# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln1.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln1.fa

X04465.1/2700-2775    AGGAGCCGUGUGA...AUUGAAAAUC...UCAUGCACGGUUUUGAAUGAGAG
Z00044.1/87253-87177  GAAAGAAGUAUGCUUU...GGAA...GAAGCUUGUACAGUUUGG....GAAG
X57546.1/2817-2907    GAGAGCCGUAUGAUAU...GAAA...GUAUCACGUACGGUUCGG....AGAG
X77508.1/2333-2408    GGGAGCGGUAUGAGCC...GAGA...GGUUCACGUACCGUUCUG....CGAG
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUU...GAAA...GAUGCAUGCACGGUUCUUA...GGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<..........>>>>>...>>>>>>>>......<<<<

X04465.1/2700-2775    AAA....................AAAUAAUUUUUUUUUUUCGACUCUAAC
Z00044.1/87253-87177  GGG..............UUUUGAUUGAUCAAAAGAAGAAUCUACUUC.AA
X57546.1/2817-2907    GGCUCUCUUAUAUGAUUGUUAUUACAAUCAGAUAGGUUUGCUACUCU.AC
X77508.1/2333-2408    AGG...............CUGCGGGGGAGGUUCCUGCGGCCUACUCA.CC
AJ277126.1/8230-8302  GGG....................AAAGCCGGUAACCGUACCUAUCCCAAU
#=GC SS_cons          .<<....................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln2.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln2.fa

AJ011856.1/37648-37722  UUGAGCUGUAUACUAU..GAAAGUAGUACGUACAGUUCUGA......GUG
X03415.1/1030-1100      UCGAGCCGUACGAGG..AGAAAGCUUCCUAUACGUUUCUAG......GGG
AJ315331.1/53-130       AGGAGCCGUAUGAGAU..GAAAAUCUCACGUACGGUUCUGUA.....AUA
AJ130746.1/1754-1835    UUGAGCCGUAUGCGAAG.GAAACUUGCACGUGCGGUUCUUUGCUUUGAGG
AF029891.1/9161-9235    UUGAGCCGUAUGCGAU..GAAAGUCGCACGUACGGUUCUUA......GAG
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>.........<<<

AJ011856.1/37648-37722  GGGG..AAAAUUUGUAAAGAUCUACCUAUCACAAU
X03415.1/1030-1100      GGGU......GUUGUUCAUCUACAUCAAUCCCAAU
AJ315331.1/53-130       GCGAUGGGCACAGUGAUGUUAUCAUCGACUAUGAU
AJ130746.1/1754-1835    GGGG..AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AF029891.1/9161-9235    GGGG..AAAGUUCGAGAGGACCUACCUAUCUCAAC
#=GC SS_cons            <.<<....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln3.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln3.fa

AJ131144.1/1753-1833    UUGAGCCGUAUGCGAG...GAAA.CUUGCACGUGCGGUUCUUUGCUUUGA
X05917.1/3244-3331      GAGAGCCAAAUGAAUU...GAAA.GAUUCAUGUUUGGUUCGG.......G
M15176.1/580-656        AGGAGCUGGAUGAGA...AGAAAC.UCUCAUGUCCAGUUUUGUA.....G
Z00044.1/44460-44392    CUGAGCCGUAUGAGG.UAAGAAA.UUCUCAAGUACGGUUCUAA......G
AF087656.1/10795-10873  UUGAGCUGUAUGCGAU...GAAA.GUCGCACGUACAGUUCUUA......G
#=GC SS_cons            ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>.........<

AJ131144.1/1753-1833    GGGGGG..............AAAGCUUGAAAGAGCCUAUCCA.UC.CU..
X05917.1/3244-3331      AAGAGAUCAUAGACAUUUUGAAAUGAAUGGAAAGAGAAUCUA.CUUUC..
M15176.1/580-656        UAGAGA.............UGGAACUAAGAAGGAACCAUCGA.CU.AU..
Z00044.1/44460-44392    GGAAGG......................AAUUGAACUACCUA.UU.CC..
AF087656.1/10795-10873  AGGAUG.............UUAAUAUAGUAAUAUUUAACGUAGCC.UCAA
#=GC SS_cons            <<<.<<................................>>...>>.>>..

AJ131144.1/1753-1833    GAU
X05917.1/3244-3331      .AU
M15176.1/580-656        AAC
Z00044.1/44460-44392    GGC
AF087656.1/10795-10873  CAG
#=GC SS_cons            ...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln4.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln4.fa

AF029891.1/9161-9235  UUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA.GAGGGGG....A
AE007285.1/6659-6583  GGGAGCGGUGUGAAUCGAGAGGUUCACGCACCGUUCUG..CGAGAGGCCGGC
X77508.1/2333-2408    GGGAGCGGUAUGAGCCGAGAGGUUCACGUACCGUUCUG..CGAGAGG.CUGC
X03481.1/524-600      AGGAGCCGUAUGAGGUGAAAAUCUCAUGUACGGUUCUGU.AGAGUGG..CAG
Z00044.1/23174-23103  UUGAGCCGGAUGAAAGGAAACUUUCACGUCCGAUUUUGAAGGGGGGG.....
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>....<<<<.<<.....

AF029891.1/9161-9235  AAGUUCGAGAGGACCUACCUAUCUCAAC
AE007285.1/6659-6583  UGGUGAAACUCCUCCGGCCUACUCA.CC
X77508.1/2333-2408    GGGGGAGGUUCCUGCGGCCUACUCA.CC
X03481.1/524-600      UAAGGGUGACUUAUCUGUCAACUUUUCC
Z00044.1/23174-23103  ...AGAUCCUAUAGAAUCCUAUCCCAAU
#=GC SS_cons          .................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln5.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln5.fa

X04465.1/19125-19199  GAAAGCCGAAUGAAUU..GAAA.AGUUCAUGUUCGGUUUGG...GA.AGAGA
AF314856.1/1250-1311  ACGAGCCACAUGCAGG..GAAA.CUUGCACGUGUGGUUCUG...GCCGGGGA
AJ131136.1/1732-1807  UUGAGCCGUAUGCGAG..GAAA.CUUGCACGUGCGGUUCUUUGAGG.GGGGA
AF029891.1/4522-4594  UUGAGCCGUAUGCCAU..GAAA.GUGGCACGUACGGUUCUGA..GG.GGGGG
X04465.1/77203-77142  AGGAGCCGGAUGAA..UCAAAAU..UUCAUGUCCGGUUUUGAA.GU.AGCGA
#=GC SS_cons          ..<<<<<<<<.<<<<<.......>>>>>...>>>>>>>>.....<<.<<.<<

X04465.1/19125-19199  UUAUAAAAUAUAUAUAUAAUCUACUUUC.AU
AF314856.1/1250-1311  .............CCCCGGUAUACU.GU.AC
AJ131136.1/1732-1807  ..AAGCUUGAAAGAGCCUAUCCAUC.CCGAU
AF029891.1/4522-4594  .AAAGUCUGAGAGGACCUACCUAUC.CC..A
X04465.1/77203-77142  ..............UCAAAUCGACU.AUAAC
#=GC SS_cons          ...................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln6.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln6.fa

X07106.1/1306-1373      UUGAGCUGUACGAGAUGAAA.GUCUCAUAUACAGUUCUUA.GGGGGGU..
X03481.1/524-600        AGGAGCCGUAUGAGGUGAAA.AUCUCAUGUACGGUUCUGU.AGAGUGGCA
Z00044.1/23174-23103    UUGAGCCGGAUGAAAGGAAA.CUUUCACGUCCGAUUUUGAAGGGGGGG..
X17395.1/1934-1994      GAGAGCUUUUUGCGGGGAAA.CUUGCAAGUACAGUUUGG..GGGGAGG..
X04465.1/101010-100933  AGGAGCCGUAUGAAAUGAAAA.UUUCAUGUACGGUUUUGCAAUAGAGAUA
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>....<<<<.<<..

X07106.1/1306-1373      .......UUAAUAGUUUACCUAUCUCAAU
X03481.1/524-600        GUAAGGGUGACUUAUCUGUCAACUUUUCC
Z00044.1/23174-23103    ....AGAUCCUAUAGAAUCCUAUCCCAAU
X17395.1/1934-1994      ............CGGGCGUCGACCCU.AC
X04465.1/101010-100933  UAAAUAGUAAUGUUCAUAUCGACUAUAAU
#=GC SS_cons            ..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln7.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln7.fa

X04465.1/21511-21432    AGGAGCCGAAUGAAAGAAAA.CUUUCACGUUCGGUUUUGAAUUAGAGG..
X86563.2/93178-93102    AGGAGCCGUAUGAGGUGAAAA.UCUCAUGUACGGUUCUGU.AGAGGGA..
AF087656.1/10795-10873  UUGAGCUGUAUGCGAUGAAA.GUCGCACGUACAGUUCUUA.GAGGAUG..
Z69899.1/2926-3021      GAGAGCCGUAUGCGGUGAAA.GUCGCACGUACGGUUCGG..AGGAGAGUU
X77508.1/2333-2408      GGGAGCGGUAUGAGCCGAGA.GGUUCACGUACCGUUCUG..CGAGAGG..
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>....<<<<.<<..

X04465.1/21511-21432    ................CAUUUUUUAUUUUUAAUAAAUGUCGA.CUAU..A
X86563.2/93178-93102    ..................CAGUAAGGAUGACUUAUCUGUCGA.CUUU..U
AF087656.1/10795-10873  ...................UUAAUAUAGUAAUAUUUAACGUAGCCUCAAC
Z69899.1/2926-3021      GUUGGUUUCUAAGGUUUCUUUAGACUAAGGACUGGCUGCUUA.UCCU..A
X77508.1/2333-2408      .................CUGCGGGGGAGGUUCCUGCGGCCUA.CUCA...
#=GC SS_cons            ......................................>>...>>>>...

X04465.1/21511-21432    AC
X86563.2/93178-93102    CC
AF087656.1/10795-10873  AG
Z69899.1/2926-3021      CA
X77508.1/2333-2408      CC
#=GC SS_cons            ..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln8.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln8.fa

X86563.2/75403-75477    UCGAGCCGGAUGAUGAA.AAAUUCUCAUGUCCGGUUCCUUU.GGGGGAU.
Z00044.1/45478-45405    AGGAGCCGUAUGAGGU.GAAAAUCUCACGUACGGUUCUGGA.ACGGAGA.
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAU.GAAAGUCGCACGUACGGUUCUUA..CCGGGGG.
X04465.1/21511-21432    AGGAGCCGAAUGAAAG.AAAACUUUCACGUUCGGUUUUGAA.UUAGAGGC
AJ130737.1/1761-1840    UUGAGCCGUAUGCGGG.GAAACUUGCACGUGCGGUUCUUUGAGGGGGGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.....<<<<.<<.

X86563.2/75403-75477    ....GGAUCCUAAAGAAUUCACCUAUCCCAAU
Z00044.1/45478-45405    .....UUCUUUCAAUUGAAUGACGACCGUAAC
AJ011856.1/26154-26228  ...AAAACUUGUAAAGGUCUACCUAUCGGGAU
X04465.1/21511-21432    AUUUUUUAUUUUUAAUAAAUGUCGACUAUAAC
AJ130737.1/1761-1840    GAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
#=GC SS_cons            .....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln9.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln9.fa

AF065404.1/6521-6444  UUGAGCCGUAUGUGCU..GAAA.GGUACAAGUACGGUUCUU.AG.GGGAG..
X05422.1/3488-3558    UUGAGCCGUACGAGA..UGAAAU.UUUCAUAUACGGUUCUCGGA.GGGGG..
X04465.1/68119-68052  UUAAGCUGUAUGCGCUU.AAAA.AGUGCUUGUACAGUUUUAUAA.GAAAA..
X72616.1/122-187      AAGAGCCGUACGAG....GCAG...CUCACGUACGGUUCGG.GAGCCGAG..
Z00044.1/12700-12613  GAGAGCCAAAUGAAUC..GAAA.GAUUCAUGUUUGGUUCGG.GA.AGGGAUU
#=GC SS_cons          ..<<<<<<<<.<<<<<.......>>>>>...>>>>>>>>...<<.<<.<<..

AF065404.1/6521-6444  ........AAAGAGUUGGUAACACCUCUGACUUACC.CGACU
X05422.1/3488-3558    ................AGUCGGGCUAGUUACCUAUC.UCAAU
X04465.1/68119-68052  ....................AAAUAAUAAAAUUAUC.UUAAU
X72616.1/122-187      ................CCCCUGCACAGGGGCUUAGG.UC.AA
Z00044.1/12700-12613  AUGGAAUUUUGGAAAGGAAUGGAAAAAUAAUCUACUUUC.AU
#=GC SS_cons          ..............................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln10.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln10.fa

X03481.1/524-600        AGGAGCCGUAUGAGGUGAAAAUCUCAUGUACGGUUCUGU......AGAGU
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGG
AJ131144.1/1753-1833    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGG
AF235045.1/658-731      GAAAGCCGUAUUCGAUGAAAGUCGUAUGUACGGCUUGG.......AGGGA
AB042240.3/88332-88259  GAAAGCCGUAUUCGAUGAAAGUCGUAUGUACGGCUUGG.......AGGGA
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<<<.

X03481.1/524-600        GGCAGUAAGGGUGACUUAUCUGUCAACUUUUCC
AJ131145.1/1727-1802    GG...AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ131144.1/1753-1833    GG..AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AF235045.1/658-731      GA.UCUUUCAUAUCUUUCGAGAUCCACCCU.AC
AB042240.3/88332-88259  GA.UCUUUCCUAUCUUUCGAGAUCCACCCU.AC
#=GC SS_cons            <<....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln11.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln11.fa

Z00044.1/23174-23103    UUGAGCCGGAUGAAAGGAAACUUUCACGUCCGAUUUUGAAGGGGGGG...
M36911.1/2445-2539      GAGAGCCGUAUGCGGUGAAAGUCGCACGUACGGUUCGG..AGGAGAGUUU
X04465.1/19125-19199    GAAAGCCGAAUGAAUUGAAAAGUUCAUGUUCGGUUUGG..GAAGAGA...
X04465.1/10044-10114    UUGAGCCGGAUGACGGAAAACUUUCAUGUCCGAUUCUUA.GGGGGGG...
AJ277126.1/35792-35885  GAGAGCCCGGUGCGGUGAAAGUCGCACGCCGGGUUCGG..GGAGAAC.UC
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>....<<<<.<<...

