# STOCKHOLM 1.0

#=GF AC   RF00006
#=GF ID   Vault
#=GF DE   Vault RNA
#=GF AU   Bateman A
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD; Bateman A
#=GF GA   25.00
#=GF TC   41.33
#=GF NC   23.46
#=GF TP   Gene;
#=GF BM   cmbuild CM SEED
#=GF BM   cmsearch --local -W 150 CM SEQDB
#=GF DR   URL; http://vaults.arc.ucla.edu/sci/sci_home.htm;
#=GF CC   This family of RNAs are found as part of the enigmatic vault
#=GF CC   ribonucleoprotein complex. The complex consists of a major
#=GF CC   vault protein (MVP), two minor vault proteins (VPARP and TEP1),
#=GF CC   and several small untranslated RNA molecules. It has been
#=GF CC   suggested that the vault complex is involved in drug
#=GF CC   resistance.
#=GF CC   We have identified a putative novel vault RNA on chromosome 5
#=GF CC   EMBL:AC005219.
#=GF SQ   11

Z11765.1/1-89                        GGUCAGCAACAGCUC.AGCGGUUACUUCUCGA.....CACGGAAUUGUAA
AF210457.1/105-240                   GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACAGUGGUUCAGUUCAU.U
AY007237.1/1-136                     GGCCAGCUUUAGCUG.AGCGGUUAC..UUUGACAGUGUUUCAGUUCAU.U
Z11771.1/1-137                       GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACGUGCUCCAGUUUGAGCA
AC116353.2/181870-181951             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGCGUGU.............C
AF058927.1/1-92                      GGYCAGCUUYAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A
AC005219.1/49915-50008               GGUCGGAGUUAGCUCAAGCGGUUAC..CUCCUCAUGCC...........G
AF058926.1/1-82                      GGYCAGCWWYAGCUC.AGCGGUUAC..UUCGAGUAC.............A
AC116353.2/174637-174718             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGAGUAC.............A
AC116353.2/166987-167078             GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A
Z97054.1/58392-58486                 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAAUGCUUUCCAUGGUUA
#=GC SS_cons                         .<<<<<.....<<<<..<<<<.......<<<<..................

Z11765.1/1-89                        UUCUG........................AAAACCUUUC...........
AF210457.1/105-240                   ACCAGCUAUUCGUAGCAGGUUCGAACAACACAACCAACCACUUACCUAAC
AY007237.1/1-136                     ACCAGCUAUUCGUAGCAGGUUCAAAUAACACAACCAACCACUUGCCUAAC
Z11771.1/1-137                       GGCUAUGUAACGUGGUCGGUUCGAGCAACACAACCAGCCGCUUGCCUAUC
AC116353.2/181870-181951             AUCAA........................ACCACCUCUC...........
AF058927.1/1-92                      AACAA........................GCAACCUGUC...........
AC005219.1/49915-50008               GACUU........................UCUAUCUGUCCAUCUCUGU..
AF058926.1/1-82                      UUGUA........................ACCACCUCUC...........
AC116353.2/174637-174718             UUGUA........................ACCACCUCUC...........
AC116353.2/166987-167078             AACAA........................GCAACCUGUC...........
Z97054.1/58392-58486                 GGAAA........................CCAACCUCUC...........
#=GC SS_cons                         ................................<<<...............

Z11765.1/1-89                        ..........GGGGUUCGAAACCCGCGGGCGCCACCUGAC
AF210457.1/105-240                   CCGUGAGUGUUUGGUUCGAGACCCGCGGGCGCUCCCUGGC
AY007237.1/1-136                     CCAUGAGUGUUUGGUUCGAGACCGGCGGGCGCUCCCUGGC
Z11771.1/1-137                       UGGUGAGUGGUUGGUUCGAGACCCGCGGGCGCUCUCUGGC
AC116353.2/181870-181951             .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGC
AF058927.1/1-92                      .......UGGGUGGUUCGARACCCGCGGCCGCUMYCUGGC
AC005219.1/49915-50008               .......GCUGGGGUUCGAGACCCGCGGGUGCUUACUGAC
AF058926.1/1-82                      .......UGGGUGGUUCGARACCCGCGGSCGCYMYCUGRC
AC116353.2/174637-174718             .......UGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGC
AC116353.2/166987-167078             .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGU
Z97054.1/58392-58486                 .......UGGGUGGUUUGAGACCCGUGGGCCCUCUCCAGU
#=GC SS_cons                         ............>>>>>>>...>>>>>>>>.....>>>>>
//
# STOCKHOLM 1.0

