# STOCKHOLM 1.0
#=GF ID U1
#=GF AC RF00003
#=GF DE U1 spliceosomal RNA
#=GF AU Griffiths-Jones SR, Mifsud W, Moxon SJ
#=GF GA 37.0
#=GF NC 37.0
#=GF TC 37.2
#=GF SE Zwieb C, The uRNA database, PMID:9016512
#=GF SS Published; PMID:2405391
#=GF TP Gene; snRNA; splicing;
#=GF BM cmbuild CM SEED
#=GF BM cmsearch -W 250 CM SEQDB
#=GF DR URL; http://psyche.uthct.edu/dbs/uRNADB/u1/u1.html;
#=GF RN [1]
#=GF RM 9016512
#=GF RT The uRNA database.
#=GF RA Zwieb C;
#=GF RL Nucleic Acids Res 1997;25:102-103.
#=GF RN [2]
#=GF RM 2405391
#=GF RT Saccharomyces cerevisiae U1 small nuclear RNA secondary structure
#=GF RT contains both universal and yeast-specific domains.
#=GF RA Kretzner L, Krol A, Rosbash M;
#=GF RL Proc Natl Acad Sci U S A 1990;87:851-855.
#=GF RN [3]
#=GF RM 7984237
#=GF RT Crystal structure at 1.92 A resolution of the RNA-binding domain of
#=GF RT the U1A spliceosomal protein complexed with an RNA hairpin.
#=GF RA Oubridge C, Ito N, Evans PR, Teo CH, Nagai K;
#=GF RL Nature 1994;372:432-438.
#=GF RN [4]
#=GF RM 11297556
#=GF RT Two functionally distinct steps mediate high affinity binding of U1A
#=GF RT protein to U1 hairpin II RNA.
#=GF RA Katsamba PS, Myszka DG, Laird-Offringa IA;
#=GF RL J Biol Chem 2001;276:21476-21481.
#=GF CC U1 is a small nuclear RNA (snRNA) component of the spliceosome
#=GF CC (involved in pre-mRNA splicing). Its 5' end forms complementary
#=GF CC base pairs with the 5' splice junction, thus defining the 5'
#=GF CC donor site of an intron.
#=GF CC There are significant differences in sequence and secondary
#=GF CC structure between metazoan and yeast U1 snRNAs, the latter being
#=GF CC much longer (568 nucleotides as compared to 164 nucleotides in
#=GF CC human). Nevertheless, secondary structure predictions suggest
#=GF CC that all U1 snRNAs share a 'common core' consisting of helices I,
#=GF CC II, the proximal region of III, and IV [1].
#=GF CC This family does not contain the larger yeast sequences.
#=GF SQ 100

X58845.1/1-161       --ACUUACCUGGCUGG-AGUUU-GCUA---UCGAUCAU-GAAG-GGUAG-
X63783.1/2024-2186   UUACUUACCUGGCUGG-AGUUU-GCUA---UCGAUCAU-GAAG-GGUAG-
X63783.1/1394-1556   UUACUUACCUGGCUGG-AGUUA-GCUA---UCGAUCAU-GAAG-GGUAG-
X63783.1/596-756     UAAAUUACAAUGUUGU-AGUUA-GCUA---UAUAUCAA-AAAA-UAUAG-
M29062.1/238-387     UUACUUACCUGGCAUG-AGUUU--CUG---CAGCACAA-GAAU-UGUGG-
AY198212.1/1-163     AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-CAAG-GUGGU-
AJ243001.2/347-509   AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-CAAG-GUGGU-
AY198211.1/1-163     AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-CAAG-GUGGU-
AY198213.1/1-163     AUACUUACCUGGCACA-GGGAA-UACC---ACGAUCAC-UAAG-GUGGU-
AY198214.1/1-163     AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-UAAG-GUGGU-
K00787.1/2-165       AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X01725.1/69-233      AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X53541.1/1195-1359   AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X04257.1/1-164       AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
J01156.1/9-172       AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X53543.1/383-547     AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X53542.1/2592-2756   AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X53544.1/117-281     AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X53544.1/1653-1817   AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-
X02585.1/923-1086    AUACUUACCUGGCAGG-CGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
X00549.1/150-313     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-
X02585.1/1513-1676   AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M59827.1/771-934     AUACUUACCUGGCAGG-GGAGC-AUCU---GUGAUCAG-CAAG-GCAGA-
X01093.1/329-492     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-
