examples/unfolded_RF00031.aln

   1 CLUSTAL
   2
   3 B.taurus.1/1-64       C-UUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGU
   4 D.melanogaster.3/1-68 G-UGGCGCU--UAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GC--------GGG
   5 D.melanogaster.2/1-63 C-AUUCAACU-UAUGAGGAUUAUUUCU-UAAA-GGCCUCU---GGC--U-------CGGA
   6 D.melanogaster.1/1-65 G-AGCC-CU---AUGAUCGAUGAUUGG-CAAA-UCCUCUC--GAGG--A-------ACCG
   7 R.norvegicus.7/1-66   C-CGGCACU--CAUGACGGUCUGCCUG-AAAA-CCAGCCC--GCUG-GU--------GGG
   8 R.norvegicus.6/1-67   G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCA-AAGAC--C-----UGUGGU
   9 R.norvegicus.5/1-62   G-UUUUUCC---AUGACGGUGUUUCCUCUAAA--UUUAC----AUG-----------GAG
  10 R.norvegicus.4/1-61   G-UCAGAUG---AUGACGGCCUGUGCA-GAAA-CCCCCAC-GUGGG--C--------UGC
  11 R.norvegicus.3/1-67   U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAGGGU--------UUG
  12 R.norvegicus.2/1-64   G-UUACAUU--GAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGU
  13 R.norvegicus.1/1-61   A-UAUUUGUU-UAUGAUGGUCACAGUG-UAAA--GUUCA----CAC-----------AGC
  14 O.aries.1/1-68        G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCU-UGGAC-GC------CUGGU
  15 M.musculus.9/1-66     C-CGGCACU--CAUGAAGGUCUGCUUG-AAAA-CCAGCCU--GCUG-GU--------GGG
  16 M.musculus.8/1-67     U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAG-GA-------CUUG
  17 O.niloticus.3/1-65    G-UGUCUCU---GUGAAGUUCGGUUUU-UAAA-AGGGUCA---UCC--A-------GAAA
  18 M.musculus.7/1-64     G-UGUCUCU---AUGAAGGAGGGGCCC-GAAG-CCCUUGU---GGG--C--------GGG
  19 O.niloticus.2/1-61    U-GUUUAUU--AAUGACGGCUACAGAU-UAAA--CCUUU----AGC-----------CUC
  20 M.musculus.6/1-61     G-UCAGAUG---AUGAUGGCCUGGGCA-GAAA-CCCCAUG--UGGG--C--------CGC
  21 O.niloticus.1/1-59    G-UUUCUCA---GUGAAGGCUACAGAU-UAAA--CCUCU----GGC-----------CUC
  22 M.musculus.5/1-66     G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUA---GAC--C-----UGUGGU
  23 M.musculus.4/1-65     G-UGUGCGA---AUGAUAACUACUGAC-GAAA-GAGCUGU-CUGCU--C-------AGUC
  24 M.musculus.3/1-64     G-GUUCUUC--CAUGAUGGUGUUUCCUCUAAA--UUUGC----ACG-----------GAG
  25 M.musculus.2/1-64     G-UUACAUU--AAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGU
  26 M.musculus.1/1-64     G-UCACCGA---AUGAUCUGCUCUGGU-CAAA-UCCUUCU---AUG--C------CAGCC
  27 C.elegans.1/1-64      G-AGGCAGCUUUGUGACGACCUUUGGC-UAAA-CUCCAUC--GUGA-GC--------GCC