#=GF AC   RF00007
#=GF ID   U12
#=GF DE   U12 minor spliceosomal RNA
#=GF AU   Griffiths-Jones SR, Mifsud W
#=GF SE   Shukla GC and Padgett RA, PMID:10199569
#=GF SS   Published; PMID:10199569
#=GF GA   10.00
#=GF TC   11.43
#=GF NC   undefined
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild CM SEED
#=GF BM   cmsearch -W 160 CM SEQDB
#=GF RN   [1]
#=GF RM   10199569
#=GF RT   Conservation of functional features of U6atac and U12 snRNAs between
#=GF RT   vertebrates and higher plants.
#=GF RA   Shukla GC, Padgett RA;
#=GF RL   RNA 1999;5:525-538.
#=GF RN   [2]
#=GF RM   9149533
#=GF RT   Pre-mRNA splicing: the discovery of a new spliceosome doubles the
#=GF RT   challenge.
#=GF RA   Tarn WY, Steitz JA;
#=GF RL   Trends Biochem Sci 1997;22:132-137.
#=GF RN   [3]
#=GF RM   11864616
#=GF RT   The divergent U12-type spliceosome is required for pre-mRNA splicing
#=GF RT   and is essential for development in Drosophila.
#=GF RA   Otake LR, Scamborova P, Hashimoto C, Steitz JA;
#=GF RL   Mol Cell 2002;9:439-446.
#=GF CC   The U12 small nuclear (snRNA), together with U4atac/U6atac, U5,
#=GF CC   and U11 snRNAs and associated proteins, forms a spliceosome that
#=GF CC   cleaves a divergent class of low-abundance pre-mRNA introns. 
#=GF CC   Although the U12 sequence is very divergent from that of U2
#=GF CC   (Rfam:RF00004), the two are functionally analogous [2].
#=GF SQ   7

L43844.1/2-149                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACAACU......CGGGGUGAC
L43843.1/2-150                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
L43846.1/332-460                    .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
L43845.1/357-512                    AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU
J04119.1/2-130                      .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
Z93241.11/76641-76790               AUGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC
AL513366.11/57716-57871             AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU
#=GC SS_cons                        ...<<<<<..........>>>>>........<<<<......<<<<.....

L43844.1/2-149                      GCCCGAGUCCUCACUACUGAUGUGAGAGGAAUUUUUGUGCGGGUACAGGU
L43843.1/2-150                      GCCCGAGUCCUCACUGCUUAUGUGAGAAGAAUUUUUGAGCGGGUAUAGGU
L43846.1/332-460                    GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
L43845.1/357-512                    GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU
J04119.1/2-130                      GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
Z93241.11/76641-76790               GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU
AL513366.11/57716-57871             GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU
#=GC SS_cons                        .>>>>>>>><<<<<.......>>>>>...........<<<<<<<...<<<

L43844.1/2-149                      CGUCCCC.GGGUGACCCGCUUACUUCGCGGGAUGCCCAGGUGCAAUGAUC
L43843.1/2-150                      UGCAAUCUGAGCGACCCGCCUACUUUGCGGGAUGCCUGGGUGACGCGAUC
L43846.1/332-460                    CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC..............
L43845.1/357-512                    CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC
J04119.1/2-130                      CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC..............
Z93241.11/76641-76790               CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCCUGGGAGUUGCGAUC
AL513366.11/57716-57871             CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC
#=GC SS_cons                        <<<<.....>>>>>>>.>>>>>>>..<<<<<<<<<.........>>>>>>

L43844.1/2-149                      UGCCCG
L43843.1/2-150                      UGCCCG
L43846.1/332-460                    ......
L43845.1/357-512                    UGCCUG
J04119.1/2-130                      ......
Z93241.11/76641-76790               UGCCCG
AL513366.11/57716-57871             UGCCUG
#=GC SS_cons                        >>>...
//
# STOCKHOLM 1.0

