>>>>>....>>>>>>>...>>...>>>>>>>......>>>>.>..>...>>.

ZEA.MA-D      UCaCuAA-GcAgacCACCAUCUU-
ORY.SA-B      uuCCauG-GCAgacCACCACCUUu
ARA.TH-E      AuCuCAu-aUGaaCCACCAUUUu-
ARA.TH-F      AuCuCAu-aUGaaCCACCAUUUU-
ZEA.MA-C      AUacUAAaGCAgacCACCAUUUUu
#=GC SS_cons  >....>...>>...>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln47.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln47.fa

LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUg-aaU-AU
LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGG-aaUG-U
TRI.AE-B      nCCGAGCU-aguugcgggAGCUUgucaCCCAugUGGGGGcauuGAGGcGGUGuggaUGCU
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUG-aaUA-U
HUM.LU-A      GCCGGuCUUAgcaacgUGGGcCUguaaCCCAagUGGGGGCauGuGGGAAAUGG-gaCU-U
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<<<.<<<<....<<.<

LYC.ES-H      UGGGCuGUaCCAgauGGUu-GGGCUUGG--UGGGcUAauuuCUGACUUGcCCuaUCCAaG
LYC.ES-C      UGAACAugcCCAgaAGGUA-GGGCUUGUG--UGAcaAuucuCUGGCcUGcCCugUCCAaG
TRI.AE-B      uGGUGcGGu-UuGuuGGCCUGGGCUUGUgaugUaaCc-uugcUGGCCUGcCCgUUCCAaG
LYC.ES-A      UGGGCuuUaCCAgaAGGUu-GGGCUUGGU--GGGcUuaguuCUGGCCUGcCCugUCCAaG
HUM.LU-A      UGGGUCAacCUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaG
#=GC SS_cons  <<<<<....<<<...<<<..<<<<<<<<...<<<.<.....<<<<<<<<.<<..<<<<.<

LYC.ES-H      CuUAGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGG
LYC.ES-C      CAaAGAGUuGGGUCUuGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCUaaAGuGGGG
TRI.AE-B      UUGGuAGU-gGgCUGGGuGGcUGGGGCgaaaGCUUCGcCUuCUCAGgC-CUuaAGuGGCA
LYC.ES-A      CACAGAGUuGGAUCucGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAGuGGGG
HUM.LU-A      CCGGGAGUuGGgcUGaGUGACCUGGgCgaagGgCUGGGUUGCgCAcgUCCUagAGuGGAG
#=GC SS_cons  <<<<<<<<.<<.<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>.>><<..>>.<<<<

LYC.ES-H      CggaaugCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCagUGGAaG
LYC.ES-C      UggacugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCagUGGAaG
TRI.AE-B      GgcaccaCGUuaggCUGguuucaCAGagcaGCGacaaCUGCC-GCUuCCAACggUGGAAG
LYC.ES-A      CGgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagUGGAaG
HUM.LU-A      GgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGGAAG
#=GC SS_cons  <......<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>

LYC.ES-H      GauaaUGGGUCGGUGuCUUA-UCAAGUUC-ag-uaacGCCuaaUGG-GUuGCU-cCAAUa
LYC.ES-C      GauaaCGaGCCAGUg-UCA-UAUAAGUUCaac-gaaUGUCUgaUGG-gcUGUU-cUAGuU
TRI.AE-B      GauaaCAGGCCGcuG-cAgc-AUGGGCCCgcuc-uGGGCCucCuA--CCcCGCcaU-AGC
LYC.ES-A      GauaaUGGGUCGGuG-UCUuAUCAAGUUCagu--aacGCCUaaUGG-GuuGCU-cCAA-U
HUM.LU-A      GauaaCGGGCCGGUG-CUAc-CUGGGUCCacc--auGcUUCACUAGgcUGACUcuUAAuA
#=GC SS_cons  >....>>>>>>>>.>.>>>..>>>>>>>>........>>>...>>>....>>>..>>>.>

LYC.ES-H      AacaAcCacCUUUu
LYC.ES-C      AaaCUACCACAUUu
TRI.AE-B      AgacCACCaUCUUu
LYC.ES-A      AaaCAACCACcUUu
HUM.LU-A      GgaCCAUUUCUUuU
#=GC SS_cons  >...>>>>.>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln48.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln48.fa

ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaauAAGGgGAUGG-gaCG-U
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
LYC.ES-F      GCCGAGCUUuguaacguGGGCUUguaaCCCGagUGGGGGCaacAAuGUGGUGG-aaUG-U
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUG-aaUA-U
HUM.JA-B      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGG-gaCU-U
#=GC SS_cons  .<<<<.<<<........>>>.>>....<<<<..>>>>>>....<<.<<<<<<<...<<.<

ARA.TH-C      UG-GGUcGauCUcAUUGGGcC-GGgUUcGGguuGGGcUA-uauucUGGCCCGcCCaUUCC
ZEA.MA-B      uuGcGAuGGu--uUCUGGGcCUGGGCUCGu--uGUGaCu-cuagcCGGCUUGcCCaUCCC
LYC.ES-F      UG-GGUccau-CUugauGGaU-GGGCUUGA--aGGGcUAauguuCUGGCCUGcCCugUCC
LYC.ES-J      UG-GGCuuUa-CCAgaAGGUu-GGGCUUGG--UGGGcUu-aguuCUGGCCUGcCCugUCC
HUM.JA-B      UA-GuUCGGc-cCAuUGGAUC-GGaUCCAGuguUAGcUG-cuugCUGGgCUGcCCaUUCC
#=GC SS_cons  <<.<<<.......<..<<<.<.<<.<<<<<...<<<.<.......<<<<<<<.<<..<<<

ARA.TH-C      AaGUUGGGAGUuGAGGCA-UGGGcUUCGAGCgaagGCU-CGGGuCUCA-UGUCUUCUagA
ZEA.MA-B      AaGUUGGuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacA
LYC.ES-F      AaGCACAGAGUuGGGUCA-AGUGGuCUAUACgaaaGUA-UAG-CCACU-UGGCCUUUagA
LYC.ES-J      AaGCACAGAGUuGGAUCA-cGAGGCCCAaAUgaaaAUa-UGGGCUUCu-UGAUUCCUaaA
HUM.JA-B      AaGCCGAGAGUuGAGCUG-ugUGAGCCGGACgaagGUC-UGGCUUGgu-CAGCUCCUaaA
#=GC SS_cons  <.<<<<<<<<<.<<<<<<..<<<.<<<<<<<....>>>.>>>>.>>>..>>>>>><<..>

ARA.TH-C      GuGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCC-UCCcGCUCUUGACg
ZEA.MA-B      GcGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAACg
LYC.ES-F      GuGGGAUggacugCGUgaggCUGguuucaCAGagcaACGacuaGU-CCCcGCUCUGUGCa
LYC.ES-J      GuGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGC-UCCcGCUCUGUGCa
HUM.JA-B      GcGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGacaaCC-UCCcGCUCUCGGCa
#=GC SS_cons  >.<<<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>>>>>>>.

ARA.TH-C      gUGGAAGGauuaCGGGCCAuUG-CCU-UCcGAgCCcacu-auGaCCCAAUaAG--CcGCU
ZEA.MA-B      gUGGGAGGauaaCAAGCCGcuG-CACuuUGAGCCCaaca-cAGaCCCAGA---uCC-UCu
LYC.ES-F      gUGGAaGGaucaCGGGCUAGUGcUCU-UUGAGUCCuaacaaaAaCCugauAG--guuGCC
LYC.ES-J      gUGGAaGGauaaUGGGUCGGuGuCUUAUCAAGUUC-ag-uaacGCCUaaUGG--GuuGCU
HUM.JA-B      gUGGAAGGauaaCGGgCCGGUG-CUGcUUGGAcCCacc--auGGUUCAcUGag-CUGAcU
#=GC SS_cons  .>>>>.>>....>>>>>>>..>.>>>.>>>>>.>>.......>.>>>..>.......>>>

ARA.TH-C      -cCGAuUGgaCCAUCaCUUU-
ZEA.MA-B      -CuuAGCAaacCaCCAUCUUu
LYC.ES-F      --UAAuUAaaCCAUCACuUUu
LYC.ES-J      -cCAA-UAaaCAACCACcUUu
HUM.JA-B      cuUAAuAGgaCCAUUUCUUuU
#=GC SS_cons  ..>>>.>>..>>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln49.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln49.fa

ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
HUM.LU-B      ---GGcCUUAgcaacgUGGGcCUguaaCCCAagUGGGggcau-GuGGGAAAUGG--aaC-
LYC.ES-M      -----------------------------CAagUGgggaugu-uAAGGUGGUgG--aaUA
ZEA.MA-G      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcau-uAAGGUGGUGc-ggaUu
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcau-GuGGGAAAUGG--aaCU
#=GC SS_cons  ...<...<<........>>...>....<<<<..>>>>........<<<<<<<.<....<.

ORY.SA-A      uUUGgugUGGAuucu-GAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCC
HUM.LU-B      AUUG----GGUCAGc--CCAGUGGauC-gGGuCCAGuguUAGcUGcuuaCUGGUCUGcCC
LYC.ES-M      -UUG----GGCuGUc--CCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCC
ZEA.MA-G      CUUuG---cGAuGGcu--UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCC
HUM.LU-C      -UUG----GGUCAac--CCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCC
#=GC SS_cons  .<<<....<<<.<....<<<<<.<..<..<<.<<<....<<<.<......<<<<<<<.<<

ORY.SA-A      gUUCCAaGuUGcGuAGU-GGGccGGaGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUCC
HUM.LU-B      aUUCCAaGCCG-GGAGUuGGGCUG-aGUGACCUGGGCgaagGCCUGGGUUGCg-CAGCUC
LYC.ES-M      ugUCCAaGCAC-AGAGUuGGAUCA-cGAGGCCCAaAUgaaaAUaUGGGCUUCu-UGAUUC
ZEA.MA-G      gUCCCAaGUUG-GuAGU-GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCU-CCAGaC
HUM.LU-C      aUUCCAaGCCG-GGAGguGGGcUG-aGggaCcugGGCgaagGCUnnnGgngCg-CA-CUC
#=GC SS_cons  .<<<<<.<<<<.<.<<<.<<<.<<..<<<<<...<<<....>>>...>>>>>..>>.>>>

ORY.SA-A      ggccCUaaAGuGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcGC
HUM.LU-B      ----CUagAGuGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGacuaCCUCCcGC
LYC.ES-M      ----CUaaAGuGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGC
ZEA.MA-G      ----CUgaAGuGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcGC
HUM.LU-C      ----cUagAcuGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgC
#=GC SS_cons  ....<<..>>.<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>

ORY.SA-A      UuCCAuCggUGGAAGGauaaCAGGCUGcuG-cACcuUGGgcccgcuu-cuGGCCCAGaGU
HUM.LU-B      UCCCGGCagUGGAAGGauaaCGGGCCGGUG-CUAcUUGGuCCa-cc--auGu-UCACUGG
LYC.ES-M      UCUGUGCagUGGAaGGauaaUGGGUCGGUGuCUUAUCAAGUUC-ag-uaacGCCuaaUGG
ZEA.MA-G      UuCCAACggUGGGAGGauaaCGGGCCGcuG-CACuuCGAGCCCaacu-caGGCCCAGAG-
HUM.LU-C      UCUCGGCagUGGAAGGauaaCGGgCcGGUG-CgccUUGagCCaaca--cuGuuCaACUGG
#=GC SS_cons  >.>>>>>..>>>>>>>....>>>>>>>..>.>>>..>>>.>>........>..>.>>>>>

ORY.SA-A      C--ccUCUA--CAA-CAgaCcaCCAUCUUU
HUM.LU-B      ucCUGACU-cuUAAUcGgaCCAUUUCCUuU
LYC.ES-M      --GUuGCU--cCAA-UAaaCaACCACCUUu
ZEA.MA-G      --CC-UCa--CuAAGcAgacCACCAUCUUu
HUM.LU-C      g-cUGACU-cuUAAuAGgaCCAUUUCUUuU
#=GC SS_cons  ...>.>>>...>>>..>..>.>>>>>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln50.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln50.fa

HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCau-GuGGGAAAUGG--gaCU
ZEA.MA-E      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcau-uAAGGUGGUGc-ggaUu
HUM.JA-A      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcau-GuGGGAGAUGG--gacu
ARA.TH-G      GUCGAGCUaUguaacgAgAGCUUguaaCCCAagUGGGGACua-uAAGAUGGUGG--aaCA
ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
#=GC SS_cons  ..<<<<<<.<......>.>>>>>....<<<<..>>>>>.......<<<<<<<<<....<.

HUM.LU-D      -UUG----GGUCAac--CUAGUGGAuC-GGGUCCAGuguUAGcUGcuuaCUGGUCUGcCC
ZEA.MA-E      CUUuG---cGAuGGcu--UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCC
HUM.JA-A      -UUG----GGUcaGc--cCAuUGGaUC-gGGUCCAGuguUAGcUGcuugCUGGUCUGcCC
ARA.TH-G      c-UG----gauCGGc--CCA-CGGGUC-GGAUUUGUuguUGGcauaggucUGGACUGcCC
ORY.SA-A      uUUGgugUGGAuucu-GAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCC
#=GC SS_cons  .<<<.....<<.......<<.<<<<<<..<<<<<<....<<<.<......<<<<<<<.<<

HUM.LU-D      aUUCCAaGCCG-GGAGUuGGGCUG-aGUGACCUgGGCgaagGCU-GGGUUGCg-CAGCUC
ZEA.MA-E      gUCCCAaGUUG-GuAGU-GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCU-CCAGaC
HUM.JA-A      aUUCCAaGCCG-AGAGUuGGGCUG-UGUGAUCUgGGCgaagGCUgGGGUCGCA-CAGCUC
ARA.TH-G      aaUCCAaGCUG-uGAGU-gAACCG-UAUGaAcCAAGCgaagGUUUGaUcCGUA-CGGUUg
ORY.SA-A      gUUCCAaGuUGcGuAGU-GGGccGGaGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUCC
#=GC SS_cons  .<<<<<.<<<<.<.<<<.<<<<<<..<<<<<...<<<....>>>...>>>>>..>>>>>>

HUM.LU-D      ----CUagAG-uGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCC-UCCc
ZEA.MA-E      ----CUgaAG-UGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCG
HUM.JA-A      ----CUaaAG-aGGAGGgcaaugCGUgaggCUGguuucaCAGagcaGCGaccaCC-UCCc
ARA.TH-G      ----CUaaAGguuGAGGguauugCGUuaggCUGgcuucaCAGagcaGCGacuaCC-UCcc
ORY.SA-A      ggccCUaaAG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCU-GCCc
#=GC SS_cons  ....<<..>>..<<<<<......<<<....<<<......>>>....>>>....>>.>>>.

HUM.LU-D      GCUCUCGGCagUGGAAGGauaaCGGGCCGGUGCUAcCUGGAUCCacc-auGcUUCACUGG
ZEA.MA-E      GCUuCCAACggUGGGAGGauaaCGGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG-
HUM.JA-A      GCUCUCGGCagUGGAAGGauaaCGGGUCGGUGCUAcUUGGGCCa-cc-auGG-UCAcUGc
ARA.TH-G      GCUCuCAGCagUGGAcGGacaaCGGUUCGacgCCAcACAAAUCCacu-auGGUCCGcUGG
ORY.SA-A      GCUuCCAuCggUGGAAGGauaaCAGGCUGcuGcACcuUGGgcccgcuucuGGCCCAGaGU
#=GC SS_cons  >>>.>>>>>..>>>>>>>....>>>>>>>..>>>>..>>>>>>.......>>>>>>.>>.

HUM.LU-D      gcUGACU-cuUAAuAGgaCCAUUUCUUuU
ZEA.MA-E      -CC-UCa--CuAAGcAgacCACCAUCUUu
HUM.JA-A      aUgcACU-cuUAAucagaCCAUCUCUUuU
ARA.TH-G      cUCGuaa-ccCGcuUGaaCCACCAUUUU-
ORY.SA-A      C-ccUCUA--CAA-CAgaCcaCCAUCUUU
#=GC SS_cons  ....>>....>>>..>..>>>>>>>>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln51.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln51.fa

ARA.TH-F      GUCGAGCUAaguaacaaUAGCUUguaaCCCAugUGGGGACauuAAGAUGGUGG-gaCAc-
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUG-aaUA-U
TRI.AE-A      nCCGAGCUCaguugcgaGAGCUUguaaCCCGagUGGGGGcauuaaaguGaUGugaacGCU
ZEA.MA-G      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgG-aaUA-U
#=GC SS_cons  ..<<<<<<<........>>>>>>....<<<<..>>>>>.....<<.<<<<<<....<<.<

ARA.TH-F      UG-GuUCGGu-UCcuCGGaUC-GGUUCUGAugugGGcauguuuCUGAGCUGcCCaGUCCA
LYC.ES-A      UG-GGCuuUa-CCAgaAGGUu-GGGCUUGGU--GGGcUuaguuCUGGCCUGcCCugUCCA
TRI.AE-A      GuuGUA-Gcg--CUGCGGGCCUGGUCUGGG--uGUGcUA-cugcUGGCCCGcCCgUUCCA
ZEA.MA-G      UuGcGAuGGcu-UUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCA
LYC.ES-M      UG-GGCuGUc-CCAgauGGCu-GGGCUUGG--UGGGcUAauuuCUGGCCUGcCCugUCCA
#=GC SS_cons  <..<<<.<<...<<..<<<<..<<<<<<<<...<<<.<......<<<<<<<.<<..<<<<

ARA.TH-F      aGCUG-UGAGU-AAUUag--uguUGAGUUGAGCgaagGCUUGGCUUGca--GGUUCU-ag
LYC.ES-A      aGCAC-AGAGUuGGAUCu---cGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCU-aa
TRI.AE-A      aGUUGcGuAGU-gGACCGcc-UGGGGCUUAuGCgaaaGC-UGGGUCUCACGGUC-CAuaa
ZEA.MA-G      aGUUG-GuAGU-GgCUGGc--GGAGGCUuuAGCggaaGCUuuGGUCUCUCCAGaCCU-ga
LYC.ES-M      aGCAC-AGAGUuGGAUCA---cGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCU-aa
#=GC SS_cons  .<<<<.<.<<<.<<<<<.....<<<<<<<<.<<....>>.>>>>>>>>..>>>>><<...

ARA.TH-F      AGucGGAGGguaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCUUCCcGCUUACAGC
LYC.ES-A      AG-uGGGGCGgaccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGC
TRI.AE-A      UG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGacaaCUGCCcGCUuCCAAC
ZEA.MA-G      AG-uGGCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcGCUuCCAAC
LYC.ES-M      AG-uGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGC
#=GC SS_cons  >>..<<<<<......<<<....<<<......>>>....>>>....>>>>>.>>>.>>>>>

ARA.TH-F      agUGGACGGaucaCGGUUUAGcg-UCgc-UCAGAACCacu--auGGcC-UGcuGGuCCGA
LYC.ES-A      agUGGAaGGauaaUGGGUCGGuG-UCUuAUCAAGUUCagu--aacGCC-UaaUGG-GuuG
TRI.AE-A      ggUGGAAGGauaaUGGGCCGcUG-CACu-CCUAGGCCaau--uGGGCCuCGCAG---CcU
ZEA.MA-G      ggUGGGAGGauaaCGGGCCGcuG-CACu-uCGAGCCCaacu-caGGCC-CAGAG--CC-U
LYC.ES-M      agUGGAaGGauaaUGGGUCGGUGuCUUA-UCAAGUUC-ag-uaacGCC-uaaUGG-GUuG
#=GC SS_cons  ..>>>>.>>....>>>>>>>..>.>>>..>>>>>>>>........>>>.>..>>..>>.>

ARA.TH-F      uCuCAuaUGaaCCACCAUUUU-
LYC.ES-A      CUcCAA-UAaaCAACCACcUUu
TRI.AE-A      ACucCAGCagacCAcC------
ZEA.MA-G      CaCuAAGcAgacCACCAUCUUu
LYC.ES-M      CUcCAA-UAaaCaACCACCUUu
#=GC SS_cons  >>..>>.>>...>>>>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln52.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln52.fa

CAE.BRI.      ACCGGGUGUCguggcgGGCGCCUgugaGUC-agcuuc--uuGACGGUaGACAAGUGugga
CAE.EL-C      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUGAGUGugga
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGUGGGagga
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu--gGGAGGCuGAGGCUGGcgga
XEN.LAE.      GCCGGGCGCuguggcguGUGCCUguaaUCC-agcuac--uuGGAGGCuuGGGCUGUcgga
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<...........>>>>>>.<<<<<<<<....