  28 H.sapiens.15/1-63     U-UUUCAUC--UAUGAGGGUGUUUCCUCUAAA--CCUACG---AGG-----------GAG
  29 H.sapiens.14/1-62     C-ACUGCUG---AUGACGAACUAUCUC-UAAC-UGGUCUU--GACC--A-------CGAG
  30 H.sapiens.13/1-64     G-UCACUGC---AUGAUCCGCUCUGGU-CAAA-CCCUUCC---AGG--C------CAGCC
  31 H.sapiens.12/1-67     C-UCUGUUA---AUGACGUCUCUCCCUCUAAA-CCCCAUU-AAGGA--C--------UGG
  32 D.rerio.1/1-66        A-UGUGGUCUUUAUGAAGGCAGGUGCA-GAAA-CUAUGCA---CUA-GU--------GGU
  33 H.sapiens.11/1-63     G-CCGGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CAC
  34 H.sapiens.10/1-62     C-CGGCACU--CAUGACGGCCUGCCUG-CAAA--CCUGC----UGG--U--------GGG
  35 S.mansoni.1/1-67      C-UCGCUAU---AUGACGAUGGCAAUC-UCAA--AUGUU----CAU--U--------GGU
  36 S.scrofa.4/1-64       C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCC----CUG-GU--------GGG
  37 S.scrofa.3/1-63       A-UUUUAUC--CAUGAAAGUGUUUCCUCUAAA--CCUAU----GUG-----------GAG
  38 S.scrofa.2/1-65       C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCCC---CUG-GU--------GGG
  39 S.scrofa.1/1-68       G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUG-UGGAC-GC------CUGGU
  40 H.sapiens.9/1-58      U-AUUUGUU--UAUGAUGGCCACAGCC-UAAA--GUACA----CAC-----------GGC
  41 H.sapiens.8/1-67      U-UUGCUUU--AAUGAGAAUAGAAACG-UAAA--CUAUGA-CCUAG-G---------GGU
  42 X.laevis.1/1-67       G-UGUUUGCA-AAUGACGACCGAUUUU-GAAA-UGGUCUCACGGCC--A-------AAAA
  43 H.sapiens.7/1-70      U-GGCGUCUU-CAUGAGGGAGGGGCCC--AAA-GCCCUUG--UGGG--C--------GGA
  44 H.sapiens.6/1-66      G-UGUGCGG---AUGAUAACUACUGAC-GAAAGAGUCAUC---GAC--C-----UCAGUU
  45 H.sapiens.5/1-57      U-UCACAGA---AUGAUGGCACCUUCC-UAA---ACCCU----CAU-----------GGG
  46 H.sapiens.4/1-71      G-ACUGACAU-UAUGAAGGCCUGUACU-GAAG-ACAGCAA--GCUG--U-------UAGU
  47 H.sapiens.3/1-68      G-ACGCUUC---AUGAUAGGAAGGACU-GAAA-AGUCUUG-UGGAC--A-----CCUGGU
  48 H.sapiens.2/1-65      G-UGUGCGG---AUGAUAACUACUGAC-GAAA-GAGUCAU-CGACU--C-------AGUU
  49 H.sapiens.1/1-63      G-CCAGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CAC
  50 M.musculus.14/1-67    C-UCUGAUA---AUGAUGUCUCUCCCU-CUAA-CUCCCAGUAAGGA--C--------UGG
  51 M.musculus.13/1-60    C-AUGCGUC--CAUGAAGUCACUGGCC-UCAA-GCCCAA----GUG-GU--------GGG
  52 M.musculus.12/1-65    C-UCAGCAG--GAUGAUGAGAAGGGCU-GAAA-UGCUGCC--AAAC--C-------AGGU
  53 M.musculus.11/1-63    U-AUUUGUG--UAUGAUGGUCACAGUG-UAAA--GUUCC----CAC-----------AGC