#=GF AC   RF00008
#=GF ID   Hammerhead_3
#=GF DE   Hammerhead ribozyme (type III)
#=GF AU   Bateman A
#=GF SE   Bateman A
#=GF SS   Published; PMID:7969422
#=GF GA   29.00
#=GF TC   29.53
#=GF NC   28.96
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild CM SEED
#=GF BM   cmsearch -W 130 CM SEQDB
#=GF RN   [1]
#=GF RM   7969422
#=GF RT   Three-dimensional structure of a hammerhead ribozyme.
#=GF RA   Pley HW, Flaherty KM, McKay DB;
#=GF RL   Nature 1994;372:68-74.
#=GF RN   [2]
#=GF RM   9506521
#=GF RT   The structural basis of hammerhead ribozyme self-cleavage.
#=GF RA   Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L,
#=GF RA   Scott WG;
#=GF RL   Cell 1998;92:665-673.
#=GF RN   [3]
#=GF RM   10899150
#=GF RT   Distribution of hammerhead and hammerhead-like RNA motifs through the
#=GF RT   GenBank.
#=GF RA   Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R;
#=GF RL   Genome Res 2000;10:1011-1019.
#=GF CC   The hammerhead ribozyme is one of the smallest catalytic
#=GF CC   RNAs. These RNAs have an endonuclease function, and most
#=GF CC   often are autocatalytic. Structurally it is composed of
#=GF CC   three base paired helices, separated by short linkers of
#=GF CC   conserved sequence. These helices are called I, II and III.
#=GF CC   We have classified hammerhead ribozymes into three types
#=GF CC   based on which helix the 5' and 3' ends of the sequence
#=GF CC   join. This family are the type III hammerheads.
#=GF CC   The conserved uridine-turn links helix I 
#=GF CC   to helix II and usually has the sequence CUGA.  Helix II and
#=GF CC   III are linked by a sequence CGAAA.  The cleavage reaction 
#=GF CC   occurs between helix III and I, and is usually a C.
#=GF CC   Hammerhead ribozymes are found in plant viroids and other
#=GF CC   small replicating sattelite RNA species.  Hammerhead
#=GF CC   ribozymes have been found in animals as well as plants.
#=GF CC   This family includes a couple of false matches currently
#=GF CC   these are EMBL:AC078923 and EMBL:BC050488. These animal
#=GF CC   sequences are not expected to be hammerhead ribozymes.
#=GF SQ   84

AJ295015.1/58-1                ACAGAGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU.....
AJ295018.1/58-1                ACAGGGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU.....
AJ536620.1/206-152             CCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA.........
AJ536615.1/1-44                .........GGGUGGUG.UGUACCAUCCCUGAUGAGUCCAA.........
AJ536612.1/206-152             UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCGA.........
AJ536617.1/1-40                .........GGGUGGUGUGUA.CCACCCCUGAUGAGUCCGA.........
AJ536614.1/206-152             UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA.........
AJ536620.1/1-40                .........GGGUGGUGUGUG.CCACCCCUGAUGAGUCCGA.........
AJ536619.1/206-152             CCACCGUC.GGAAAGUG.UGUACUUUCCCUGAUGAGUCCGA.........
AJ550911.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA.......
AF170503.1/280-333             GAAAGGUC.UGUGCUU......AGCACACUGACGAGUUCCUGA.......
AF170504.1/284-337             GAUAAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ550912.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA.......
AJ247113.1/134-53              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
AJ241833.1/282-334             AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ241841.1/57-3                CAAAAGUU.UGGGCUAA.....AGCCCACUGAUGAGCCGCUGA.......
AJ241839.1/282-334             GAUGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ550901.1/282-334             GAAGAGUC..GCGCUA......AGCGCACUGAUGAGUCUUUGA.......
AJ005298.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ241819.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ005320.1/281-333             GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ005310.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AF339740.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCGUUGA.......
AJ241828.1/56-3                CAUAAGUC.UGGGUUA......AGCCCACUGAUGAGCCGUUGA.......
AJ550906.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUCGCUGC.......
AJ550903.1/281-333             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ241831.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ241840.1/56-3                CAGAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AJ005303.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ005312.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AJ550906.1/282-334             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ550907.1/56-3                CAUAAGUC.UGGGCUU......AGCCUACUGAUGAGUCGCUGC.......