CAE.BRI.      UGGAGugaAGGGAGGaguCcugUGGGUGuuGUcgGCAACggC-ga-cCGAGCGUCCGuGC
CAE.EL-C      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
HOM.SA-B      UCGCUugaGCcCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-gGGGUGUCCgCAC
FUG.RUB.      UCGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgU-cgau-CGGGUGUCCgUAC
XEN.LAE.      UCGCUugaGUcCAGGaguUcugggCUG-CACUGaGCUAUgU-cgau-CGGGUGUCCgCAC
#=GC SS_cons  <<<<<...<<.<<<<...<...<<<<<..<<<..<<<<<.<......<<<<<<<<<..<<

CAE.BRI.      CAaGCGCUGCGUCGCCaGGGGUCuCCGGUCggaaGGCUGGcGGUCCCgGGCG-CauaagG
CAE.EL-C      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUG-CauaagG
HOM.SA-B      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGG
FUG.RUB.      UAaGuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCG-CCuaaGG
XEN.LAE.      UAaGuUCGGUAUCAAUaUGGUGuUCCuGGGggagCCUcGGAuCACCAgGUUGcUCuaaGG
#=GC SS_cons  <<.<.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>>.<.....>

CAE.BRI.      aGUGGUgcac-gGCUcaggGCCgaaaGGCagcaGGCaaaaGCCACcGCGCGGUGCagUGG
CAE.EL-C      aGUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGG
HOM.SA-B      aGGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAG
FUG.RUB.      aGGGGUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAG
XEN.LAE.      aGGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACCCCcGUGCCGAuCagUAG
#=GC SS_cons  .<<<<<......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>..>>>

CAE.BRI.      C-CGGauaGCGCUUGuG-aGUUGUcGCu-CGCCCAcaGCCUCUCUgauacCUUCAgacCA
CAE.EL-C      C-CGGacaGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCA
HOM.SA-B      UG-GGaucGCGCCUgu-GaAUAGCCACUG-CAcUCcaGCCUGaGCaacauAGCGAgacCC
FUG.RUB.      UG-GGaucGCGCCCGu-GaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUC
XEN.LAE.      UG-GGaucGCGCCUGu-GaAUAGCCGGUG-CAGaacaGCCUGaACaacacAGCGAgacAC
#=GC SS_cons  >..>>...>>>>>>>..>.>>>>>.>>>..>>>>>..>>>>>.>>.....>>>>>...>>

CAE.BRI.      CUUGUCa--uu
CAE.EL-C      CUUGUCacu--
HOM.SA-B      CGUCUCu----
FUG.RUB.      AGUCUUu----
XEN.LAE.      AGUUCu-----
#=GC SS_cons  >>>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln53.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln53.fa

CAE.EL-D      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUAAGUGugga
HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCuGGagga
RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGacaGagga
CAE.EL-B      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUAGAUAAGUGugga
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGcCcGccgga
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<...........>>>>>>.<<<<<.<<....

CAE.EL-D      UGGAGugaGAGGAGGaguCcugUGUAUGucGUcgUCuACgU-cgac-CGAGCGUCCGuGC
HOM.SA-A      UCGCUugaGUcCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
RAT.RAT.      UCGCUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
CAE.EL-B      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
GAL.GAL.      UCGCUugaGCCCAGGaguUcuggGCUG-CAGUGcGCUAUgC-cgag-CGGGCGUCCgCGc
#=GC SS_cons  <<<<<...<<<<<<<...<...<<.<<..<<<..<<<<<.<......<<<<<<<<<..<<

CAE.EL-D      CAaGCGCUACGUCACCaGGGGaUAACUGUCggaaGGCGGUUAgUCCCgGGUGCauaagGa
HOM.SA-A      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
RAT.RAT.      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
CAE.EL-B      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGa
GAL.GAL.      UAaGGCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCuaaGGa
#=GC SS_cons  <<.<.<<<<<<<<<<<.<<<<...<<<<<<....>>>>>>...>>>>.>>>><.....>.

CAE.EL-D      GUCGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCGACcGCGUGGUGCagUGGC
HOM.SA-A      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
RAT.RAT.      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
CAE.EL-B      GUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGC
GAL.GAL.      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaC
#=GC SS_cons  <<<<<......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>..>>>>

CAE.EL-D      -CGGaccGCGCUUGuaA-GUuGAcACa-CAUACAcaGCCUUCUCgauacCUUCAgacCAC
HOM.SA-A      G-GGaucGCGCCUGu-GaAUAGCCACUG-CAcUCcaGCCUGuGCaacauAGCGAgacCCc
RAT.RAT.      G-GGaucGCGCCUGu-GaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGAgacCcc
CAE.EL-B      -CGGacuGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCAC
GAL.GAL.      G-GGaucGCGCCUGu-GaAUAGCCACUG-CAGCguaGCCUGGGCaacauAGCGAgaccCu
#=GC SS_cons  ..>>...>>>>>>>..>.>>>>>.>>>..>>.>>..>>>>>>>>.....>>>>>...>>.

CAE.EL-D      UUAUCa-uuu
HOM.SA-A      GUCUCu--uu
RAT.RAT.      gUCUCuu---
CAE.EL-B      UUGUUU-uu-
GAL.GAL.      GuCUCc----
#=GC SS_cons  >>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln54.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln54.fa

CAE.BRI.      ACC-GGGUGUCguggcgGGCGCCUgugaGUC-agcuuc--uuGACGGUaGACAAGUGugg
DRO.MEL.      GaCuGGAAGg-uuggca-gCUUCUguaaUCA-cgcuuc--ugUGAGgUcuGAUUGUGG-g
HOM.SA-B      GCC-GGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGUGGGagg
ORI.CUN.      GCC-GGGCGCGguggcgCGCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCcGGagg
RAT.NOR.      GCC-GGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGACaGGagg
#=GC SS_cons  <<<.<<<<<.<......>.>>>>>....<<<...........>>>>>>.<<<<<.<<...

CAE.BRI.      aUGGAGugaAGGGAGGa---guCcugUGGGUGuuGUcgGCAACggC-ga-cCGAGCGUCC
DRO.MEL.      aUGGCCugaGGcUGGGaucuacUgcguaGcgGacCAGc-UCAUgUU-ga-CGGaACGUCC
HOM.SA-B      aUCGCUugaGCcCAGGa---guUcugGGcUG-UAGUGcGCUAUgC-cgau-gGGGUGUCC
ORI.CUN.      aUCGCUugaGUCCAGGa---guUcugGGcUG-UcGUGcGCUAUgC-cgau-CGGGUGUCC
RAT.NOR.      aUCGaUugaGUCCAGGa---guUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCC
#=GC SS_cons  .<<<<<...<<.<<<<......<...<<.<<...<<<.<<<<<.<......<<<<<<<<<

CAE.BRI.      GuGCCAaGCGCUGCGUCGCCaGGGGUCuCCGGUCggaaGGCUGGcGGUCCCgGGCGCaua
DRO.MEL.      gCACUAaGCUUGCCAUCAAUaUGGGUGCCAUGGAggagUCCGUGGCAUUCAgGUUGgCua
HOM.SA-B      gCACUAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCua
ORI.CUN.      gCACUAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCua
RAT.NOR.      gCACUAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCua
#=GC SS_cons  .<<<<<.<.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<..

CAE.BRI.      agGaGUGGUgcac--gGCUcaggGCCgaaaGGCagcaGGCaaaaGCCACcGCGCGGUGCa
DRO.MEL.      aGgaGGGAUgaac-cgGGCcaggGGUgaaaACCagcaGCCaagaGUUCCcGUGGUAGGCa
HOM.SA-B      aGGaGGGGUgaacc-GGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCa
ORI.CUN.      aGGaGGGGUgaacc-GGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCa
RAT.NOR.      aGGaGGGGUgaacc-GGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCa
#=GC SS_cons  .>>.<<<<<.......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>.

CAE.BRI.      gUGGC-CGGauaGCGCUUG-uG-aGUUGUcGCu-CGCCCAcaGCCUCUCUgauacCUUCA
DRO.MEL.      gUAGUG-GGauaGCGUaCCG-GA-GUGGaCUGc-CguUaucaGCCCAaCCgauauGGUUG
HOM.SA-B      gUAGUG-GGaucGCGCCUg-u-GaAUAGCCACUG-CAcUCcaGCCUGaGCaacauAGCGA
ORI.CUN.      gUAGUG-GGaucGCGCCUG-u-GaAUAGCCACuG-CAcUCcaGCCUGGGCaacauAGCGA
RAT.NOR.      gUAGUG-GGaucGCGCCUG-u-GaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAgCGA
#=GC SS_cons  .>>>>>.>>...>>>>>>>...>.>>>>>>>>...>>.>>..>>>>>.>>.....>>>>>

CAE.BRI.      gacCACUUGUCauu-
DRO.MEL.      gaCCACAAUC--uuu
HOM.SA-B      gacCCCGUCUCu---
ORI.CUN.      gacCCuGUCUCc---
RAT.NOR.      gacCC-GUCUCu---
#=GC SS_cons  ...>>.>>>>>....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln55.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln55.fa

RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGGacaGaggaU
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGcCcGccggaU
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCcGGaggaU
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu-gGGAGGCuGAGGCUGGcggaU
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGACaGGaggaU
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

RAT.RAT.      CGCUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
GAL.GAL.      CGCUugaGCCCAGGaguUcuggGCUG-CAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAa
ORI.CUN.      CGCUugaGUCCAGGaguUcugGGcUG-UcGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
FUG.RUB.      CGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgUcgauCGGGUGUCCgUACUAa
RAT.NOR.      CGaUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
#=GC SS_cons  <<<<...<<<<<<<...<...<<.<<.<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

RAT.RAT.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
GAL.GAL.      GGCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCuaaGGaGGG
ORI.CUN.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
FUG.RUB.      GuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCuaaGGaGGG
RAT.NOR.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<

RAT.RAT.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
GAL.GAL.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGGG
ORI.CUN.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
FUG.RUB.      GUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAGUGGG
RAT.NOR.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
#=GC SS_cons  <<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>

RAT.RAT.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGAgacCccgUCUC
GAL.GAL.      aucGCGCCUGuGaAUAGCCACUG-CAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUC
ORI.CUN.      aucGCGCCUGuGaAUAGCCACuG-CAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUC
FUG.RUB.      aucGCGCCCGuGaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUCAGUCUU
RAT.NOR.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUC
#=GC SS_cons  ...>>>>>>>.>.>>>>>>>>>>.>>.>>..>>>>>>>>.....>>>>>...>>.>>>>>

RAT.RAT.      uu
GAL.GAL.      c-
ORI.CUN.      c-
FUG.RUB.      u-
RAT.NOR.      u-
#=GC SS_cons  ..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln56.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln56.fa

CAE.BRI.      ACCGGGUGUCguggcgGGCGCCUgugaGUC-agcuuc--uuGACGGUaGACAAGUGugga
CAE.EL-B      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUAGAUAAGUGugga
CAE.EL-C      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUGAGUGugga
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGUGGGagga
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCcGGagga
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<...........>>>>>>.<<<<<<<<....

CAE.BRI.      UGGAGugaAGGGAGGaguCcugUGGGUGuuGUcgGCAACggC-ga-cCGAGCGUCCGuGC
CAE.EL-B      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
CAE.EL-C      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
HOM.SA-B      UCGCUugaGCcCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-gGGGUGUCCgCAC
ORI.CUN.      UCGCUugaGUCCAGGaguUcugGGcUG-UcGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
#=GC SS_cons  <<<<<...<<<<<<<...<...<<.<<...<<..<<<<<.<......<<<<<<<<<..<<

CAE.BRI.      CAaGCGCUGCGUCGCCaGGGGUCuCCGGUCggaaGGCUGGcGGUCCCgGGCGCauaagGa
CAE.EL-B      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGa
CAE.EL-C      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGa
HOM.SA-B      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
ORI.CUN.      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
#=GC SS_cons  <<.<.<<<<<<<<<<<.<<<<...<<<<<<....>>>>>>...>>>>.>>>><.....>.

CAE.BRI.      GUGGUgcac-gGCUcaggGCCgaaaGGCagcaGGCaaaaGCCACcGCGCGGUGCagUGGC
CAE.EL-B      GUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGC
CAE.EL-C      GUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGC
HOM.SA-B      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
ORI.CUN.      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
#=GC SS_cons  <<<<<......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>..>>>>

CAE.BRI.      -CGGauaGCGCUUGuG-aGUUGUcGCu-CGCCCAcaGCCUCUCUgauacCUUCAgacCAC
CAE.EL-B      -CGGacuGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCAC
CAE.EL-C      -CGGacaGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCAC
HOM.SA-B      G-GGaucGCGCCUgu-GaAUAGCCACUG-CAcUCcaGCCUGaGCaacauAGCGAgacCCC
ORI.CUN.      G-GGaucGCGCCUGu-GaAUAGCCACuG-CAcUCcaGCCUGGGCaacauAGCGAgacCCu
#=GC SS_cons  ..>>...>>>>>>>..>.>>>>>.>>...>>.>>..>>>>>>>>.....>>>>>...>>>

CAE.BRI.      UUGUCa--uu
CAE.EL-B      UUGUUU--uu
CAE.EL-C      UUGUCacu--
HOM.SA-B      GUCUCu----
ORI.CUN.      GUCUCc----
#=GC SS_cons  >>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln57.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln57.fa

RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGacaGagga
CAE.EL-C      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUGAGUGugga
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGUGGGagga
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu--gGGAGGCuGAGGCUGGcgga
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGACaGGagga
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<...........>>>>>>.<<<<<.<<....

RAT.RAT.      UCGCUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
CAE.EL-C      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
HOM.SA-B      UCGCUugaGCcCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-gGGGUGUCCgCAC
FUG.RUB.      UCGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgU-cgau-CGGGUGUCCgUAC
RAT.NOR.      UCGaUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
#=GC SS_cons  <<<<<...<<<<<<<...<...<<.<<..<<<<.<<<<<.<......<<<<<<<<<.<<<

RAT.RAT.      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
CAE.EL-C      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGa
HOM.SA-B      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
FUG.RUB.      UAaGuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCuaaGGa
RAT.NOR.      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
#=GC SS_cons  <<.<.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.

RAT.RAT.      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
CAE.EL-C      GUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGC
HOM.SA-B      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
FUG.RUB.      GGGGUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAGU
RAT.NOR.      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
#=GC SS_cons  <<<<<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>

RAT.RAT.      G-GGaucGCGCCUGu-GaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGAgacCcc
CAE.EL-C      -CGGacaGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCAC
HOM.SA-B      G-GGaucGCGCCUgu-GaAUAGCCACUG-CAcUCcaGCCUGaGCaacauAGCGAgacCCC
FUG.RUB.      G-GGaucGCGCCCGu-GaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUCA
RAT.NOR.      G-GGaucGCGCCUGu-GaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAgCGAgacCC-
#=GC SS_cons  >.>>...>>>>>>>..>.>>>>>>>>>..>>.>>..>>>>>>>>.....>>>>>...>>.

RAT.RAT.      gUCUCuu-
CAE.EL-C      UUGUCacu
HOM.SA-B      GUCUCu--
FUG.RUB.      GUCUUu--
RAT.NOR.      GUCUCu--
#=GC SS_cons  >>>>>...
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln58.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln58.fa

RAT.RAT.      GCC-GGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGacaGagg
CAE.EL-B      ACC-GAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUAGAUAAGUGugg
DRO.MEL.      GaCuGGAAGg-uuggca-gCUUCUguaaUCA-cgcuuc--ugUGAGgUcuGAUUGUGG-g
GAL.GAL.      GCC-GGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGcCcGccgg
FUG.RUB.      GCC-GGGUACGguggcgCGUGCCUguaaUCCaagcuacu--gGGAGGCuGAGGCUGGcgg
#=GC SS_cons  <<<.<<<<<.<......>.>>>>>....<<<...........>>>>>>.<<<<<.<<...

RAT.RAT.      aUCGCUugaGUCCAGGa---guUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCC
CAE.EL-B      aUGGAGugaGAGGAGGa---guCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCC
DRO.MEL.      aUGGCCugaGGcUGGGaucuacUgcguaGcgGacCAGc-UCAUgUU-ga-CGGaACGUCC
GAL.GAL.      aUCGCUugaGCCCAGGa---guUcuggGCUG-CAGUGcGCUAUgC-cgag-CGGGCGUCC
FUG.RUB.      aUCGCUugaGCUCAGGa---guUcugGGCUuC-AGCGgaCUAUgU-cgau-CGGGUGUCC
#=GC SS_cons  .<<<<<...<<<<<<<......<....<<<...<<<<..<<<<.<......<<<<<<<<<

RAT.RAT.      gCACUAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCua
CAE.EL-B      GuGCCAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCaua
DRO.MEL.      gCACUAaGCUUGCCAUCAAUaUGGGUGCCAUGGAggagUCCGUGGCAUUCAgGUUGgCua
GAL.GAL.      gCGcUAaGGCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCua
FUG.RUB.      gUACUAaGuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCua
#=GC SS_cons  .<<<<<.<.<<<<<<<<<<<.<<<<<.<<<<<<<....>>>>>>>.>>>>>.>>>><<..

RAT.RAT.      aGGaGGGGUgaacc-GGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCa
CAE.EL-B      agGaGUGGUggau--gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCa
DRO.MEL.      aGgaGGGAUgaac-cgGGCcaggGGUgaaaACCagcaGCCaagaGUUCCcGUGGUAGGCa
GAL.GAL.      aGGaGGGGUgaacc-GGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCa
FUG.RUB.      aGGaGGGGUgcccc-GGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCa
#=GC SS_cons  .>>.<<<<<.......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>.

RAT.RAT.      gUAGUG-GGaucGCGCCUG-u-GaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGA
CAE.EL-B      gUGGC-CGGacuGCGCUUG-uGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCA
DRO.MEL.      gUAGUG-GGauaGCGUaCCG-GA-GUGGaCUGc-CguUaucaGCCCAaCCgauauGGUUG
GAL.GAL.      gUAaCG-GGaucGCGCCUG-u-GaAUAGCCACUG-CAGCguaGCCUGGGCaacauAGCGA
FUG.RUB.      gUAGUG-GGaucGCGCCCG-u-GaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGG
#=GC SS_cons  .>>>>>.>>...>>>>>>>...>.>>>>.>>>>...>>>...>>>>>>>>.....>>>>>

RAT.RAT.      gacCccgUCUCuu---
CAE.EL-B      gacCACUUGUUU-uu-
DRO.MEL.      gaCCACAAUC---uuu
GAL.GAL.      gaccCuGuCUCc----
FUG.RUB.      gacUCAGUCUUu----
#=GC SS_cons  ...>>.>>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln59.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln59.fa

CAE.EL-A      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUAAGUGugga
CAE.BRI.      ACCGGGUGUCguggcgGGCGCCUgugaGUC-agcuuc--uuGACGGUaGACAAGUGugga
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu--gGGAGGCuGAGGCUGGcgga
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGACaGGagga
XEN.LAE.      GCCGGGCGCuguggcguGUGCCUguaaUCC-agcuac--uuGGAGGCuuGGGCUGUcgga
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<...........>>>>>>.<<<<<<<<....