X01091.1/442-605     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-
X01092.1/374-537     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-
V00444.1/1-162       --ACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-
J00914.1/146-309     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-
Y00131.1/944-1108    AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-
M32270.1/371-535     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-
J00645.1/51-213      AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
K03128.1/241-77      AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-
M32271.1/288-452     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
K02430.1/690-853     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
X12936.1/575-738     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
V01266.1/1-168       --ACUUACCUGGCAGG-GAGAU--ACC---AUGAUCAC-GAAG-GUGUU-
M14386.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
V00590.1/1-162       --ACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M14385.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
DQ058356.1/1-168     AUGUCUUCGUGGCGGG-GGAGA-GACGCUGUUGGUCCU-GAUAAAGUGU-
M14586.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
V00591.1/394-557     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
DQ058357.1/1-164     AUACUUAACUGGCAAG-GGAAA-UAAC---AUGAUCAUUAAAG-GUGGA-
M14587.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
K00529.1/225-388     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M14585.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
K00788.1/2-165       AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M28012.1/108-271     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M28013.1/108-271     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
J00318.1/433-596     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M14387.1/399-562     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
M38483.1/1-164       AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-
DQ092354.1/1778-1949 AUACUUACCUGACGGU-GAAGC-AAAC---CUGGUCAA-CAUG-GGGCU-
X75936.1/1034-1195   AUACUUACCUGGCGCA-GGGGU-AGCA---UUGAUCAA-GAAG-GAUGC-
M27880.1/1-161       AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-
X56629.1/421-582     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-
X01749.1/448-609     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-
X04994.1/620-781     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-
X04993.1/647-808     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-
L22246.1/3195-3356   AGACUUAUUUGGUUGG-GAGGA-UUUC---GUAAUCAG--AAG-GCGGG-
L22246.1/5535-5699   AAACUAACCUGGCUGG-GAGGCAUCUC---GCGAUCAU-GAAG-GCGGG-
L22246.1/2071-2235   AAACUAACCUGGCUGG-GGGGCAUCUC---GCGAUCAU-GAAG-GCGGG-
L22246.1/4551-4714   AAACUUACCUGGCUGG-GAGGC-UUUC---GUGAUCAU-GAAG-GCGGA-
X51371.1/181-345     AAACUUACCUGGCUGG-GGGUUAUUUC---GCGAUCAC-AAAG-GCGGA-
M73768.1/361-517     AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-CAAG-GCUCC-
L25914.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-
L25915.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-
L25921.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-
L25916.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-
L25917.1/1-158       AAACUUACUUGGCGCC-GGGAC-CAGG---GUGAUCAC-GAAU-GCCCU-
L25919.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-
X13841.1/396-551     AUACAUACCUGGCCGG-GGGAA-GUCG---GUGAUCAA-GACG-GCCGA-
X13842.1/1-150       ------ACCUGGCCGG-GGGAA-GUCG---GUGAUCAA-GACG-GCCGA-
X70869.1/1-161       AUACUUACCUGGCCCG-CUUCU-CGAG---GUGGUCAC-CAUG-GCCUC-
X06880.1/1-162       AUACUUACCUGUCCGG-CCUGC-GACC---UCGAGCAA-GAAG-GGGGU-
X69334.1/1-160       AUACUUACCUGGACGG-GGUCG-ACGA---GCGAUCAA-GAAG-GCUCG-
X69333.1/1-157       ----UUACCUGGACGG-GGUCG-ACGA---GCGAUCAA-GAAG-GCUCG-