Z00044.1/23174-23103    .......................AGAUCCUAUAGAAUCCUAUC.CCAAU
M36911.1/2445-2539      UUGGUUUCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUAUC.CU.AC
X04465.1/19125-19199    ..................UUAUAAAAUAUAUAUAUAAUCUACUUUC.AU
X04465.1/10044-10114    .......................AAUUCUAUAAAUAACCUAUC.CCAAU
AJ277126.1/35792-35885  UCUGUAACUAAAAUAUUUCGGUAUCACGUUAUGGUUAGUCACU.CC.AC
#=GC SS_cons            .....................................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln12.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln12.fa

M68929.1/41010-41093  GUGAGCCGUGUAAUGG..GCAA..CUAUUUCGCACGGUUCGG...AGGGCAC
AJ130737.1/1761-1840  UUGAGCCGUAUGCGGG..GAAA..CUUGCACGUGCGGUUCUUUGAGGGGGGG
Z00044.1/84143-84067  AGGAGCUGGAUGAGA..AGAAA..CUCUCACGUCCGGUUCUGUA.GUAGAGA
AF029891.1/9161-9235  UUGAGCCGUAUGCGAU..GAAA..GUCGCACGUACGGUUCUUA..GAGGGGG
X04465.1/754-816      AAAAGCCGUAUUCG..UUGAAAAU..CGGAUGUACGGUUUGG...AGGGAGA
#=GC SS_cons          ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>.....<<<<.<<

M68929.1/41010-41093  UUCAGUAAGCCCUACAAGGGCUGAAGUCUUGACCCCUAU
AJ130737.1/1761-1840  .......GAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
Z00044.1/84143-84067  .........UGGAAUUCAGAAACAACCAUCAACUAUAAC
AF029891.1/9161-9235  ..........AAAGUUCGAGAGGACCUACCUAUCUCAAC
X04465.1/754-816      ....................UAAAAAAAUCCACCCU.AC
#=GC SS_cons          ............................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln13.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln13.fa

AF029891.1/9161-9235    UUGAGCCGUAUGCGAUGAAA.GUCGCACGUACGGUUCUUA..GAGGGGG.
X04465.1/79649-79574    AAAAGCUGUAUGCUU.GAAAA.AAGCUUGUACAGUUUGG...GAAGAGAU
AF087656.1/10795-10873  UUGAGCUGUAUGCGAUGAAA.GUCGCACGUACAGUUCUUA..GAGGAUG.
X03481.1/524-600        AGGAGCCGUAUGAGGUGAAA.AUCUCAUGUACGGUUCUGU..AGAGUGG.
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAGGAAA.CUUGCACGUGCGGUUCUUUGAGGGGGGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.....<<<<.<<.

AF029891.1/9161-9235    ...AAAGUUCGAGAGGACCUACCUA.UCUC..AAC
X04465.1/79649-79574    UUUAAUAUAAAAAAUUUAAAAUCUA.CUUC...AA
AF087656.1/10795-10873  ..UUAAUAUAGUAAUAUUUAACGUAGCCUCAACAG
X03481.1/524-600        .CAGUAAGGGUGACUUAUCUGUCAA.CUUU..UCC
AJ131145.1/1727-1802    ....AAGCUUGAAAGAGCCUACCCA.UCCC..GAU
#=GC SS_cons            .....................>>...>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln14.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln14.fa

X05917.1/3244-3331      GAGAGCCAAAUGAAUU...GAAA...GAUUCAUGUUUGGUUCGG....GA
X01088.1/1893-1955      GAGAGCUUUUUGCGGG...GAAA...CUUGCAAGUAAAGUUUGG....GG
AB042240.3/88332-88259  GAAAGCCGUAUUCGAU...GAAA...GUCGUAUGUACGGCUUGG....AG
AF200692.2/21112-21025  GAGAGCCGGAUGCGCU...GAAA...GGUGCACGUCCGGUUCGG....GG
X04465.1/2700-2775      AGGAGCCGUGUGA...AUUGAAAAUC...UCAUGCACGGUUUUGAAUGAG
#=GC SS_cons            ..<<<<<<<<.<<<<<..........>>>>>...>>>>>>>>......<<

X05917.1/3244-3331      AGAGAUCAUAGACAUUUUGAAAUGAAUGGAAAGAGAAUCUACUUUC..AU
X01088.1/1893-1955      GGAGG..........................CGGGCGUCGACC.CAACCU
AB042240.3/88332-88259  GGAGA.............UCUUUCCUAUCUUUCGAGAUCCACC.CU..AC
AF200692.2/21112-21025  AGGAGAGGCAGGGAAAUAGUCCGACUACGCCCUGCCUCUUACU.CU.UAC
X04465.1/2700-2775      AGAAA................AAAUAAUUUUUUUUUUUCGACU.CU.AAC
#=GC SS_cons            <<.<<................................>>..>>.>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln15.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln15.fa

AB042240.3/88332-88259  GAAAGCCGUAUUCGAU..GAAA..GUCGUAUGUACGGCUUGG....AG.G
AJ316582.1/98150-98072  AGGAGCCGUGUGAGAU..GAAA..GUCUCAUGCACGGUUUUGAAUGAG.A
X04465.1/754-816        AAAAGCCGUAUUCG..UUGAAAAU..CGGAUGUACGGUUUGG....AG.G
X72616.1/122-187        AAGAGCCGUACGAG....GCAG....CUCACGUACGGUUCGG....GAGC
V00712.1/1227-1289      GAGAGCUUUUUGCGGG..GAAA..CUUGCAAGUCAAGUUUGG....GG.G
#=GC SS_cons            ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>......<<.<

AB042240.3/88332-88259  GAGAUCUUUCCUAUCUUUCGAGAUCCACCCU..AC
AJ316582.1/98150-98072  GAAAGAAGUGAGGAAUCCUCUUUUCGACUCU.GAC
X04465.1/754-816        GAGA...........UAAAAAAAUCCACCCU..AC
X72616.1/122-187        CGAG.....CCCCUGCACAGGGGCUUAGGUC..AA
V00712.1/1227-1289      GAGG.............CGGGCGUCGACCCAACCU
#=GC SS_cons            <.<<...................>>..>>>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln16.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln16.fa

AJ131145.1/1727-1802    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGG..
Y08501.1/133100-133176  GUGAGCGCAUGCGGG.GAGACCCGCACGUACGGUUUUU...AGGGGGAUC
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA..UGGGGGG..
AF029891.1/4522-4594    UUGAGCCGUAUGCCAUGAAAGUGGCACGUACGGUUCUGA..GGGGGGG..
X62341.1/1274-1336      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGG...GGGGAGA..
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

AJ131145.1/1727-1802    ....AAGCUUGAAAGAGCCUACCCAUCCC.GAU
Y08501.1/133100-133176  UGGCCGAAAGACCGGCCGGCGCCCACCCG..AC
AJ277126.1/6413-6487    ...AAAACGAGAGAUCGUCUACCUAUCCA.ACU
AF029891.1/4522-4594    ...AAAGUCUGAGAGGACCUACCUAUCCC...A
X62341.1/1274-1336      ...............CGGGCGUCGACCCAACCU
#=GC SS_cons            .....................>>..>>>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln17.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln17.fa

AP000423.1/1844-1752  GAAAGCUGUGUGCA..AUGAAAAA..UGCAAGCACGGUUUGG...GGAGGGG
M36911.1/2445-2539    GAGAGCCGUAUGCGGU..GAAA..GUCGCACGUACGGUUCGG...AGGAGAG
AJ130737.1/1761-1840  UUGAGCCGUAUGCGGG..GAAA..CUUGCACGUGCGGUUCUUUGAGGGGGGG
L36897.1/2659-2743    GAAAGCCGUAUGAUGG..GAAA..CUAUCACGUACGGUUUGG...GAAAGGC
U13767.1/4803-4881    GGGAGCCGUGUGCAGC..GAAA..GUUGCACGCACGGAUCUAAC.AGAGAGG
#=GC SS_cons          ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>.....<<<<.<<

AP000423.1/1844-1752  ..UUUUUUACCUUUUUUUUUUCAUUUUAACAAGGAGAUUAUCUACUCC.AU
M36911.1/2445-2539    UUUUUGGUUUCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUAUCCU.AC
AJ130737.1/1761-1840  ...................GAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
L36897.1/2659-2743    ..........UCUUUAACACGUGGCAACAUAGGUUAAUUUGCUAUUUC.AU
U13767.1/4803-4881    ...................GACGGGGAAUAAUAUCCCCUCUCGACUCUAAC
#=GC SS_cons          ........................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln18.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln18.fa

AJ277126.1/6413-6487  GUGAGCCGUGUGCGAU...GAAA..GUCGCAAGCACGGUUCUGA.UGGGGGG
Z00044.1/1956-1845    GAAAGCCGUGUGCA...AUGAAAAA..UGCAAGCACGGCUUGG..GGAGGGG
X03834.1/1418-1494    GGGAGCCGGAUGAGA...AGAAAC..UCUCAUGUCCGGUUCUGUAGUAGAGA
Z00044.1/44460-44392  CUGAGCCGUAUGAGG.UAAGAAA..UUCUCAAGUACGGUUCUAA.GGGAAGG
X07106.1/1306-1373    UUGAGCUGUACGAGAU...GAAA..GUCUCAUAUACAGUUCUUA.GGGGGGU
#=GC SS_cons          ..<<<<<<<<.<<<<<.........>>>>>...>>>>>>>>....<<<<.<<

AJ277126.1/6413-6487  .......................................AAAACGAGAGAUC
Z00044.1/1956-1845    UCUUUACUUGUUUAUUUAAUUUAAGAUUAACAUUUAUUUUAUUUAACAAGGA
X03834.1/1418-1494    ......................................UGGAAUAGGGAAAU
Z00044.1/44460-44392  ...............................................AAUUG
X07106.1/1306-1373    ..............................................UUAAUA
#=GC SS_cons          ....................................................

AJ277126.1/6413-6487  GUCUACCUAUCCAACU
Z00044.1/1956-1845    ACUUAUCUACUCC.AU
X03834.1/1418-1494    AACCAUCAACUAUAAC
Z00044.1/44460-44392  AACUACCUAUUCCGGC
X07106.1/1306-1373    GUUUACCUAUCUCAAU
#=GC SS_cons          .....>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln19.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln19.fa

X07106.1/1306-1373      UUGAGCUGUACGAGAUGAAAGUCUCAUAUACAGUUCUUA..GGGGGGU..
AF200692.2/21112-21025  GAGAGCCGGAUGCGCUGAAAGGUGCACGUCCGGUUCGG...GGAGGAG..
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGG..
X04336.1/3210-3313      GAGAGCCGUAUGCAGGGAAACUUGCACGUACGGUUCGG...AGGGAGGUC
Z00044.1/23174-23103    UUGAGCCGGAUGAAAGGAAACUUUCACGUCCGAUUUUGAA.GGGGGGG..
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

X07106.1/1306-1373      ....................................UUAAUAGUUUACCU
AF200692.2/21112-21025  ...............AGGCAGGGAAAUAGUCCGACUACGCCCUGCCUCUU
AJ131145.1/1727-1802    ..............................AAGCUUGAAAGAGCCUACCC
X04336.1/3210-3313      UCUCGUUGCCAGUUCUAAUCUAUUGAUAAGGAUCACGGUGCGGGUUAUCG
Z00044.1/23174-23103    .................................AGAUCCUAUAGAAUCCU
#=GC SS_cons            ...............................................>>.

X07106.1/1306-1373      AUCUCAAU
AF200692.2/21112-21025  ACUCUUAC
AJ131145.1/1727-1802    AUCCCGAU
X04336.1/3210-3313      ACCCU.AC
Z00044.1/23174-23103    AUCCCAAU
#=GC SS_cons            .>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln20.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln20.fa

AB042240.3/34087-34170  GAGAGCCAAAUGAAUC...GAAA....GAUUCAUGUUUGGUUCGG....G
M68929.1/49817-49892    UUGAGCCGUAUGCGG....GAAA...ACUCGCACGUACGGUUCUUA...G
X62341.1/1274-1336      GAGAGCUUUUUGCGGG...GAAA....CUUGCAAGUACAGUUUGG....G
X63625.1/1815-1875      GAGAGCUUUUUGCGGG...GAAA....CUUGCAAGUACAGUUUGG....A
X04465.1/2700-2775      AGGAGCCGUGUGA...AUUGAAAAUC....UCAUGCACGGUUUUGAAUGA
#=GC SS_cons            ..<<<<<<<<.<<<<<...........>>>>>...>>>>>>>>......<

AB042240.3/34087-34170  AAGAGAUCAUAAAAGUUGUAAACUUACAAAAUAAUCUACUUUC..AU
M68929.1/49817-49892    GGGGGG.........GAAAGCUUGAGAGGGCCUACCUAUC.CC.GAC
X62341.1/1274-1336      GGGAGA......................CGGGCGUCGACC.CAACCU
X63625.1/1815-1875      GGGAGG......................CGGGCGUCGACC.CA..AC
X04465.1/2700-2775      GAGAAA............AAAUAAUUUUUUUUUUUCGACU.CU.AAC
#=GC SS_cons            <<<.<<............................>>..>>.>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln21.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln21.fa

AF235045.1/658-731    GAAAGCCGUAUUCGAU..GAAA..GUCGUAUGUACGGCUUGG..AGGGAGA.
X55026.1/77786-77867  GAGAGCCGUAUGAUGG..GAAA..CUAUCACGUACGGUUCGG..GAAAAGGU
X04465.1/71857-71924  UUAAGCUGUAAGAUUA..UAAA..UAAUCAUUUACGGUUUUUC.GAGGGGG.
AJ277126.1/9249-9325  AGGAGCCGUAUGAAUG..GAGA..CAUUCACGUACGGUUUUGGAGUAGCAG.
X04465.1/754-816      AAAAGCCGUAUUCG..UUGAAAAU..CGGAUGUACGGUUUGG..AGGGAGA.
#=GC SS_cons          ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>....<<<<.<<.