CAE.EL-A      UGGAGugaGAGGAGGaguCcugUGUAUGucGUugUCuACgUC-ga-cCGAGCGUCCGuGC
CAE.BRI.      UGGAGugaAGGGAGGaguCcugUGGGUGuuGUcgGCAACggC-ga-cCGAGCGUCCGuGC
FUG.RUB.      UCGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgU-cgau-CGGGUGUCCgUAC
RAT.NOR.      UCGaUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
XEN.LAE.      UCGCUugaGUcCAGGaguUcugggCUG-CACUGaGCUAUgU-cgau-CGGGUGUCCgCAC
#=GC SS_cons  <<<<<...<<<<<<<...<...<<<<<...<<..<<<<<.<......<<<<<<<<<..<<

CAE.EL-A      CAaGCGCUACGUCACCaGGGGaUAACUGUCggaaGGCGGUUAgUCCCgGGUG-CauaagG
CAE.BRI.      CAaGCGCUGCGUCGCCaGGGGUCuCCGGUCggaaGGCUGGcGGUCCCgGGCG-CauaagG
FUG.RUB.      UAaGuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCG-CCuaaGG
RAT.NOR.      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGG
XEN.LAE.      UAaGuUCGGUAUCAAUaUGGUGuUCCuGGGggagCCUcGGAuCACCAgGUUGcUCuaaGG
#=GC SS_cons  <<.<.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>>.<.....>

CAE.EL-A      aGUCGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCGACcGCGUGGUGCagUGG
CAE.BRI.      aGUGGUgcac-gGCUcaggGCCgaaaGGCagcaGGCaaaaGCCACcGCGCGGUGCagUGG
FUG.RUB.      aGGGGUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAG
RAT.NOR.      aGGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAG
XEN.LAE.      aGGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACCCCcGUGCCGAuCagUAG
#=GC SS_cons  .<<<<<......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>..>>>

CAE.EL-A      C-CGGaccGCGCUUGuGA-GUuGAcACa-CAUACGcaGCCUUCUCgauacCUUCAgacCA
CAE.BRI.      C-CGGauaGCGCUUGuG-aGUUGUcGCu-CGCCCAcaGCCUCUCUgauacCUUCAgacCA
FUG.RUB.      UG-GGaucGCGCCCGu-GaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUC
RAT.NOR.      UG-GGaucGCGCCUGu-GaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAgCGAgacCC
XEN.LAE.      UG-GGaucGCGCCUGu-GaAUAGCCGGUG-CAGaacaGCCUGaACaacacAGCGAgacAC
#=GC SS_cons  >..>>...>>>>>>>..>.>>>>>.>>...>>>>>..>>>>>>>>.....>>>>>...>>

CAE.EL-A      CUUAUCauuu
CAE.BRI.      CUUGUCauu-
FUG.RUB.      AGUCUUu---
RAT.NOR.      -GUCUCu---
XEN.LAE.      AGUUCu----
#=GC SS_cons  >>>>>>....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln60.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln60.fa

HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGCuGGaggaU
RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGGacaGaggaU
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGUGGGaggaU
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu-gGGAGGCuGAGGCUGGcggaU
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGACaGGaggaU
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

HOM.SA-A      CGCUugaGUcCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
RAT.RAT.      CGCUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
HOM.SA-B      CGCUugaGCcCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgaugGGGUGUCCgCACUAa
FUG.RUB.      CGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgUcgauCGGGUGUCCgUACUAa
RAT.NOR.      CGaUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
#=GC SS_cons  <<<<...<<.<<<<...<...<<.<<.<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

HOM.SA-A      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
RAT.RAT.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
HOM.SA-B      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
FUG.RUB.      GuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCuaaGGaGGG
RAT.NOR.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<

HOM.SA-A      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
RAT.RAT.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
HOM.SA-B      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
FUG.RUB.      GUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAGUGGG
RAT.NOR.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
#=GC SS_cons  <<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>

HOM.SA-A      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUC
RAT.RAT.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGAgacCccgUCUC
HOM.SA-B      aucGCGCCUguGaAUAGCCACUG-CAcUCcaGCCUGaGCaacauAGCGAgacCCCGUCUC
FUG.RUB.      aucGCGCCCGuGaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUCAGUCUU
RAT.NOR.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUC
#=GC SS_cons  ...>>>>>>>.>.>>>>>>>>>>.>>.>>..>>>>>.>>.....>>>>>...>>.>>>>>

HOM.SA-A      u-uu
RAT.RAT.      uu--
HOM.SA-B      u---
FUG.RUB.      u---
RAT.NOR.      u---
#=GC SS_cons  ....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln61.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln61.fa

CAE.EL-A      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUAAGUGugga
CAE.EL-B      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUAGAUAAGUGugga
CAE.EL-C      ACCGAGCGUCguggcgGGCGCUUgugaGUC-agcuuc--uuGACGGUaGAUGAGUGugga
CAN.SPE.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCaGGagga
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu--gGGAGGCuGAGGCUGGcgga
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<...........>>>>>>.<<<<<<<<....

CAE.EL-A      UGGAGugaGAGGAGGaguCcugUGUAUGucGUugUCuACgUC-ga-cCGAGCGUCCGuGC
CAE.EL-B      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
CAE.EL-C      UGGAGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGC
CAN.SPE.      UCGCUugaGCcCAGGaguUcugGGcUG-CAGUGcGCUAUgC-cgau-CGGGUGUCCgCAC
FUG.RUB.      UCGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgU-cgau-CGGGUGUCCgUAC
#=GC SS_cons  <<<<<...<<<<<<<...<...<<<<<<.<<<..<<<<<.<......<<<<<<<<<..<<

CAE.EL-A      CAaGCGCUACGUCACCaGGGGaUAACUGUCggaaGGCGGUUAgUCCCgGGUGCauaagGa
CAE.EL-B      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGa
CAE.EL-C      CAaGCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGa
CAN.SPE.      UAaGuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGa
FUG.RUB.      UAaGuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCuaaGGa
#=GC SS_cons  <<.<.<<<<<<<<<<<.<<<<..<<<<<<<....>>>>>>>..>>>>.>>>><.....>.

CAE.EL-A      GUCGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCGACcGCGUGGUGCagUGGC
CAE.EL-B      GUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGC
CAE.EL-C      GUGGUggau-gGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGC
CAN.SPE.      GGGGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGU
FUG.RUB.      GGGGUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAGU
#=GC SS_cons  <<<<<......<<<....<<<....>>>....>>>....>>>>>.>>>>>>>.>..>>>>

CAE.EL-A      -CGGaccGCGCUUGuGA-GUuGAcACa-CAUACGcaGCCUUCUCgauacCUUCAgacCAC
CAE.EL-B      -CGGacuGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCAC
CAE.EL-C      -CGGacaGCGCUUGuGA-GUUGAcACG-UAUACAcaGCCUUCUCaauacCUUCAgacCAC
CAN.SPE.      G-GGaucGCGCCUGu-GaAUAGCCACUG-CAcUCcaGCCUGuGCaacauAGCGAgacCCc
FUG.RUB.      G-GGaucGCGCCCGu-GaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUCA
#=GC SS_cons  ..>>...>>>>>>>..>.>>>>>.>>>.>>>>>>..>>>>>>>>.....>>>>>...>>>

CAE.EL-A      UUAUCa--uuu
CAE.EL-B      UUGUUU--uu-
CAE.EL-C      UUGUCacu---
CAN.SPE.      GUCUCu-----
FUG.RUB.      GUCUUu-----
#=GC SS_cons  >>>>>......
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln62.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln62.fa

LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGGaaUA-UU
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUgaaU-AUU
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUGaaUA-UU
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<..<<.<<

LYC.ES-E      GGGCuGUcCCAgauGGCuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGUAC
LYC.ES-G      GGGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGCAC
LYC.ES-H      GGGCuGUaCCAgauGGUuGGGCUUGG-UGGGcUAauuuCUGACUUGcCCuaUCCAaGCuU
LYC.ES-B      GGGCuGUaCCAgauGGUuGGGCUUGGu-GGGcUAauuuCUGACUUGcCCuaUCCAaGCUU
LYC.ES-A      GGGCuuUaCCAgaAGGUuGGGCUUGGU-GGGcUuaguuCUGGCCUGcCCugUCCAaGCAC
#=GC SS_cons  <<<<.<<.<<<...<<<.<<<<<<<<..<<<.<<....<<<<.<<<.<<..<<<<.<<<<

LYC.ES-E      AGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgg
LYC.ES-G      AGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgg
LYC.ES-H      AGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgg
LYC.ES-B      AGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgg
LYC.ES-A      AGAGUuGGAUCucGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAGuGGGGCGg
#=GC SS_cons  <<<<<.<<<<<..<<<<.<<<.<<....>>.>>>.>>>>..>>>>>.<..>..<<<<<..

LYC.ES-E      acc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGau
LYC.ES-G      accgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGau
LYC.ES-H      aaugCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCagUGGAaGGau
LYC.ES-B      aaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggUGGAaGGau
LYC.ES-A      accgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagUGGAaGGau
#=GC SS_cons  ....<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>..

LYC.ES-E      aaCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGUUcUAGuUAaaCUA
LYC.ES-G      aaCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCA
LYC.ES-H      aaUGGGUCGGUGuCUUA-UCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAAUaAacaAc
LYC.ES-B      aaCGAGUCGGUG-UUC-uCUGAGUCCagu-aauGCCugaUGGGCuGCUcUAAuUAaaCCA
LYC.ES-A      aaUGGGUCGGuG-UCUuAUCAAGUUCagu-aacGCCUaaUGGGuuGCUcCAA-UAaaCAA
#=GC SS_cons  ..>>>.>>>>>>.>>>..>>>>>>>>.......>>>...>>>>>.>>>.>>>.>>..>>>

LYC.ES-E      CCACaUUuu
LYC.ES-G      CCACuUUu-
LYC.ES-H      CacCUUUu-
LYC.ES-B      CCACuUUu-
LYC.ES-A      CCACcUUu-
#=GC SS_cons  >>>>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln63.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln63.fa

LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUgaaU-AUU
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGGaaUA-UU
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUA-UU
#=GC SS_cons  <.<<<<<<<<......>>>>>>>....<<<<..>>>>>.>...<<.<<<<<<<..<<.<<

LYC.ES-G      GGGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACA
LYC.ES-H      GGGCuGUaCCAgauGGUuGGGCUUGGUGGGcUAauuuCUGACUUGcCCuaUCCAaGCuUA
LYC.ES-O      GGGCuGUcCCAgauGGCuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACA
LYC.ES-I      GGGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-M      GGGCuGUcCCAgauGGCuGGGCUUGGUGGGcUAauuuCUGGCCUGcCCugUCCAaGCACA
#=GC SS_cons  <<<<.<<.<<<...<<<.<<<<<<<<.<<<.<<....<<<<.<<<.<<..<<<<.<<<<<

LYC.ES-G      GAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgga
LYC.ES-H      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgga
LYC.ES-O      GAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgga
LYC.ES-I      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
LYC.ES-M      GAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCgga
#=GC SS_cons  <<<<.<<<<<..<<<<.<<<.<<....>>.>>>.>>>>..>>>>>.<..>..<<<<<...

LYC.ES-G      ccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGaua
LYC.ES-H      augCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCagUGGAaGGaua
LYC.ES-O      ccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGaua
LYC.ES-I      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
LYC.ES-M      ccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGaua
#=GC SS_cons  ...<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>...

LYC.ES-G      aCGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCACC
LYC.ES-H      aUGGGUCGGUGuCUUAUCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAAUaAacaAcCa
LYC.ES-O      aCGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCACC
LYC.ES-I      aCGAGUCGGUGuUCU-CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCACC
LYC.ES-M      aUGGGUCGGUGuCUUAUCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAA-UAaaCaACC
#=GC SS_cons  .>>>.>>>>>>.>>>.>>>>>>>>.......>>>...>>>>>.>>>.>>>.>>..>>>>>

LYC.ES-G      ACuUUu
LYC.ES-H      cCUUUu
LYC.ES-O      ACUUU-
LYC.ES-I      AUuUUu
LYC.ES-M      ACCUUu
#=GC SS_cons  >>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln64.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln64.fa

LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGGaaUAUUG
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUAUUG
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGGaaUAUUG
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUGaaUAUUG
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUGUUG
#=GC SS_cons  <.<<<<<<<<......>>>>>>>....<<<<..>>>>>.>...<<.<<<<<<<..<<<<<

LYC.ES-E      GGCuGUcCCAgauGGCuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGUACA
LYC.ES-K      GGCuuUaCCAgaAGGUuGGGCUUGG-UGGGcUuaguuCUGGCCUGcCCugUCCAaGCACA
LYC.ES-O      GGCuGUcCCAgauGGCuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACA
LYC.ES-A      GGCuuUaCCAgaAGGUuGGGCUUGGU-GGGcUuaguuCUGGCCUGcCCugUCCAaGCACA
LYC.ES-N      GGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
#=GC SS_cons  <<<..<.<<<...<<<.<<<<<<<<..<<<.<.....<<<<.<<<.<<..<<<<.<<<<<

LYC.ES-E      GAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgga
LYC.ES-K      GAGUaGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGcGGGGCgga
LYC.ES-O      GAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgga
LYC.ES-A      GAGUuGGAUCucGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAGuGGGGCGga
LYC.ES-N      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
#=GC SS_cons  <<<<.<<<<<..<<<<<<<<.<<....>>.>>>>>>>>..>>>>><<..>>.<<<<<...

LYC.ES-E      cc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGaua
LYC.ES-K      ccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGaua
LYC.ES-O      ccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGaua
LYC.ES-A      ccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagUGGAaGGaua
LYC.ES-N      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
#=GC SS_cons  ...<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>...

LYC.ES-E      aCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGUUcUAGuUAaaCUAC
LYC.ES-K      aUGGGUCGGuGuCUUA-UCAAGUUC-aguaacGCCUaaUGGGuuGCUcCAA-UAaaCAAC
LYC.ES-O      aCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCAC
LYC.ES-A      aUGGGUCGGuG-UCUuAUCAAGUUCagu-aacGCCUaaUGGGuuGCUcCAA-UAaaCAAC
LYC.ES-N      aCGAGUCGGUGuUCU--CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCAC
#=GC SS_cons  .>>>.>>>>.>.>>>..>>>>>>>>.......>>>...>>>>..>>>.>>>.>>..>>>>

LYC.ES-E      CACaUUuu
LYC.ES-K      CACcUUu-
LYC.ES-O      CACUUU--
LYC.ES-A      CACcUUu-
LYC.ES-N      CAUuUUu-
#=GC SS_cons  >>>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln65.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln65.fa

LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGGaaUAUUG
LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUAUUG
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUGUUG
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUAUUG
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<..<<<<<

LYC.ES-E      GGCuGUcCCAgauGGCuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGUACAG
LYC.ES-G      GGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACAG
LYC.ES-J      GGCuuUaCCAgaAGGUuGGGCUUGGUGGGcUuaguuCUGGCCUGcCCugUCCAaGCACAG
LYC.ES-N      GGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUAG
LYC.ES-M      GGCuGUcCCAgauGGCuGGGCUUGGUGGGcUAauuuCUGGCCUGcCCugUCCAaGCACAG
#=GC SS_cons  <<<.<<.<<<...<<<.<<<<<<<<.<<<.<<....<<<<.<<<.<<..<<<<.<<<<<<

LYC.ES-E      AGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUggac
LYC.ES-G      AGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUggac
LYC.ES-J      AGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCggac
LYC.ES-N      AGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCggaa
LYC.ES-M      AGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCggac
#=GC SS_cons  <<<.<<<<<..<<<<<<<<.<<....>>.>>>>>>>>..>>>>><<..>>.<<<<<....

LYC.ES-E      c-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGauaa
LYC.ES-G      cgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGauaa
LYC.ES-J      cgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGauaa
LYC.ES-N      ugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGauaa
LYC.ES-M      cgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGauaa
#=GC SS_cons  ..<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>....

LYC.ES-E      CGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGUUcUAGuUAaaCUACCA
LYC.ES-G      CGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCACCA
LYC.ES-J      UGGGUCGGuGuCUUAUCAAGUUC-aguaacGCCUaaUGGGuuGCUcCAA-UAaaCAACCA
LYC.ES-N      CGAGUCGGUGuUCU-CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCACCA
LYC.ES-M      UGGGUCGGUGuCUUAUCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAA-UAaaCaACCA
#=GC SS_cons  >>>.>>>>>>.>>>.>>>>>>>>.......>>>...>>>>>.>>>.>>>.>>..>>>>>>

LYC.ES-E      CaUUuu
LYC.ES-G      CuUUu-
LYC.ES-J      CcUUu-
LYC.ES-N      UuUUu-
LYC.ES-M      CCUUu-
#=GC SS_cons  >.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln66.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln66.fa

LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUAUUG
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGGaaUAUUG
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUAUUG
#=GC SS_cons  <.<<<<<<<<......>>>>>>>....<<<<..>>>>>.>...<<.<<<<<<<..<<<<<

LYC.ES-G      GGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACAG
LYC.ES-J      GGCuuUaCCAgaAGGUuGGGCUUGGUGGGcUuaguuCUGGCCUGcCCugUCCAaGCACAG
LYC.ES-O      GGCuGUcCCAgauGGCuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACAG
LYC.ES-I      GGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUAG
LYC.ES-M      GGCuGUcCCAgauGGCuGGGCUUGGUGGGcUAauuuCUGGCCUGcCCugUCCAaGCACAG
#=GC SS_cons  <<<.<<.<<<...<<<.<<<<<<<<.<<<.<<....<<<<.<<<.<<..<<<<.<<<<<<

LYC.ES-G      AGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUggac
LYC.ES-J      AGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCggac
LYC.ES-O      AGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUggac
LYC.ES-I      AGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCggaa
LYC.ES-M      AGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCggac
#=GC SS_cons  <<<.<<<<<..<<<<<<<<.<<....>>.>>>>>>>>..>>>>><<..>>.<<<<<....

LYC.ES-G      cgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGauaa
LYC.ES-J      cgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGauaa
LYC.ES-O      cgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGauaa
LYC.ES-I      ugCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGauaa
LYC.ES-M      cgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGauaa
#=GC SS_cons  ..<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>....

LYC.ES-G      CGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCACCA
LYC.ES-J      UGGGUCGGuGuCUUAUCAAGUUC-aguaacGCCUaaUGGGuuGCUcCAA-UAaaCAACCA
LYC.ES-O      CGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCACCA
LYC.ES-I      CGAGUCGGUGuUCU-CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCACCA
LYC.ES-M      UGGGUCGGUGuCUUAUCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAA-UAaaCaACCA
#=GC SS_cons  >>>.>>>>>>.>>>.>>>>>>>>.......>>>...>>>>>.>>>.>>>.>>..>>>>>>

LYC.ES-G      CuUUu
LYC.ES-J      CcUUu
LYC.ES-O      CUUU-
LYC.ES-I      UuUUu
LYC.ES-M      CCUUu
#=GC SS_cons  >.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln67.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln67.fa

LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGGaaUGUUG
LYC.ES-E      GUCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAgGUGGUGGaaUAUUG
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-J      GUCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUAUUG
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUGUUG
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<..<<<<<

LYC.ES-C      AACAugcCCAgaAGGUAGGGCUUGUG-UGAcaAuucuCUGGCcUGcCCugUCCAaGCAaA
LYC.ES-E      GGCuGUcCCAgauGGCuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGUACA
LYC.ES-B      GGCuGUaCCAgauGGUuGGGCUUGGu-GGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-J      GGCuuUaCCAgaAGGUuGGGCUUGG-UGGGcUuaguuCUGGCCUGcCCugUCCAaGCACA
LYC.ES-N      GGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
#=GC SS_cons  <<<..<.<<<...<<<.<<<<<<<<..<<<.<<....<<<<<<<<.<<..<<<<.<<<<<

LYC.ES-C      GAGUuGGGUCUuGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCUaaAGuGGGGUgga
LYC.ES-E      GAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgga
LYC.ES-B      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgga
LYC.ES-J      GAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCgga
LYC.ES-N      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
#=GC SS_cons  <<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>>>>.<..>..<<<<<...

LYC.ES-C      cugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCagUGGAaGGaua
LYC.ES-E      cc-CGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGaua
LYC.ES-B      augCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggUGGAaGGaua
LYC.ES-J      ccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGaua
LYC.ES-N      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
#=GC SS_cons  ...<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>...

