t/data/rfam_tests.stk

   1 # STOCKHOLM 1.0
   2
   3 #=GF AC   RF00006
   4 #=GF ID   Vault
   5 #=GF DE   Vault RNA
   6 #=GF AU   Bateman A
   7 #=GF SE   Bateman A
   8 #=GF SS   Predicted; PFOLD; Bateman A
   9 #=GF GA   25.00
  10 #=GF TC   41.33
  11 #=GF NC   23.46
  12 #=GF TP   Gene;
  13 #=GF BM   cmbuild CM SEED
  14 #=GF BM   cmsearch --local -W 150 CM SEQDB
  15 #=GF DR   URL; http://vaults.arc.ucla.edu/sci/sci_home.htm;
  16 #=GF CC   This family of RNAs are found as part of the enigmatic vault
  17 #=GF CC   ribonucleoprotein complex. The complex consists of a major
  18 #=GF CC   vault protein (MVP), two minor vault proteins (VPARP and TEP1),
  19 #=GF CC   and several small untranslated RNA molecules. It has been
  20 #=GF CC   suggested that the vault complex is involved in drug
  21 #=GF CC   resistance.
  22 #=GF CC   We have identified a putative novel vault RNA on chromosome 5
  23 #=GF CC   EMBL:AC005219.
  24 #=GF SQ   11
  25
  26 Z11765.1/1-89                        GGUCAGCAACAGCUC.AGCGGUUACUUCUCGA.....CACGGAAUUGUAA
  27 AF210457.1/105-240                   GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACAGUGGUUCAGUUCAU.U
  28 AY007237.1/1-136                     GGCCAGCUUUAGCUG.AGCGGUUAC..UUUGACAGUGUUUCAGUUCAU.U
  29 Z11771.1/1-137                       GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACGUGCUCCAGUUUGAGCA
  30 AC116353.2/181870-181951             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGCGUGU.............C
  31 AF058927.1/1-92                      GGYCAGCUUYAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A
  32 AC005219.1/49915-50008               GGUCGGAGUUAGCUCAAGCGGUUAC..CUCCUCAUGCC...........G
  33 AF058926.1/1-82                      GGYCAGCWWYAGCUC.AGCGGUUAC..UUCGAGUAC.............A
  34 AC116353.2/174637-174718             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGAGUAC.............A
  35 AC116353.2/166987-167078             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A
  36 Z97054.1/58392-58486                 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAAUGCUUUCCAUGGUUA
  37 #=GC SS_cons                         .<<<<<.....<<<<..<<<<.......<<<<..................
  38
  39 Z11765.1/1-89                        UUCUG........................AAAACCUUUC...........
  40 AF210457.1/105-240                   ACCAGCUAUUCGUAGCAGGUUCGAACAACACAACCAACCACUUACCUAAC
  41 AY007237.1/1-136                     ACCAGCUAUUCGUAGCAGGUUCAAAUAACACAACCAACCACUUGCCUAAC
  42 Z11771.1/1-137                       GGCUAUGUAACGUGGUCGGUUCGAGCAACACAACCAGCCGCUUGCCUAUC
  43 AC116353.2/181870-181951             AUCAA........................ACCACCUCUC...........
  44 AF058927.1/1-92                      AACAA........................GCAACCUGUC...........
  45 AC005219.1/49915-50008               GACUU........................UCUAUCUGUCCAUCUCUGU..
  46 AF058926.1/1-82                      UUGUA........................ACCACCUCUC...........
  47 AC116353.2/174637-174718             UUGUA........................ACCACCUCUC...........
  48 AC116353.2/166987-167078             AACAA........................GCAACCUGUC...........
  49 Z97054.1/58392-58486                 GGAAA........................CCAACCUCUC...........
  50 #=GC SS_cons                         ................................<<<...............