AF235045.1/658-731    .......UCUUUCAUAUCUUUCGAGAUCCACCCU.AC
X55026.1/77786-77867  AUAUAUACUGAUAAGAGGUAUACGUAUCUAGUUC.AU
X04465.1/71857-71924  ...............AACUUUAGUAACCUAUCUCAAU
AJ277126.1/9249-9325  .......GAUAUAUGGUAACAUGUACUUGACUAUAAG
X04465.1/754-816      ..................UAAAAAAAUCCACCCU.AC
#=GC SS_cons          ..........................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln22.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln22.fa

X04336.1/3210-3313      GAGAGCCGUAUGCAGG.GAAA.CUUGCACGUACGGUUCGG..AGGGAGGU
X04465.1/101010-100933  AGGAGCCGUAUGAAAU.GAAAA.UUUCAUGUACGGUUUUGCAAUAGAGA.
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAU.GAAA.GUCGCACGUACGGUUCUUA.CCGGGGG.
Z00044.1/84143-84067    AGGAGCUGGAUGAGA.AGAAA.CUCUCACGUCCGGUUCUGUAGUAGAGA.
U77945.1/1848-1919      AACCGCCGUGUACG...GAAC...CGUACGCACGGUGGUG..UGAGAGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

X04336.1/3210-3313      CUCUCGUUGCCAGUUCUAAUCUAUUGAUAAGGAUCACGGUGCGGGUUAUC
X04465.1/101010-100933  ............................UAUAAAUAGUAAUGUUCAUAUC
AJ011856.1/26154-26228  ..............................AAAACUUGUAAAGGUCUACC
Z00044.1/84143-84067    .............................UGGAAUUCAGAAACAACCAUC
U77945.1/1848-1919      ...........................ACGGCGGGUGUGAAUCCGCCUCC
#=GC SS_cons            ................................................>>

X04336.1/3210-3313      GACCCU.AC
X04465.1/101010-100933  GACUAUAAU
AJ011856.1/26154-26228  UAUCGGGAU
Z00044.1/84143-84067    AACUAUAAC
U77945.1/1848-1919      UACUCG.AU
#=GC SS_cons            ..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln23.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln23.fa

AP000423.1/1844-1752    GAAAGCUGUGUGCA...AUGAAAAA..UGCAAGCACGGUUUGG..GGAGG
Z00044.1/23174-23103    UUGAGCCGGAUGAAAG...GAAA..CUUUCACGUCCGAUUUUGAAGGGGG
X02819.1/3326-3410      GAGAGCCGUAUAAUUAC..GAAA..GUAUCCCGUACGGUUCGG..UGACG
U41288.1/3118-3192      UUGAGCCGUAUGCGAU...GAAA..GUUGCACGUACGGUUCUUA.CCGGG
AB042240.3/34087-34170  GAGAGCCAAAUGAAUC...GAAA..GAUUCAUGUUUGGUUCGG..GAAGA
#=GC SS_cons            ..<<<<<<<<.<<<<<.........>>>>>...>>>>>>>>....<<<<.

AP000423.1/1844-1752    GGUUUUUUACCUUUUUUUUUUCAUUUUAACAAGGAGAUUAUCUACU.CC.
Z00044.1/23174-23103    GG........................AGAUCCUAUAGAAUCCUAUC.CCA
X02819.1/3326-3410      AG..........CCGUGUCAACCCUGCAAAGGGAAUGCGUCUUAGUUCA.
U41288.1/3118-3192      GG....................AAAGCUUGAGAGAGCCUACCUAUC.GGA
AB042240.3/34087-34170  GA..........UCAUAAAAGUUGUAAACUUACAAAAUAAUCUACUUUC.
#=GC SS_cons            <<......................................>>..>>.>>.

AP000423.1/1844-1752    AU
Z00044.1/23174-23103    AU
X02819.1/3326-3410      AU
U41288.1/3118-3192      AC
AB042240.3/34087-34170  AU
#=GC SS_cons            ..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln24.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln24.fa

AF029891.1/4522-4594  UUGAGCCGUAUGCCAUGAAA.GUGGCACGUACGGUUCUGAGGGGGGG.....
X04465.1/79649-79574  AAAAGCUGUAUGCUU.GAAAA.AAGCUUGUACAGUUUGG.GAAGAGA.....
X04465.1/28100-28187  GAAAGCCGUAUGCAGU.AAAAAUUGCAAGUACGGUUUGG.GAAGAGAUGAUU
AJ277126.1/2879-2953  UUCAGCCGUGUGCGGUGAAA.GUCGCACGCACGGUUGUGAGGGGGGG.....
X07106.1/1306-1373    UUGAGCUGUACGAGAUGAAA.GUCUCAUAUACAGUUCUUAGGGGGGU.....
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>...<<<<.<<.....

AF029891.1/4522-4594  ..........AAAGUCUGAGAGGACCUACCUAUCCC..A
X04465.1/79649-79574  ......UUUUAAUAUAAAAAAUUUAAAAUCUACUUC.AA
X04465.1/28100-28187  UUAUUUUUAUUGAAAAAAAAAUUAUUUAUCUACUUC.AU
AJ277126.1/2879-2953  ..........AAAAUCUGUGAAGAUCUACCUAUCCCGAU
X07106.1/1306-1373    .................UUAAUAGUUUACCUAUCUCAAU
#=GC SS_cons          ............................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln25.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln25.fa

AJ131147.1/1719-1794  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA....
AJ277126.1/9249-9325  AGGAGCCGUAUGAAUGGAGACAUUCACGUACGGUUUUGGA.GUAGCAG...G
AJ131136.1/1732-1807  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGA....
AB027572.1/1941-1862  AGGAGCCGAAUGAAAUCAAAAUUUCAUGUUCGGUUUUGAA.UUAGAGACGUU
AJ277126.1/2879-2953  UUCAGCCGUGUGCGGUGAAAGUCGCACGCACGGUUGUGA..GGGGGGG....
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<....

AJ131147.1/1719-1794  .AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ277126.1/9249-9325  AUAUAUGGUAACAUGUACUUGACUAUAAG
AJ131136.1/1732-1807  .AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AB027572.1/1941-1862  AAAAAUAAUCAACCAACGUCGACUAUAAC
AJ277126.1/2879-2953  AAAAUCUGUGAAGAUCUACCUAUCCCGAU
#=GC SS_cons          ..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln26.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln26.fa

X73671.1/1293-1367      UUGAGCCGUAUGCGAU.GAAA.GUUGCACGUACGGUUCUUA.AGAGGGG.
X04465.1/10044-10114    UUGAGCCGGAUGACGG.AAAA.CUUUCAUGUCCGAUUCUUA.GGGGGGG.
AJ011856.1/37648-37722  UUGAGCUGUAUACUAU.GAAA.GUAGUACGUACAGUUCUGA.GUGGGGG.
M81726.1/5191-5288      GUGAGCCGUAUGAUGG.GCAA.CUAUCUCCUGCGGUUCGG..AGAGGACU
X03834.1/1418-1494      GGGAGCCGGAUGAGA.AGAAAC.UCUCAUGUCCGGUUCUGUAGUAGAGA.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

X73671.1/1293-1367      ........................AAAAUGAGUGAUCAUCUACCUAUUCU
X04465.1/10044-10114    ............................AAUUCUAUAAAUAACCUAUCCC
AJ011856.1/37648-37722  ........................AAAAUUUGUAAAGAUCUACCUAUCAC
M81726.1/5191-5288      CAGCUGUUAGUUAGUACCCCCGUCGGUUUCGGGGUGGACCCUUUUACUCU
X03834.1/1418-1494      .......................UGGAAUAGGGAAAUAACCAUCAACUAU
#=GC SS_cons            ..........................................>>..>>>>

X73671.1/1293-1367      AAC
X04465.1/10044-10114    AAU
AJ011856.1/37648-37722  AAU
M81726.1/5191-5288      .AU
X03834.1/1418-1494      AAC
#=GC SS_cons            ...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln27.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln27.fa

X04336.1/3210-3313      GAGAGCCGUAUGCAGGGAAACUUGCACGUACGGUUCGG...AGGGAGGUC
AJ131136.1/1732-1807    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGA..
X17395.1/1934-1994      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGG...GGGGAGG..
AF074613.1/60570-60649  UUGAGCCGUAUGCCGGGAAACUGGCACGUACGGUUCUU...AGGGGGC..
AJ277126.1/8230-8302    UUGAGCCGUGUGCGUUGAAAGAUGCAUGCACGGUUCUUA..GGGGGGG..
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

X04336.1/3210-3313      UCUCGUUGCCAGUUCUAAUCUAUUGAUAAGGAUCACGGUGCGGGUUAUCG
AJ131136.1/1732-1807    ..............................AAGCUUGAAAGAGCCUAUCC
X17395.1/1934-1994      .........................................CGGGCGUCG
AF074613.1/60570-60649  .........................GGUGAUGCAGUAAUGCAUCACUGCU
AJ277126.1/8230-8302    ...............................AAAGCCGGUAACCGUACCU
#=GC SS_cons            ...............................................>>.

X04336.1/3210-3313      ACCCU...AC
AJ131136.1/1732-1807    AUCCC..GAU
X17395.1/1934-1994      ACCCU...AC
AF074613.1/60570-60649  ACCCGAUCGU
AJ277126.1/8230-8302    AUCCC..AAU
#=GC SS_cons            .>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln28.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln28.fa

AP000397.1/37693-37753  GAGAGCUUUUUGCGGG...GAAA..CUUGCAAGUACAGUUUGG...GGGG
X04465.1/4746-4826      UUAAGCCAUACAGA..GUUGAAAA..UAUCAUAUAUGGUUUUCA..AGGG
Z00044.1/1956-1845      GAAAGCCGUGUGCA...AUGAAAAA..UGCAAGCACGGCUUGG...GGAG
AJ131136.1/1732-1807    UUGAGCCGUAUGCGAG...GAAA..CUUGCACGUGCGGUUCUUUGAGGGG
AY005806.1/723-797      UCGAGCUGGAUGAU...UAAAAA..UUAUCAUGUCCAGUUCCCUC.GGGG
#=GC SS_cons            ..<<<<<<<<.<<<<<.........>>>>>...>>>>>>>>.....<<<<

AP000397.1/37693-37753  AGG...............................................
X04465.1/4746-4826      GGG..................................AAAAAGAAUUAUA
Z00044.1/1956-1845      GGGUCUUUACUUGUUUAUUUAAUUUAAGAUUAACAUUUAUUUUAUUUAAC
AJ131136.1/1732-1807    GGA........................................AAGCUUG
AY005806.1/723-797      GAU........................................GGAUCUA
#=GC SS_cons            .<<...............................................

AP000397.1/37693-37753  ....CGGGCGUCGACCCA.AC
X04465.1/4746-4826      AAAUCUAAAACCUAUCCUAAU
Z00044.1/1956-1845      AAGGAACUUAUCUACUCC.AU
AJ131136.1/1732-1807    AAAGAGCCUAUCCAUCCCGAU
AY005806.1/723-797      UAAGAAUUCACCUAUCCCAAU
#=GC SS_cons            ..........>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln29.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln29.fa

V00712.1/1227-1289      GAGAGCUUUUUGCGGGGAAACUUGCAAGUCAAGUUUGG.GGGGAGG....
AJ277126.1/2879-2953    UUCAGCCGUGUGCGGUGAAAGUCGCACGCACGGUUGUGAGGGGGGG..AA
AF087656.1/10795-10873  UUGAGCUGUAUGCGAUGAAAGUCGCACGUACAGUUCUUAGAGGAUG.UUA
X03481.1/524-600        AGGAGCCGUAUGAGGUGAAAAUCUCAUGUACGGUUCUGUAGAGUGGCAGU
AB042240.3/88332-88259  GAAAGCCGUAUUCGAUGAAAGUCGUAUGUACGGCUUGG.AGGGAGA.UCU
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>...<<<<.<<....

V00712.1/1227-1289      ..........CGGGCGUCGA.CCCA.ACCU
AJ277126.1/2879-2953    AAUCUGUGAAGAUCUACCUA.UCCC..GAU
AF087656.1/10795-10873  AUAUAGUAAUAUUUAACGUAGCCUCAACAG
X03481.1/524-600        AAGGGUGACUUAUCUGUCAA.CUUU..UCC
AB042240.3/88332-88259  UUCCUAUCUUUCGAGAUCCA.CCCU...AC
#=GC SS_cons            ................>>...>>>>.....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln30.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln30.fa

U41288.1/27369-27451    GAGAGCCGUAUGCGGU.GAAA.GUUGCACGUACGGUUCGG..UGGGAGGU
X03834.1/1418-1494      GGGAGCCGGAUGAGA.AGAAAC.UCUCAUGUCCGGUUCUGUAGUAGAGA.
AJ277126.1/33096-33168  GCGAGCCGUAUGAUGG.GAAA.CUAUCACGUACGGUUCUG..AGGGCAA.
U13767.1/4803-4881      GGGAGCCGUGUGCAGC.GAAA.GUUGCACGCACGGAUCUAACAGAGAGG.
X04465.1/47942-47868    AGGAGCCGUAUGAAGU.UUAA.ACUUCAUGUACGGUUUUGAAACGGAGU.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

U41288.1/27369-27451    UUCUUAUAUCCCUCGUGGAGUAGGCUAUCGACC.CA.AC
X03834.1/1418-1494      ........UGGAAUAGGGAAAUAACCAUCAACU.AUAAC
AJ277126.1/33096-33168  ..........GGUAUAUUCUAAAUGCCUUGACCCCU.AC
U13767.1/4803-4881      ......GACGGGGAAUAAUAUCCCCUCUCGACU.CUAAC
X04465.1/47942-47868    ..........UUAUUUUAAAUAAAUUAACAACC.GUAAC
#=GC SS_cons            ...........................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln31.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln31.fa

AJ316582.1/73932-73872  UUGAACCGUAUGCAUC.AAAAGGCGCAUGUACGGUUCCUAAGGGAUA...
X03698.1/100-176        AGAAGCCGUAUGAAAU.GAAAAUAUCAAGUACGGUUUUGUAAAGUGA...
AF087656.1/10795-10873  UUGAGCUGUAUGCGAU.GAAAGUCGCACGUACAGUUCUUAGAGGAUG...
M36911.1/2445-2539      GAGAGCCGUAUGCGGU.GAAAGUCGCACGUACGGUUCGG.AGGAGAGUUU
X02819.1/3326-3410      GAGAGCCGUAUAAUUACGAAAGUAUCCCGUACGGUUCGG.UGACGAG...
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>...<<<<.<<...

AJ316582.1/73932-73872  .................................CAAUUUUA.CC.CU..A
X03698.1/100-176        .................CAAUUUAGGUAACUUAUUUGUCAA.CU.UU..U
AF087656.1/10795-10873  ..................UUAAUAUAGUAAUAUUUAACGUAGCC.UCAAC
M36911.1/2445-2539      UUGGUUUCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUA.UC.CU...
X02819.1/3326-3410      .........CCGUGUCAACCCUGCAAAGGGAAUGCGUCUUA.GUUCA...
#=GC SS_cons            .....................................>>...>>.>>...