AF170503.1/55-3                CAUAAGUC.UGGGCUU......AG.CCACUGACGAGUCGCUGG.......
Y14700.1/133-53                .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC
AJ005321.1/281-333             GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ241845.1/282-335             GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ005322.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGACGAGCCGUUGA.......
M83545.1/56-3                  CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGUCGCUGA.......
AJ005305.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGACGAGCCGCUGG.......
AJ550908.1/281-334             GAAGAGUC.UGCGCUU......AGCGCACUCAUGAGUCUCUGA.......
AJ550909.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUUGCUGC.......
AJ241843.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCACUGA.......
AF170523.1/55-3                CAAAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA.......
AF170509.1/56-3                CAUAAGUC.UAGGCUU......AGCCCACUGAUGAGCCGUUGA.......
AJ241847.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUUUCUGA.......
AJ241823.1/282-335             AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUAA.......
AJ247122.1/132-52              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
AJ005300.1/282-335             UAAGAGUC.UGUGGUA......AGCACACUGAUGAGUCUCUGA.......
AJ005302.1/281-334             AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ005318.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AF339739.1/56-3                CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGGCGUUGA.......
AJ241838.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCUGCUGA.......
AJ247121.1/133-53              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC
AJ550911.1/282-335             GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
AJ550898.1/282-335             GAAGAGUC.UGCGCUA......AGCGCACUGAUGAGUCUUUGA.......
AF170516.1/283-335             GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ005319.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA.......
AJ550899.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC.......
AF170519.1/55-3                CAUAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA.......
AJ247116.1/133-53              .UCCAGUC.GAGACCUGAAGUGGGUUUACUGAUGAGGCUGUGGAGAGAGC
AJ550907.1/281-333             AAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA.......
AJ241850.1/282-334             UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AF170499.1/56-3                CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA.......
AF170520.1/282-335             GAUAAGUC.UGUGCUU......AGCACACUGAUGAGUCUCUGA.......
AJ005299.1/282-335             UAAGAGUC.UGUGCUA......AGCACACUGAUGAAUCUCUGA.......
AJ005312.1/282-335             GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUAUGA.......
AJ550909.1/282-333             GAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA.......
AJ005322.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
AJ005294.1/282-334             UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ247123.1/132-52              .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC
AJ550900.1/56-3                CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC.......
AJ241830.1/282-334             AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA.......
AJ241831.1/281-334             GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA.......
M83545.1/282-335               GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
AJ550910.1/282-336             GAAGAGUCCUGCGCUU......AGCGCACUGACGAGUCUCUGA.......
AJ005314.1/281-334             AAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA.......
Y12833.1/339-285               CCGCUAUA.UGGGGAUGUGUG.UCCCUACUGACGAGUUCAA.........
M63666.1/246-192               CCGGUGUC.UCAAGGUGCGUA.CCUUGACUGAUGAGUCCGA.........
J02439.1/42-95                 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCGA.........
J02386.1/42-95                 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCAA.........
M33000.1/55-110                ACGCUGUC.UGUACUUGUAUC.AGUACACUGACGAGUCCCU.........
M33001.1/56-111                ACGCUGUC.UGUACUUAUAUC.AGUACACUGACGAGUCCCU.........
D00685.1/1-46                  .........GCCAGACGU.GGACCCGGCCUGAUGAGUCCGAAA.......
M17439.1/1-48                  .........ACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGU.........
#=GC SS_cons                   .<<<<<<..<<<<<.........>>>>>.......<<<<...........