  51
  52 Z11765.1/1-89                        ..........GGGGUUCGAAACCCGCGGGCGCCACCUGAC
  53 AF210457.1/105-240                   CCGUGAGUGUUUGGUUCGAGACCCGCGGGCGCUCCCUGGC
  54 AY007237.1/1-136                     CCAUGAGUGUUUGGUUCGAGACCGGCGGGCGCUCCCUGGC
  55 Z11771.1/1-137                       UGGUGAGUGGUUGGUUCGAGACCCGCGGGCGCUCUCUGGC
  56 AC116353.2/181870-181951             .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGC
  57 AF058927.1/1-92                      .......UGGGUGGUUCGARACCCGCGGCCGCUMYCUGGC
  58 AC005219.1/49915-50008               .......GCUGGGGUUCGAGACCCGCGGGUGCUUACUGAC
  59 AF058926.1/1-82                      .......UGGGUGGUUCGARACCCGCGGSCGCYMYCUGRC
  60 AC116353.2/174637-174718             .......UGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGC
  61 AC116353.2/166987-167078             .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGU
  62 Z97054.1/58392-58486                 .......UGGGUGGUUUGAGACCCGUGGGCCCUCUCCAGU
  63 #=GC SS_cons                         ............>>>>>>>...>>>>>>>>.....>>>>>
  64 //
  65 # STOCKHOLM 1.0
  66
  67 #=GF AC   RF00007
  68 #=GF ID   U12
  69 #=GF DE   U12 minor spliceosomal RNA
  70 #=GF AU   Griffiths-Jones SR, Mifsud W
  71 #=GF SE   Shukla GC and Padgett RA, PMID:10199569
  72 #=GF SS   Published; PMID:10199569
  73 #=GF GA   10.00
  74 #=GF TC   11.43
  75 #=GF NC   undefined
  76 #=GF TP   Gene; snRNA; splicing;
  77 #=GF BM   cmbuild CM SEED
  78 #=GF BM   cmsearch -W 160 CM SEQDB
  79 #=GF RN   [1]
  80 #=GF RM   10199569
  81 #=GF RT   Conservation of functional features of U6atac and U12 snRNAs between
  82 #=GF RT   vertebrates and higher plants.
  83 #=GF RA   Shukla GC, Padgett RA;
  84 #=GF RL   RNA 1999;5:525-538.
  85 #=GF RN   [2]
  86 #=GF RM   9149533
  87 #=GF RT   Pre-mRNA splicing: the discovery of a new spliceosome doubles the
  88 #=GF RT   challenge.
  89 #=GF RA   Tarn WY, Steitz JA;
  90 #=GF RL   Trends Biochem Sci 1997;22:132-137.
  91 #=GF RN   [3]
  92 #=GF RM   11864616
  93 #=GF RT   The divergent U12-type spliceosome is required for pre-mRNA splicing
  94 #=GF RT   and is essential for development in Drosophila.
  95 #=GF RA   Otake LR, Scamborova P, Hashimoto C, Steitz JA;
  96 #=GF RL   Mol Cell 2002;9:439-446.
  97 #=GF CC   The U12 small nuclear (snRNA), together with U4atac/U6atac, U5,
  98 #=GF CC   and U11 snRNAs and associated proteins, forms a spliceosome that
  99 #=GF CC   cleaves a divergent class of low-abundance pre-mRNA introns.
 100 #=GF CC   Although the U12 sequence is very divergent from that of U2
 101 #=GF CC   (Rfam:RF00004), the two are functionally analogous [2].
 102 #=GF SQ   7
 103
 104 L43844.1/2-149                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACAACU......CGGGGUGAC
 105 L43843.1/2-150                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
 106 L43846.1/332-460                    .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
 107 L43845.1/357-512                    AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU
 108 J04119.1/2-130                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
 109 Z93241.11/76641-76790               AUGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
 110 AL513366.11/57716-57871             AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU
 111 #=GC SS_cons                        ...<<<<<..........>>>>>........<<<<......<<<<.....
 112
 113 L43844.1/2-149                      GCCCGAGUCCUCACUACUGAUGUGAGAGGAAUUUUUGUGCGGGUACAGGU
 114 L43843.1/2-150                      GCCCGAGUCCUCACUGCUUAUGUGAGAAGAAUUUUUGAGCGGGUAUAGGU
 115 L43846.1/332-460                    GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
 116 L43845.1/357-512                    GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU
 117 J04119.1/2-130                      GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
 118 Z93241.11/76641-76790               GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
 119 AL513366.11/57716-57871             GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU
 120 #=GC SS_cons                        .>>>>>>>><<<<<.......>>>>>...........<<<<<<<...<<<