AJ316582.1/73932-73872  AU
X03698.1/100-176        CC
AF087656.1/10795-10873  AG
M36911.1/2445-2539      AC
X02819.1/3326-3410      AU
#=GC SS_cons            ..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln32.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln32.fa

AY005806.1/723-797      UCGAGCUGGAUGAU..UAAAAAUUAUCAUGUCCAGUUCCCUCGGGGGAU.
M68929.1/41010-41093    GUGAGCCGUGUAAUGG..GCAACUAUUUCGCACGGUUCGG..AGGGCACU
U13767.1/4803-4881      GGGAGCCGUGUGCAGC..GAAAGUUGCACGCACGGAUCUAACAGAGAGG.
AB042240.3/34087-34170  GAGAGCCAAAUGAAUC..GAAAGAUUCAUGUUUGGUUCGG..GAAGAGAU
X04465.1/19125-19199    GAAAGCCGAAUGAAUU..GAAAAGUUCAUGUUCGGUUUGG..GAAGAGA.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

AY005806.1/723-797      ..........GGAUCUAUAAGAAUUCACCUAUC.CCAAU
M68929.1/41010-41093    UCAGUAAGCCCUACAAGGGCUGAAGUCUUGACC.CCUAU
U13767.1/4803-4881      ......GACGGGGAAUAAUAUCCCCUCUCGACU.CUAAC
AB042240.3/34087-34170  CAUAAAAGUUGUAAACUUACAAAAUAAUCUACUUUC.AU
X04465.1/19125-19199    ........UUAUAAAAUAUAUAUAUAAUCUACUUUC.AU
#=GC SS_cons            ...........................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln33.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln33.fa

X04465.1/47942-47868  AGGAGCCGUAUGAAGU...UUAA.ACUUCAUGUACGGUUUUGAA.ACGGAGU
X04465.1/4746-4826    UUAAGCCAUACAGA..GUUGAAAA.UAUCAUAUAUGGUUUUCA..AGGGGGG
AE007285.1/6659-6583  GGGAGCGGUGUGAAUC...GAGA.GGUUCACGCACCGUUCUG...CGAGAGG
L36897.1/2659-2743    GAAAGCCGUAUGAUGG...GAAA.CUAUCACGUACGGUUUGG...GAAAGGC
AJ130737.1/1761-1840  UUGAGCCGUAUGCGGG...GAAA.CUUGCACGUGCGGUUCUUUGAGGGGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>.....<<<<.<<

X04465.1/47942-47868  .............UUAUUUUAAAUAAAUUAACAACCGUAAC
X04465.1/4746-4826    .......AAAAAGAAUUAUAAAAUCUAAAACCUAUCCUAAU
AE007285.1/6659-6583  ........CCGGCUGGUGAAACUCCUCCGGCCUACUCA.CC
L36897.1/2659-2743    UCUUUAACACGUGGCAACAUAGGUUAAUUUGCUAUUUC.AU
AJ130737.1/1761-1840  .........GAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
#=GC SS_cons          ..............................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln34.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln34.fa

M36911.1/2445-2539      GAGAGCCGUAUGCGGU.GAAA.GUCGCACGUACGGUUCGG..AGGAGAGU
X04465.1/73150-73215    UGGAGCCGGAUGAUA.UUAAAU.UAUCAUGUCCGAUUCUUU.GGGGGGA.
Z00044.1/12700-12613    GAGAGCCAAAUGAAUC.GAAA.GAUUCAUGUUUGGUUCGG..GAAGGGA.
U13767.1/4803-4881      GGGAGCCGUGUGCAGC.GAAA.GUUGCACGCACGGAUCUAACAGAGAGG.
AB042240.3/88332-88259  GAAAGCCGUAUUCGAU.GAAA.GUCGUAUGUACGGCUUGG..AGGGAGA.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

M36911.1/2445-2539      UUUUGGUUUCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUAUC.CU.A
X04465.1/73150-73215    ..............................CUUUUUUAAUCUACC.UUAA
Z00044.1/12700-12613    .......UUAUGGAAUUUUGGAAAGGAAUGGAAAAAUAAUCUACUUUC.A
U13767.1/4803-4881      ..................GACGGGGAAUAAUAUCCCCUCUCGACU.CUAA
AB042240.3/88332-88259  ....................UCUUUCCUAUCUUUCGAGAUCCACC.CU.A
#=GC SS_cons            .......................................>>..>>.>>..

M36911.1/2445-2539      C
X04465.1/73150-73215    U
Z00044.1/12700-12613    U
U13767.1/4803-4881      C
AB042240.3/88332-88259  C
#=GC SS_cons            .
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln35.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln35.fa

X04465.1/101010-100933  AGGAGCCGUAUGAAAU.GAAAA.UUUCAUGUACGGUUUUGCAAUAGAGAU
M15176.1/580-656        AGGAGCUGGAUGAGA.AGAAAC.UCUCAUGUCCAGUUUUGUAGUAGAGA.
Z00044.1/84143-84067    AGGAGCUGGAUGAGA.AGAAA.CUCUCACGUCCGGUUCUGUAGUAGAGA.
X01088.1/1893-1955      GAGAGCUUUUUGCGGG.GAAA.CUUGCAAGUAAAGUUUGG..GGGGAGG.
X07106.1/1306-1373      UUGAGCUGUACGAGAU.GAAA.GUCUCAUAUACAGUUCUUA.GGGGGGU.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

X04465.1/101010-100933  AUAAAUAGUAAUGUUCAUAUCGACUAU.AAU
M15176.1/580-656        UGGAACUAAGAAGGAACCAUCGACUAU.AAC
Z00044.1/84143-84067    UGGAAUUCAGAAACAACCAUCAACUAU.AAC
X01088.1/1893-1955      .............CGGGCGUCGACCCAACCU
X07106.1/1306-1373      ........UUAAUAGUUUACCUAUCUC.AAU
#=GC SS_cons            ...................>>..>>>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln36.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln36.fa

Y08501.1/133100-133176  GUGAGCGCAUGCGGG.GAGACCCGCACGUACGGUUUUU...AG.GGGGAU
AJ316582.1/78387-78450  UUGAGCUGUACGAGAUGAAAGUCUCAUAUACGGUUCUCA..GA.GGGGG.
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGG.GGGAA.
X72616.1/122-187        AAGAGCCGUACGAG..GCAG..CUCACGUACGGUUCGG...GAGCCGAG.
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..CC.GGGGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<.<<.<<.

Y08501.1/133100-133176  CUGGCCGAAAGACCGGCCGGCGCCCACCCG.AC
AJ316582.1/78387-78450  ...............AGUUCCGCCUAUCUCAAU
AJ131147.1/1719-1794    .....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
X72616.1/122-187        ........CCCCUGCACAGGGGCUUAGGUC.AA
AJ011856.1/26154-26228  ....AAAACUUGUAAAGGUCUACCUAUCGGGAU
#=GC SS_cons            ......................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln37.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln37.fa

AB042240.3/34087-34170  GAGAGCCAAAUGAAUCGAAAGAUUCAUGUUUGGUUCGG.GAAGAGAUCAU
X04465.1/10044-10114    UUGAGCCGGAUGACGGAAAACUUUCAUGUCCGAUUCUUAGGGGGGG....
AF065404.1/6521-6444    UUGAGCCGUAUGUGCUGAAAGGUACAAGUACGGUUCUU.AGGGGAG....
AF074613.1/60570-60649  UUGAGCCGUAUGCCGGGAAACUGGCACGUACGGUUCUU.AGGGGGC....
X01088.1/1893-1955      GAGAGCUUUUUGCGGGGAAACUUGCAAGUAAAGUUUGG.GGGGAGG....
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>...<<<<.<<....

AB042240.3/34087-34170  AAAAGUUGUAAACUUACAAAAUAAUCUACUUUC...AU
X04465.1/10044-10114    ..........AAUUCUAUAAAUAACCUAUC.CC..AAU
AF065404.1/6521-6444    ..AAAGAGUUGGUAACACCUCUGACUUACC.CG..ACU
AF074613.1/60570-60649  ..GGUGAUGCAGUAAUGCAUCACUGCUACC.CGAUCGU
X01088.1/1893-1955      ..................CGGGCGUCGACC.CA.ACCU
#=GC SS_cons            ........................>>..>>.>>.....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln38.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln38.fa

U77945.1/1848-1919    AACCGCCGUGUACG....GAAC....CGUACGCACGGUGGUG.UGAGAGG..
X03481.1/524-600      AGGAGCCGUAUGAGGU..GAAA..AUCUCAUGUACGGUUCUGUAGAGUGG..
Z00044.1/1956-1845    GAAAGCCGUGUGCA..AUGAAAAA..UGCAAGCACGGCUUGG.GGAGGGGUC
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUU..GAAA..GAUGCAUGCACGGUUCUUAGGGGGGG..
X17375.2/29364-29438  UUGAGCCGUGUGCGGU..GAAA..GUCGCAUGCACGGUUCUACUGGGGGG..
#=GC SS_cons          ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>...<<<<.<<..

U77945.1/1848-1919    ..................................ACGGCGGGUGUGAAUCCG
X03481.1/524-600      ...................................CAGUAAGGGUGACUUAU
Z00044.1/1956-1845    UUUACUUGUUUAUUUAAUUUAAGAUUAACAUUUAUUUUAUUUAACAAGGAAC
AJ277126.1/8230-8302  .......................................AAAGCCGGUAACC
X17375.2/29364-29438  .....................................AAAGCCUGAGAGGGC
#=GC SS_cons          ....................................................

U77945.1/1848-1919    CCUCCUACUCG.AU
X03481.1/524-600      CUGUCAACUUUUCC
Z00044.1/1956-1845    UUAUCUACUCC.AU
AJ277126.1/8230-8302  GUACCUAUCCCAAU
X17375.2/29364-29438  CUACCUAUCCAACU
#=GC SS_cons          ...>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln39.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln39.fa

AE007285.1/6659-6583  GGGAGCGGUGUGAAUC...GAGA.GGUUCACGCACCGUUCUG.......CGA
X04465.1/77203-77142  AGGAGCCGGAUGAA...UCAAAAU..UUCAUGUCCGGUUUUGAA.....GUA
AB027572.1/1941-1862  AGGAGCCGAAUGAAAU...CAAA.AUUUCAUGUUCGGUUUUGAA.....UUA
X86563.2/93178-93102  AGGAGCCGUAUGAGGU...GAAAA.UCUCAUGUACGGUUCUGU......AGA
AJ130746.1/1754-1835  UUGAGCCGUAUGCGAAG..GAAA.CUUGCACGUGCGGUUCUUUGCUUUGAGG
#=GC SS_cons          ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>.........<<<

AE007285.1/6659-6583  GAGGCCGGCUGGUGAAACUCCUCCGGCCUACUCA.CC
X04465.1/77203-77142  GCGA.................UCAAAUCGACUAUAAC
AB027572.1/1941-1862  GAGACGUUAAAAAUAAUCAACCAACGUCGACUAUAAC
X86563.2/93178-93102  GGGA..CAGUAAGGAUGACUUAUCUGUCGACUUUUCC
AJ130746.1/1754-1835  GGGG....AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
#=GC SS_cons          <.<<......................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln40.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln40.fa

U41288.1/3118-3192      UUGAGCCGUAUGCGAU.GAAAGUUGCACGUACGGUUCUUA.CCGGGGG..
X86563.2/75403-75477    UCGAGCCGGAUGAUGAA.AAAUUCUCAUGUCCGGUUCCUUUGGGGGAU..
X55026.1/77786-77867    GAGAGCCGUAUGAUGG.GAAACUAUCACGUACGGUUCGG..GAAAAGGUA
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAU.GAAAGUCGCAAGCACGGUUCUGA.UGGGGGG..
AJ316582.1/78387-78450  UUGAGCUGUACGAGAU.GAAAGUCUCAUAUACGGUUCUCA.GAGGGGG..
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>....<<<<.<<..

U41288.1/3118-3192      .......AAAGCUUGAGAGAGCCUACCUAUCGGAAC
X86563.2/75403-75477    ........GGAUCCUAAAGAAUUCACCUAUCCCAAU
X55026.1/77786-77867    UAUAUACUGAUAAGAGGUAUACGUAUCUAGUUC.AU
AJ277126.1/6413-6487    .......AAAACGAGAGAUCGUCUACCUAUCCAACU
AJ316582.1/78387-78450  ..................AGUUCCGCCUAUCUCAAU
#=GC SS_cons            .........................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln41.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln41.fa

AJ131144.1/1753-1833    UUGAGCCGUAUGCGAG..GAAA..CUUGCACGUGCGGUUCUUUGCUUUGA
AF065404.1/6521-6444    UUGAGCCGUAUGUGCU..GAAA..GGUACAAGUACGGUUCUU.......A
Z00044.1/1956-1845      GAAAGCCGUGUGCA..AUGAAAAA..UGCAAGCACGGCUUGG.......G
AB042240.3/88332-88259  GAAAGCCGUAUUCGAU..GAAA..GUCGUAUGUACGGCUUGG.......A
AF029891.1/4522-4594    UUGAGCCGUAUGCCAU..GAAA..GUGGCACGUACGGUUCUGA......G
#=GC SS_cons            ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>.........<

AJ131144.1/1753-1833    GGGGGG.......................................AAAGC
AF065404.1/6521-6444    GGGGAG...................................AAAGAGUUG
Z00044.1/1956-1845      GAGGGGUCUUUACUUGUUUAUUUAAUUUAAGAUUAACAUUUAUUUUAUUU
AB042240.3/88332-88259  GGGAGA......................................UCUUUC
AF029891.1/4522-4594    GGGGGG.......................................AAAGU
#=GC SS_cons            <<<.<<............................................

AJ131144.1/1753-1833    UUGAAAGAGCCUAUCCAUCCUGAU
AF065404.1/6521-6444    GUAACACCUCUGACUUACCCGACU
Z00044.1/1956-1845      AACAAGGAACUUAUCUACUCC.AU
AB042240.3/88332-88259  CUAUCUUUCGAGAUCCACCCU.AC
AF029891.1/4522-4594    CUGAGAGGACCUACCUAUCCC..A
#=GC SS_cons            .............>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln42.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln42.fa

X17395.1/1934-1994    GAGAGCUUUUUGCGGG..GAAACUUGCAAGUACAGUUUGG..GGGGAGG...
AF029891.1/4522-4594  UUGAGCCGUAUGCCAU..GAAAGUGGCACGUACGGUUCUGA.GGGGGGG...
AY005806.1/723-797    UCGAGCUGGAUGAU..UAAAAAUUAUCAUGUCCAGUUCCCUCGGGGGAU...
U41288.1/27369-27451  GAGAGCCGUAUGCGGU..GAAAGUUGCACGUACGGUUCGG..UGGGAGGUUU
X04465.1/19125-19199  GAAAGCCGAAUGAAUU..GAAAAGUUCAUGUUCGGUUUGG..GAAGAGA...
#=GC SS_cons          ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<...