LYC.ES-C      aCGaGCCAGUg-UCA-UAUAAGUUCaacgaaUGUCUgaUGGgcUGUUcUAGuUAaaCUAC
LYC.ES-E      aCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGUUcUAGuUAaaCUAC
LYC.ES-B      aCGAGUCGGUG-UUC-uCUGAGUCCagu-aauGCCugaUGGGCuGCUcUAAuUAaaCCAC
LYC.ES-J      aUGGGUCGGuGuCUUA-UCAAGUUC-aguaacGCCUaaUGGGuuGCUcCAA-UAaaCAAC
LYC.ES-N      aCGAGUCGGUGuUCU--CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCAC
#=GC SS_cons  .>>>>>>>>>>.>>>..>>>>>>>>.......>>>...>>>>..>>>.>>>.>>..>>>>

LYC.ES-C      CACAUUu-
LYC.ES-E      CACaUUuu
LYC.ES-B      CACuUUu-
LYC.ES-J      CACcUUu-
LYC.ES-N      CAUuUUu-
#=GC SS_cons  >>>.>>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln68.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln68.fa

LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUgaaU-AUU
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUA-UU
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGGaaUA-UU
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUG-UU
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<..<<.<<

LYC.ES-H      GGGCuGUaCCAgauGGUuGGGCUUGGUGGGcUAauuuCUGACUUGcCCuaUCCAaGCuUA
LYC.ES-K      GGGCuuUaCCAgaAGGUuGGGCUUGGUGGGcUuaguuCUGGCCUGcCCugUCCAaGCACA
LYC.ES-O      GGGCuGUcCCAgauGGCuGGGCUUGGuGGGcUAauuuCUGGcCUGcCCuaUCCAaGCACA
LYC.ES-I      GGGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-N      GGGCuGUaCCAgauGGUuGGGCUUGGuGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
#=GC SS_cons  <<<<.<<.<<<...<<<.<<<<<<<<.<<<.<<....<<<<<<<<.<<..<<<<.<<<<<

LYC.ES-H      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgga
LYC.ES-K      GAGUaGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGcGGGGCgga
LYC.ES-O      GAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgga
LYC.ES-I      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
LYC.ES-N      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
#=GC SS_cons  <<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>>>>.<..>..<<<.<...

LYC.ES-H      augCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCagUGGAaGGaua
LYC.ES-K      ccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGaua
LYC.ES-O      ccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGaua
LYC.ES-I      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
LYC.ES-N      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
#=GC SS_cons  ...<<<....<<<......>>>....>>>....>.>>>.>>>>>>>>>..>>>>.>>...

LYC.ES-H      aUGGGUCGGUGuCUUAUCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAAUaAacaAcCa
LYC.ES-K      aUGGGUCGGuGuCUUAUCAAGUUC-aguaacGCCUaaUGGGuuGCUcCAA-UAaaCAACC
LYC.ES-O      aCGGaCCGGUGcCUU-CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCACC
LYC.ES-I      aCGAGUCGGUGuUCU-CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCACC
LYC.ES-N      aCGAGUCGGUGuUCU-CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCACC
#=GC SS_cons  .>>>>>>>>>>.>>>.>>>>>>>>.......>>>...>>>>>.>>>.>>>.>>..>>>>>

LYC.ES-H      cCUUUu
LYC.ES-K      ACcUUu
LYC.ES-O      ACUUU-
LYC.ES-I      AUuUUu
LYC.ES-N      AUuUUu
#=GC SS_cons  >>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln69.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln69.fa

LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGGaaUGUUG
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUGaaUAUUG
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUAUUG
#=GC SS_cons  <.<<<<<<<<......>>>>>>>....<<<<..>>>>>.>...<<.<<<<<<<..<<<<<

LYC.ES-C      AACAugcCCAgaAGGUAGGGCUUGUG-UGAcaAuucuCUGGCcUGcCCugUCCAaGCAaA
LYC.ES-B      GGCuGUaCCAgauGGUuGGGCUUGGu-GGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-A      GGCuuUaCCAgaAGGUuGGGCUUGGU-GGGcUuaguuCUGGCCUGcCCugUCCAaGCACA
LYC.ES-I      GGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-M      GGCuGUcCCAgauGGCuGGGCUUGG-UGGGcUAauuuCUGGCCUGcCCugUCCAaGCACA
#=GC SS_cons  <<<..<.<<<...<<<.<<<<<<<<..<<<.<<....<<<<<<<<.<<..<<<<.<<<<<

LYC.ES-C      GAGUuGGGUCUuGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCUaaAGuGGGGUgga
LYC.ES-B      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgga
LYC.ES-A      GAGUuGGAUCucGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAGuGGGGCGga
LYC.ES-I      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
LYC.ES-M      GAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCgga
#=GC SS_cons  <<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>>>>.<..>..<<<<<...

LYC.ES-C      cugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCagUGGAaGGaua
LYC.ES-B      augCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggUGGAaGGaua
LYC.ES-A      ccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagUGGAaGGaua
LYC.ES-I      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
LYC.ES-M      ccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGaua
#=GC SS_cons  ...<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>...

LYC.ES-C      aCGaGCCAGUg-UCA-UAUAAGUUCaacgaaUGUCUgaUGGgcUGUUcUAGuUAaaCUAC
LYC.ES-B      aCGAGUCGGUG-UUC-uCUGAGUCCagu-aauGCCugaUGGGCuGCUcUAAuUAaaCCAC
LYC.ES-A      aUGGGUCGGuG-UCUuAUCAAGUUCagu-aacGCCUaaUGGGuuGCUcCAA-UAaaCAAC
LYC.ES-I      aCGAGUCGGUGuUCU--CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCAC
LYC.ES-M      aUGGGUCGGUGuCUUA-UCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAA-UAaaCaAC
#=GC SS_cons  .>>>>>>>>>>.>>>..>>>>>>>>.......>>>...>>>>..>>>.>>>.>>..>>>>

LYC.ES-C      CACAUUu
LYC.ES-B      CACuUUu
LYC.ES-A      CACcUUu
LYC.ES-I      CAUuUUu
LYC.ES-M      CACCUUu
#=GC SS_cons  >>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln70.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln70.fa

LYC.ES-G      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-H      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAAGugGuUgaaU-AUU
LYC.ES-B      GUCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUG-UU
LYC.ES-K      GUUGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGACaucAAaGUGGUUGaaUA-UU
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUguuAAGGUGGUGGaaUA-UU
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<..>>>>>>>...<<.<<<<<<<..<<.<<

LYC.ES-G      GGGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGCAC
LYC.ES-H      GGGCuGUaCCAgauGGUuGGGCUUGG-UGGGcUAauuuCUGACUUGcCCuaUCCAaGCuU
LYC.ES-B      GGGCuGUaCCAgauGGUuGGGCUUGGu-GGGcUAauuuCUGACUUGcCCuaUCCAaGCUU
LYC.ES-K      GGGCuuUaCCAgaAGGUuGGGCUUGG-UGGGcUuaguuCUGGCCUGcCCugUCCAaGCAC
LYC.ES-O      GGGCuGUcCCAgauGGCuGGGCUUGG-uGGGcUAauuuCUGGcCUGcCCuaUCCAaGCAC
#=GC SS_cons  <<<<.<<.<<<...<<<.<<<<<<<<..<<<.<<....<<<<.<<<.<<..<<<<.<<<<

LYC.ES-G      AGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgg
LYC.ES-H      AGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgg
LYC.ES-B      AGAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGGCgg
LYC.ES-K      AGAGUaGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGcGGGGCgg
LYC.ES-O      AGAGUuGGAUCauGUGGUCCAaUUgaaaGAaUGGGCUACuaGAUUCCUaaAGuGGGGUgg
#=GC SS_cons  <<<<<.<<<<<..<<<<.<<<.<<....>>.>>>.>>>>..>>>>>.<..>..<<<<<..

LYC.ES-G      accgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGau
LYC.ES-H      aaugCGUgaggCUGguuucaCAGagcaGUGaacaGCUCCcGCUCUGuGCagUGGAaGGau
LYC.ES-B      aaugCGUgaggCUGguuucaCAGagcaACGauaaGUUUCcGCUCUAAGCggUGGAaGGau
LYC.ES-K      accgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGau
LYC.ES-O      accgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGCUUUGUGCagUGGAaGGau
#=GC SS_cons  ....<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>.>>..

LYC.ES-G      aaCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCA
LYC.ES-H      aaUGGGUCGGUGuCUUA-UCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAAUaAacaAc
LYC.ES-B      aaCGAGUCGGUG-UUC-uCUGAGUCCagu-aauGCCugaUGGGCuGCUcUAAuUAaaCCA
LYC.ES-K      aaUGGGUCGGuGuCUUA-UCAAGUUC-aguaacGCCUaaUGGGuuGCUcCAA-UAaaCAA
LYC.ES-O      aaCGGaCCGGUGcCUU--CCAAGUUCcauuaauGCCugaUGGGCuGCUcCAAuUAaaCCA
#=GC SS_cons  ..>>>.>>>>>>.>>>..>>>>>>>>.......>>>...>>>>>.>>>.>>>.>>..>>>

LYC.ES-G      CCACuUUu
LYC.ES-H      CacCUUUu
LYC.ES-B      CCACuUUu
LYC.ES-K      CCACcUUu
LYC.ES-O      CCACUUU-
#=GC SS_cons  >>>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln71.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln71.fa

LYC.ES-C      GCCGAGCUCAguagcgUGGGCUUguaaCUCAagUGAGGGCaucAGUGUGGUGGaaUGUUG
LYC.ES-A      GgCGAGCUUAguaacgUGGGCUUguaaUCCAagUGGAGaCaucAAaGUGGUUGaaUAUUG
LYC.ES-I      GCCGAGCUUAguaaugUGGGCUUguaaCCCAaaUGGGGGCauuAAuGUGGUGGaaUGUUG
LYC.ES-N      GUUGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGAUguuAAuGUGGUGGaaUGUUG
LYC.ES-M      -----------------------------CAagUGgggauguuAAGGUGGUgGaaUAUUG
#=GC SS_cons  <.<<<<<<<<......>>>>>>>....<<<<..>>>>>.>...<<.<<<<<<<..<<<<<

LYC.ES-C      AACAugcCCAgaAGGUAGGGCUUGUG-UGAcaAuucuCUGGCcUGcCCugUCCAaGCAaA
LYC.ES-A      GGCuuUaCCAgaAGGUuGGGCUUGGU-GGGcUuaguuCUGGCCUGcCCugUCCAaGCACA
LYC.ES-I      GGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-N      GGCuGUaCCAgauGGUuGGGCUUGG-uGGGcUAauuuCUGACUUGcCCuaUCCAaGCUUA
LYC.ES-M      GGCuGUcCCAgauGGCuGGGCUUGG-UGGGcUAauuuCUGGCCUGcCCugUCCAaGCACA
#=GC SS_cons  <<<..<.<<<...<<<.<<<<<<<<..<<<.<<....<<<<<<<<.<<..<<<<.<<<<<

LYC.ES-C      GAGUuGGGUCUuGUGGgCCAAGCgaagGCUUGGgCUGCuGGGCUCCUaaAGuGGGGUgga
LYC.ES-A      GAGUuGGAUCucGAGGCCCAaAUgaaaAUaUGGGCUUCuuGAUUCCUaaAGuGGGGCGga
LYC.ES-I      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
LYC.ES-N      GAGUuGGAUCAuGUGGcCCAaUUgaagAAaUGGaCUACuUGAUUCgUaaAguGGGgCgga
LYC.ES-M      GAGUuGGAUCAcGAGGCCCAaAUgaaaAUaUGGGCUUCuUGAUUCCUaaAGuGGGGCgga
#=GC SS_cons  <<<<.<<<<<<.<<<<.<<<.<<....>>.>>>.>>>>.>>>>>>.<..>..<<<.<...

LYC.ES-C      cugCGUgaggCUGguuucaCAGagcaACGaauaGCUCCcGCUCUgUGCagUGGAaGGaua
LYC.ES-A      ccgCAUgaggCUGgcuucaCAGagcaGUGaa-CGCUCCcGCUCUGUGCagUGGAaGGaua
LYC.ES-I      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
LYC.ES-N      augCGUgaggCUGguuucaCAGagcaACGauaaG-UUUcGCUCUAAGCggUGGAaGGaua
LYC.ES-M      ccgCAUgaggCUGgcuucaCAGagcaGUGaacaGCUCCcGCUCUGUGCagUGGAaGGaua
#=GC SS_cons  ...<<<....<<<......>>>....>>>....>.>>>.>>>>>>>>>..>>>>.>>...

LYC.ES-C      aCGaGCCAGUg-UCA-UAUAAGUUCaacgaaUGUCUgaUGGgcUGUUcUAGuUAaaCUAC
LYC.ES-A      aUGGGUCGGuG-UCUuAUCAAGUUCagu-aacGCCUaaUGGGuuGCUcCAA-UAaaCAAC
LYC.ES-I      aCGAGUCGGUGuUCU--CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCAC
LYC.ES-N      aCGAGUCGGUGuUCU--CUGAGUCC-aguaacGCCugaUGGGUuGCUcCAAuUAaaCCAC
LYC.ES-M      aUGGGUCGGUGuCUUA-UCAAGUUC-aguaacGCCuaaUGGGUuGCUcCAA-UAaaCaAC
#=GC SS_cons  .>>>>>>>>>>.>>>..>>>>>>>>.......>>>...>>>>..>>>.>>>.>>..>>>>

LYC.ES-C      CACAUUu
LYC.ES-A      CACcUUu
LYC.ES-I      CAUuUUu
LYC.ES-N      CAUuUUu
LYC.ES-M      CACCUUu
#=GC SS_cons  >>>.>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln72.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln72.fa

HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCuGGagga
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGcCcGccgga
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCcGGagga
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGACaGGagga
XEN.LAE.      GCCGGGCGCuguggcguGUGCCUguaaUCC-agcuac--uuGGAGGCuuGGGCUGUcgga
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<.........>>>>>>>.<<<<<.<<....

HOM.SA-A      UCGCUugaGUcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
GAL.GAL.      UCGCUugaGCCCAGGaguUcuggGCUGCAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAa
ORI.CUN.      UCGCUugaGUCCAGGaguUcugGGcUGUcGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
RAT.NOR.      UCGaUugaGUCCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
XEN.LAE.      UCGCUugaGUcCAGGaguUcugggCUGCACUGaGCUAUgUcgauCGGGUGUCCgCACUAa
#=GC SS_cons  <<<<<...<<.<<<<...<....<.<<<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

HOM.SA-A      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
GAL.GAL.      GGCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUG-CCuaaGGaGG
ORI.CUN.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
RAT.NOR.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
XEN.LAE.      GuUCGGUAUCAAUaUGGUGuUCCuGGGggagCCUcGGAuCACCAgGUUGcUCuaaGGaGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<.<<<....>>>.>>..>>>>>.>>>>.<<...>>.<<

HOM.SA-A      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
GAL.GAL.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGG
ORI.CUN.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
RAT.NOR.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
XEN.LAE.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACCCCcGUGCCGAuCagUAGUGG
#=GC SS_cons  <<<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>

HOM.SA-A      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUC
GAL.GAL.      GaucGCGCCUGuGaAUAGCCACUGCAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUC
ORI.CUN.      GaucGCGCCUGuGaAUAGCCACuGCAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUC
RAT.NOR.      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUC
XEN.LAE.      GaucGCGCCUGuGaAUAGCCGGUGCAGaacaGCCUGaACaacacAGCGAgacACAGUUCu
#=GC SS_cons  >...>>>>>>>.>.>>>>>>>>>>>>.>...>>>>>.>>.....>>>>>...>>.>>>>>

HOM.SA-A      uuu
GAL.GAL.      c--
ORI.CUN.      c--
RAT.NOR.      u--
XEN.LAE.      ---
#=GC SS_cons  ...
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln73.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln73.fa

HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCuGGagga
CAN.SPE.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCaGGagga
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacuc-GGGAGGCuGAGGUGGGagga
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGACaGGagga
XEN.LAE.      GCCGGGCGCuguggcguGUGCCUguaaUCC-agcuac--uuGGAGGCuuGGGCUGUcgga
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<.........>>>>>>>.<<<<<.<<....

HOM.SA-A      UCGCUugaGUcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
CAN.SPE.      UCGCUugaGCcCAGGaguUcugGGcUGCAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
HOM.SA-B      UCGCUugaGCcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgaugGGGUGUCCgCACUAa
RAT.NOR.      UCGaUugaGUCCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
XEN.LAE.      UCGCUugaGUcCAGGaguUcugggCUGCACUGaGCUAUgUcgauCGGGUGUCCgCACUAa
#=GC SS_cons  <<<<<...<<.<<<<...<...<<.<<<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

HOM.SA-A      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
CAN.SPE.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
HOM.SA-B      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
RAT.NOR.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
XEN.LAE.      GuUCGGUAUCAAUaUGGUGuUCCuGGGggagCCUcGGAuCACCAgGUUGcUCuaaGGaGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>>.<<...>>.<<

HOM.SA-A      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
CAN.SPE.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
HOM.SA-B      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
RAT.NOR.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
XEN.LAE.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACCCCcGUGCCGAuCagUAGUGG
#=GC SS_cons  <<<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>

HOM.SA-A      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUC
CAN.SPE.      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUC
HOM.SA-B      GaucGCGCCUguGaAUAGCCACUGCAcUCcaGCCUGaGCaacauAGCGAgacCCCGUCUC
RAT.NOR.      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUC
XEN.LAE.      GaucGCGCCUGuGaAUAGCCGGUGCAGaacaGCCUGaACaacacAGCGAgacACAGUUCu
#=GC SS_cons  >...>>>>>>>.>.>>>>>>>>>>>>.>>..>>>>>.>>.....>>>>>...>>.>>>>>

HOM.SA-A      uuu
CAN.SPE.      u--
HOM.SA-B      u--
RAT.NOR.      u--
XEN.LAE.      ---
#=GC SS_cons  ...
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln74.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln74.fa

HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGCuGGaggaU
RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGGacaGaggaU
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGcCcGccggaU
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGUGGGaggaU
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCcGGaggaU
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

HOM.SA-A      CGCUugaGUcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
RAT.RAT.      CGCUugaGUCCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
GAL.GAL.      CGCUugaGCCCAGGaguUcuggGCUGCAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAaG
HOM.SA-B      CGCUugaGCcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgaugGGGUGUCCgCACUAaG
ORI.CUN.      CGCUugaGUCCAGGaguUcugGGcUGUcGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
#=GC SS_cons  <<<<...<<.<<<<...<...<<.<<<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.<

HOM.SA-A      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
RAT.RAT.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
GAL.GAL.      GCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCuaaGGaGGGG
HOM.SA-B      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
ORI.CUN.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
#=GC SS_cons  .<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<<

HOM.SA-A      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
RAT.RAT.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
GAL.GAL.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGGGa
HOM.SA-B      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
ORI.CUN.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
#=GC SS_cons  <.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>.

HOM.SA-A      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUCu-
RAT.RAT.      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGGGCaacauAGCGAgacCccgUCUCuu
GAL.GAL.      ucGCGCCUGuGaAUAGCCACUGCAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUCc-
HOM.SA-B      ucGCGCCUguGaAUAGCCACUGCAcUCcaGCCUGaGCaacauAGCGAgacCCCGUCUCu-
ORI.CUN.      ucGCGCCUGuGaAUAGCCACuGCAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUCc-
#=GC SS_cons  ..>>>>>>>.>.>>>>>>>>>>>>.>>..>>>>>.>>.....>>>>>...>>.>>>>>..