 121
 122 L43844.1/2-149                      CGUCCCC.GGGUGACCCGCUUACUUCGCGGGAUGCCCAGGUGCAAUGAUC
 123 L43843.1/2-150                      UGCAAUCUGAGCGACCCGCCUACUUUGCGGGAUGCCUGGGUGACGCGAUC
 124 L43846.1/332-460                    CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC..............
 125 L43845.1/357-512                    CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC
 126 J04119.1/2-130                      CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC..............
 127 Z93241.11/76641-76790               CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCCUGGGAGUUGCGAUC
 128 AL513366.11/57716-57871             CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC
 129 #=GC SS_cons                        <<<<.....>>>>>>>.>>>>>>>..<<<<<<<<<.........>>>>>>
 130
 131 L43844.1/2-149                      UGCCCG
 132 L43843.1/2-150                      UGCCCG
 133 L43846.1/332-460                    ......
 134 L43845.1/357-512                    UGCCUG
 135 J04119.1/2-130                      ......
 136 Z93241.11/76641-76790               UGCCCG
 137 AL513366.11/57716-57871             UGCCUG
 138 #=GC SS_cons                        >>>...
 139 //
 140 # STOCKHOLM 1.0
 141
 142 #=GF AC   RF00008
 143 #=GF ID   Hammerhead_3
 144 #=GF DE   Hammerhead ribozyme (type III)
 145 #=GF AU   Bateman A
 146 #=GF SE   Bateman A
 147 #=GF SS   Published; PMID:7969422
 148 #=GF GA   29.00
 149 #=GF TC   29.53
 150 #=GF NC   28.96
 151 #=GF TP   Gene; ribozyme;
 152 #=GF BM   cmbuild CM SEED
 153 #=GF BM   cmsearch -W 130 CM SEQDB
 154 #=GF RN   [1]
 155 #=GF RM   7969422
 156 #=GF RT   Three-dimensional structure of a hammerhead ribozyme.
 157 #=GF RA   Pley HW, Flaherty KM, McKay DB;
 158 #=GF RL   Nature 1994;372:68-74.
 159 #=GF RN   [2]
 160 #=GF RM   9506521
 161 #=GF RT   The structural basis of hammerhead ribozyme self-cleavage.
 162 #=GF RA   Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L,
 163 #=GF RA   Scott WG;
 164 #=GF RL   Cell 1998;92:665-673.
 165 #=GF RN   [3]
 166 #=GF RM   10899150
 167 #=GF RT   Distribution of hammerhead and hammerhead-like RNA motifs through the
 168 #=GF RT   GenBank.
 169 #=GF RA   Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R;
 170 #=GF RL   Genome Res 2000;10:1011-1019.
 171 #=GF CC   The hammerhead ribozyme is one of the smallest catalytic
 172 #=GF CC   RNAs. These RNAs have an endonuclease function, and most
 173 #=GF CC   often are autocatalytic. Structurally it is composed of
 174 #=GF CC   three base paired helices, separated by short linkers of
 175 #=GF CC   conserved sequence. These helices are called I, II and III.
 176 #=GF CC   We have classified hammerhead ribozymes into three types
 177 #=GF CC   based on which helix the 5' and 3' ends of the sequence
 178 #=GF CC   join. This family are the type III hammerheads.
 179 #=GF CC   The conserved uridine-turn links helix I
 180 #=GF CC   to helix II and usually has the sequence CUGA.  Helix II and
 181 #=GF CC   III are linked by a sequence CGAAA.  The cleavage reaction
 182 #=GF CC   occurs between helix III and I, and is usually a C.
 183 #=GF CC   Hammerhead ribozymes are found in plant viroids and other
 184 #=GF CC   small replicating sattelite RNA species.  Hammerhead
 185 #=GF CC   ribozymes have been found in animals as well as plants.
 186 #=GF CC   This family includes a couple of false matches currently
 187 #=GF CC   these are EMBL:AC078923 and EMBL:BC050488. These animal
 188 #=GF CC   sequences are not expected to be hammerhead ribozymes.