S72336.1/2-161       AUACUUACCUGGACGG-GGUCG-ACGG---GCGAUCAA-GAAG-GCCCG-
X69329.1/1-160       AUACUUACCUGGACGG-GGUCG-ACGG---GCGAUCAA-GAAG-GCCCG-
X69328.1/1-158       --ACUUACCUGGACGG-GGUCG-ACGG---CCGAUCAA-GAAG-GGUCG-
Z11883.1/2839-2998   AUACUUACCUGGACGG-GGUUA-AUGG---GCGAUCAA-UAAG-ACCCA-
Z11883.1/1496-1656   UUACUUACCUGGACGG-GGUCA-AUGG---GCAAUCAA-UAAG-ACCCA-
Z11881.1/1515-1675   AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAA-UAAG-ACCUA-
Z11881.1/315-475     AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAA-UAAG-ACCUA-
Z11883.1/3441-3603   UUACUG--GUGGGUGGCGGAGA-AGAGAUCGUGACAUC-GUAG-ACCUA-
Z11883.1/361-521     AUACUUACCUGGACGG-GGUCA-AUGG---ACGAUCAA-UAAG-ACCCA-
Z11881.1/2581-2742   AUACUUACCUGGACGG-GGUCA-AUGG---GUGAUCAA-UAAG-ACCCAA
Z11882.1/353-512     AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAA-UAAG-ACCCA-
X14414.1/152-312     AUACUUACCUGGACGG-GGUCA-AUAG---GCGAUCAA-UAAG-ACCCA-
X14417.1/177-340     AUACUUACCUGGACGG-GGUCA-AUGG---GUAAUCAA-GAAG-UUCCA-
X14415.1/175-335     UUACUUACCUGGACGG-GGUCA-AUUG---GCGAUCAU-GAAG-GUCCA-
X14419.1/178-338     AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAU-GAAC-ACCCA-
X14416.1/171-331     AUACUUACCUGGACGG-GGUCU-AUGG---GCGAUCAU-GUAG-GUCCA-
X06809.1/232-392     AUACUUACCUGGACGG-GGUCA-AUGG---AUGAUCAA-GAAG-GUCCA-
X06810.1/261-421     AUACUUACCUGGACGG-GGUCA-AUGG---AUGAUCAA-UAAG-GUCCA-
J03563.1/352-512     AUACUUACCUGGACGG-GGUCA-AUGG---AUGAUCUA-UAAG-GUCCA-
X15926.1/1-161       AUACUUACCUGGAUGG-GGUCG-AUGG---GUGAUCAU-GAAG-GCCCA-
X15927.1/1-160       AUACUUACCUGGAUGG-GGUCA-AUGG---GUGAUCAA-GAAG-GCCCA-
X15928.1/1-160       AUACUUACCUGGAUGG-GGUCA-AUGG---GUGAUCAU-GAAG-GCCCA-
AY222070.1/1-157     AUACUUACCUGGACGG-GGUCG-UUGG---GUGAUCAU-GAAG-AUCCG-
#=GC SS_cons         ...........<<<<<.<<<<<..<<<...<<............>>>>>.
#=GC RF              xxxxxxxxxxxxxxxx.xxxxx.xxxx...xxxxxxxx.xxxx.xxxxx.

X58845.1/1-161       CGGCUU---AGG-GUGGAGCAGGUCAUU-----GCACAAAAGAUGU-CUG
X63783.1/2024-2186   CGGCUU---AGG-GUGGAGCAGGUCAUU-----GCACAAAAGAUGU-CUG
X63783.1/1394-1556   CGGCUU---AGG-GUGGAGCAGGUCAUU-----GCACAAAAGAUGU-CUG
X63783.1/596-756     CAACUA---AGG--UGGAGCAAGUCAUU-----GUACUAAAGAUGU-UUG
M29062.1/238-387     AGACUCA--GUU-AUUUGUCUUGGCAUU-----GCACUG-AGCCCU-G-A
AY198212.1/1-163     UCCCCC---AAG-ACGAGGCUCACCAUU-----GCACUC-CGG-UG-GCG
AJ243001.2/347-509   UCCCCC---AAG-ACGAGGCUCACCAUU-----GCACUC-CGG-UG-GCG
AY198211.1/1-163     UCCCCC---AAG-ACGAGGCUCACCAUU-----GCACUC-CGG-UG-GCG
AY198213.1/1-163     UCCCCCA--AGG-CGAGGCUCA-CCAUU-----GCACCU-CGG--UGGCG
AY198214.1/1-163     UCCCCCA--AGG-CGAGGCCCC-CCAUU-----GCACUU-CGG-UG-GUG
K00787.1/2-165       UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X01725.1/69-233      UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X53541.1/1195-1359   UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X04257.1/1-164       UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
J01156.1/9-172       UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X53543.1/383-547     UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X53542.1/2592-2756   UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X53544.1/117-281     UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X53544.1/1653-1817   UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAG
X02585.1/923-1086    UCUCCCA--GGG-CGAGGCUCAGCCAUU-----GCACUC-CGG-CU-GUG
X00549.1/150-313     UCUCCCA--GGG-CGAGGCUCAGCCAUU-----GCACUC-CGG-UU-GUG
X02585.1/1513-1676   UCUCCCA--GGG-CGAGGCUCAGCCAUU-----GCACUC-CGG-CC-GUG
M59827.1/771-934     GCUCCCA--GGG-UGAGGCUCAUCCAUU-----GCACAU-CGGAUU--UG
X01093.1/329-492     UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUG
X01091.1/442-605     UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUG
X01092.1/374-537     UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUG
V00444.1/1-162       UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUG
J00914.1/146-309     UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUG
Y00131.1/944-1108    UUUCCCA--GGG-CGAGGCUCACCCAUUU----GCACUGUUGGGGU-GUG
M32270.1/371-535     UUUCCCA--GGG-CGAGGCUCACCCAUU-----GCACUU-UGGGGU-GUG
J00645.1/51-213      UUUCCCA--GGG-CGAGGUGUAUCCAUU-----GCA-UC-CGG-AU-GUG
K03128.1/241-77      UUUCCCA--GGG-CGAGGCUCACCCAUU-----GCACUU-UGGGGU-GUG
M32271.1/288-452     UUUCCCA--GGG-CGAGGCUCACCCAUU-----GCACUU-UGGGGU-GUG
K02430.1/690-853     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
X12936.1/575-738     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
V01266.1/1-168       UUCUCUCCAGGG-CGUGGUCUAUCCAUUGAGGCGCACUC-CGU-GG-AUG
M14386.1/106-268     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
V00590.1/1-162       UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
M14385.1/106-268     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
DQ058356.1/1-168     UUUUCUUG-GGG-GAGGGUUUUUACUUU-----GUGUUU-GGGAUG-UGU
M14586.1/106-268     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
V00591.1/394-557     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
DQ058357.1/1-164     UUUUUCA--GGG-UGAGGUUUGUCUCUU-----GCAUUG-UGG-AU-GUG
M14587.1/106-268     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
K00529.1/225-388     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
M14585.1/106-268     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
K00788.1/2-165       UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
M28012.1/108-271     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
M28013.1/108-271     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
J00318.1/433-596     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
M14387.1/399-562     UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
M38483.1/1-164       UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUG
DQ092354.1/1778-1949 UCUUCC---AGGGUGAGGCUUUUGCAUU-----GCACUU-CGCCUG-G-G
X75936.1/1034-1195   ACCCCC---AGG-ACGAGGCUUGCUAUU-----GCACAC-CGG-CU--CG
M27880.1/1-161       ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UG
X56629.1/421-582     ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UG
X01749.1/448-609     ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UG
X04994.1/620-781     ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UG
X04993.1/647-808     ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UG
L22246.1/3195-3356   ACCUCCA--UGG-CGAGGCUUGGUCAUU-----GCACUUUCGA-CC-AGG
L22246.1/5535-5699   ACCUCCA--UGG-CGAGGUUUGGCCAUU-----GCACUUUCGG-CC-AGG
L22246.1/2071-2235   ACCUCCA--UGG-UGAGGUCUGGUCAUU-----GCACUUCCGA-CC-AGG
L22246.1/4551-4714   ACCUCCA--UGG-UGAGGCUUGGUCAUU-----GCACUUUCGA-CC-AGG
X51371.1/181-345     AUCCCCA--UGG-UUAGGCCUACCCAUU-----GCACUUUUGGUGC-GGG
M73768.1/361-517     GACCCCA--GGU-GGAGGCUCA-GCAUU-----GCACUC-CGC--U-GUG
L25914.1/1-159       GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGG
L25915.1/1-159       GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGG
L25921.1/1-159       GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGG
L25916.1/1-159       GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGG
L25917.1/1-158       GGCCCCA--GGU-GGAGGCUCG-CCAUU-----GCACUC-CGG--C-GUG
L25919.1/1-159       GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGG
X13841.1/396-551     GUCCCU---AGU-UGGGGUACCUCUCCU-----GCACUU-GAGAGG-G-G
X13842.1/1-150       GUCCCU---AGU-UGGGGAACCUCUCCU-----GCACUU-GAGAGG-G-G
X70869.1/1-161       GGUUGU---GUG-GUCGGUCUUCACCUU-----GCACUU-UGU-GA-GGG
X06880.1/1-162       CUAGGUA--GUG-CUUGUACCUCGCCUU-----GUACUA-UGCUUG-GGG
X69334.1/1-160       UGGCCU---GGG-UCAGUGGUCCACAUU-----GCACUU-GGU-GG-AUG
X69333.1/1-157       UGGCCU---AGG-UUAGUGGCCCACAUU-----GCACUU-GGUGGGUG-C