HOM.SA-A      uu
RAT.RAT.      --
GAL.GAL.      --
HOM.SA-B      --
ORI.CUN.      --
#=GC SS_cons  ..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln75.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln75.fa

RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGGacaGaggaU
CAN.SPE.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCaGGaggaU
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGcCcGccggaU
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGUGGGaggaU
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu-gGGAGGCuGAGGCUGGcggaU
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

RAT.RAT.      CGCUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
CAN.SPE.      CGCUugaGCcCAGGaguUcugGGcUG-CAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
GAL.GAL.      CGCUugaGCCCAGGaguUcuggGCUG-CAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAa
HOM.SA-B      CGCUugaGCcCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgaugGGGUGUCCgCACUAa
FUG.RUB.      CGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgUcgauCGGGUGUCCgUACUAa
#=GC SS_cons  <<<<...<<.<<<<...<...<<.<<.<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

RAT.RAT.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
CAN.SPE.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
GAL.GAL.      GGCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCuaaGGaGGG
HOM.SA-B      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
FUG.RUB.      GuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCuaaGGaGGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<

RAT.RAT.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
CAN.SPE.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
GAL.GAL.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGGG
HOM.SA-B      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
FUG.RUB.      GUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAGUGGG
#=GC SS_cons  <<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>

RAT.RAT.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGAgacCccgUCUC
CAN.SPE.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUC
GAL.GAL.      aucGCGCCUGuGaAUAGCCACUG-CAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUC
HOM.SA-B      aucGCGCCUguGaAUAGCCACUG-CAcUCcaGCCUGaGCaacauAGCGAgacCCCGUCUC
FUG.RUB.      aucGCGCCCGuGaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUCAGUCUU
#=GC SS_cons  ...>>>>>>>.>.>>>>>>>>>>.>>.>>..>>>>>.>>.....>>>>>...>>.>>>>>

RAT.RAT.      uu
CAN.SPE.      u-
GAL.GAL.      c-
HOM.SA-B      u-
FUG.RUB.      u-
#=GC SS_cons  ..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln76.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln76.fa

RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGacaGagga
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGcCcGccgga
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacuc-GGGAGGCuGAGGCcGGagga
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacuc-GGGAGGCuGAGACaGGagga
XEN.LAE.      GCCGGGCGCuguggcguGUGCCUguaaUCC-agcuac--uuGGAGGCuuGGGCUGUcgga
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<.........>>>>>>>.<<<<<.<<....

RAT.RAT.      UCGCUugaGUCCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
GAL.GAL.      UCGCUugaGCCCAGGaguUcuggGCUGCAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAa
ORI.CUN.      UCGCUugaGUCCAGGaguUcugGGcUGUcGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
RAT.NOR.      UCGaUugaGUCCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
XEN.LAE.      UCGCUugaGUcCAGGaguUcugggCUGCACUGaGCUAUgUcgauCGGGUGUCCgCACUAa
#=GC SS_cons  <<<<<...<<<<<<<...<....<.<<<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

RAT.RAT.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
GAL.GAL.      GGCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUG-CCuaaGGaGG
ORI.CUN.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
RAT.NOR.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
XEN.LAE.      GuUCGGUAUCAAUaUGGUGuUCCuGGGggagCCUcGGAuCACCAgGUUGcUCuaaGGaGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<.<<<....>>>.>>..>>>>>.>>>>.<<...>>.<<

RAT.RAT.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
GAL.GAL.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGG
ORI.CUN.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
RAT.NOR.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGG
XEN.LAE.      GGUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACCCCcGUGCCGAuCagUAGUGG
#=GC SS_cons  <<<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>

RAT.RAT.      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGGGCaacauAGCGAgacCccgUCUC
GAL.GAL.      GaucGCGCCUGuGaAUAGCCACUGCAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUC
ORI.CUN.      GaucGCGCCUGuGaAUAGCCACuGCAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUC
RAT.NOR.      GaucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUC
XEN.LAE.      GaucGCGCCUGuGaAUAGCCGGUGCAGaacaGCCUGaACaacacAGCGAgacACAGUUCu
#=GC SS_cons  >...>>>>>>>.>.>>>>>>>>>>>>.>...>>>>>>>>.....>>>>>...>>.>>>>>

RAT.RAT.      uu
GAL.GAL.      c-
ORI.CUN.      c-
RAT.NOR.      u-
XEN.LAE.      --
#=GC SS_cons  ..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln77.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln77.fa

HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGCuGGaggaU
CAN.SPE.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCaGGaggaU
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGcCcGccggaU
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCcGGaggaU
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGACaGGaggaU
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

HOM.SA-A      CGCUugaGUcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
CAN.SPE.      CGCUugaGCcCAGGaguUcugGGcUGCAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
GAL.GAL.      CGCUugaGCCCAGGaguUcuggGCUGCAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAaG
ORI.CUN.      CGCUugaGUCCAGGaguUcugGGcUGUcGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
RAT.NOR.      CGaUugaGUCCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
#=GC SS_cons  <<<<...<<.<<<<...<...<<.<<<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.<

HOM.SA-A      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
CAN.SPE.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
GAL.GAL.      GCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCuaaGGaGGGG
ORI.CUN.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
RAT.NOR.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
#=GC SS_cons  .<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<<

HOM.SA-A      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
CAN.SPE.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
GAL.GAL.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGGGa
ORI.CUN.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
RAT.NOR.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
#=GC SS_cons  <.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>.

HOM.SA-A      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUCuu
CAN.SPE.      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUCu-
GAL.GAL.      ucGCGCCUGuGaAUAGCCACUGCAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUCc-
ORI.CUN.      ucGCGCCUGuGaAUAGCCACuGCAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUCc-
RAT.NOR.      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUCu-
#=GC SS_cons  ..>>>>>>>.>.>>>>>>>>>>>>.>>..>>>>>.>>.....>>>>>...>>.>>>>>..

HOM.SA-A      u
CAN.SPE.      -
GAL.GAL.      -
ORI.CUN.      -
RAT.NOR.      -
#=GC SS_cons  .
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln78.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln78.fa

HOM.SA-A      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGCuGGaggaU
CAN.SPE.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCaGGaggaU
GAL.GAL.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGcCcGccggaU
HOM.SA-B      GCCGGGCGCGguggcgCGUGCCUguagUCCCagcuacucGGGAGGCuGAGGUGGGaggaU
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCcGGaggaU
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

HOM.SA-A      CGCUugaGUcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
CAN.SPE.      CGCUugaGCcCAGGaguUcugGGcUGCAGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
GAL.GAL.      CGCUugaGCCCAGGaguUcuggGCUGCAGUGcGCUAUgCcgagCGGGCGUCCgCGcUAaG
HOM.SA-B      CGCUugaGCcCAGGaguUcugGGcUGUAGUGcGCUAUgCcgaugGGGUGUCCgCACUAaG
ORI.CUN.      CGCUugaGUCCAGGaguUcugGGcUGUcGUGcGCUAUgCcgauCGGGUGUCCgCACUAaG
#=GC SS_cons  <<<<...<<.<<<<...<...<<.<<<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.<

HOM.SA-A      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
CAN.SPE.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
GAL.GAL.      GCCGGCAUCAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUGCCuaaGGaGGGG
HOM.SA-B      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
ORI.CUN.      uUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGGG
#=GC SS_cons  .<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<<

HOM.SA-A      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
CAN.SPE.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
GAL.GAL.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCCGGUCagUAaCGGGa
HOM.SA-B      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
ORI.CUN.      UgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGGa
#=GC SS_cons  <.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>.

HOM.SA-A      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUCuu
CAN.SPE.      ucGCGCCUGuGaAUAGCCACUGCAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUCu-
GAL.GAL.      ucGCGCCUGuGaAUAGCCACUGCAGCguaGCCUGGGCaacauAGCGAgaccCuGuCUCc-
HOM.SA-B      ucGCGCCUguGaAUAGCCACUGCAcUCcaGCCUGaGCaacauAGCGAgacCCCGUCUCu-
ORI.CUN.      ucGCGCCUGuGaAUAGCCACuGCAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUCc-
#=GC SS_cons  ..>>>>>>>.>.>>>>>>>>>>>>.>>..>>>>>.>>.....>>>>>...>>.>>>>>..

HOM.SA-A      u
CAN.SPE.      -
GAL.GAL.      -
HOM.SA-B      -
ORI.CUN.      -
#=GC SS_cons  .
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln79.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln79.fa

RAT.RAT.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGGacaGaggaU
CAN.SPE.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCaGGaggaU
ORI.CUN.      GCCGGGCGCGguggcgCGCGCCUguagUCCCagcuacucGGGAGGCuGAGGCcGGaggaU
FUG.RUB.      GCCGGGUACGguggcgCGUGCCUguaaUCCaagcuacu-gGGAGGCuGAGGCUGGcggaU
RAT.NOR.      GCCGGGCGcGguggcgCaCGCCUguagUCCCagcuacucGGGAGGCuGAGACaGGaggaU
#=GC SS_cons  <<<<<<<<.<......>.>>>>>....<<<<........>>>>>>>.<<<<<.<<....<

RAT.RAT.      CGCUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
CAN.SPE.      CGCUugaGCcCAGGaguUcugGGcUG-CAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
ORI.CUN.      CGCUugaGUCCAGGaguUcugGGcUG-UcGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
FUG.RUB.      CGCUugaGCUCAGGaguUcugGGCUuC-AGCGgaCUAUgUcgauCGGGUGUCCgUACUAa
RAT.NOR.      CGaUugaGUCCAGGaguUcugGGcUG-UAGUGcGCUAUgCcgauCGGGUGUCCgCACUAa
#=GC SS_cons  <<<<...<<<<<<<...<...<<.<<.<<<<<.<<<<<.<....<<<<<<<<<.<<<<<.

RAT.RAT.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
CAN.SPE.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
ORI.CUN.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
FUG.RUB.      GuuCGGUAUCGAUaUGGUGcUCCUGGGggagCCCGGGAuCACCAgGUCGCCuaaGGaGGG
RAT.NOR.      GuUCGGCAUCAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUGCCuaaGGaGGG
#=GC SS_cons  <.<<<<<<<<<<<.<<<<<..<<<<<<....>>>>>>..>>>>>.>>>><<...>>.<<<

RAT.RAT.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
CAN.SPE.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
ORI.CUN.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
FUG.RUB.      GUgccccGGCCcaggUCGgaaaCGAagcaGGUCaaaGCCCCcGUGCCGcuCagUAGUGGG
RAT.NOR.      GUgaaccGGCCcaggUCGgaaaCGGagcaGGUCaaaACUCCcGUGCUGAuCagUAGUGGG
#=GC SS_cons  <<.....<<<<....<<<....>>>....>>>>...>>>>>.>>>>>>>.>..>>>>>>>

RAT.RAT.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAGCGAgacCccgUCUC
CAN.SPE.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGuGCaacauAGCGAgacCCcGUCUC
ORI.CUN.      aucGCGCCUGuGaAUAGCCACuG-CAcUCcaGCCUGGGCaacauAGCGAgacCCuGUCUC
FUG.RUB.      aucGCGCCCGuGaAUAGaCGCU-GuAGUUcaACCUGAGUaacacAGCGGgacUCAGUCUU
RAT.NOR.      aucGCGCCUGuGaAUAGCCACUG-CAcUCcaGCCUGGGCaacauAgCGAgacCC-GUCUC
#=GC SS_cons  ...>>>>>>>.>.>>>>>>>>>>.>>.>>..>>>>>>>>.....>>>>>...>>.>>>>>

RAT.RAT.      uu
CAN.SPE.      u-
ORI.CUN.      c-
FUG.RUB.      u-
RAT.NOR.      u-
#=GC SS_cons  ..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln80.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln80.fa

ZEA.MA-E      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ZEA.MA-D      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ZEA.MA-G      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGUGcggaUuCU
ZEA.MA-B      nCCGAGCUCUguagcgAGAGCUUguaaCCCGagCGGGGGcauuAAGGUGGcGcggaUGCU
ZEA.MA-F      nCCGAGCUCUguagcgAGAGCUUguaaCCUaagcGGGGGcauuAAGGUGGUGuggaUGUU
#=GC SS_cons  .<<<<<<<<<......>>>>>>>....<<<<..>>>>>>....<<<<<<<<<....<.<<

ZEA.MA-E      UuGcGAuGGcuUUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCAa
ZEA.MA-D      UuGcGAuGGcuUUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCAa
ZEA.MA-G      UuGcGAuGGcuUUCUGGGCCcGGGCUCGcuauGUGcCuuuggcCGGCCUGcCCgUCCCAa
ZEA.MA-B      uuGcGAuGGu-uUCUGGGcCUGGGCUCGu--uGUGaCucuagcCGGCUUGcCCaUCCCAa
ZEA.MA-F      UccUGAcGGa-UUCUGgGcCUGGGCUUGU-auGUGcCAcuggcCGGCCUGcCCgUUCCAa
#=GC SS_cons  <.<.<<.<<..<<<<<<<.<.<<<<<<<....<<<.<......<<<<<<<.<<.<<<<<.

ZEA.MA-E      GUUGGuAGUGgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUgaAGUG
ZEA.MA-D      GUUGGuAGUGgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUgaAGuG
ZEA.MA-G      GUUGGuAGUGgCUGGcGGAGGCUuuAGCggaaGCU-uuGGUCUCU-CCAGaCCUgaAGuG
ZEA.MA-B      GUUGGuAGUGUCUGaCGGGG-CUCuAGCgaaaGCUuuGGGuCUCUG-CAGACCUacAGcG
ZEA.MA-F      GUUGGuuGUGgCUGGuGGGG-CUCGGGCgaagGCC-UGGGcCUCU-UUAGaCCUgaAGcG
#=GC SS_cons  <<<<<.<<<<.<<<<.<<<<.<<..<<<....>>>...>>.>>>>.>>>>.><<..>>.<

ZEA.MA-E      GCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCGGCUuCCAACggUG
ZEA.MA-D      GCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuCCAACggUG
ZEA.MA-G      GCAGgaauggCGUgaggCUGgcuucaCAGagcaGCGaucaCU-GCCcGCUuCCAACggUG
ZEA.MA-B      GCAGgaauggCGUaaggCUGgcuucaCAGagcaGCGaucaCUcGCCcACUuCCAACggUG
ZEA.MA-F      GCAGgcauggCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCuuCCAACggUG
#=GC SS_cons  <<<<......<<<....<<<......>>>....>>>....>>.>>>.>>>.>>>>>..>>

ZEA.MA-E      GGAGGauaaCGGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG-CCUCaCuAAGcAg
ZEA.MA-D      GGAGGauaaCAGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG-CCUCaCuAAGcAg
ZEA.MA-G      GGAGGauaaCGGGCCGcuGCACuuCGAGCCCaacucaGGCCCAGAG-CCUCaCuAAGcAg
ZEA.MA-B      GGAGGauaaCAAGCCGcuGCACuuUGAGCCCaacacAGaCCCAGA-uCCUCuCuuAGCAa
ZEA.MA-F      GGAGGauaaCAGGCCGcUGCAUuGCAAGCCCaacucGGuC-CAGAG-CCUCAuuAAACAg
#=GC SS_cons  >>>>>....>>>>>>>..>>>>..>>>>>>>......>.>>>>>>>.>>>>.>.>>>.>.

ZEA.MA-E      acCACCAUCUUu
ZEA.MA-D      acCACCAUCUU-
ZEA.MA-G      acCACCAUCUUu
ZEA.MA-B      acCaCCAUCUUu
ZEA.MA-F      acCACCAUCUUu
#=GC SS_cons  ..>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln81.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln81.fa

HUM.LU-A      GCCGGuCUUAgcaacgUGGGcCUguaaCCCAagUGGGGGCauGuGGGAAAUGGgaCU-UU
HUM.LU-D      GaCGGGCUUAgcaacgUGGGCCUguaaCCCAagUGGGGgCauGuGGGAAAUGGgaCU-UU
HUM.JA-B      ---GGcCU-AgcaacgUgGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGGgaCU-UU
HUM.LU-B      ---GGcCUUAgcaacgUGGGcCUguaaCCCAagUGGGggcauGuGGGAAAUGGaaC-AUU
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcauGuGGGAAAUGGaaCU-UU
#=GC SS_cons  ...<<.<<<<......>>>>.>>....<<<<..>>>>.....<.<<<<<<<<<..<<.<<

HUM.LU-A      GGGUCAacCUAGUGGAuCGGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaGCC
HUM.LU-D      GGGUCAacCUAGUGGAuCGGGUCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaGCC
HUM.JA-B      AGuUCGGccCAuUGGAUCGGaUCCAGuguUAGcUGcuugCUGGgCUGcCCaUUCCAaGCC
HUM.LU-B      GGGUCAGcCCAGUGGauCgGGuCCAGuguUAGcUGcuuaCUGGUCUGcCCaUUCCAaGCC
HUM.LU-C      GGGUCAacCCAGUgGunCgGGncCAGugcuaGcUGcuuaCCcGgCUGcCCaUUCCAaGCC
#=GC SS_cons  <<<<<<..<<<<<<<..<.<<.<<<<...<<<.<<....<<<<.<<<.<<.<<<<<.<<<

HUM.LU-A      GGGAGUuGGgcUGaGUGACCUGGgCgaagGgCUGGGUUGCgCAcgUCCUagAGuGGAGGg
HUM.LU-D      GGGAGUuGGGCUGaGUGACCUgGGCgaagGCU-GGGUUGCgCAGCUCCUagAGuGGAGGg
HUM.JA-B      GAGAGUuGAGCUGugUGAGCCGGACgaagGUCUGGCUUGguCAGCUCCUaaAGcGGAGGg
HUM.LU-B      GGGAGUuGGGCUGaGUGACCUGGGCgaagGCCUGGGUUGCgCAGCUCCUagAGuGGAGGg
HUM.LU-C      GGGAGguGGGcUGaGggaCcugGGCgaagGCUnnnGgngCgCA-CUCcUagAcuGGAGGg
#=GC SS_cons  <<<<<<.<<<.<<.<<<<<<<.<<<....>>>.>>>>>>>.>>.>>><<..>>.<<<<<.

HUM.LU-A      caaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGGAAGGa
HUM.LU-D      caaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcGCUCUCGGCagUGGAAGGa
HUM.JA-B      caaugCGUgaggCUGguuucaCAGagcaGCGacaaCCUCCcGCUCUCGGCagUGGAAGGa
HUM.LU-B      caaugCGUgaggCUGguuucaCAGagcaGCGacuaCCUCCcGCUCCCGGCagUGGAAGGa
HUM.LU-C      caaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgCUCUCGGCagUGGAAGGa
#=GC SS_cons  .....<<<....<<<......>>>....>>>....>>>>>.>>>>>>>>>..>>>>>>>.

HUM.LU-A      uaaCGGGCCGGUGCUAcCUGGGUCCaccauGcUUCACUAGg-cUGACUcuUAAuAGgaCC
HUM.LU-D      uaaCGGGCCGGUGCUAcCUGGAUCCaccauGcUUCACUGGg-cUGACUcuUAAuAGgaCC
HUM.JA-B      uaaCGGgCCGGUGCUGcUUGGAcCCaccauGGUUCAcUGag-CUGAcUcuUAAuAGgaCC
HUM.LU-B      uaaCGGGCCGGUGCUAcUUGGuCCa-ccauGu-UCACUGGucCUGACUcuUAAUcGgaCC
HUM.LU-C      uaaCGGgCcGGUGCgccUUGagCCaacacuGuuCaACUGGg-cUGACUcuUAAuAGgaCC
#=GC SS_cons  ...>>>.>>>>>>>>>.>>>>.>>......>..>>>>>>>...>>>>>..>>>.>>..>>

HUM.LU-A      AUUUCUUuU
HUM.LU-D      AUUUCUUuU
HUM.JA-B      AUUUCUUuU
HUM.LU-B      AUUUCCUuU
HUM.LU-C      AUUUCUUuU
#=GC SS_cons  >>>>>>>.>
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln82.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln82.fa

CAE.EL-A      ACCGAGCGUCguggcgGGCGCUUgugaGUCagcuucuuGACGGUaGAUAAGUGuggaUGG
CAE.EL-D      ACCGAGCGUCguggcgGGCGCUUgugaGUCagcuucuuGACGGUaGAUAAGUGuggaUGG
CAE.BRI.      ACCGGGUGUCguggcgGGCGCCUgugaGUCagcuucuuGACGGUaGACAAGUGuggaUGG
CAE.EL-B      ACCGAGCGUCguggcgGGCGCUUgugaGUCagcuucuuGACGGUAGAUAAGUGuggaUGG
CAE.EL-C      ACCGAGCGUCguggcgGGCGCUUgugaGUCagcuucuuGACGGUaGAUGAGUGuggaUGG
#=GC SS_cons  <<<<<<<<<<......>>>>>>>....<<<........>>>>>>.<<<<<<<<....<<<

CAE.EL-A      AGugaGAGGAGGaguCcugUGUAUGucGUugUCuACgUC-ga-cCGAGCGUCCGuGCCAa
CAE.EL-D      AGugaGAGGAGGaguCcugUGUAUGucGUcgUCuACgU-cgac-CGAGCGUCCGuGCCAa
CAE.BRI.      AGugaAGGGAGGaguCcugUGGGUGuuGUcgGCAACggC-ga-cCGAGCGUCCGuGCCAa
CAE.EL-B      AGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGCCAa
CAE.EL-C      AGugaGAGGAGGaguCcugUGUAUGuCGUugUCAACgUC-ga-cCGAGCGUCCGuGCCAa
#=GC SS_cons  <<...<<<<<<<...<...<<<<<<..<<..<<.<<.<<.....<<<<<<<<<<.<<<<.