X17395.1/1934-1994    ...................CGGGCGUCGACC.CU.AC
AF029891.1/4522-4594  .......AAAGUCUGAGAGGACCUACCUAUC.CC..A
AY005806.1/723-797    ........GGAUCUAUAAGAAUUCACCUAUC.CCAAU
U41288.1/27369-27451  CUUAUAUCCCUCGUGGAGUAGGCUAUCGACC.CA.AC
X04465.1/19125-19199  ......UUAUAAAAUAUAUAUAUAAUCUACUUUC.AU
#=GC SS_cons          .........................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln43.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln43.fa

AF065404.1/6521-6444    UUGAGCCGUAUGUGCU.GAAAGGUACAAGUACGGUUCUU..AGGGGAG..
X03415.1/1030-1100      UCGAGCCGUACGAGG.AGAAAGCUUCCUAUACGUUUCUAG.GGGGGGU..
M36911.1/2445-2539      GAGAGCCGUAUGCGGU.GAAAGUCGCACGUACGGUUCGG..AGGAGAGUU
AJ315331.1/53-130       AGGAGCCGUAUGAGAU.GAAAAUCUCACGUACGGUUCUGUAAUAGCGA..
AJ277126.1/35792-35885  GAGAGCCCGGUGCGGU.GAAAGUCGCACGCCGGGUUCGG..GGAGAAC.U
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>....<<<<.<<..

AF065404.1/6521-6444    ................AAAGAGUUGGUAACACCUCUGACUUACCCGACU
X03415.1/1030-1100      ........................GUUGUUCAUCUACAUCAAUCCCAAU
M36911.1/2445-2539      UUUGGUUUCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUAUCCU.AC
AJ315331.1/53-130       ..................UGGGCACAGUGAUGUUAUCAUCGACUAUGAU
AJ277126.1/35792-35885  CUCUGUAACUAAAAUAUUUCGGUAUCACGUUAUGGUUAGUCACUCC.AC
#=GC SS_cons            ......................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln44.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln44.fa

X04465.1/10044-10114    UUGAGCCGGAUGACGGAAAACUUUCAUGUCCGAUUCUUA...GG.GGGGG
Z00044.1/45478-45405    AGGAGCCGUAUGAGGUGAAAAUCUCACGUACGGUUCUGGA..AC.GGAGA
AJ316582.1/98150-98072  AGGAGCCGUGUGAGAUGAAAGUCUCAUGCACGGUUUUGAAUGAG.AGAAA
AJ277126.1/8230-8302    UUGAGCCGUGUGCGUUGAAAGAUGCAUGCACGGUUCUUA...GG.GGGGG
AF314856.1/1250-1311    ACGAGCCACAUGCAGGGAAACUUGCACGUGUGGUUCUG....GCCGGGGA
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>......<<.<<.<<

X04465.1/10044-10114    .....AAUUCUAUAAAUAACCUAUCCCAAU
Z00044.1/45478-45405    ...UUCUUUCAAUUGAAUGACGACCGUAAC
AJ316582.1/98150-98072  GAAGUGAGGAAUCCUCUUUUCGACUCUGAC
AJ277126.1/8230-8302    ...AAAGCCGGUAACCGUACCUAUCCCAAU
AF314856.1/1250-1311    .............CCCCGGUAUACUGU.AC
#=GC SS_cons            ...................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln45.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln45.fa

AF314856.1/1250-1311    ACGAGCCACAUGCAGGGAAACUUGCACGUGUGGUUCUG....GCCGGGGA
AJ316582.1/73932-73872  UUGAACCGUAUGCAUCAAAAGGCGCAUGUACGGUUCCUA...AG.GGAUA
X04465.1/19125-19199    GAAAGCCGAAUGAAUUGAAAAGUUCAUGUUCGGUUUGG....GA.AGAGA
AJ316582.1/98150-98072  AGGAGCCGUGUGAGAUGAAAGUCUCAUGCACGGUUUUGAAUGAG.AGAAA
AJ251292.1/2399-2492    AGGAGCCGUAUGCAUUGAAAGAUGCACGUACGGUUCUA....GG.GGAGA
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>......<<.<<.<<

AF314856.1/1250-1311    .................................CCCCGGUAUACU.GU.A
AJ316582.1/73932-73872  ...................................CAAUUUUACC.CUAA
X04465.1/19125-19199    ....................UUAUAAAAUAUAUAUAUAAUCUACUUUC.A
AJ316582.1/98150-98072  ....................GAAGUGAGGAAUCCUCUUUUCGACU.CUGA
AJ251292.1/2399-2492    GGGCUUGAUCUUCCAUUAUUUUAAUAUUGGACUCGGGUUCUUAUC.CU.A
#=GC SS_cons            .......................................>>..>>.>>..

AF314856.1/1250-1311    C
AJ316582.1/73932-73872  U
X04465.1/19125-19199    U
AJ316582.1/98150-98072  C
AJ251292.1/2399-2492    C
#=GC SS_cons            .
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln46.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln46.fa

X04465.1/2700-2775      AGGAGCCGUGUGA...AUUGAAAAUC...UCAUGCACGGUUUUGAAUGAG
AP000397.1/37693-37753  GAGAGCUUUUUGCGGG...GAAA...CUUGCAAGUACAGUUUGG....GG
X55026.1/77786-77867    GAGAGCCGUAUGAUGG...GAAA...CUAUCACGUACGGUUCGG....GA
Z00044.1/45478-45405    AGGAGCCGUAUGAGGU...GAAA...AUCUCACGUACGGUUCUGGA..AC
X04465.1/77203-77142    AGGAGCCGGAUGAA...UCAAAAU....UUCAUGUCCGGUUUUGAA..GU
#=GC SS_cons            ..<<<<<<<<.<<<<<..........>>>>>...>>>>>>>>......<<

X04465.1/2700-2775      AGAAA...........AAAUAAUUUUUUUUUUUCGACUCUAAC
AP000397.1/37693-37753  GGAGG.....................CGGGCGUCGACCCA.AC
X55026.1/77786-77867    AAAGGUAUAUAUACUGAUAAGAGGUAUACGUAUCUAGUUC.AU
Z00044.1/45478-45405    GGAGA...........UUCUUUCAAUUGAAUGACGACCGUAAC
X04465.1/77203-77142    AGCGA......................UCAAAUCGACUAUAAC
#=GC SS_cons            <<.<<...........................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln47.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln47.fa

AF200692.2/21112-21025  GAGAGCCGGAUGCGCU..GAAA...GGUGCACGUCCGGUUCGG....GGA
M68929.1/49817-49892    UUGAGCCGUAUGCGG...GAAA..ACUCGCACGUACGGUUCUUA...GGG
AJ316582.1/98150-98072  AGGAGCCGUGUGAGAU..GAAA...GUCUCAUGCACGGUUUUGAAUGAGA
AJ316582.1/78387-78450  UUGAGCUGUACGAGAU..GAAA...GUCUCAUAUACGGUUCUCA...GAG
X04465.1/754-816        AAAAGCCGUAUUCG..UUGAAAAU...CGGAUGUACGGUUUGG....AGG
#=GC SS_cons            ..<<<<<<<<.<<<<<.........>>>>>...>>>>>>>>......<<<

AF200692.2/21112-21025  GGAGAGGCAGGGAAAUAGUCCGACUACGCCCUGCCUCUUACUCUUAC
M68929.1/49817-49892    GGGG.............GAAAGCUUGAGAGGGCCUACCUAUCCCGAC
AJ316582.1/98150-98072  GAAA.............GAAGUGAGGAAUCCUCUUUUCGACUCUGAC
AJ316582.1/78387-78450  GGGG.........................AGUUCCGCCUAUCUCAAU
X04465.1/754-816        GAGA........................UAAAAAAAUCCACCCU.AC
#=GC SS_cons            <.<<................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln48.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln48.fa

X73671.1/1293-1367  UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA.AGAGGGG....AAA
Y18999.2/2881-2957  UUGAGCCGGAUGAGGGGCGACUCUCAUGUCCGGUUCUU..AGGGGACGGCGGCG
U13767.1/4803-4881  GGGAGCCGUGUGCAGCGAAAGUUGCACGCACGGAUCUAACAGAGAGG.GACGGG
X03698.1/100-176    AGAAGCCGUAUGAAAUGAAAAUAUCAAGUACGGUUUUGU.AAAGUGA..CAAUU
X62341.1/1274-1336  GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGG..GGGGAGA.......
#=GC SS_cons        ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>....<<<<.<<.......

X73671.1/1293-1367  AUGAGUGAUCAUCUACCUAUUCU.AAC
Y18999.2/2881-2957  CAGUAAUGCGCUGCUGUUACCCG..AC
U13767.1/4803-4881  GAAUAAUAUCCCCUCUCGACUCU.AAC
X03698.1/100-176    UAGGUAACUUAUUUGUCAACUUU.UCC
X62341.1/1274-1336  .........CGGGCGUCGACCCAACCU
#=GC SS_cons        ...............>>..>>>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln49.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln49.fa

Z00044.1/1956-1845    GAAAGCCGUGUGCA...AUGAAAAA..UGCAAGCACGGCUUGG.GGAGGGGU
Y18999.2/2881-2957    UUGAGCCGGAUGAGGG...GCGA..CUCUCAUGUCCGGUUCUU.AGGGGAC.
X04465.1/4746-4826    UUAAGCCAUACAGA..GUUGAAAA..UAUCAUAUAUGGUUUUCAAGGGGGG.
X04465.1/19125-19199  GAAAGCCGAAUGAAUU...GAAA..AGUUCAUGUUCGGUUUGG.GAAGAGA.
M81726.1/5191-5288    GUGAGCCGUAUGAUGG...GCAA..CUAUCUCCUGCGGUUCGG.AGAGGAC.
#=GC SS_cons          ..<<<<<<<<.<<<<<.........>>>>>...>>>>>>>>...<<<<.<<.

Z00044.1/1956-1845    CUUUACUUGUUUAUUUAAUUUAAGAUUAACAUUUAUUUUAUUUAACAAGGAA
Y18999.2/2881-2957    ..................................GGCGGCGCAGUAAUGCGC
X04465.1/4746-4826    .................................AAAAAGAAUUAUAAAAUCU
X04465.1/19125-19199  .....................................UUAUAAAAUAUAUAU
M81726.1/5191-5288    .............UCAGCUGUUAGUUAGUACCCCCGUCGGUUUCGGGGUGGA
#=GC SS_cons          ....................................................

Z00044.1/1956-1845    CUUAUCUACU.CC.AU
Y18999.2/2881-2957    UGCUGUUACC.CG.AC
X04465.1/4746-4826    AAAACCUAUC.CUAAU
X04465.1/19125-19199  AUAAUCUACUUUC.AU
M81726.1/5191-5288    CCCUUUUACU.CU.AU
#=GC SS_cons          ....>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln50.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln50.fa

AF200692.2/21112-21025  GAGAGCCGGAUGCGCU..GAAA..GGUGCACGUCCGGUUCGG..GGAGGA
AP000423.1/1844-1752    GAAAGCUGUGUGCA..AUGAAAAA..UGCAAGCACGGUUUGG..GGAGGG
U41288.1/27369-27451    GAGAGCCGUAUGCGGU..GAAA..GUUGCACGUACGGUUCGG..UGGGAG
AJ251292.1/2399-2492    AGGAGCCGUAUGCAUU..GAAA..GAUGCACGUACGGUUCUA..GGGGAG
X04465.1/47942-47868    AGGAGCCGUAUGAAGU..UUAA..ACUUCAUGUACGGUUUUGAAACGGAG
#=GC SS_cons            ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>....<<<<.<

AF200692.2/21112-21025  G.......AGGCAGGGAAAUAGUCCGACUACGCCCUGCCUCUUACUCUUA
AP000423.1/1844-1752    G.UUUUUUACCUUUUUUUUUUCAUUUUAACAAGGAGAUUAUCUACUCC.A
U41288.1/27369-27451    G...........UUUCUUAUAUCCCUCGUGGAGUAGGCUAUCGACCCA.A
AJ251292.1/2399-2492    AGGGCUUGAUCUUCCAUUAUUUUAAUAUUGGACUCGGGUUCUUAUCCU.A
X04465.1/47942-47868    U......................UUAUUUUAAAUAAAUUAACAACCGUAA
#=GC SS_cons            <.......................................>>..>>>>..

AF200692.2/21112-21025  C
AP000423.1/1844-1752    U
U41288.1/27369-27451    C
AJ251292.1/2399-2492    C
X04465.1/47942-47868    C
#=GC SS_cons            .
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln51.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln51.fa

X03834.1/1418-1494  GGGAGCCGGAUGAGA...AGAAAC.UCUCAUGUCCGGUUCUGUAGUAGAGA...
U77945.1/1848-1919  AACCGCCGUGUACG.....GAAC...CGUACGCACGGUGGUG..UGAGAGG...
L36897.1/2659-2743  GAAAGCCGUAUGAUGG...GAAA.CUAUCACGUACGGUUUGG..GAAAGGCUCU
X04465.1/4746-4826  UUAAGCCAUACAGA..GUUGAAAA.UAUCAUAUAUGGUUUUCA.AGGGGGG...
Y18999.2/2881-2957  UUGAGCCGGAUGAGGG...GCGA.CUCUCAUGUCCGGUUCUU..AGGGGAC...
#=GC SS_cons        ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>....<<<<.<<...