  54 M.musculus.10/1-66    C-CGGCACU--CAUGAAGGUCUGCCUG-AAAA-CCAGCCU--GCUG-GU--------GGG
  55 B.taurus.7/1-61       U-UUUGCCC---AUGAAGGUGUUCCCUCUAAA--CCUAC----GUG-----------GAG
  56 B.taurus.6/1-67       G-AUGCGUC--CAUGAAGUCACCAGCC-CCAA-GCCCCUC---GUG-GU--------GGG
  57 B.taurus.5/1-61       G-CCAGAUG---AUGAGGACCUGUGCG-GAAA-CCCCCCG--CGGG--C--------UGC
  58 B.taurus.4/1-64       ACUUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGU
  59 G.gallus.3/1-73       U-AUUUCUU--UGUGAUGACCGAUUUU-GAAA-UGGGUUU---CUC--UAAUGCCAGGAA
  60 B.taurus.3/1-66       C-CCGGUGCC-UAUGACGGUCUGUCUG-AAAA-CCAGCCC---CUG-GU--------GGG
  61 G.gallus.2/1-60       U-AUUUGUC---AUGACAGUCACAGCA-UAAA--GCGCA----GAC-----------GGC
  62 B.taurus.2/1-64       C-UUGCGUU--AAUGAGAACAGAAACG-AAAA--CUAUAA-CCUAG-G---------GGU
  63 G.gallus.1/1-63       G-UGUGUUU---AUGAAGAGCACUAAC-AAAA-GAGUAAU-UGACU--C-------AGUU
  64
  65 B.taurus.1/1-64       UUC-U-G-UUGGAU--GGUUG-------GCAAC
  66 D.melanogaster.3/1-68 CAA-U-U-GCUGAU---UACG---AUUAACCAC
  67 D.melanogaster.2/1-63 AAU-A-G-UCUGAA---CCU--------UAUUG
  68 D.melanogaster.1/1-65 AUC-G-U-UGAGAA--CCCCU-----UUGCCUU
  69 R.norvegicus.7/1-66   GCA-G-U-CCCGAG-GACCUG-------GCGUG
  70 R.norvegicus.6/1-67   CUU-U-C-UUCGAU--GUUCU-------GCGGC
  71 R.norvegicus.5/1-62   AAA-C-A-CCUGAU-UUCCAG------AAAAAU
  72 R.norvegicus.4/1-61   -CA-G-G-UUUGAA---CCC--------CUGGC
  73 R.norvegicus.3/1-67   UGUCG-A-UCUGCU--AAUUG-------GCAAA
  74 R.norvegicus.2/1-64   UUC-U-G-UUGGAU--AGCUC-------GUAAU
  75 R.norvegicus.1/1-61   UGU-G-A-CUUGAU--UUUUA-------AAAAU
  76 O.aries.1/1-68        CCU-U-C-CUUGAU--GUUCU------CACGGC
  77 M.musculus.9/1-66     GCA-G-U-CCUGAG-GACCUG-------GCGUG
  78 M.musculus.8/1-67     UGU-AGA-UCUGAU--AAUUG-------GCAAA
  79 O.niloticus.3/1-65    ACC-G-ACACUGAU--GUUUC------CGACAC
  80 M.musculus.7/1-64     CCU-C-C-CCUGAG---CCCG----UCUGUGGU
  81 O.niloticus.2/1-61    UGG-A-G-CCAGAU--GCAUU------CAAACA
  82 M.musculus.6/1-61     CCA-G-G-UUUGAA---CCC--------CUGGC
  83 O.niloticus.1/1-59    UGG-A-G-CCAGAU--GCAUU-------GAAAC
  84 M.musculus.5/1-66     CUU-U-C-CUCGAU--GUUCC------UGCGGC
  85 M.musculus.4/1-65     UGU-G-G-UUGGAU---GUAG------UCACAC
  86 M.musculus.3/1-64     AAA-C-A-CCUGAU-UUCCAG-----GAAAAUC
  87 M.musculus.2/1-64     UUC-U-G-UUGGAU--AGCUU-------GUAAU