CAE.EL-A      GCGCUACGUCACCaGGGGaUAACUGUCggaaGGCGGUUAgUCCCgGGUGCauaagGaGUC
CAE.EL-D      GCGCUACGUCACCaGGGGaUAACUGUCggaaGGCGGUUAgUCCCgGGUGCauaagGaGUC
CAE.BRI.      GCGCUGCGUCGCCaGGGGUCuCCGGUCggaaGGCUGGcGGUCCCgGGCGCauaagGaGUG
CAE.EL-B      GCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGaGUG
CAE.EL-C      GCGCUGCGUCACCaGGGGaUGACUGUCggaaGAUGGUCAgUCCCgGGUGCauaagGaGUG
#=GC SS_cons  <<<<<<<<<<<<<.<<<<.<<<<<<<<....>>>>>>>>.>>>>.>>>><.....>.<<<

CAE.EL-A      GUggaugGUUcaggACCgaaaGGUagcaGACaaaaGCGACcGCGUGGUGCagUGGCCGGa
CAE.EL-D      GUggaugGUUcaggACCgaaaGGUagcaGACaaaaGCGACcGCGUGGUGCagUGGCCGGa
CAE.BRI.      GUgcacgGCUcaggGCCgaaaGGCagcaGGCaaaaGCCACcGCGCGGUGCagUGGCCGGa
CAE.EL-B      GUggaugGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGCCGGa
CAE.EL-C      GUggaugGUUcaggACCgaaaGGUagcaGACaaaaGCCACcGCGCGGUGCagUGGCCGGa
#=GC SS_cons  <<.....<<<....<<<....>>>....>>>....>>>>>.>>>>>>>>>..>>>>>>>.

CAE.EL-A      ccGCGCUUGuGA-GUuGAcACaCAUACGcaGCCUUCUCgauacCUUCAgacCACUUAUCa
CAE.EL-D      ccGCGCUUGuaA-GUuGAcACaCAUACAcaGCCUUCUCgauacCUUCAgacCACUUAUCa
CAE.BRI.      uaGCGCUUGuG-aGUUGUcGCuCGCCCAcaGCCUCUCUgauacCUUCAgacCACUUGUCa
CAE.EL-B      cuGCGCUUGuGA-GUUGAcACGUAUACAcaGCCUUCUCaauacCUUCAgacCACUUGUUU
CAE.EL-C      caGCGCUUGuGA-GUUGAcACGUAUACAcaGCCUUCUCaauacCUUCAgacCACUUGUCa
#=GC SS_cons  ..>>>>>>>.>>.>>.>>.>>.>>>>>>..>>>>>>>>.....>>>>>...>>>>>>>>.

CAE.EL-A      --uuu
CAE.EL-D      --uuu
CAE.BRI.      --uu-
CAE.EL-B      --uu-
CAE.EL-C      cu---
#=GC SS_cons  .....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln83.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln83.fa

ARA.TH-C      GUCGAaCUCaguaacgcGGGcUUgugaUCCAagUGGAGACaa-uAAGGgGAUGG--gaCG
LYC.ES-O      GcCGAGCUUAguaacgUGGGCUUguaaCCCAagUGGGGaUgu-uAAGGUGGUGG--aaUA
ARA.TH-D      GUCGAGCUaaguaacgagAGCUUgugaCCCGagUGGGGACaa-uAAGGUGGUGG--aaCA
HUM.LU-C      ---GGucUUAgcaacuUGGucCUguaaCCCAagUGGGggcau-GuGGGAAAUGG--aaCU
ORY.SA-A      GCCGaGCUCaguagcgaGAGCcUguaaCCCaagcGGGGGCacuAAAGGUGGcuGcggaUG
#=GC SS_cons  <.<<<.<<<........>>>.>>....<<<<..>>>>>.>....<<<<<<<<<<....<<

ARA.TH-C      -UUG----GGUcGauCUcAUUGGGcC-GGgUUcGGguuGGGcUAuauucUGGCCCGcCCa
LYC.ES-O      -UUG----GGCuGUc-CCAgauGGCu-GGGCUUGG--uGGGcUAauuuCUGGcCUGcCCu
ARA.TH-D      G-uG----GuUCaAu-UCcuCGGGUC-GGAcCUGAugcuGAcaUauaucUGAGCUGcCCa
HUM.LU-C      -UUG----GGUCAac-CCAGUgGunC-gGGncCAGugcuaGcUGcuuaCCcGgCUGcCCa
ORY.SA-A      uUUGgugUGGAuucuGAUcCUGGGCCccaugUUGu--uGUaaUc-uugcUGGCUUGcCCg
#=GC SS_cons  .<<<....<<<.....<<..<.<<.<..<..<<<<....<<.<<.....<<<.<<<.<<.

ARA.TH-C      UUCCAaGUUG-GGAGUuGAGGCA-UGGGcUUCGAGCgaagGCUCGGGuCUCA-UGUCUU-
LYC.ES-O      aUCCAaGCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACu-aGAUUC-
ARA.TH-D      GUCCAaGCUG-UGAGu-AAUCUG-UgUGGGUCAGGCgaagGCUUGACUCAgG-CGGAUU-
HUM.LU-C      UUCCAaGCCG-GGAGguGGGcUG-aGggaCcugGGCgaagGCUnnnGgngCg-CA-CUC-
ORY.SA-A      UUCCAaGuUGcGuAGU-GGGccGGaGGGGCuuuGGCgaagGCCuuuGCUUUgCUucUCCg
#=GC SS_cons  <<<<<.<<<<.<<<<..<<<.<<..<<<.<...<<<....>>>...>.>>>..>>.>>>.

ARA.TH-C      ---CUagAG-uGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUccaCCUCCcGC
LYC.ES-O      ---CUaaAG-uGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaaaACUUCcGC
ARA.TH-D      ---CUaaAGucGGAGGguaaugCGUgaggCUGguuucaCAGagcaGCGacuaCUUCCcuC
HUM.LU-C      ---cUagAc-uGGAGGgcaaugCGUgaggCUGgcuucaCAGagcaGCGacuaCCUCCcgC
ORY.SA-A      gccCUaaAG-uGGCAGgcacagCGUgaggCUGgcuucaCAGagcaGCGaucaCUGCCcGC
#=GC SS_cons  ...<<..>>..<<<<<......<<<....<<<......>>>....>>>....>>>>>..>

ARA.TH-C      UCUUGACggUGGAAGGauuaCGGGCCAuUG-CCU-UCcGAgCCcacu-auGaCCCAAUaA
LYC.ES-O      UUUGUGCagUGGAaGGauaaCGGaCCGGUGcCUU-CCAAGUUCcau-uaauGCCugaUGG
ARA.TH-D      UUACAGCagUGGAUGGaucaUAGUUCGaAg-UCucUCAGaUCCacu--auGGCCCGcuGG
HUM.LU-C      UCUCGGCagUGGAAGGauaaCGGgCcGGUG-CgccUUGagCCaaca--cuGuuCaACUGG
ORY.SA-A      UuCCAuCggUGGAAGGauaaCAGGCUGcuG-cACcuUGGgcccgcuu-cuGGCCCAGaGU
#=GC SS_cons  >>>>>>>..>>>>>>>....>>>.>>>.>>.>>..>>>>..>........>.>>.>..>>

ARA.TH-C      G-CcGCU--cCGAuUGgaCCAUCaCUUU-
LYC.ES-O      -GCuGCU--cCAAuUAaaCCACCACUUU-
ARA.TH-D      uUcGAuC--uCucCUGgaCCACCACUUU-
HUM.LU-C      gcUGACU-cuUAAuAGgaCCAUUUCUUuU
ORY.SA-A      C-ccUCUA--CAA-CAgaCcaCCAUCUUU
#=GC SS_cons  ....>>>...>>>.>>..>>>>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln84.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln84.fa

HOM.SA-B      GCCGGGCGCGgug--gcgCGUGCCUguagUCCCagcuacuc-GGGAGGC---uGAGGUGG
HUM.LU-A      GCCGGuCUUA--gcaacgUGGGcCUguaaCCCAag-------UGGGGGCauGuGGGAAAU
CAE.BRI.      ACCGGGUGUCgug--gcgGGCGCCUgugaGUC-agcuuc--uuGACGGU---aGACAAGU
ZEA.MA-B      nCCGAGCUCU--guagcgAGAGCUUguaaCCCGag-------CGGGGGcauuAAGGUGGc
SCH.POM.      cGC---------------------uguaa----ug-----------GC-------uUGGU
#=GC SS_cons  .<<<<.<<<<........>>>>.>>....<<<...........>>>>>.....<<<<<<<

HOM.SA-B      GaggaUCGCUu---gaGCcCAGGa----guUcugGGcUG---UAGUGc-GCUAUgC----
HUM.LU-A      GG--gaCU--UUG---GGUCAac--CUAGUG-GAuC-------GGGUCCAGuguUAGcUG
CAE.BRI.      GuggaUGGAGu---gaAGGGAGGa----guCcugUGGGUG--uuGUcg-GCAACggC---
ZEA.MA-B      Gc-ggaUGC-UuuG--cGAuGGu---uUCUG-GGcCU------GGGCUCGu--uGUGaCu
SCH.POM.      CG--aaGUGUUUa--GUACUcCCaa--------uaGUGCAUGUUCgGUGGucuc------
#=GC SS_cons  <.....<<<.......<<<<<<........<....<.......<<<<..<..........

HOM.SA-B      cgau------gGGGUGUCCgCACUAaGuUCGGCAU----CAAUaUGGUGacCUCCCGgga
HUM.LU-A      -cuu--aCUGGUC-UGcCCaUUCCA-aGCCG-GGAGUuGGgcUG-aGUGACCUGGgCgaa
CAE.BRI.      -ga------cCGAGCGUCCGuGCCAaGCGCUGCGU----CGCCaGGGGUCuCCGGUCgga
ZEA.MA-B      -cua--gcCGGCU-UGcCCaUCCCA-aGUUG-GuAGU-GUCUGaCGGGG-CUCuAGCgaa
SCH.POM.      ----GGGUucGAGUCUCgcuUuCG-auCCCucGAUc--UGCCAcgUcUgUuCGAAGAgua
#=GC SS_cons  ..........<<<.<<.<<.<<<<<..<<<<.<<<....<<<<..<<<<..<<<<<<...

HOM.SA-B      gCGG-GGGacCACCAgGUUG-CCuaaGGaGGGGUgaacc-GGCCcaggUCGgaa--aCGG
HUM.LU-A      gGgC-UGGGUUGCg-CAcgUCCU-agAGuGGAGGgcaau-gCGUgaggCUGgcuucaCAG
CAE.BRI.      aGGC-UGGcGGUCCCgGGCG-CauaagGaGUGGUgcac--gGCUcaggGCCgaa--aGGC
ZEA.MA-B      aGCUuuGGGuCUCUG-CAGACCU-acAGcGGCAGgaaug-gCGUaaggCUGgcuucaCAG
SCH.POM.      gUCU-UCGuG-GcAacUGGCAGUuaaACCguGuaguac-cGAUGgaggUUGgaa--aCAA
#=GC SS_cons  .>>>.>>>..>>>>..>>>>.<<...>>.<<<<<.......<<<....<<<......>>>

HOM.SA-B      agcaGGUCaaaAC-UCCc--GUGCUGAuCag-UAGUG-GG-aucGCGCCUg------u--
HUM.LU-A      agcaGCGacuaCC-UCCcGCUCU-CGGCag--UGGAA-GG-auaaCG-GGCCGG----UG
CAE.BRI.      agcaGGCaaaaGC-CACc--GCGCGGUGCag-UGGC-CGG-auaGCGCUUG------u--
ZEA.MA-B      agcaGCGaucaCUcGCCcACUuC-CAACgg--UGGGA-GG-auaaCA-AGCCGc----uG
SCH.POM.      ugcaCAUCa--cuaCcgG--GUCuuGGGcagugCG-AuagcgauGGGAUUC--ACCU---
#=GC SS_cons  ....>>>....>>.>>>...>>>.>>>>....>>>>>.>>.....>>.>>>.........

HOM.SA-B      -GaAUAGC--CACUG---CAcUC-caG------CCUGaGCaa--cauAGCGAgacCCCGU
HUM.LU-A      CUAc--CUGGGUCCacc--auGcUU-CACUAGg-cUGACU--cuUAA-uAGg-aCCAUUU
CAE.BRI.      G-aGUUGU--cGCu---CGCCCA-caG------CCUCUCUga--uacCUUCAgacCACUU
ZEA.MA-B      CACu--uUGAGCCCaaca-cAGaCC-CAGA---uCC-UCu---CuuA-GCAa-acCaCCA
SCH.POM.      -------UCGCaGGAUGUGCAU-----------GGaAGUAU----AAACACa-aCGGUCG
#=GC SS_cons  .......>..>>>>.......>....>.......>>>>>>........>>>....>>>>>

HOM.SA-B      CUCu---
HUM.LU-A      CUUuU--
CAE.BRI.      GUCa-uu
ZEA.MA-B      UCUUu--
SCH.POM.      uu-----
#=GC SS_cons  >>>....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln85.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln85.fa

RAT.NOR.      GCCGGGCGcGgug--gcgCaCGCCUguagUCCCagcuacucGGGAGGC---uGAGACaGG
LYC.ES-H      GUUGAGCUUA--guaacgUGGGCUUguaaUCCAag------UGGAGACaucAAAGugGuU
ARA.TH-G      GUCGAGCUaU--guaacgAgAGCUUguaaCCCAag------UGGGGACuauAAGAUGGUG
ZEA.MA-B      nCCGAGCUCU--guagcgAGAGCUUguaaCCCGag------CGGGGGcauuAAGGUGGcG
LYC.ES-G      GCCGAGCUUA--guaaugUGGGCUUguaaCCCAaa------UGGGGGCauuAAuGUGGUG
#=GC SS_cons  <<<<<<<<.<........>.>>>>>....<<<<........>>>>>>>...<<<<<<<.<

RAT.NOR.      aggaUCGaUu---gaGUCCAGGa---guUcugGGcUGUAGUGc-GCUAUgC----cgau-
LYC.ES-H      g--aaU-A-UUG---GGCuGUa-CCAgau-GGUu----GGGCUUGG--UGGGcUA-auuu
ARA.TH-G      G--aaCAc--UG---gauCGGc-CCA-CG-GGUC----GGAUUUGUuguUGGcau-aggu
ZEA.MA-B      c-ggaUGC-UuuG--cGAuGGu--uUCUG-GGcCU---GGGCUCGu--uGUGaCu-cuag
LYC.ES-G      G--aaUG--UUG---GGCuGUa-CCAgau-GGUu----GGGCUUGG--uGGGcUA-auuu
#=GC SS_cons  .....<<.........<<.<<....<....<<<.....<<<<<<<<...<<<........

RAT.NOR.      ---CGGGUGUCCgCACUAaGuUCGGCAU----CAAUaUGGUGacCUCCCGggagCGG-GG
LYC.ES-H      CUGACU-UGcCCuaUCCA-aGCuU-AGAGUuGGAUCA-uGUGGcCCAaUUgaagAAa-UG
ARA.TH-G      cUGGAC-UGcCCaaUCCA-aGCUG-uGAGU-gAACCG-UAUGaAcCAAGCgaagGUU-UG
ZEA.MA-B      cCGGCU-UGcCCaUCCCA-aGUUG-GuAGU-GUCUGaCGGGG-CUCuAGCgaaaGCUuuG
LYC.ES-G      CUGGcC-UGcCCuaUCCA-aGCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAa-UG
#=GC SS_cons  .<<<<<.<<.<<..<<<<..<<<<.<<<<<..<<<<...<<<..<<<.<<....>>..>>

RAT.NOR.      GacCACCAgGUUG-CCuaaGG-aGGGGUgaaccGGCCcaggUCGgaa--aCGGagcaGGU
LYC.ES-H      GaCUACu-UGAUUCgU-aaAg-uGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUG
ARA.TH-G      aUcCGUA-CGGUUgCU-aaAGguuGAGGguauugCGUuaggCUGgcuucaCAGagcaGCG
ZEA.MA-B      GGuCUCUG-CAGACCU-acAG-cGGCAGgaauggCGUaaggCUGgcuucaCAGagcaGCG
LYC.ES-G      GGCUACu-aGAUUCCU-aaAG-uGGGGUggaccgCGUgaggCUGguuucaCAGagcaACG
#=GC SS_cons  >..>>>...>>>>.<<...>>..<<<<<......<<<....<<<......>>>....>>>

RAT.NOR.      CaaaAC-UCCc--GUGCUGAuCagUAGUGGGaucGCGCCUG---u----GaAUAGC--CA
LYC.ES-H      aacaGC-UCCcGCUCU-GuGCag-UGGAaGGauaaUG-GGUCGG-UGuCUUA--UCAAGU
ARA.TH-G      acuaCC-UCccGCUCu-CAGCag-UGGAcGGacaaCG-GUUCGa-cg-CCAc--ACAAAU
ZEA.MA-B      aucaCUcGCCcACUuC-CAACgg-UGGGAGGauaaCA-AGCCGc-uG-CACu--uUGAGC
LYC.ES-G      aaaaAC-UUCcGCUUU-GUGCag-UGGAaGGauaaCG-GaCCGG-UGcCUU---CCAAGU
#=GC SS_cons  ....>>.>>>.>>>>>.>>>>...>>>>.>>....>>.>>>>>.....>>>...>>>>>>

RAT.NOR.      CUG---CAcUC-caG------CCUGGGCaa--cauAgCGAgacCC-GUCUCu-
LYC.ES-H      UC-ag-uaacGCC-uaaUGG--GUuGCU---cCAA-UaAa-caAcCacCUUUu
ARA.TH-G      CCacu--auGGUC-CGcUGGc-UCGuaa--ccCGc-uUGa-aCCACCAUUUU-
ZEA.MA-B      CCaaca-cAGaCC-CAGA---uCC-UCu---CuuA-GCAa-acCaCCAUCUUu
LYC.ES-G      UCcau-uaauGCC-ugaUGG--GCuGCU---cCAA-uUAa-aCCACCACuUUu
#=GC SS_cons  >>........>>>....>....>>.>>..........>>....>.>>>>>>>.
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln86.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln86.fa

CAE.EL-D      ACCGAGCGUCgug--gcgGGCGCUUgugaGUC-agcuuc--uuGACGGU---aGAUAAGU
GAL.GAL.      GCCGGGCGcGgug--gcgCaCGCCUguagUCCCagcuacuc-GGGAGGC---uGAGcCcG
LYC.ES-O      GcCGAGCUUA--guaacgUGGGCUUguaaCCCAag-------UGGGGaUguuAAGGUGGU
ZEA.MA-D      nCCGAGCUCU--guagcgAGAGCUUguaaCCCGag-------CGGGGGcauuAAGGUGGU
YAR.LI-B      aGC---------------------uguaa----ug-----------GCauu---uuGUCG
#=GC SS_cons  .<<<<<<<.<........>.>>>>>....<<<...........>>>>>.....<<<<<<<

CAE.EL-D      GuggaUGGAGu---gaGAGGAGGa--------------------------------guCc
GAL.GAL.      ccggaUCGCUu---gaGCCCAGGa--------------------------------guUc
LYC.ES-O      GG--aaUA--UUG---GGCuGUc------------------------------CCAgau-
ZEA.MA-D      Gc-ggaUuC-UUuG--cGAuGGcu------------------------------UUCUG-
YAR.LI-B      ga-GUgGUAAAU---cGCCUUCUuguugugcguucgaguucuggacucugcac-------
#=GC SS_cons  ......<<<.......<<<.<<......................................