X03834.1/1418-1494  ........UGGAAUAGGGAAAUAACCAUCAACUAUAAC
U77945.1/1848-1919  ......ACGGCGGGUGUGAAUCCGCCUCCUACUCG.AU
L36897.1/2659-2743  UUAACACGUGGCAACAUAGGUUAAUUUGCUAUUUC.AU
X04465.1/4746-4826  ....AAAAAGAAUUAUAAAAUCUAAAACCUAUCCUAAU
Y18999.2/2881-2957  .....GGCGGCGCAGUAAUGCGCUGCUGUUACCCG.AC
#=GC SS_cons        ...........................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln52.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln52.fa

Z00044.1/87253-87177    GAAAGAAGUAUGCUUU.GGAA.GAAGCUUGUACAGUUUGG..GAAGGGG.
AF029891.1/9161-9235    UUGAGCCGUAUGCGAU.GAAA.GUCGCACGUACGGUUCUUA.GAGGGGG.
M15176.1/580-656        AGGAGCUGGAUGAGA.AGAAAC.UCUCAUGUCCAGUUUUGUAGUAGAGA.
Z00044.1/84143-84067    AGGAGCUGGAUGAGA.AGAAA.CUCUCACGUCCGGUUCUGUAGUAGAGA.
Y08501.1/133100-133176  GUGAGCGCAUGCGGG..GAGA.CCCGCACGUACGGUUUUU..AGGGGGAU
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

Z00044.1/87253-87177    UUUUGAUUGAUCAAAAGAAGAAUCUACUUC.AA
AF029891.1/9161-9235    ....AAAGUUCGAGAGGACCUACCUAUCUCAAC
M15176.1/580-656        ...UGGAACUAAGAAGGAACCAUCGACUAUAAC
Z00044.1/84143-84067    ...UGGAAUUCAGAAACAACCAUCAACUAUAAC
Y08501.1/133100-133176  CUGGCCGAAAGACCGGCCGGCGCCCACCCG.AC
#=GC SS_cons            ......................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln53.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln53.fa

Y08501.1/133100-133176  GUGAGCGCAUGCGGG.GAGACCCGCACGUACGGUUUUU...AGGGGGA..
V00694.1/5204-5294      GAGAGCCGUAUGAUAUGAAAGUAUCACGUACGGUUCGG...AGAGGGCUC
X71404.1/2822-2898      AGGAGCCGUAUGAGGUGAAAGUCUCAAGUACGGUUUUGA..AGACCAG..
X17375.2/29364-29438    UUGAGCCGUGUGCGGUGAAAGUCGCAUGCACGGUUCUAC..UGGGGGG..
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA..
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

Y08501.1/133100-133176  ...........UCUGGCCGAAAGACCGGCCGGCGCCCACCCG.AC
V00694.1/5204-5294      UUUUAUAUGAAUGUUAUUACAUUCAGAUAGGUUUGCUACUCU.AC
X71404.1/2822-2898      ..............CAGGAUUGGUGACAGUCUUGCUGAGUUUAAU
X17375.2/29364-29438    ................AAAGCCUGAGAGGGCCUACCUAUCCAACU
AJ131147.1/1719-1794    .................AAGCUUGAAAGAGCCUAUCCAUCCCGAU
#=GC SS_cons            ..................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln54.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln54.fa

M68929.1/49817-49892    UUGAGCCGUAUGCGG..GAAAACUCGCACGUACGGUUCUUA.GGGGGGG.
AP000397.1/37693-37753  GAGAGCUUUUUGCGGG.GAAA.CUUGCAAGUACAGUUUGG..GGGGAGG.
U13767.1/4803-4881      GGGAGCCGUGUGCAGC.GAAA.GUUGCACGCACGGAUCUAACAGAGAGG.
L36897.1/2659-2743      GAAAGCCGUAUGAUGG.GAAA.CUAUCACGUACGGUUUGG..GAAAGGCU
X86563.2/75403-75477    UCGAGCCGGAUGAUGAA.AAA.UUCUCAUGUCCGGUUCCUUUGGGGGAU.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

M68929.1/49817-49892    ..........GAAAGCUUGAGAGGGCCUACCUAUCCCGAC
AP000397.1/37693-37753  .......................CGGGCGUCGACCCA.AC
U13767.1/4803-4881      ........GACGGGGAAUAAUAUCCCCUCUCGACUCUAAC
L36897.1/2659-2743      CUUUAACACGUGGCAACAUAGGUUAAUUUGCUAUUUC.AU
X86563.2/75403-75477    ............GGAUCCUAAAGAAUUCACCUAUCCCAAU
#=GC SS_cons            .............................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln55.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln55.fa

L36897.1/2659-2743      GAAAGCCGUAUGAUGGGAAACUAUCACGUACGGUUUGG.......GA.AA
AP000397.1/37693-37753  GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGG.......GG.GG
AJ131144.1/1753-1833    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAG.GG
X72616.1/122-187        AAGAGCCGUACGAG..GCAG..CUCACGUACGGUUCGG.......GAGCC
X05917.1/3244-3331      GAGAGCCAAAUGAAUUGAAAGAUUCAUGUUUGGUUCGG.......GA.AG
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<.<<

L36897.1/2659-2743      GGC..UCUUUAACACGUGGCAACAUAGGUUAAUUUGCUAUU.UC.AU
AP000397.1/37693-37753  AGG..........................CGGGCGUCGACC.CA.AC
AJ131144.1/1753-1833    GGG..............AAAGCUUGAAAGAGCCUAUCCAUC.CUGAU
X72616.1/122-187        GAG..................CCCCUGCACAGGGGCUUAGG.UC.AA
X05917.1/3244-3331      AGAUCAUAGACAUUUUGAAAUGAAUGGAAAGAGAAUCUACUUUC.AU
#=GC SS_cons            .<<................................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln56.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln56.fa

AP000397.1/37693-37753  GAGAGCUUUUUGCGGG..GAAACUUGCAAGUACAGUUUGG..GGGGAGG.
AJ277126.1/9249-9325    AGGAGCCGUAUGAAUG..GAGACAUUCACGUACGGUUUUGGAGUAGCAG.
M36911.1/2445-2539      GAGAGCCGUAUGCGGU..GAAAGUCGCACGUACGGUUCGG..AGGAGAGU
AY005806.1/723-797      UCGAGCUGGAUGAU..UAAAAAUUAUCAUGUCCAGUUCCCUCGGGGGAU.
X73671.1/1293-1367      UUGAGCCGUAUGCGAU..GAAAGUUGCACGUACGGUUCUUA.AGAGGGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

AP000397.1/37693-37753  .................................CGGGCGUCGACCCA.AC
AJ277126.1/9249-9325    ....................GAUAUAUGGUAACAUGUACUUGACUAUAAG
M36911.1/2445-2539      UUUUGGUUUCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUAUCCU.AC
AY005806.1/723-797      ......................GGAUCUAUAAGAAUUCACCUAUCCCAAU
X73671.1/1293-1367      .....................AAAAUGAGUGAUCAUCUACCUAUUCUAAC
#=GC SS_cons            .......................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln57.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln57.fa

AF087656.1/10795-10873  UUGAGCUGUAUGCGAU...GAAA..GUCGCACGUACAGUUCUUA......
Z00044.1/1956-1845      GAAAGCCGUGUGCA...AUGAAAAA..UGCAAGCACGGCUUGG.......
Z00044.1/87253-87177    GAAAGAAGUAUGCUUU...GGAA..GAAGCUUGUACAGUUUGG.......
X02819.1/3326-3410      GAGAGCCGUAUAAUUAC..GAAA..GUAUCCCGUACGGUUCGG.......
AJ130746.1/1754-1835    UUGAGCCGUAUGCGAAG..GAAA..CUUGCACGUGCGGUUCUUUGCUUUG
#=GC SS_cons            ..<<<<<<<<.<<<<<.........>>>>>...>>>>>>>>.........

AF087656.1/10795-10873  GAGGAUG......................................UUAAU
Z00044.1/1956-1845      GGAGGGGUCUUUACUUGUUUAUUUAAUUUAAGAUUAACAUUUAUUUUAUU
Z00044.1/87253-87177    GAAGGGG...................................UUUUGAUU
X02819.1/3326-3410      UGACGAG.............................CCGUGUCAACCCUG
AJ130746.1/1754-1835    AGGGGGG.......................................AAAG
#=GC SS_cons            <<<<.<<...........................................

AF087656.1/10795-10873  AUAGUAAUAUUUAACGUAGCC.UCAACAG
Z00044.1/1956-1845      UAACAAGGAACUUAUCUA.CU.CC...AU
Z00044.1/87253-87177    GAUCAAAAGAAGAAUCUA.CU.UC...AA
X02819.1/3326-3410      CAAAGGGAAUGCGUCUUA.GUUCA...AU
AJ130746.1/1754-1835    CUUGAAAGAGCCUAUCCA.UC.CU..GAU
#=GC SS_cons            ..............>>...>>.>>.....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln58.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln58.fa

X04465.1/21511-21432    AGGAGCCGAAUGAAAG.AAAA.CUUUCACGUUCGGUUUUGAAUUAGAGG.
Y08501.1/133100-133176  GUGAGCGCAUGCGGG..GAGA.CCCGCACGUACGGUUUUU..AGGGGGA.
M68929.1/120754-120816  GGGAGCCGGAUGAGGGAGAAAUUUCUCACGUCCGGAUCUU..UGAGAGC.
X73671.1/1293-1367      UUGAGCCGUAUGCGAU.GAAA.GUUGCACGUACGGUUCUUA.AGAGGGG.
Z69899.1/2926-3021      GAGAGCCGUAUGCGGU.GAAA.GUCGCACGUACGGUUCGG..AGGAGAGU
#=GC SS_cons            ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>....<<<<.<<.

X04465.1/21511-21432    .................CAUUUUUUAUUUUUAAUAAAUGUCGACUAUAAC
Y08501.1/133100-133176  ................UCUGGCCGAAAGACCGGCCGGCGCCCACCCG.AC
M68929.1/120754-120816  .................................CUCCGGGCUACUCU.CU
X73671.1/1293-1367      .....................AAAAUGAGUGAUCAUCUACCUAUUCUAAC
Z69899.1/2926-3021      UGUUGGUUUCUAAGGUUUCUUUAGACUAAGGACUGGCUGCUUAUCCUACA
#=GC SS_cons            .......................................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln59.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln59.fa

AY005806.1/723-797    UCGAGCUGGAUGAU...UAAAAAUUAUCAUGUCCAGUUCCCUCGG.GGGAU.
AF065404.1/6521-6444  UUGAGCCGUAUGUGCU...GAAAGGUACAAGUACGGUUCUU..AG.GGGAGA
Z00044.1/87253-87177  GAAAGAAGUAUGCUUU...GGAAGAAGCUUGUACAGUUUGG..GA.AGGGGU
Z00044.1/44460-44392  CUGAGCCGUAUGAGG.UAAGAAAUUCUCAAGUACGGUUCUAA.GG.GAAGG.
AF314856.1/1250-1311  ACGAGCCACAUGCAGG...GAAACUUGCACGUGUGGUUCUG..GCCGGGGA.
#=GC SS_cons          ..<<<<<<<<.<<<<<.......>>>>>...>>>>>>>>....<<.<<.<<.

AY005806.1/723-797    ....GGAUCUAUAAGAAUUCACCUAUCCCAAU
AF065404.1/6521-6444  AAGAGUUGGUAACACCUCUGACUUACCCGACU
Z00044.1/87253-87177  UUUGAUUGAUCAAAAGAAGAAUCUACUUC.AA
Z00044.1/44460-44392  ...........AAUUGAACUACCUAUUCCGGC
AF314856.1/1250-1311  ...............CCCCGGUAUACUGU.AC
#=GC SS_cons          .....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln60.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln60.fa

AJ277126.1/6413-6487  GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA.UGGGGGG.....
X77508.1/2333-2408    GGGAGCGGUAUGAGCCGAGAGGUUCACGUACCGUUCUG..CGAGAGG.....
U41288.1/27369-27451  GAGAGCCGUAUGCGGUGAAAGUUGCACGUACGGUUCGG..UGGGAGGUUUCU
Z00044.1/45478-45405  AGGAGCCGUAUGAGGUGAAAAUCUCACGUACGGUUCUGGAACGGAGA.....
X04465.1/71857-71924  UUAAGCUGUAAGAUUAUAAAUAAUCAUUUACGGUUUUUC.GAGGGGG.....
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>....<<<<.<<.....

AJ277126.1/6413-6487  .....AAAACGAGAGAUCGUCUACCUAUCCAACU
X77508.1/2333-2408    ..CUGCGGGGGAGGUUCCUGCGGCCUACUCA.CC
U41288.1/27369-27451  UAUAUCCCUCGUGGAGUAGGCUAUCGACCCA.AC
Z00044.1/45478-45405  .......UUCUUUCAAUUGAAUGACGACCGUAAC
X04465.1/71857-71924  ............AACUUUAGUAACCUAUCUCAAU
#=GC SS_cons          .......................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln61.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln61.fa

X04465.1/73150-73215    UGGAGCCGGAUGAUA..UUAAAU..UAUCAUGUCCGAUUCUUU.GGGGGG
AJ277126.1/33096-33168  GCGAGCCGUAUGAUGG..GAAA..CUAUCACGUACGGUUCUG..AGGGCA
X04465.1/77203-77142    AGGAGCCGGAUGAA..UCAAAAU...UUCAUGUCCGGUUUUGAAGUAGCG
L36897.1/2659-2743      GAAAGCCGUAUGAUGG..GAAA..CUAUCACGUACGGUUUGG..GAAAGG
X04465.1/754-816        AAAAGCCGUAUUCG..UUGAAAAU..CGGAUGUACGGUUUGG..AGGGAG
#=GC SS_cons            ..<<<<<<<<.<<<<<........>>>>>...>>>>>>>>....<<<<.<

X04465.1/73150-73215    A.....................CUUUUUUAAUCUACC.UUAAU
AJ277126.1/33096-33168  A.............GGUAUAUUCUAAAUGCCUUGACCCCU.AC
X04465.1/77203-77142    A.........................UCAAAUCGACU.AUAAC
L36897.1/2659-2743      CUCUUUAACACGUGGCAACAUAGGUUAAUUUGCUAUU.UC.AU
X04465.1/754-816        A......................UAAAAAAAUCCACC.CU.AC
#=GC SS_cons            <..............................>>..>>.>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln62.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln62.fa

X60045.1/1000-1142   GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG...............
X72287.1/717-859     GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG...............
Y12731.1/1118-1260   GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG...............
AF143421.1/868-1007  GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUAG
AF143424.1/944-1083  GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUCAUUCU
#=GC SS_cons         ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.................

X60045.1/1000-1142   .........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUGCA
X72287.1/717-859     .........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUGCA
Y12731.1/1118-1260   .........AGAGCACUUAAUUAGAAUGAGAGGUUCACCACCACAUCAUUGCA
AF143421.1/868-1007  AAUGUUCCUGGGGGUA...........................CCACAUCAUU
AF143424.1/944-1083  AAUGUUCCUGGGGGUA...........................CCACAUCAUU
#=GC SS_cons         .........<<<<.<<.....................................

X60045.1/1000-1142   UGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUCACUUCU
X72287.1/717-859     UGCAAGGGGAGCUCGCUCGAUUCGCAAAUUGGUCCGACUCGUAAUUCACUUCU
Y12731.1/1118-1260   UGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUAACUUCU
AF143421.1/868-1007  GCAAGGGUAAAAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCC
AF143424.1/944-1083  GCAAGGGUAACAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCC
#=GC SS_cons         ...................................................>>

X60045.1/1000-1142   GACUCUGU
X72287.1/717-859     GACUCCGU
Y12731.1/1118-1260   GACUCCGU
AF143421.1/868-1007  GACCCUGU
AF143424.1/944-1083  GACCCUGU
#=GC SS_cons         ..>>>>..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln63.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln63.fa

X60045.1/1000-1142    GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG..............
X72287.1/717-859      GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG..............
AF143425.1/760-901    GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUCAUUC
AF143423.1/825-965    GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUA
AF080083.1/1551-1683  GAGAGCCGUGUGAUGGGUGACUAUCCAGCACGGUUCGG..............
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>................

X60045.1/1000-1142    ..........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUG
X72287.1/717-859      ..........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUG
AF143425.1/760-901    GAAU......GGGGUGA...................ACCACCACAUCAUUGC
AF143423.1/825-965    GAAUGUUCCUGGGGGGU..........................ACCACAUCA
AF080083.1/1551-1683  ..........AGAGCAC..........UUUUAGUCUGCGUUGGUGAAUGAAA
#=GC SS_cons          ..........<<<<.<<...................................