 189 #=GF SQ   84
 190
 191 AJ295015.1/58-1                ACAGAGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU.....
 192 AJ295018.1/58-1                ACAGGGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU.....
 193 AJ536620.1/206-152             CCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA.........
 194 AJ536615.1/1-44                .........GGGUGGUG.UGUACCAUCCCUGAUGAGUCCAA.........
 195 AJ536612.1/206-152             UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCGA.........
 196 AJ536617.1/1-40                .........GGGUGGUGUGUA.CCACCCCUGAUGAGUCCGA.........
 197 AJ536614.1/206-152             UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA.........
 198 AJ536620.1/1-40                .........GGGUGGUGUGUG.CCACCCCUGAUGAGUCCGA.........
 199 AJ536619.1/206-152             CCACCGUC.GGAAAGUG.UGUACUUUCCCUGAUGAGUCCGA.........
 200 AJ550911.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA.......
 201 AF170503.1/280-333             GAAAGGUC.UGUGCUU......AGCACACUGACGAGUUCCUGA.......
 202 AF170504.1/284-337             GAUAAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
 203 AJ550912.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA.......
 204 AJ247113.1/134-53              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
 205 AJ241833.1/282-334             AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 206 AJ241841.1/57-3                CAAAAGUU.UGGGCUAA.....AGCCCACUGAUGAGCCGCUGA.......
 207 AJ241839.1/282-334             GAUGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 208 AJ550901.1/282-334             GAAGAGUC..GCGCUA......AGCGCACUGAUGAGUCUUUGA.......
 209 AJ005298.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
 210 AJ241819.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
 211 AJ005320.1/281-333             GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 212 AJ005310.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
 213 AF339740.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCGUUGA.......
 214 AJ241828.1/56-3                CAUAAGUC.UGGGUUA......AGCCCACUGAUGAGCCGUUGA.......
 215 AJ550906.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUCGCUGC.......
 216 AJ550903.1/281-333             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
 217 AJ241831.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
 218 AJ241840.1/56-3                CAGAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
 219 AJ005303.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
 220 AJ005312.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
 221 AJ550906.1/282-334             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
 222 AJ550907.1/56-3                CAUAAGUC.UGGGCUU......AGCCUACUGAUGAGUCGCUGC.......
 223 AF170503.1/55-3                CAUAAGUC.UGGGCUU......AG.CCACUGACGAGUCGCUGG.......
 224 Y14700.1/133-53                .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC
 225 AJ005321.1/281-333             GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 226 AJ241845.1/282-335             GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
 227 AJ005322.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGACGAGCCGUUGA.......
 228 M83545.1/56-3                  CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGUCGCUGA.......
 229 AJ005305.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGACGAGCCGCUGG.......
 230 AJ550908.1/281-334             GAAGAGUC.UGCGCUU......AGCGCACUCAUGAGUCUCUGA.......
 231 AJ550909.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUUGCUGC.......
 232 AJ241843.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCACUGA.......
 233 AF170523.1/55-3                CAAAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA.......
 234 AF170509.1/56-3                CAUAAGUC.UAGGCUU......AGCCCACUGAUGAGCCGUUGA.......
 235 AJ241847.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUUUCUGA.......
 236 AJ241823.1/282-335             AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUAA.......
 237 AJ247122.1/132-52              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
 238 AJ005300.1/282-335             UAAGAGUC.UGUGGUA......AGCACACUGAUGAGUCUCUGA.......
 239 AJ005302.1/281-334             AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
 240 AJ005318.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
 241 AF339739.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGGCGUUGA.......
 242 AJ241838.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCUGCUGA.......
 243 AJ247121.1/133-53              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
 244 AJ550911.1/282-335             GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
 245 AJ550898.1/282-335             GAAGAGUC.UGCGCUA......AGCGCACUGAUGAGUCUUUGA.......
 246 AF170516.1/283-335             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
 247 AJ005319.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
 248 AJ550899.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC.......
 249 AF170519.1/55-3                CAUAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA.......
 250 AJ247116.1/133-53              .UCCAGUC.GAGACCUGAAGUGGGUUUACUGAUGAGGCUGUGGAGAGAGC
 251 AJ550907.1/281-333             AAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA.......
 252 AJ241850.1/282-334             UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 253 AF170499.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