CAE.EL-D      ugUGUAUG--ucGUcg-UCuACgU----cgac----CGAGCGUCCGuGCCA-aGCGCUAC
GAL.GAL.      uggGCUG---CAGUGc-GCUAUgC----cgag----CGGGCGUCCgCGcUA-aGGCCGGC
LYC.ES-O      GGCu-------GGGCUUGG--uGGGcUA-auuuCUGGcC-UGcCCuaUCCA--aGCAC-A
ZEA.MA-D      GGCCc------GGGCUCGcuauGUGcCu-uuggcCGGCC-UGcCCgUCCCA--aGUUG-G
YAR.LI-B      -------uGgGcUAc--------------------UUUGUUGUCCUuuCCGAauUCUGCG
#=GC SS_cons  ............<<...<.....<............<<<.<<.<<..<<<<...<<<<.<

CAE.EL-D      GU------CACCaGGGGaUAACUGUCggaaGGCGGUUAgUCCCgGGUG-CauaagGaGUC
GAL.GAL.      AU------CAAUaUGGUGaGCCcCGGggagCCGaGGCaCACCAgGUUG-CCuaaGGaGGG
LYC.ES-O      GAGUu--GGAUCa-uGUGGUCCAaUUgaaaGAaUGGGCUACu-aGAUUCCU-aaAGuGGG
ZEA.MA-D      uAGU---GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCU-CCAGaCCU-gaAGuGGC
YAR.LI-B      Gu---ugAUGGGcGUCUCG-GuCUGAguaaUCGGcUuUGAGAUuUCCGUUCuaaGAuUAA
#=GC SS_cons  <<......<<<<..<<<<<<<..<<<....>>>..>>>>>>>..>>>>.<<...>>.<<<

CAE.EL-D      GUggau--gGUUcaggACCgaa--aGGUagcaGACaaaaGC-GACc--GCGUGGUGCag-
GAL.GAL.      GUgaacc-GGCCcaggUCGgaa--aCGGagcaGGUCaaaAC-UCCc--GUGCCGGUCag-
LYC.ES-O      GUggacc-gCGUgaggCUGguuucaCAGagcaACGaaaaAC-UUCcGCUUU-GUGCag--
ZEA.MA-D      AGgaaug-gCGUgaggCUGgcuucaCAGagcaGCGaucaCUcGCCcGCUuC-CAACgg--
YAR.LI-B      cuggga-uaCUUcaguGGAgca--aUCCagcaGAGauc-cagUUG----CCGUGGGuaUg
#=GC SS_cons  <<.......<<<....<<<......>>>....>>>....>>.>>>...>>>.>>>>....

CAE.EL-D      -UGGC-CGGaccGCGCUUG-------u---aA-GUuGA--cACa---CAUACA-caG---
GAL.GAL.      -UAaCG-GGaucGCGCCUG-------u----GaAUAGC--CACUG---CAGCg-uaG---
LYC.ES-O      -UGGAa-GGauaaCG-GaCCGG-----UGcCUU---CCAAGUUCcau-uaauGCC-ugaU
ZEA.MA-D      -UGGGA-GGauaaCA-GGCCGc-----uG-CACu--uCGAGCCCaacu-caGGCC-CAGA
YAR.LI-B      gCGG-uGGGauaGCAACAAA-guggu------------auaUGuUaU-------------
#=GC SS_cons  .>>>>..>>....>>.>>>............>.....>...>>.................

CAE.EL-D      --CCUUCUCga-uacCUUCAg-acCACUUAUCauuu
GAL.GAL.      --CCUGGGCaa-cauAGCGAg-accCuGuCUCc---
LYC.ES-O      GG-GCuGCU--cCAA-uUAa--aCCACCACUUU---
ZEA.MA-D      G--CC-UCa--CuAA-GcAg--acCACCAUCUU---
YAR.LI-B      --GGAAGGU----AUUUGCaAU-caCGACucuc---
#=GC SS_cons  ...>>.>>>.......>>>......>>>>>>>....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln87.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln87.fa

FUG.RUB.      GCCGGGUACGgug--gcgCGUGCCUguaaUCCaagcuacu-gGGAGGC---uGAGGCUGG
HOM.SA-A      GCCGGGCGCGgug--gcgCGUGCCUguagUCCCagcuacucGGGAGGC---uGAGGCuGG
LYC.ES-L      ------------------------------------------------------------
ORI.CUN.      GCCGGGCGCGgug--gcgCGCGCCUguagUCCCagcuacucGGGAGGC---uGAGGCcGG
LYC.ES-G      GCCGAGCUUA--guaaugUGGGCUUguaaCCCAaa------UGGGGGCauuAAuGUGGUG
#=GC SS_cons  <<<<<<<<<<........>>>>>>>....<<<..........>>>>>>....<.<<<.<<

FUG.RUB.      cggaUCGCUu--gaGCUCAGGa---guUcugGGCUuC-AGCGg-aCUAUgU----cgau-
HOM.SA-A      aggaUCGCUu--gaGUcCAGGa---guUcugGGcUG-UAGUGc-GCUAUgC----cgau-
LYC.ES-L      -------G-UUG--GGUuGac-CCAgau-GGUu-----GGGUUCGg--UaGGcUuauagu
ORI.CUN.      aggaUCGCUu--gaGUCCAGGa---guUcugGGcUG-UcGUGc-GCUAUgC----cgau-
LYC.ES-G      G--aaUG--UUG--GGCuGUa-CCAgau-GGUu-----GGGCUUGG--uGGGcUA-auuu
#=GC SS_cons  .....<<<......<<<.<<...........<......<<<<..<<..<.<.........

FUG.RUB.      ---CGGGUGUCCgUACUAaGuuCGGUAU----CGAUaUGGUGcUCCUGGGggagCCC-GG
HOM.SA-A      ---CGGGUGUCCgCACUAaGuUCGGCAU----CAAUaUGGUGacCUCCCGggagCGG-GG
LYC.ES-L      CUGGCC-UGcCCucUCCA-aGCAU-GGAGUuGGAUCA-cGUGGCUUAGUCgaaaGACcUG
ORI.CUN.      ---CGGGUGUCCgCACUAaGuUCGGCAU----CAAUaUGGUGacCUCCCGggagCGG-GG
LYC.ES-G      CUGGcC-UGcCCuaUCCA-aGCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAa-UG
#=GC SS_cons  ...<<<.<<.<<..<<<<...<<<.<<<....<<<<...<<<..<<<<<<....>>>.>>

FUG.RUB.      GAuCACCAgGUCG-CCuaaGGaGGGGUgccccGGCCcaggUCGgaa--aCGAagcaGGUC
HOM.SA-A      GacCACCAgGUUG-CCuaaGGaGGGGUgaaccGGCCcaggUCGgaa--aCGGagcaGGUC
LYC.ES-L      GGUUGCu-UGAUUCCU-aaAGuGGGGUggacugCGUgaggCUGguuucaCAGagcaACGa
ORI.CUN.      GacCACCAgGUUG-CCuaaGGaGGGGUgaaccGGCCcaggUCGgaa--aCGGagcaGGUC
LYC.ES-G      GGCUACu-aGAUUCCU-aaAGuGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGa
#=GC SS_cons  >..>>>...>>>>.<<...>>.<<<<<......<<<....<<<......>>>....>>>.

FUG.RUB.      aaaGCCCCc--GUGCCGcuCagUAGUGGGaucGCGCCCG---u----GaAUAGa--CGCU
HOM.SA-A      aaaACUCCc--GUGCUGAuCagUAGUGGGaucGCGCCUG---u----GaAUAGC--CACU
LYC.ES-L      acaGCUUCcGCUCU-GUGCag-UGGAaGGauaaCG-GGUCAG-uG-CUcA--gCGAGUCC
ORI.CUN.      aaaACUCCc--GUGCUGAuCagUAGUGGGaucGCGCCUG---u----GaAUAGC--CACu
LYC.ES-G      aaaACUUCcGCUUU-GUGCag-UGGAaGGauaaCG-GaCCGG-UGcCUU---CCAAGUUC
#=GC SS_cons  ...>>>>>...>>>.>>>....>>>>.>>....>>.>>>........>.>..>>..>>>>

FUG.RUB.      ---GuAGUU-caA-----CCUGAGUaa-cacAGCGGgacUCAGUCUUu---
HOM.SA-A      G---CAcUC-caG-----CCUGuGCaa-cauAGCGAgacCCcGUCUCu-uu
LYC.ES-L      -aguuaacGCCcugaUGG-gCuGCU--cCAA-Cuaa-accaccacuuu---
ORI.CUN.      G---CAcUC-caG-----CCUGGGCaa-cauAGCGAgacCCuGUCUCc---
LYC.ES-G      cau-uaauGCC-ugaUGG-GCuGCU--cCAA-uUAa-aCCACCACuUUu--
#=GC SS_cons  ........>..........>>.>>>.......>>>....>>.>>>.>....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln88.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln88.fa

SCH.POM.      cGC--------------------uguaa----ug-----GC-------uUGGUCG-aaGU
LEP.COL.      GcC-GGAGC---cu----uGCUCUguaaCCU-u-cgGGGGcU--uucaccAGCUg-aACA
ZEA.MA-B      nCC-GAGCUCUguagcgAGAGCUUguaaCCCGag-CGGGGGcauuAAGGUGGcGcggaUG
LYC.ES-H      GUU-GAGCUUAguaacgUGGGCUUguaaUCCAag-UGGAGACaucAAAGugGuUg-aaU-
TET.ROS.      GCCaGGGUAg--ca----aUGCCUgugacCu---cguGuGGC--auaaacaaugUaGUUA
#=GC SS_cons  .<<.<<<<<..........>>>>>.....<.......>.>>..........<.<....<<

SCH.POM.      GUUUa--GUACUcCCaa---------uaGUGCAUGUUCgGUGGucuc---------GGGU
LEP.COL.      GG----gaGCUgucu----ggaccaGCaUAGGg--uGcUuG-C-GGCgUU---ga-----
ZEA.MA-B      C-UuuG--cGAuGGu----uUCUG-GGcCU------GGGCUCGu--uGUGaCucua--gc
LYC.ES-H      A-UUG---GGCuGUa---CCAgau-GGUu-------GGGCUUGG--UGGGcUAauu--uC
TET.ROS.      gaau--aGucAGaGuAug--------agAGUUUGAugagaCAGUUuGc--u--aa-----
#=GC SS_cons  <........<<..<..............<<......<...<<<.................

SCH.POM.      ucGAGUCUCgcuUuCG--auCCCucGAUc--UGCCAcg-----UcUgUuCGAAGAguagU
LEP.COL.      -CGUGGUGcUCU-GCuuGGCuG-UGUGU----CGGAGGccuccGGGUGCcCCCUUgcagA
ZEA.MA-B      CGGCU-UGcCCaUCCCA--aGUUG-GuAGU-GUCUGaC-----GGGG-CUCuAGCgaaaG
LYC.ES-H      UGACU-UGcCCuaUCCA--aGCuU-AGAGUuGGAUCA------uGUGGcCCAaUUgaagA
TET.ROS.      -GAGUGUGcCCgUUCC-aaACAGUGAGU----UGCUaU-----GGUGGAaaCCUAguaaU
#=GC SS_cons  .<<<<.<<.<<..<<<....<<.<.<<<....<<<<.......<<<<<..<<<<<....>

SCH.POM.      CU-UCGuG-GcAacUGGCAGUuaaACCguGuaguac-cGAUGgaggUUGgaa--aCAAug
LEP.COL.      AGgGGcGCGCCCCCUCCG--UuaaA-GUaGAGGaac-UGGGUcaggCCGgca--aCGGag
ZEA.MA-B      CUuuGGGuCUCUG-CAGACCU-acAGcGGCAGgaaug-gCGUaaggCUGgcuucaCAGag
LYC.ES-H      Aa-UGGaCUACu-UGAUUCgU-aaAguGGGGCggaau-gCGUgaggCUGguuucaCAGag
TET.ROS.      AG-GacUUCACCAgGGCA-UUaaaGAGcUGAGgaac-cgCCUcaggCUGgca--aCAGaa
#=GC SS_cons  >>.>>..>>>>>..>>>>..<...>....<<<.......<<<....<<<......>>>..

SCH.POM.      caCAUCa--cuaCcgG--GUCuuGGGcagu-gCG-AuagcgauGGGAUUC--ACCU----
LEP.COL.      caGCCCA-CCU-C-GC--GCACGuCuGCCgu-uGC-AGA-accaCACCGCG--------G
ZEA.MA-B      caGCGaucaCUcGCCcACUuC-CAACgg---UGGGA-GG-auaaCA-AGCCGc---uG-C
LYC.ES-H      caGUGaacaGC-UCCcGCUCU-GuGCag---UGGAa-GG-auaaUG-GGUCGG---UGuC
TET.ROS.      caGGGaaaaCU-UGcC--GCUUAUUGUggu--GGAA-GG-auaaCAUACUC---------
#=GC SS_cons  ..>>>....>>.>.....>>>.>.>>......>>>..>>.....>>.>>>>.........

SCH.POM.      ------UCGCaGGAUGUGCAU------------GGaAGUAU---AAACACa---aCGGUC
LEP.COL.      A-GCCuG-UcAuC---aCCUGcGC---------cccaGGCga---uCCUGUg---aAGCU
ZEA.MA-B      ACu--uUGAGCCCaaca-cAGaCC-CAGA----uCC-UCu--CuuA-GCAa---acCaCC
LYC.ES-H      UUA--UCAAGUUC-ag-uaacGCC-uaaUGG---GUuGCU--cCAA-UaAa---caAcCa
TET.ROS.      -aUuAACUG-----UCAAGCUaaucgg----uUcUgCUauUc------UGAUca-Gacac
#=GC SS_cons  ......>>>...>......>>.............>..>>........>>>......>.>.

SCH.POM.      Guu---
LEP.COL.      uu----
ZEA.MA-B      AUCUUu
LYC.ES-H      cCUUUu
TET.ROS.      u-----
#=GC SS_cons  ......
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln89.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln89.fa

ORI.CUN.      GCCGGGCGCGgug--gcgCGCGCCUguagUCCCagcuacuc-GGGAGGC---uGAGGCcG
LEP.COL.      GcCGGAGC-----cu----uGCUCUguaaCCU-u-------cgGGGGcU--uucaccAGC
ARA.TH-E      GUCGAGCUaA--guaacaUgAGCUUguaaCCCAug-------UGGGGACauuuAGAUGGU
LEI.MAJ.      GcCGGAGC-----uc----uGCUCUguaaCCU-u-------cgGGGGcU---aaccAGGC
LYC.ES-A      GgCGAGCUUA--guaacgUGGGCUUguaaUCCAag-------UGGAGaCaucAAaGUGGU
#=GC SS_cons  <.<<<<<<............>>>>>....<<<...........>>>>.>.......<<<<

ORI.CUN.      GaggaUCGCUu--gaGUCCAGGa---guUcugGGcUG-UcGUGc-GCUAUgC----cgau
LEP.COL.      Ug--aACAGG---gaGCUgucu--ggaccaGCaUAGGguGcUuG-C-GGCgUU----ga-
ARA.TH-E      GG--aaCAc--UG--GuUCGGg-UCcaCG-GGCC-----GGUUCUGuuguUGGcau-guu
LEI.MAJ.      UU--aGCGGgG--aGGaCGUGGa----ccaGCgaGGGUgauuuG-C-UGCgUU----ga-
LYC.ES-A      UG--aaUA--UUG--GGCuuUa-CCAgaA-GGUu-----GGGCUUGGU--GGGcUu-agu
#=GC SS_cons  <.....<<.......<.<..<.........<<.........<.<.<.<...<<.......

ORI.CUN.      ----CGGGUGUCCgCACUA-aGuUCGGCAU----CAAUaU-----GGUGacCUCCCGgga
LEP.COL.      ---CGUGGUGcUCU-GCuuGGCuG-UGUGU----CGGAGGccuccGGGUGCcCCCUUgca
ARA.TH-E      uCUGGGC-UGcCCaGUCCA--aGCUG-UGAGU-AAGaCG------UgUGuGUCAAGCgaa
LEI.MAJ.      ---CGUGGUGcUCU-GCuuGGCuG-UGUGU----CGGuGUg----gCuUGCCcCCCUgca
LYC.ES-A      uCUGGCC-UGcCCugUCCA--aGCAC-AGAGUuGGAUCu------cGAGGCCCAaAUgaa
#=GC SS_cons  ...<<<<.<<.<<..<<......<.<.<<<....<<<<........<<<.<<<<<<<...

ORI.CUN.      gCGG-GGGacCACCAgGUUG---CCuaaGG-aGGGGUgaacc-GGCCcaggUCGgaa--a
LEP.COL.      gAAGgGGcGCGCCCCCUCCG----UuaaA--GUaGAGGaac-UGGGUcaggCCGgca--a
ARA.TH-E      gGCU-UGGCuCAaA-CGgCUU--CU-aaAGuuGGAGGguaau-gCGUgaggCUGguuuca
LEI.MAJ.      gAGG-GuGGCGcGgGU-CCGccg-UugaA--GcgaGGGaac-cGGGUcaggCCGgaa--a
LYC.ES-A      aAUa-UGGGCUUCu-uGAUUC--CU-aaAG-uGGGGCGgacc-gCAUgaggCUGgcuuca
#=GC SS_cons  .>>>.>>>>.>>>...>>>>....<...>...<.<<<.......<<<....<<<......

ORI.CUN.      CGGagcaGGUCaaaACUCCc--GUGCUGAuCag--UAGUG-GGaucGCGCCUG---u---
LEP.COL.      CGGagcaGCCCA-CCUC-GC--GCACGuCuGCCgu-uGC-AGAaccaCACCGCG-----G
ARA.TH-E      CAGagcaGCGacuaCUUCCcGCUUA-CAGCag---UGGAC-GGaucaCA-GUUUAG-cgU
LEI.MAJ.      CGGagcaGCCCa-CCCc-aC--GCACGuCcGCCgu-uGC-AGAaucaCACCGCG-----G
LYC.ES-A      CAGagcaGUGaa-CGCUCCcGCUCU-GUGCag---UGGAa-GGauaaUG-GGUCGG-uGU
#=GC SS_cons  >>>....>>>....>>>.>...>>>.>.>........>>..>>....>>.>>>>.....>

ORI.CUN.      GaAUAGC--CACuG---CAcUC-caG-------CCUGGGCaa-cauAGCGAgacCCuGUC
LEP.COL.      A-GCCuG-UcAuC---aCCUGcGC---------cccaGGCga---uCCUGUg-aAGCUuu
ARA.TH-E      CGc--uCAGAACCacu--auGGCC-UGcuGGu--CCGAuC--uCAu-aUGa-aCCACCAU
LEI.MAJ.      A-GCAuGuCc----gcACUUgaGC--------cCCACGcUU----CgUCGCg-AAGCCUu
LYC.ES-A      CUu-AUCAAGUUCagu--aacGCC-UaaUGG---GuuGCU--cCAA--UAa-aCAACCAC
#=GC SS_cons  >...>.>.>.>...........>>..........>..>.>........>>....>>>>>.