X60045.1/1000-1142    CAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUCACU
X72287.1/717-859      CAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUUGGUCCGACUCGUAAUUCACU
AF143425.1/760-901    AAGGGUAACAGAGCUCGCUCGAUUCGCAGAUUGGUUUGACCCGGAAUUCACU
AF143423.1/825-965    UUGCAAGGGUAACAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACU
AF080083.1/1551-1683  GCCCCCCCCCAUCAAGCAAGAAAGAAGCGGCUCUUCCCACGGCGGAGUCACC
#=GC SS_cons          ....................................................

X60045.1/1000-1142    UCUGACUCUGU
X72287.1/717-859      UCUGACUCCGU
AF143425.1/760-901    UUCGACCCUGU
AF143423.1/825-965    UCCGACCCUGU
AF080083.1/1551-1683  AUUGACUCUAU
#=GC SS_cons          .>>..>>>>..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln64.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln64.fa

X72287.1/717-859      GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG..............
Y12731.1/1118-1260    GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG..............
AF143423.1/825-965    GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUA
AF143421.1/868-1007   GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUA
AF080083.1/1551-1683  GAGAGCCGUGUGAUGGGUGACUAUCCAGCACGGUUCGG..............
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>................

X72287.1/717-859      ..........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUG
Y12731.1/1118-1260    ..........AGAGCACUUAAUUAGAAUGAGAGGUUCACCACCACAUCAUUG
AF143423.1/825-965    GAAUGUUCCUGGGGGGU..........................ACCACAUCA
AF143421.1/868-1007   GAAUGUUCCUGGGGGUA...........................CCACAUCA
AF080083.1/1551-1683  ..........AGAGCAC..........UUUUAGUCUGCGUUGGUGAAUGAAA
#=GC SS_cons          ..........<<<<.<<...................................

X72287.1/717-859      CAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUUGGUCCGACUCGUAAUUCACU
Y12731.1/1118-1260    CAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUAACU
AF143423.1/825-965    UUGCAAGGGUAACAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACU
AF143421.1/868-1007   UUGCAAGGGUAAAAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACU
AF080083.1/1551-1683  GCCCCCCCCCAUCAAGCAAGAAAGAAGCGGCUCUUCCCACGGCGGAGUCACC
#=GC SS_cons          ....................................................

X72287.1/717-859      UCUGACUCCGU
Y12731.1/1118-1260    UCUGACUCCGU
AF143423.1/825-965    UCCGACCCUGU
AF143421.1/868-1007   UCCGACCCUGU
AF080083.1/1551-1683  AUUGACUCUAU
#=GC SS_cons          .>>..>>>>..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln65.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln65.fa

X60045.1/1000-1142   GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG...............
Y12731.1/1118-1260   GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG...............
AF143425.1/760-901   GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUCAUUCG
AF143421.1/868-1007  GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUAG
AF143424.1/944-1083  GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUCAUUCU
#=GC SS_cons         ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.................

X60045.1/1000-1142   .........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUGCA
Y12731.1/1118-1260   .........AGAGCACUUAAUUAGAAUGAGAGGUUCACCACCACAUCAUUGCA
AF143425.1/760-901   AAU......GGGGUGA...................ACCACCACAUCAUUGCAA
AF143421.1/868-1007  AAUGUUCCUGGGGGUA...........................CCACAUCAUU
AF143424.1/944-1083  AAUGUUCCUGGGGGUA...........................CCACAUCAUU
#=GC SS_cons         .........<<<<.<<.....................................

X60045.1/1000-1142   UGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUCACUUCU
Y12731.1/1118-1260   UGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUAACUUCU
AF143425.1/760-901   GGGUAACAGAGCUCGCUCGAUUCGCAGAUUGGUUUGACCCGGAAUUCACUUUC
AF143421.1/868-1007  GCAAGGGUAAAAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCC
AF143424.1/944-1083  GCAAGGGUAACAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCC
#=GC SS_cons         ...................................................>>

X60045.1/1000-1142   GACUCUGU
Y12731.1/1118-1260   GACUCCGU
AF143425.1/760-901   GACCCUGU
AF143421.1/868-1007  GACCCUGU
AF143424.1/944-1083  GACCCUGU
#=GC SS_cons         ..>>>>..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln66.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln66.fa

X60045.1/1000-1142    GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG..............
Y12731.1/1118-1260    GUGAGCCGUGUGAUGGGAAACCUUCCCGCACGGUUCGG..............
AF143423.1/825-965    GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUA
AF143421.1/868-1007   GUGAGCCGUGUGAUGGGAAACCUCCCCGCACGGUUCGGAGAGCACUUAAUUA
AF080083.1/1551-1683  GAGAGCCGUGUGAUGGGUGACUAUCCAGCACGGUUCGG..............
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>................

X60045.1/1000-1142    ..........AGAGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAUUG
Y12731.1/1118-1260    ..........AGAGCACUUAAUUAGAAUGAGAGGUUCACCACCACAUCAUUG
AF143423.1/825-965    GAAUGUUCCUGGGGGGU..........................ACCACAUCA
AF143421.1/868-1007   GAAUGUUCCUGGGGGUA...........................CCACAUCA
AF080083.1/1551-1683  ..........AGAGCAC..........UUUUAGUCUGCGUUGGUGAAUGAAA
#=GC SS_cons          ..........<<<<.<<...................................

X60045.1/1000-1142    CAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUCACU
Y12731.1/1118-1260    CAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUAACU
AF143423.1/825-965    UUGCAAGGGUAACAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACU
AF143421.1/868-1007   UUGCAAGGGUAAAAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACU
AF080083.1/1551-1683  GCCCCCCCCCAUCAAGCAAGAAAGAAGCGGCUCUUCCCACGGCGGAGUCACC
#=GC SS_cons          ....................................................

X60045.1/1000-1142    UCUGACUCUGU
Y12731.1/1118-1260    UCUGACUCCGU
AF143423.1/825-965    UCCGACCCUGU
AF143421.1/868-1007   UCCGACCCUGU
AF080083.1/1551-1683  AUUGACUCUAU
#=GC SS_cons          .>>..>>>>..
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln67.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln67.fa

AJ130746.1/1754-1835  UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AF029891.1/9161-9235  UUGAGCCGUAUGCGAU.GAAAGUCGCACGUACGGUUCUUA......GAGGGG
AJ277126.1/6413-6487  GUGAGCCGUGUGCGAU.GAAAGUCGCAAGCACGGUUCUGA......UGGGGG
X17375.2/29364-29438  UUGAGCCGUGUGCGGU.GAAAGUCGCAUGCACGGUUCUAC......UGGGGG
AF029891.1/4522-4594  UUGAGCCGUAUGCCAU.GAAAGUGGCACGUACGGUUCUGA......GGGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<.<

AJ130746.1/1754-1835  GAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AF029891.1/9161-9235  GAAAGUUCGAGAGGACCUACCUAUCUCAAC
AJ277126.1/6413-6487  GAAAACGAGAGAUCGUCUACCUAUCCAACU
X17375.2/29364-29438  GAAAGCCUGAGAGGGCCUACCUAUCCAACU
AF029891.1/4522-4594  GAAAGUCUGAGAGGACCUACCUAUCCC..A
#=GC SS_cons          <..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln68.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln68.fa

AJ130746.1/1754-1835    UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGG
AJ131144.1/1753-1833    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGCUUUGAGGG
AJ131136.1/1732-1807    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGG
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAU.GAAAGUCGCACGUACGGUUCUUA......CCGG
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<

AJ130746.1/1754-1835    GGGAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131144.1/1753-1833    GGGAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131136.1/1732-1807    GGA.AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ131145.1/1727-1802    GGG.AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ011856.1/26154-26228  GGGAAAACUUGUAAAGGUCUACCUAUCGGGAU
#=GC SS_cons            .<<..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln69.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln69.fa

AJ131136.1/1732-1807  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGA.AAG
AJ131147.1/1719-1794  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA.AAG
AF029891.1/9161-9235  UUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..GAGGGGGAAAG
AJ277126.1/2879-2953  UUCAGCCGUGUGCGGUGAAAGUCGCACGCACGGUUGUGA..GGGGGGGAAAA
U41288.1/3118-3192    UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA..CCGGGGGAAAG
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<....

AJ131136.1/1732-1807  CUUGAAAGAGCCUAUCCAUCCCGAU
AJ131147.1/1719-1794  CUUGAAAGAGCCUAUCCAUCCCGAU
AF029891.1/9161-9235  UUCGAGAGGACCUACCUAUCUCAAC
AJ277126.1/2879-2953  UCUGUGAAGAUCUACCUAUCCCGAU
U41288.1/3118-3192    CUUGAGAGAGCCUACCUAUCGGAAC
#=GC SS_cons          ..............>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln70.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln70.fa

AJ130737.1/1761-1840  UUGAGCCGUAUGCGGGGAAA.CUUGCACGUGCGGUUCUUUGAGGGGGGGGAG
M68929.1/49817-49892  UUGAGCCGUAUGCGG.GAAAACUCGCACGUACGGUUCUUA..GGGGGGG..G
AJ277126.1/6413-6487  GUGAGCCGUGUGCGAUGAAA.GUCGCAAGCACGGUUCUGA..UGGGGGG...
AF029891.1/4522-4594  UUGAGCCGUAUGCCAUGAAA.GUGGCACGUACGGUUCUGA..GGGGGGG...
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUUGAAA.GAUGCAUGCACGGUUCUUA..GGGGGGG...
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.....<<<<.<<...

AJ130737.1/1761-1840  CUUGCUCGAAAGAGCCUACCUAUCCCGAU
M68929.1/49817-49892  AAAGCUUGAGAGGGCCUACCUAUCCCGAC
AJ277126.1/6413-6487  AAAACGAGAGAUCGUCUACCUAUCCAACU
AF029891.1/4522-4594  AAAGUCUGAGAGGACCUACCUAUCCC..A
AJ277126.1/8230-8302  ..AAAGCCGGUAACCGUACCUAUCCCAAU
#=GC SS_cons          ..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln71.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln71.fa

AJ131144.1/1753-1833    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGG
AJ130737.1/1761-1840    UUGAGCCGUAUGCGGGGAAACUUGCACGUGCGGUUCUUUGA....GGGGG
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA......CCGGG
X73671.1/1293-1367      UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA......AGAGG
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<<<.

AJ131144.1/1753-1833    GG...AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ130737.1/1761-1840    GGGAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
AJ131147.1/1719-1794    AA....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ011856.1/26154-26228  GG...AAAACUUGUAAAGGUCUACCUAUCGGGAU
X73671.1/1293-1367      GG...AAAAUGAGUGAUCAUCUACCUAUUCUAAC
#=GC SS_cons            <<.....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln72.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln72.fa

AJ130737.1/1761-1840    UUGAGCCGUAUGCGGGGAAA.CUUGCACGUGCGGUUCUUUGAGGGGGGGG
M68929.1/49817-49892    UUGAGCCGUAUGCGG.GAAAACUCGCACGUACGGUUCUUA..GGGGGGG.
AJ011856.1/37648-37722  UUGAGCUGUAUACUAUGAAA.GUAGUACGUACAGUUCUGA..GUGGGGG.
X73671.1/1293-1367      UUGAGCCGUAUGCGAUGAAA.GUUGCACGUACGGUUCUUA..AGAGGGG.
AF029891.1/4522-4594    UUGAGCCGUAUGCCAUGAAA.GUGGCACGUACGGUUCUGA..GGGGGGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.....<<<<.<<.

AJ130737.1/1761-1840    AGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
M68929.1/49817-49892    .GAAAGCUUGAGAGGGCCUACCUAUCCCGAC
AJ011856.1/37648-37722  ..AAAAUUUGUAAAGAUCUACCUAUCACAAU
X73671.1/1293-1367      ..AAAAUGAGUGAUCAUCUACCUAUUCUAAC
AF029891.1/4522-4594    ..AAAGUCUGAGAGGACCUACCUAUCCC..A
#=GC SS_cons            ....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln73.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln73.fa

AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA.A
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..CCGGGGGAA
AJ277126.1/2879-2953    UUCAGCCGUGUGCGGUGAAAGUCGCACGCACGGUUGUGA..GGGGGGGAA
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA..UGGGGGGAA
X17375.2/29364-29438    UUGAGCCGUGUGCGGUGAAAGUCGCAUGCACGGUUCUAC..UGGGGGGAA
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

AJ131147.1/1719-1794    AGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ011856.1/26154-26228  AACUUGUAAAGGUCUACCUAUCGGGAU
AJ277126.1/2879-2953    AAUCUGUGAAGAUCUACCUAUCCCGAU
AJ277126.1/6413-6487    AACGAGAGAUCGUCUACCUAUCCAACU
X17375.2/29364-29438    AGCCUGAGAGGGCCUACCUAUCCAACU
#=GC SS_cons            ................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln74.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln74.fa

AJ130746.1/1754-1835    UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGG
AJ131136.1/1732-1807    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGG
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAU.GAAAGUCGCACGUACGGUUCUUA......CCGG
AJ011856.1/37648-37722  UUGAGCUGUAUACUAU.GAAAGUAGUACGUACAGUUCUGA......GUGG
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<

AJ130746.1/1754-1835    GGGAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131136.1/1732-1807    GGA.AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ131145.1/1727-1802    GGG.AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ011856.1/26154-26228  GGGAAAACUUGUAAAGGUCUACCUAUCGGGAU
AJ011856.1/37648-37722  GGGAAAAUUUGUAAAGAUCUACCUAUCACAAU
#=GC SS_cons            .<<..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln75.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln75.fa

AJ131144.1/1753-1833  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGGG
AJ131147.1/1719-1794  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGGAA
AJ277126.1/6413-6487  GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA......UGGGGGG
X17375.2/29364-29438  UUGAGCCGUGUGCGGUGAAAGUCGCAUGCACGGUUCUAC......UGGGGGG
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUUGAAAGAUGCAUGCACGGUUCUUA......GGGGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<<<.<<

AJ131144.1/1753-1833  AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131147.1/1719-1794  .AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ277126.1/6413-6487  AAAACGAGAGAUCGUCUACCUAUCCAACU
X17375.2/29364-29438  AAAGCCUGAGAGGGCCUACCUAUCCAACU
AJ277126.1/8230-8302  ..AAAGCCGGUAACCGUACCUAUCCCAAU
#=GC SS_cons          ..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln76.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln76.fa

AJ131147.1/1719-1794  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA.AAG
AF029891.1/9161-9235  UUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..GAGGGGGAAAG
X17375.2/29364-29438  UUGAGCCGUGUGCGGUGAAAGUCGCAUGCACGGUUCUAC..UGGGGGGAAAG
X73671.1/1293-1367    UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA..AGAGGGGAAAA
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUUGAAAGAUGCAUGCACGGUUCUUA..GGGGGGG..AA
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<....