  88 M.musculus.1/1-64     AGG-G-U-GGUGAU--GACCC-------GUGAC
  89 C.elegans.1/1-64      UCU-G-G-UCUGAU---GC---------GCCUC
  90 H.sapiens.15/1-63     GAA-C-A-CCUGAU---CUUA-----CAGAAAA
  91 H.sapiens.14/1-62     CUA-G-U-UCUGAA---UU-G-------CAGGG
  92 H.sapiens.13/1-64     AGA-G-U-GGGGAU--GGUCU-------GUGAC
  93 H.sapiens.12/1-67     GAG-A-G-GCAGAGCAAGCCU-------CAGAG
  94 D.rerio.1/1-66        GUC-U-G-UCUGAU--GUUUG-------GCCAU
  95 H.sapiens.11/1-63     CCA-U-G-UCCGAG---CCCC-------CUGGC
  96 H.sapiens.10/1-62     GCA-G-A-CCCGAA-AAUCCA-------GCGUG
  97 S.mansoni.1/1-67      UGC-C-A-UUUGAU--GAAAUCAGUUUUGUGUG
  98 S.scrofa.4/1-64       GCA-G-A-CUCGAG-AACCUG-------GCGUG
  99 S.scrofa.3/1-63       GAA-C-A-CCUGAU-GUCCAG------GAAAAU
 100 S.scrofa.2/1-65       GCA-G-A-CUCGAG-AACCUG-------GCGUG
 101 S.scrofa.1/1-68       CCU-U-C-CCUGAU--GUUCU------CAUGGC
 102 H.sapiens.9/1-58      UGU-G-A-CUUGAU---UCA--------AAAGA
 103 H.sapiens.8/1-67      UUC-U-G-UUGGAU-AAUUAG-----CAGUUUA
 104 X.laevis.1/1-67       CUC-GUG-UCCGAC---AUC--------AACCC
 105 H.sapiens.7/1-70      CCU-C-C-CCUGAG---CCUGUCUGAGGGGCCA
 106 H.sapiens.6/1-66      AGU-G-G-UUGGAU---GUAG------UCACAU
 107 H.sapiens.5/1-57      UGG-U-G-UCUGAG--AGGC--------GUGAA
 108 H.sapiens.4/1-71      ACA-G-A-CCAGAU--GCUUU--CUUGGCAGGC
 109 H.sapiens.3/1-68      CUU-U-C-CCUGAU--GUUCU------CGUGGC
 110 H.sapiens.2/1-65      AGU-G-G-UUGGAU---GUAG------UCACAU
 111 H.sapiens.1/1-63      CCA-U-G-UCCGAG---CCCC-------CUGGC
 112 M.musculus.14/1-67    GAG-A-G-GCUGAACAAACCU-------CAGAG
 113 M.musculus.13/1-60    CAG-U-G-ACAGAA---GA---------GCUGC
 114 M.musculus.12/1-65    CCU-U-U-UCUGAU--GGUGG-------CUGGG
 115 M.musculus.11/1-63    UGU-G-A-CUUGAU--UUUUA----AAAAUGUC
 116 M.musculus.10/1-66    GCA-G-U-CCUGAG-GACCUG-------GCGUG
 117 B.taurus.7/1-61       GAA-U-G-CCUGAU-GUCCAG-------GAAAA
 118 B.taurus.6/1-67       UGG-U-G-AUGGAA-CCGUCA-----AAGCAGU
 119 B.taurus.5/1-61       CCA-U-G-UCUGAG---CCC--------CUGGC
 120 B.taurus.4/1-64       UUC-U-G-UUGGAU--GGUUG-------GCAA-
 121 G.gallus.3/1-73       AUC-GUG-UCUGAU---GUUG-----UCAAGUA
 122 B.taurus.3/1-66       GCA-G-A-CCUGAG-AACCUG-------GCGUG
 123 G.gallus.2/1-60       UGU-G-A-CCUGAU--UUUAG------AAAAUA
 124 B.taurus.2/1-64       UUC-U-G-UUGGAU--GGUUG-------GCAAC
 125 G.gallus.1/1-63       GGU-G-U-UCAGAU--GCU---------CUCAC
 126