AJ295015.1/58-1                ...............GCGUUGAACAGAAACUCUGC
AJ295018.1/58-1                ...............GCGUUGAACAGAAACUCUGC
AJ536620.1/206-152             ...................AAGGGCGAAACGGUAC
AJ536615.1/1-44                ...................AAGGACGAAAUGG...
AJ536612.1/206-152             ...................AAGGGCGAAACGGUAC
AJ536617.1/1-40                ...................AAGGACGAA.......
AJ536614.1/206-152             ...................AAGGGCGAAACGGUAC
AJ536620.1/1-40                ...................AAGGACGAA.......
AJ536619.1/206-152             ...................AAGGACGAAACGGUAC
AJ550911.1/56-3                .................AACGCAACGAAACUUUUG
AF170503.1/280-333             .................AAUGGAACGAAACCUUUU
AF170504.1/284-337             .................AAUGAGACGAAACUUAUC
AJ550912.1/56-3                .................GAUGCGACGAAACUUUUG
AJ247113.1/134-53              AAAUUGCUUUACUCCCGCACAAGCCGAAACUGGA.
AJ241833.1/282-334             .................AAUGAGACGAAACUCUUU
AJ241841.1/57-3                .................AAUGCGGCGAAACUUUUG
AJ241839.1/282-334             .................AAUGAGACGAAACUCAUA
AJ550901.1/282-334             .................GAUAAGACGAAACUCUUC
AJ005298.1/56-3                .................GAUACGGCGAAACUUUUG
AJ241819.1/56-3                .................AAUACGGCGAAACUUUUG
AJ005320.1/281-333             .................AAUGAGACGAAACUCUUU
AJ005310.1/56-3                .................AAUGCGGCGAAACUUUUG
AF339740.1/56-3                .................GAUACGGCGGAACUUAUG
AJ241828.1/56-3                .................GAUACGGCGAAACUUAUG
AJ550906.1/56-3                .................GAUGCGACGAAACUUAUG
AJ550903.1/281-333             .................AAUGAGACGAAACUCUUU
AJ241831.1/56-3                .................GAUACGGCGAAACUUCUG
AJ241840.1/56-3                .................AAUGCGGCGAAACUUUUG
AJ005303.1/56-3                .................GAUACGGCGAAACUUUUG
AJ005312.1/56-3                .................AAUGCGGCUAAACUUUUG
AJ550906.1/282-334             .................GAUGAGACGAAACUCUUC
AJ550907.1/56-3                .................GAUGCGACGAAACUUAUG
AF170503.1/55-3                .................GAUACGGCGAAACUUAUG
Y14700.1/133-53                GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA.
AJ005321.1/281-333             .................AAUGAGACGAAACUCUUG
AJ241845.1/282-335             .................AAUGAGACGAAACUCAUG
AJ005322.1/56-3                .................GAUACGGCGAAACUUAUG
M83545.1/56-3                  .................AAUGCGACGAAACUUAUG
AJ005305.1/56-3                .................GAUACGGCGAAACUUUUG
AJ550908.1/281-334             .................GAUGAGACGAAACUCUUC
AJ550909.1/56-3                .................GAUGCAACGAAACUUAUG
AJ241843.1/56-3                .................AAUGCGGCGAAACUUUUG
AF170523.1/55-3                .................GAUACGGCGAAACUUUUG
AF170509.1/56-3                .................GAUACGGCGAAACUUAUG
AJ241847.1/281-334             .................AAUGAGACGAAACUCUUG
AJ241823.1/282-335             .................AAUGAGACGAAACUCUUU
AJ247122.1/132-52              UAUUGCUUUACUCCCG.CACAAGCCGAAACUGGA.
AJ005300.1/282-335             .................AAUGAGACGAAACUCUUG
AJ005302.1/281-334             .................AUUGAGACGAAACUCUUG
AJ005318.1/56-3                .................GAUACGGUGAAACUUAUG
AF339739.1/56-3                .................GAUACGGCGAAACUUAUG
AJ241838.1/56-3                .................AAUGCGGCAAAACUUUUG
AJ247121.1/133-53              UUUCGCUUUACUCCCG.CACAAGCCGAAACUGGA.
AJ550911.1/282-335             .................AAUGAGACGAAACUCUUC
AJ550898.1/282-335             .................AAUAAGACGAAACUCUUC
AF170516.1/283-335             .................AAUGAGACGAAACUCUUC
AJ005319.1/56-3                .................GAUACGGCGAAACUUAUG
AJ550899.1/56-3                .................GAUAAGGCGAAACUUAUG
AF170519.1/55-3                .................GAUACGGCGAAACUUAUG
AJ247116.1/133-53              GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA.
AJ550907.1/281-333             .................GAUGAGACGAAACUCUUC
AJ241850.1/282-334             .................AAAGAGACGAAACUCUUU
AF170499.1/56-3                .................AAUGCGGCGAAACUUUUG
AF170520.1/282-335             .................AAUGAGACGAAACUUAUC
AJ005299.1/282-335             .................AAUGAGACGAAACUCUUG
AJ005312.1/282-335             .................AAUGAGACGAAACUCAUA
AJ550909.1/282-333             ..................AUGAGACGAAACUCUUC
AJ005322.1/281-334             .................AAUGAGACGAAACUCUUU
AJ005294.1/282-334             .................AAUGAGACGAAACUCUUG
AJ247123.1/132-52              GAAAGCUUUACUCCCG.CACAAGCCGAAACUGGA.
AJ550900.1/56-3                .................GACAAGGCGAAACUUAUG
AJ241830.1/282-334             .................AAUGAGACGAAACUCUUG
AJ241831.1/281-334             .................AAUGAGACGAAACUCUUA
M83545.1/282-335               .................GAUGAGACGAAACUCUUC
AJ550910.1/282-336             .................GAUGAGACGAAACUCUUC
AJ005314.1/281-334             .................AAUGAGACGAAACUCUUU
Y12833.1/339-285               ...................AAGAACGAAAUAGUUA
M63666.1/246-192               ...................AAGGACGAAACACCAG
J02439.1/42-95                 ...................AAGGACGAAACGGAUG
J02386.1/42-95                 ...................AAGGACGAAACGGAUG
M33000.1/55-110                ..................AAAGGACGAAACAGCGC
M33001.1/56-111                ..................AAAGGACGAAACAGCGC
D00685.1/1-46                  .....................GGACGAAACAGUA.
M17439.1/1-48                  ...................GAGGACGAAACAGGAC
#=GC SS_cons                   .....................>>>>...>>>>>>.
//