ORI.CUN.      UCc-
LEP.COL.      ----
ARA.TH-E      UUu-
LEI.MAJ.      ----
LYC.ES-A      cUUu
#=GC SS_cons  ....
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln90.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln90.fa

SCH.POM.      cGC----------------------uguaa----ug-----------GC-------uUGG
DRO.MEL.      GaCuGGAAGg-uug--gca-gCUUCUguaaUCA-cgcuuc--ugUGAGgU---cuGAUUG
YAR.LI-B      aGC----------------------uguaa----ug-----------GCauu---uuGUC
ZEA.MA-G      nCC-GAGCUCU--guagcgAGAGCUUguaaCCCGag-------CGGGGGcauuAAGGUGG
RAT.RAT.      GCC-GGGCGcGgug--gcgCaCGCCUguagUCCCagcuacuc-GGGAGGC---uGAGGac
#=GC SS_cons  .<<............................................>>........<<<

SCH.POM.      UCG--aaGUGUUUa--GUACUcCCaa----------------------------------
DRO.MEL.      UGG-gaUGGCCu---gaGGcUGGGau----------------------------cuacUg
YAR.LI-B      Gga-GUgGUAAAU---cGCCUUCUuguugugcguucgaguucuggacucugcac------
ZEA.MA-G      UGc-ggaUuC-UUuG--cGAuGGcu-----------------------------UUCUG-
RAT.RAT.      aGaggaUCGCUu---gaGUCCAGGa-------------------------------guUc
#=GC SS_cons  <<.....<<<<......<<<<<<<....................................

SCH.POM.      -uaGUGCAUGUUCgGUGGucuc----------GGGUucGAGUCUCgcuUuCG--auCCCu
DRO.MEL.      cguaGcgG--acCAGc--UCAUgUU----ga------CGGaACGUCCgCACUA-aGCUUG
YAR.LI-B      -------uGgGcUAc----------------------UUUGUUGUCCUuuCCGAauUCUG
ZEA.MA-G      GGCCc------GGGCUCGcuauGUGcCu-uug--gcCGGCC-UGcCCgUCCCA--aGUUG
RAT.RAT.      ugGGcUG---UAGUGc-GCUAUgC----cgau------CGGGUGUCCgCACUA-aGuUCG
#=GC SS_cons  ............<<<.......................<<<<<<<<<.<.<<<...<<<<

SCH.POM.      cGAUc---UGCCAcgUcUgUuCGAAGAguagUCUUCGuG-GcAacUGGCAGUuaaACCgu
DRO.MEL.      CCAU-----CAAUaUGGGUGCCAUGGAggagUCCGUGGCAUUCAgGUUG-gCuaaGgaGG
YAR.LI-B      CGGu--ugAUGGGcGUCUCG-GuCUGAguaaUCGGcUuUGAGAUuUCCGUUCuaaGAuUA
ZEA.MA-G      -GuAGU--GgCUGGcGGAGGCUuuAGCggaaGCUuuGGUCUCU-CCAGaCCU-gaAGuGG
RAT.RAT.      GCAU-----CAAUaUGGUGacCUCCCGggagCGGGGGacCACCAgGUUG-CCuaaGGaGG
#=GC SS_cons  .<<<.....<<<<..<<<<<.<.<<<<....>>>>.>.>>>>>..>>>>.<<...>>.<<

SCH.POM.      Guaguac-cGAUGgaggUUGgaa--aCAAugcaCAUCa--cuaCcgG--GUCuuGGGcag
DRO.MEL.      GAUgaac-cgGGCcaggGGUgaa--aACCagcaGCCaagaGU-UCCc--GUGGUAGGCag
YAR.LI-B      Acuggga-uaCUUcaguGGAgca--aUCCagcaGAGauc-cagUUG----CCGUGGGuaU
ZEA.MA-G      CAGgaaug-gCGUgaggCUGgcuucaCAGagcaGCGaucaCU-GCCcGCUuC-CAACgg-
RAT.RAT.      GGUgaacc-GGCCcaggUCGgaa--aCGGagcaGGUCaaaAC-UCCc--GUGCUGAuCag
#=GC SS_cons  <.........<<<....<<<......>>>....>>>.......>>>...>>>.>>>>...

SCH.POM.      u-gCG-AuagcgauGGGAUUC--ACCU-----------UCGCaGGAUGUGCAU-------
DRO.MEL.      --UAGUG-GG-auaGCGUaCCG---------GA-GUGGa--CUGc---CguUau-caG--
YAR.LI-B      ggCGG-uGGG-auaGCAACAAA-guggu-----------auaUGuUaU------------
ZEA.MA-G      --UGGGA-GG-auaaCG-GGCCGc-----uGCACu--uCGAGCCCaacu-caGGCC-CAG
RAT.RAT.      --UAGUG-GG-aucGCGCCUG-------u---GaAUAGC--CACUG---CAcUC-caG--
#=GC SS_cons  ..>>>.>.>>....>>>>>>>....................>>>................

SCH.POM.      --GGaAGUAU---AAACACa--aCGGUCGuu------
DRO.MEL.      --CCCAaCCga-uauGGUUGg-aCCACAAUC---uuu
YAR.LI-B      --GGAAGGU----AUUUGCaAU-caCGACucuc----
ZEA.MA-G      AG-CC-UCa--CuAA-GcAg--acCACCAUCUUu---
RAT.RAT.      --CCUGGGCaa-cauAGCGAg-acCccgUCUCuu---
#=GC SS_cons  ..>>>>>>>......>>>>.....>>>>>........
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln91.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln91.fa

LYC.ES-J      GUCGAGCUUA--guaacgUGGGCUUguaaUCCAag------UGGAGACaucAAaGUGGUU
LYC.ES-G      GCCGAGCUUA--guaaugUGGGCUUguaaCCCAaa------UGGGGGCauuAAuGUGGUG
LYC.ES-H      GUUGAGCUUA--guaacgUGGGCUUguaaUCCAag------UGGAGACaucAAAGugGuU
ORI.CUN.      GCCGGGCGCGgug--gcgCGCGCCUguagUCCCagcuacucGGGAGGC---uGAGGCcGG
RAT.RAT.      GCCGGGCGcGgug--gcgCaCGCCUguagUCCCagcuacucGGGAGGC---uGAGGacaG
#=GC SS_cons  <<<<<<<<<<........>>>>>>>....<<<<........>>>>>>>....<.<<...<

LYC.ES-J      G--aaUA--UUG--GGCuuUa-CCAgaA-GGUu----GGGCUUGG--UGGGcUu-aguuC
LYC.ES-G      G--aaUG--UUG--GGCuGUa-CCAgau-GGUu----GGGCUUGG--uGGGcUA-auuuC
LYC.ES-H      g--aaU-A-UUG--GGCuGUa-CCAgau-GGUu----GGGCUUGG--UGGGcUA-auuuC
ORI.CUN.      aggaUCGCUu--gaGUCCAGGa---guUcugGGcUGUcGUGc-GCUAUgC----cgau--
RAT.RAT.      aggaUCGCUu--gaGUCCAGGa---guUcugGGcUGUAGUGc-GCUAUgC----cgau--
#=GC SS_cons  .....<<.......<<<.<<...........<.....<<<<..<<..<.<..........

LYC.ES-J      UGGCC-UGcCCugUCCA-aGCAC-AGAGUuGGAUCA-cGAGGCCCAaAUgaaaAUaUGGG
LYC.ES-G      UGGcC-UGcCCuaUCCA-aGCAC-AGAGUuGGAUCa-uGUGGUCCAaUUgaaaGAaUGGG
LYC.ES-H      UGACU-UGcCCuaUCCA-aGCuU-AGAGUuGGAUCA-uGUGGcCCAaUUgaagAAaUGGa
ORI.CUN.      --CGGGUGUCCgCACUAaGuUCGGCAU----CAAUaUGGUGacCUCCCGggagCGGGGGa
RAT.RAT.      --CGGGUGUCCgCACUAaGuUCGGCAU----CAAUaUGGUGacCUCCCGggagCGGGGGa
#=GC SS_cons  ..<<<.<<.<<..<<<<...<<<.<<<....<<<<...<<<..<<<.<<....>>.>>>.

LYC.ES-J      CUUCu-UGAUUCCU-aaAGuGGGGCggaccgCAUgaggCUGgcuucaCAGagcaGUGaac
LYC.ES-G      CUACu-aGAUUCCU-aaAGuGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaaa
LYC.ES-H      CUACu-UGAUUCgU-aaAguGGGGCggaaugCGUgaggCUGguuucaCAGagcaGUGaac
ORI.CUN.      cCACCAgGUUG-CCuaaGGaGGGGUgaaccGGCCcaggUCGgaa--aCGGagcaGGUCaa
RAT.RAT.      cCACCAgGUUG-CCuaaGGaGGGGUgaaccGGCCcaggUCGgaa--aCGGagcaGGUCaa
#=GC SS_cons  .>>>...>>>>.<<...>>.<<<<<......<<<....<<<......>>>....>>>...

LYC.ES-J      aGCUCCcGCUCU-GUGCag-UGGAaGGauaaUG-GGUCGG-uGuCUUA--UCAAGUUC-a
LYC.ES-G      aACUUCcGCUUU-GUGCag-UGGAaGGauaaCG-GaCCGG-UGcCUU---CCAAGUUCca
LYC.ES-H      aGCUCCcGCUCU-GuGCag-UGGAaGGauaaUG-GGUCGG-UGuCUUA--UCAAGUUC-a
ORI.CUN.      aACUCCc--GUGCUGAuCagUAGUGGGaucGCGCCUG---u----GaAUAGC--CACuG-
RAT.RAT.      aACUCCc--GUGCUGAuCagUAGUGGGaucGCGCCUG---u----GaAUAGC--CACUG-
#=GC SS_cons  .>>>>>...>>>.>>>....>>>>.>>....>>.>>>........>.>..>>..>>>>..

LYC.ES-J      guaacGCC-UaaUGG-GuuGCU--cCAA--UAa-aCAACCACcUUu
LYC.ES-G      uuaauGCC-ugaUGG-GCuGCU--cCAA-uUAa-aCCACCACuUUu
LYC.ES-H      guaacGCC-uaaUGG-GUuGCU--cCAA-UaAa-caAcCacCUUUu
ORI.CUN.      -CAcUC-caG-----CCUGGGCaa-cauAGCGAgacCCuGUCUCc-
RAT.RAT.      -CAcUC-caG-----CCUGGGCaa-cauAGCGAgacCccgUCUCuu
#=GC SS_cons  .....>..........>>.>>>........>>....>...>>.>..
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln92.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln92.fa

LYC.ES-I      GCCGAGCUUA--guaaugUGGGCUUguaaCCCAaa-----UGGGGGCauuAAuGUGGUGG
CAE.EL-B      ACCGAGCGUCgug--gcgGGCGCUUgugaGUC-agcuucuuGACGGU---AGAUAAGUGu
LYC.ES-G      GCCGAGCUUA--guaaugUGGGCUUguaaCCCAaa-----UGGGGGCauuAAuGUGGUGG
ARA.TH-C      GUCGAaCUCa--guaacgcGGGcUUgugaUCCAag-----UGGAGACaauAAGGgGAUGG
TRI.AE-C      ------------------------------------------------------------
#=GC SS_cons  <<<<<.<<<..........>>>.>>....<<<.........>>>>>>...<<.<.<<<<.

LYC.ES-I      --aaUG--UUG--GGCuGUa--CCAgau-GGUu-----GGGCUUGG--uGGGcUAauuuC
CAE.EL-B      ggaUGGAGu--gaGAGGAGGa----guCcugUGUAUGuCGUug-UCAACgUC---ga---
LYC.ES-G      --aaUG--UUG--GGCuGUa--CCAgau-GGUu-----GGGCUUGG--uGGGcUAauuuC
ARA.TH-C      --gaCG--UUG--GGUcGau-CUcAUUG-GGcC-----GGgUUcGGguuGGGcUAuauuc
TRI.AE-C      ----------------------------------------------------------gG
#=GC SS_cons  ....<<.......<<<.<....................<<....<<....<<........

LYC.ES-I      UGACU-UGcCCuaUCCA-aGCUU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGG
CAE.EL-B      -cCGAGCGUCCGuGCCAaGCGCUGCGU----CACCaG-GGGaUGACUGUCggaaGAUGGU
LYC.ES-G      UGGcC-UGcCCuaUCCA-aGCAC-AGAGUuGGAUCa--uGUGGUCCAaUUgaaaGAaUGG
ARA.TH-C      UGGCC-CGcCCaUUCCA-aGUUG-GGAGUuGAGGCA--UGGGcUUCGAGCgaagGCUCGG
TRI.AE-C      UGGUC-UGcCCgUUCCA-aGUUGaGuAGU-gGACCGcuUGGGGCCUAuGCgaaaGU-UGG
#=GC SS_cons  <<<<<.<<.<<..<<<<..<<<<.<<<<<..<<<<....<<<<<<<<.<<....>>.>>>

LYC.ES-I      aCUACu-UGAUUCgU-aaAguGGGgCggaaugCGUgaggCUGguuucaCAGagcaACGau
CAE.EL-B      CAgUCCCgGGUG-CauaagGaGUGGUggau-gGUUcaggACCgaa--aGGUagcaGACaa
LYC.ES-G      GCUACu-aGAUUCCU-aaAGuGGGGUggaccgCGUgaggCUGguuucaCAGagcaACGaa
ARA.TH-C      GuCUCA-UGUCUUCU-agAGuGGGGGagaccGCGUgaggCUGguuucaCAGagcaGCGUc
TRI.AE-C      GCCUCA-CGGUC-CAuaaUGuGGCAGgcaccgCGUgaggCUGgcuucaCAGagcaGCGac
#=GC SS_cons  >>>>>...>>>>.<<...>>.<<<<<......<<<....<<<......>>>....>>>..

LYC.ES-I      aaG-UUUcGCUCU-AAGCgg-UGGAa-GGauaaCG-AGUCGG-UGuUCU---CUGAGUCC
CAE.EL-B      aaGCCACc--GCGCGGUGCagUGGC-CGGacuGCGCUUG---u---GA-GUUGA--cACG
LYC.ES-G      aaACUUCcGCUUU-GUGCag-UGGAa-GGauaaCG-GaCCGG-UGcCUU---CCAAGUUC
ARA.TH-C      caCCUCCcGCUCU-UGACgg-UGGAA-GGauuaCG-GGCCAu-UG-CCU---UCcGAgCC
TRI.AE-C      aaCUGCCcGCUuC-CAACgg-UGGAA-GGauaaCG-GGCCGC-ug-cacu--ccuaggcc
#=GC SS_cons  ..>>>>>.>>>>>.>>>>...>>>>..>>....>>.>>>>>.....>>....>>....>>

LYC.ES-I      -ag-uaacGCC-ugaUGG--GUuGCU--cCAA-uUAa-aCCACCAUuUUu--
CAE.EL-B      ---UAUACA-caG------CCUUCUCaa-uacCUUCAgacCACUUGUUU-uu
LYC.ES-G      cau-uaauGCC-ugaUGG--GCuGCU--cCAA-uUAa-aCCACCACuUUu--
ARA.TH-C      cacu-auGaCC-CAAUaAG--CcGCU--cCGA-uUGg-aCCAUCaCUUU---
TRI.AE-C      gcu--ugggcc-ucguag---ccua---cuccagc-g-accaccauc-----
#=GC SS_cons  .....................>.>>>........>>....>>>>.>.>>...
//
# STOCKHOLM 1.0

#=GF AC  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln93.fa
#=GF ID  SRP|BRAliBaseII/data-set1/SRP/unaligned/aln93.fa

LYC.ES-A      GgC-GAGCUUAguaacgUGGGCUUguaaUCCAag-UGGAGaCaucAAaGUGGUUGaaUA-
SCH.POM.      cGC--------------------uguaa----ug-----GC-------uUGGUCGaaGUG
TET.THE.      GCCaGGGUAg--ca----aUACCUgugucUA---uaUGuGGC--auaaacAaugUaGGUU
ARA.TH-A      GUC-GAGCUAaguaacaaUAGCUUguaaCCCAug-UGGGGACauuAAGAUGGUGGgaCAc
LYC.ES-B      GUC-GAGCUUAguaaugUGGGCUUguaaCCCAaa-UGGGGGCauuAAuGUGGUGGaaUG-
#=GC SS_cons  <<<.<<<<<..........>>>>>.....<<.....>>.>>>.......<<<<<<..<<.

LYC.ES-A      -UUG---GGCuuUa---CCAgaAGGUu-------GGGCUUGGU--GGGcUuagu--uCUG
SCH.POM.      UUUa--GUACUcCCaa--------uaGUGCAUGUUCgGUGGucuc---------GGGUuc
TET.THE.      gugauaGAUAGgAuAug-------agAGUUUGAugagaCAGUUuGc--u--aa------G
ARA.TH-A      -UG----GUUcGGu---UCcuCGGaUC-------GGUUCUGAugugGGcauguu--uCUG
LYC.ES-B      -UUG---GGCuGUa---CCAgauGGUu-------GGGCUUGGu--GGGcUAauu--uCUG
#=GC SS_cons  .<<....<<<..<.....................<<.<<<<<...............<.<

LYC.ES-A      GCC-UGcCCugUCCA--aGCAC-AGAGUuGGAUCu--cGAGGCCCAaAUgaaaAUaUGGG
SCH.POM.      GAGUCUCgcuUuCG--auCCCucGAUc--UGCCAcg-UcUgUuCGAAGAguagUCUUCGu
TET.THE.      AGUGUGcCCgcUCC-aaACAAUGAGU----UGCUaU-GGUGGuaaCCUAguaaUAGGacu
ARA.TH-A      AGC-UGcCCaGUCCA--aGCUG-UGAGU-AAUUaG-uguUGAGUUGAGCgaagGCUUGGC
LYC.ES-B      ACU-UGcCCuaUCCA--aGCUU-AGAGUuGGAUCA--uGUGGcCCAaUUgaagAAaUGGa
#=GC SS_cons  <<<.<<.<<..<<<....<<<<.<<<...<<<<<.....<<<.<<<.<<....>>.>>>.

LYC.ES-A      CUUCu-uGAUUCCU-aaAG-uGGGGCGgacc-gCAUgaggCUGgcuucaCAGagcaGUGa
SCH.POM.      G-GcAacUGGCAGUuaaAC-CguGuaguac-cGAUGgaggUUGgaa--aCAAugcaCAUC
TET.THE.      CCACCAgGGCA-UUaaaGA-GcUAAGgaaa-cgCCUcaggCUGgca--aCAGaacaGGGa
ARA.TH-A      UCAug-CaGGUUCU-agAGucGGAGGguaau-gCGUgaggCUGgcuucaCAGagcaGCGa
LYC.ES-B      CUACu-UGAUUCgU-aaAg-uGGGGCggaau-gCGUgaggCUGguuucaCAGagcaACGa
#=GC SS_cons  >>>....>>>>><<...>>...<<<<.......<<<....<<<......>>>....>>>.

LYC.ES-A      a-CGC-UCCcGCUCU-GUGCag--UGGAa-GG-auaaUG-GGUCGG---uGUCUu-AUCA
SCH.POM.      a--cuaCcgG--GUCuuGGGcagugCG-AuagcgauGGGAUUC--ACCU---------UC
TET.THE.      aaaCU-UGcC--GCUUGUUGUggu-GGAa-GG-auaaCAUACUC---------aUuAACU
ARA.TH-A      cuaCU-UCCcGCUUA-CAGCag--UGGAC-GG-aucaCG-GUUUAG---cgUCgc--UCA
LYC.ES-B      uaaGU-UUCcGCUCU-AAGCgg--UGGAa-GG-auaaCG-AGUCGG---UGUUC--uCUG
#=GC SS_cons  ...>>.>>....>>>.>>>>.....>>>..>>.....>>.>>>>.>...........>>>

LYC.ES-A      AGUUCagu--aacGCC-UaaUGG---GuuGCU--cCAA--UAa-aCAACCACcUUu
SCH.POM.      GCaGGAUGUGCAU------------GGaAGUAU---AAACACa-aCGGUCGuu---
TET.THE.      G-----UCAAACUaaucgg----uUcUaCUAUCa----aAGCCa-GacaUu-----
ARA.TH-A      GAACCacu--auGGcC-UGcuGG---UCcGAU--cuCAuaUGa-aCCACCAUUUU-
LYC.ES-B      AGUCCagu--aauGCC-ugaUGG---GCuGCU--cUAA-uUAa-aCCACCACuUUu
#=GC SS_cons  >>.>>.....................>..>>>....>>..>>...>>>>>>.....
//