 254 AF170520.1/282-335             GAUAAGUC.UGUGCUU......AGCACACUGAUGAGUCUCUGA.......
 255 AJ005299.1/282-335             UAAGAGUC.UGUGCUA......AGCACACUGAUGAAUCUCUGA.......
 256 AJ005312.1/282-335             GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUAUGA.......
 257 AJ550909.1/282-333             GAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA.......
 258 AJ005322.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
 259 AJ005294.1/282-334             UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 260 AJ247123.1/132-52              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC
 261 AJ550900.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC.......
 262 AJ241830.1/282-334             AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
 263 AJ241831.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
 264 M83545.1/282-335               GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
 265 AJ550910.1/282-336             GAAGAGUCCUGCGCUU......AGCGCACUGACGAGUCUCUGA.......
 266 AJ005314.1/281-334             AAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
 267 Y12833.1/339-285               CCGCUAUA.UGGGGAUGUGUG.UCCCUACUGACGAGUUCAA.........
 268 M63666.1/246-192               CCGGUGUC.UCAAGGUGCGUA.CCUUGACUGAUGAGUCCGA.........
 269 J02439.1/42-95                 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCGA.........
 270 J02386.1/42-95                 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCAA.........
 271 M33000.1/55-110                ACGCUGUC.UGUACUUGUAUC.AGUACACUGACGAGUCCCU.........
 272 M33001.1/56-111                ACGCUGUC.UGUACUUAUAUC.AGUACACUGACGAGUCCCU.........
 273 D00685.1/1-46                  .........GCCAGACGU.GGACCCGGCCUGAUGAGUCCGAAA.......
 274 M17439.1/1-48                  .........ACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGU.........
 275 #=GC SS_cons                   .<<<<<<..<<<<<.........>>>>>.......<<<<...........