AJ131147.1/1719-1794  CUUGAAAGAGCCUAUCCAUCCCGAU
AF029891.1/9161-9235  UUCGAGAGGACCUACCUAUCUCAAC
X17375.2/29364-29438  CCUGAGAGGGCCUACCUAUCCAACU
X73671.1/1293-1367    UGAGUGAUCAUCUACCUAUUCUAAC
AJ277126.1/8230-8302  AGCCGGUAACCGUACCUAUCCCAAU
#=GC SS_cons          ..............>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln77.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln77.fa

AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA.A
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..CCGGGGGAA
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA..UGGGGGGAA
X17375.2/29364-29438    UUGAGCCGUGUGCGGUGAAAGUCGCAUGCACGGUUCUAC..UGGGGGGAA
AF029891.1/4522-4594    UUGAGCCGUAUGCCAUGAAAGUGGCACGUACGGUUCUGA..GGGGGGGAA
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

AJ131147.1/1719-1794    AGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ011856.1/26154-26228  AACUUGUAAAGGUCUACCUAUCGGGAU
AJ277126.1/6413-6487    AACGAGAGAUCGUCUACCUAUCCAACU
X17375.2/29364-29438    AGCCUGAGAGGGCCUACCUAUCCAACU
AF029891.1/4522-4594    AGUCUGAGAGGACCUACCUAUCCC..A
#=GC SS_cons            ................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln78.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln78.fa

AJ131144.1/1753-1833  UUGAGCCGUAUGCGAGGAAA.CUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AJ131145.1/1727-1802  UUGAGCCGUAUGCGAGGAAA.CUUGCACGUGCGGUUCUUUGA....GGGGGG
M68929.1/49817-49892  UUGAGCCGUAUGCGG.GAAAACUCGCACGUACGGUUCUUA......GGGGGG
U41288.1/3118-3192    UUGAGCCGUAUGCGAUGAAA.GUUGCACGUACGGUUCUUA......CCGGGG
X17375.2/29364-29438  UUGAGCCGUGUGCGGUGAAA.GUCGCAUGCACGGUUCUAC......UGGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<.<

AJ131144.1/1753-1833  G.AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131145.1/1727-1802  G..AAGCUUGAAAGAGCCUACCCAUCCCGAU
M68929.1/49817-49892  GGAAAGCUUGAGAGGGCCUACCUAUCCCGAC
U41288.1/3118-3192    G.AAAGCUUGAGAGAGCCUACCUAUCGGAAC
X17375.2/29364-29438  G.AAAGCCUGAGAGGGCCUACCUAUCCAACU
#=GC SS_cons          <...................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln79.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln79.fa

AJ131144.1/1753-1833  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGGG
AJ131145.1/1727-1802  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGGGG
AJ131147.1/1719-1794  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGGAA
U41288.1/3118-3192    UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA......CCGGGGG
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUUGAAAGAUGCAUGCACGGUUCUUA......GGGGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<<<.<<

AJ131144.1/1753-1833  AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131145.1/1727-1802  .AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ131147.1/1719-1794  .AAGCUUGAAAGAGCCUAUCCAUCCCGAU
U41288.1/3118-3192    AAAGCUUGAGAGAGCCUACCUAUCGGAAC
AJ277126.1/8230-8302  ..AAAGCCGGUAACCGUACCUAUCCCAAU
#=GC SS_cons          ..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln80.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln80.fa

AJ131145.1/1727-1802  UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGG.AAG
AJ277126.1/2879-2953  UUCAGCCGUGUGCGGUGAAAGUCGCACGCACGGUUGUGA..GGGGGGGAAAA
AJ277126.1/6413-6487  GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA..UGGGGGGAAAA
X73671.1/1293-1367    UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA..AGAGGGGAAAA
AJ277126.1/8230-8302  UUGAGCCGUGUGCGUUGAAAGAUGCAUGCACGGUUCUUA..GGGGGGG..AA
#=GC SS_cons          ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<....

AJ131145.1/1727-1802  CUUGAAAGAGCCUACCCAUCCCGAU
AJ277126.1/2879-2953  UCUGUGAAGAUCUACCUAUCCCGAU
AJ277126.1/6413-6487  CGAGAGAUCGUCUACCUAUCCAACU
X73671.1/1293-1367    UGAGUGAUCAUCUACCUAUUCUAAC
AJ277126.1/8230-8302  AGCCGGUAACCGUACCUAUCCCAAU
#=GC SS_cons          ..............>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln81.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln81.fa

AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAA.CUUGCACGUGCGGUUCUUUGAGGGGGAA.
M68929.1/49817-49892    UUGAGCCGUAUGCGG.GAAAACUCGCACGUACGGUUCUUA..GGGGGGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAA.GUCGCACGUACGGUUCUUA..CCGGGGG.
U41288.1/3118-3192      UUGAGCCGUAUGCGAUGAAA.GUUGCACGUACGGUUCUUA..CCGGGGG.
X73671.1/1293-1367      UUGAGCCGUAUGCGAUGAAA.GUUGCACGUACGGUUCUUA..AGAGGGG.
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.....<<<<.<<.

AJ131147.1/1719-1794    .AAGCUUGAAAGAGCCUAUCCAUCCCGAU
M68929.1/49817-49892    AAAGCUUGAGAGGGCCUACCUAUCCCGAC
AJ011856.1/26154-26228  AAAACUUGUAAAGGUCUACCUAUCGGGAU
U41288.1/3118-3192      AAAGCUUGAGAGAGCCUACCUAUCGGAAC
X73671.1/1293-1367      AAAAUGAGUGAUCAUCUACCUAUUCUAAC
#=GC SS_cons            ..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln82.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln82.fa

AJ130746.1/1754-1835  UUGAGCCGUAUGCGAAGGAAA.CUUGCACGUGCGGUUCUUUGCUUUGAGGGG
AJ131144.1/1753-1833  UUGAGCCGUAUGCGAG.GAAA.CUUGCACGUGCGGUUCUUUGCUUUGAGGGG
M68929.1/49817-49892  UUGAGCCGUAUGCGG..GAAAACUCGCACGUACGGUUCUUA......GGGGG
AF029891.1/9161-9235  UUGAGCCGUAUGCGAU.GAAA.GUCGCACGUACGGUUCUUA......GAGGG
AJ277126.1/2879-2953  UUCAGCCGUGUGCGGU.GAAA.GUCGCACGCACGGUUGUGA......GGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<......>>>>>...>>>>>>>>.........<<<<.

AJ130746.1/1754-1835  GG.AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131144.1/1753-1833  GG.AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
M68929.1/49817-49892  GGGAAAGCUUGAGAGGGCCUACCUAUCCCGAC
AF029891.1/9161-9235  GG.AAAGUUCGAGAGGACCUACCUAUCUCAAC
AJ277126.1/2879-2953  GG.AAAAUCUGUGAAGAUCUACCUAUCCCGAU
#=GC SS_cons          <<...................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln83.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln83.fa

AJ131144.1/1753-1833    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA......CCGGG
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUCUGA......UGGGG
U41288.1/3118-3192      UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA......CCGGG
X73671.1/1293-1367      UUGAGCCGUAUGCGAUGAAAGUUGCACGUACGGUUCUUA......AGAGG
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<<<.

AJ131144.1/1753-1833    GGAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ011856.1/26154-26228  GGAAAACUUGUAAAGGUCUACCUAUCGGGAU
AJ277126.1/6413-6487    GGAAAACGAGAGAUCGUCUACCUAUCCAACU
U41288.1/3118-3192      GGAAAGCUUGAGAGAGCCUACCUAUCGGAAC
X73671.1/1293-1367      GGAAAAUGAGUGAUCAUCUACCUAUUCUAAC
#=GC SS_cons            <<..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln84.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln84.fa

AJ131144.1/1753-1833    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGG
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGG
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGA....GGGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA......CCGGG
X17375.2/29364-29438    UUGAGCCGUGUGCGGUGAAAGUCGCAUGCACGGUUCUAC......UGGGG
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.........<<<<.

AJ131144.1/1753-1833    GGAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131145.1/1727-1802    GG.AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ131147.1/1719-1794    AA.AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ011856.1/26154-26228  GGAAAACUUGUAAAGGUCUACCUAUCGGGAU
X17375.2/29364-29438    GGAAAGCCUGAGAGGGCCUACCUAUCCAACU
#=GC SS_cons            <<..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln85.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln85.fa

AJ130746.1/1754-1835    UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGG
AJ131136.1/1732-1807    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGG
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGG
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAU.GAAAGUCGCACGUACGGUUCUUA......CCGG
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAU.GAAAGUCGCAAGCACGGUUCUGA......UGGG
#=GC SS_cons            ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<

AJ130746.1/1754-1835    GGGAAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131136.1/1732-1807    GGA.AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ131147.1/1719-1794    GAA.AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ011856.1/26154-26228  GGGAAAACUUGUAAAGGUCUACCUAUCGGGAU
AJ277126.1/6413-6487    GGGAAAACGAGAGAUCGUCUACCUAUCCAACU
#=GC SS_cons            .<<..................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln86.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln86.fa

AJ130737.1/1761-1840    UUGAGCCGUAUGCGGGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGGGA
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGGG..
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAGGAAACUUGCACGUGCGGUUCUUUGAGGGGGAA..
AF029891.1/9161-9235    UUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..GAGGGGG..
AJ011856.1/26154-26228  GUGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUCUUA..CCGGGGG..
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>.....<<<<.<<..

AJ130737.1/1761-1840    GCUUGCUCGAAAGAGCCUACCUAUCCCGAU
AJ131145.1/1727-1802    ..AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ131147.1/1719-1794    ..AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AF029891.1/9161-9235    .AAAGUUCGAGAGGACCUACCUAUCUCAAC
AJ011856.1/26154-26228  .AAAACUUGUAAAGGUCUACCUAUCGGGAU
#=GC SS_cons            ...................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln87.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln87.fa

AJ130746.1/1754-1835  UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AJ131144.1/1753-1833  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AJ130737.1/1761-1840  UUGAGCCGUAUGCGGG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131136.1/1732-1807  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131147.1/1719-1794  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGA
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<.<

AJ130746.1/1754-1835  G...AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131144.1/1753-1833  G...AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ130737.1/1761-1840  GGAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
AJ131136.1/1732-1807  A....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ131147.1/1719-1794  A....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
#=GC SS_cons          <.....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln88.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln88.fa

AJ130746.1/1754-1835  UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AJ130737.1/1761-1840  UUGAGCCGUAUGCGGG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131136.1/1732-1807  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131145.1/1727-1802  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131147.1/1719-1794  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGA
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<.<

AJ130746.1/1754-1835  G...AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ130737.1/1761-1840  GGAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
AJ131136.1/1732-1807  A....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ131145.1/1727-1802  G....AAGCUUGAAAGAGCCUACCCAUCCCGAU
AJ131147.1/1719-1794  A....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
#=GC SS_cons          <.....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln89.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln89.fa

AJ130746.1/1754-1835  UUGAGCCGUAUGCGAAGGAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AJ131144.1/1753-1833  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGCUUUGAGGGGG
AJ130737.1/1761-1840  UUGAGCCGUAUGCGGG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131136.1/1732-1807  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
AJ131145.1/1727-1802  UUGAGCCGUAUGCGAG.GAAACUUGCACGUGCGGUUCUUUGA....GGGGGG
#=GC SS_cons          ..<<<<<<<<.<<<<<.....>>>>>...>>>>>>>>.........<<<<.<

AJ130746.1/1754-1835  G...AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ131144.1/1753-1833  G...AAAGCUUGAAAGAGCCUAUCCAUCCUGAU
AJ130737.1/1761-1840  GGAGCUUGCUCGAAAGAGCCUACCUAUCCCGAU
AJ131136.1/1732-1807  A....AAGCUUGAAAGAGCCUAUCCAUCCCGAU
AJ131145.1/1727-1802  G....AAGCUUGAAAGAGCCUACCCAUCCCGAU
#=GC SS_cons          <.....................>>..>>>>...
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln90.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln90.fa

V00712.1/1227-1289      GAGAGCUUUUUGCGGGGAAACUUGCAAGUCAAGUUUGGGGGGAGGCGGGC
X62341.1/1274-1336      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGACGGGC
AP000397.1/37693-37753  GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGGCGGGC
X17395.1/1934-1994      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGGCGGGC
X63625.1/1815-1875      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGAGGGAGGCGGGC
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>..<<<<.<<.....

V00712.1/1227-1289      GUCGACCCAACCU
X62341.1/1274-1336      GUCGACCCAACCU
AP000397.1/37693-37753  GUCGACCCA..AC
X17395.1/1934-1994      GUCGACCCU..AC
X63625.1/1815-1875      GUCGACCCA..AC
#=GC SS_cons            .>>..>>>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln91.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln91.fa

V00712.1/1227-1289      GAGAGCUUUUUGCGGGGAAACUUGCAAGUCAAGUUUGGGGGGAGGCGGGC
X01088.1/1893-1955      GAGAGCUUUUUGCGGGGAAACUUGCAAGUAAAGUUUGGGGGGAGGCGGGC
X62341.1/1274-1336      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGACGGGC
AP000397.1/37693-37753  GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGGCGGGC
X17395.1/1934-1994      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGGCGGGC
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>..<<<<.<<.....

V00712.1/1227-1289      GUCGACCCAACCU
X01088.1/1893-1955      GUCGACCCAACCU
X62341.1/1274-1336      GUCGACCCAACCU
AP000397.1/37693-37753  GUCGACCCA..AC
X17395.1/1934-1994      GUCGACCCU..AC
#=GC SS_cons            .>>..>>>>....
//
# STOCKHOLM 1.0

#=GF AC  RF00029|BRAliBaseII/data-set1/g2intron/unaligned/aln92.fa
#=GF ID  Intron_gpII|BRAliBaseII/data-set1/g2intron/unaligned/aln92.fa

V00712.1/1227-1289      GAGAGCUUUUUGCGGGGAAACUUGCAAGUCAAGUUUGGGGGGAGGCGGGC
X01088.1/1893-1955      GAGAGCUUUUUGCGGGGAAACUUGCAAGUAAAGUUUGGGGGGAGGCGGGC
AP000397.1/37693-37753  GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGGCGGGC
X17395.1/1934-1994      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGGGGGAGGCGGGC
X63625.1/1815-1875      GAGAGCUUUUUGCGGGGAAACUUGCAAGUACAGUUUGGAGGGAGGCGGGC
#=GC SS_cons            ..<<<<<<<<.<<<<<....>>>>>...>>>>>>>>..<<<<.<<.....

V00712.1/1227-1289      GUCGACCCAACCU
X01088.1/1893-1955      GUCGACCCAACCU
AP000397.1/37693-37753  GUCGACCCA..AC
X17395.1/1934-1994      GUCGACCCU..AC
X63625.1/1815-1875      GUCGACCCA..AC
#=GC SS_cons            .>>..>>>>....
//