 276
 277 AJ295015.1/58-1                ...............GCGUUGAACAGAAACUCUGC
 278 AJ295018.1/58-1                ...............GCGUUGAACAGAAACUCUGC
 279 AJ536620.1/206-152             ...................AAGGGCGAAACGGUAC
 280 AJ536615.1/1-44                ...................AAGGACGAAAUGG...
 281 AJ536612.1/206-152             ...................AAGGGCGAAACGGUAC
 282 AJ536617.1/1-40                ...................AAGGACGAA.......
 283 AJ536614.1/206-152             ...................AAGGGCGAAACGGUAC
 284 AJ536620.1/1-40                ...................AAGGACGAA.......
 285 AJ536619.1/206-152             ...................AAGGACGAAACGGUAC
 286 AJ550911.1/56-3                .................AACGCAACGAAACUUUUG
 287 AF170503.1/280-333             .................AAUGGAACGAAACCUUUU
 288 AF170504.1/284-337             .................AAUGAGACGAAACUUAUC
 289 AJ550912.1/56-3                .................GAUGCGACGAAACUUUUG
 290 AJ247113.1/134-53              AAAUUGCUUUACUCCCGCACAAGCCGAAACUGGA.
 291 AJ241833.1/282-334             .................AAUGAGACGAAACUCUUU
 292 AJ241841.1/57-3                .................AAUGCGGCGAAACUUUUG
 293 AJ241839.1/282-334             .................AAUGAGACGAAACUCAUA
 294 AJ550901.1/282-334             .................GAUAAGACGAAACUCUUC
 295 AJ005298.1/56-3                .................GAUACGGCGAAACUUUUG
 296 AJ241819.1/56-3                .................AAUACGGCGAAACUUUUG
 297 AJ005320.1/281-333             .................AAUGAGACGAAACUCUUU
 298 AJ005310.1/56-3                .................AAUGCGGCGAAACUUUUG
 299 AF339740.1/56-3                .................GAUACGGCGGAACUUAUG
 300 AJ241828.1/56-3                .................GAUACGGCGAAACUUAUG
 301 AJ550906.1/56-3                .................GAUGCGACGAAACUUAUG
 302 AJ550903.1/281-333             .................AAUGAGACGAAACUCUUU
 303 AJ241831.1/56-3                .................GAUACGGCGAAACUUCUG
 304 AJ241840.1/56-3                .................AAUGCGGCGAAACUUUUG
 305 AJ005303.1/56-3                .................GAUACGGCGAAACUUUUG
 306 AJ005312.1/56-3                .................AAUGCGGCUAAACUUUUG
 307 AJ550906.1/282-334             .................GAUGAGACGAAACUCUUC
 308 AJ550907.1/56-3                .................GAUGCGACGAAACUUAUG
 309 AF170503.1/55-3                .................GAUACGGCGAAACUUAUG
 310 Y14700.1/133-53                GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA.
 311 AJ005321.1/281-333             .................AAUGAGACGAAACUCUUG
 312 AJ241845.1/282-335             .................AAUGAGACGAAACUCAUG
 313 AJ005322.1/56-3                .................GAUACGGCGAAACUUAUG
 314 M83545.1/56-3                  .................AAUGCGACGAAACUUAUG
 315 AJ005305.1/56-3                .................GAUACGGCGAAACUUUUG
 316 AJ550908.1/281-334             .................GAUGAGACGAAACUCUUC
 317 AJ550909.1/56-3                .................GAUGCAACGAAACUUAUG
 318 AJ241843.1/56-3                .................AAUGCGGCGAAACUUUUG
 319 AF170523.1/55-3                .................GAUACGGCGAAACUUUUG
 320 AF170509.1/56-3                .................GAUACGGCGAAACUUAUG
 321 AJ241847.1/281-334             .................AAUGAGACGAAACUCUUG
 322 AJ241823.1/282-335             .................AAUGAGACGAAACUCUUU
 323 AJ247122.1/132-52              UAUUGCUUUACUCCCG.CACAAGCCGAAACUGGA.
 324 AJ005300.1/282-335             .................AAUGAGACGAAACUCUUG
 325 AJ005302.1/281-334             .................AUUGAGACGAAACUCUUG
 326 AJ005318.1/56-3                .................GAUACGGUGAAACUUAUG
 327 AF339739.1/56-3                .................GAUACGGCGAAACUUAUG
 328 AJ241838.1/56-3                .................AAUGCGGCAAAACUUUUG
 329 AJ247121.1/133-53              UUUCGCUUUACUCCCG.CACAAGCCGAAACUGGA.
 330 AJ550911.1/282-335             .................AAUGAGACGAAACUCUUC
 331 AJ550898.1/282-335             .................AAUAAGACGAAACUCUUC
 332 AF170516.1/283-335             .................AAUGAGACGAAACUCUUC
 333 AJ005319.1/56-3                .................GAUACGGCGAAACUUAUG
 334 AJ550899.1/56-3                .................GAUAAGGCGAAACUUAUG
 335 AF170519.1/55-3                .................GAUACGGCGAAACUUAUG
 336 AJ247116.1/133-53              GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA.
 337 AJ550907.1/281-333             .................GAUGAGACGAAACUCUUC
 338 AJ241850.1/282-334             .................AAAGAGACGAAACUCUUU
 339 AF170499.1/56-3                .................AAUGCGGCGAAACUUUUG
 340 AF170520.1/282-335             .................AAUGAGACGAAACUUAUC
 341 AJ005299.1/282-335             .................AAUGAGACGAAACUCUUG
 342 AJ005312.1/282-335             .................AAUGAGACGAAACUCAUA
 343 AJ550909.1/282-333             ..................AUGAGACGAAACUCUUC
 344 AJ005322.1/281-334             .................AAUGAGACGAAACUCUUU
 345 AJ005294.1/282-334             .................AAUGAGACGAAACUCUUG
 346 AJ247123.1/132-52              GAAAGCUUUACUCCCG.CACAAGCCGAAACUGGA.
 347 AJ550900.1/56-3                .................GACAAGGCGAAACUUAUG
 348 AJ241830.1/282-334             .................AAUGAGACGAAACUCUUG
 349 AJ241831.1/281-334             .................AAUGAGACGAAACUCUUA
 350 M83545.1/282-335               .................GAUGAGACGAAACUCUUC
 351 AJ550910.1/282-336             .................GAUGAGACGAAACUCUUC
 352 AJ005314.1/281-334             .................AAUGAGACGAAACUCUUU
 353 Y12833.1/339-285               ...................AAGAACGAAAUAGUUA
 354 M63666.1/246-192               ...................AAGGACGAAACACCAG
 355 J02439.1/42-95                 ...................AAGGACGAAACGGAUG
 356 J02386.1/42-95                 ...................AAGGACGAAACGGAUG
 357 M33000.1/55-110                ..................AAAGGACGAAACAGCGC
 358 M33001.1/56-111                ..................AAAGGACGAAACAGCGC
 359 D00685.1/1-46                  .....................GGACGAAACAGUA.
 360 M17439.1/1-48                  ...................GAGGACGAAACAGGAC
 361 #=GC SS_cons                   .....................>>>>...>>>>>>.
 362 //