S72336.1/2-161       UGGCU----GGG-UCAAUGGCUCACAUU-----GCACUU-GGUGGGUG-C
X69329.1/1-160       UGGCU----GGG-UCAAUGGCUCACAUU-----GCACUU-GGUGGGUG-C
X69328.1/1-158       UGGCCU---AGA--UCAAUGGUCACAUU-----GCACCU-GGUGAG-CGC
Z11883.1/2839-2998   UGGGCCU--AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
Z11883.1/1496-1656   UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
Z11881.1/1515-1675   UGGCCU---AGG-CUUGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
Z11881.1/315-475     UGGCCU---AGG-CUUGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
Z11883.1/3441-3603   UGGCUU---AGA-UUGAUGACCUCCAUU-----GCACUU-UGGAGG-GGU
Z11883.1/361-521     UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
Z11881.1/2581-2742   UGACCC---AGG-CUUGUGACCUACAUU-----GCACUU-UGGAGG-GGU
Z11882.1/353-512     UGGCCU---AGG-CUUGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
X14414.1/152-312     UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGU
X14417.1/177-340     UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUA-AGGAGG-GGU
X14415.1/175-335     UGGCCU---AGG-UUGGUAACCUCCAUU-----GCACUU-AGGAGA-GGU
X14419.1/178-338     UGGCCU---AGG-UUGGUGACCAUCAUU-----GCACUU-UGAAGG-GGU
X14416.1/171-331     UGGCCU---AGG-UUGGUGACUUUCAUU-----GCACUU-UGGAGG-GGU
X06809.1/232-392     UGGCCU---AGG-GAAGUAACCUCCAUU-----GCACUG-AGGAGG-GGU
X06810.1/261-421     UGGCCU---AGG-GAAGUAACCUCCAUU-----GCACUU-AGGAGG-GGU
J03563.1/352-512     UGGCCU---AGG-GAAGUGACCUUCAUU-----GCACUC-AGAAGG-GGU
X15926.1/1-161       UGGCU----AGG-AUUGUGACCUCCAUU-----GCACUU-AGGAGG-GGU
X15927.1/1-160       UGGCU----AGG-CAAGUGACCUCCAUU-----GCACUU-AGGAGG-GGU
X15928.1/1-160       UGGCU----AGG-CAAGUGACUUCCAUU-----GCACUU-AGGAGG-GGU
AY222070.1/1-157     UGGCCUA--GCG-UGGUGGC---UUCCU-----GCACUU-GAGGU----G
#=GC SS_cons         >>>>>>...<<<.......<<<.<<................>>..>.>.>
#=GC RF              xxxxxx...xxx.xxxxxxxxxxxxxxx.....xxxxxx.xxx.xx.xxx

X58845.1/1-161       UAAUA---------CCUUAUUGUUC-CCCGU---GCGG---GGAACCGAA
X63783.1/2024-2186   UAAUA---------CCUUAUUGUUC-CCCGU---GCGG---GGAACCGAA
X63783.1/1394-1556   UAAUA---------CCUUAUUGUUC-CCCGU---GCGG---GGAACCGAA
X63783.1/596-756     UAAUA---------CCUUG--AUGUUCCCGC----UGG--GAGCAAUA--
M29062.1/238-387     CGAAU---------AACUGUGGACUGGCUAA----GGU--CAG-CUCCG-
AY198212.1/1-163     CUGACC--------CUUG-CGAUGACCCCAAAU-GUGG--GUU-ACUCG-
AJ243001.2/347-509   CUGACC--------CUUG-CAAUGACCCCAAAU-GUGG--GUU-ACUCG-
AY198211.1/1-163     CUGACC--------CUUG-CGAGGACCCCAAAU-GUGG--GUU-ACUCG-
AY198213.1/1-163     CUGAC---------CCUUGCGAUGACCCCAAAU-GUGG--GUU-ACUCG-
AY198214.1/1-163     UUGAC---------CCUUGCGAUGAUCCCAAAU-GUGG--AUU-ACUCG-
K00787.1/2-165       UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X01725.1/69-233      UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X53541.1/1195-1359   UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X04257.1/1-164       UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
J01156.1/9-172       UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X53543.1/383-547     UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X53542.1/2592-2756   UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X53544.1/117-281     UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X53544.1/1653-1817   UUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-
X02585.1/923-1086    CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
X00549.1/150-313     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
X02585.1/1513-1676   CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAAGUCG-
M59827.1/771-934     CUGAC---------CCCUGCGAUGUCCCCAAAU-GCGG---GAUUCUCG-
X01093.1/329-492     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
X01091.1/442-605     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
X01092.1/374-537     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
V00444.1/1-162       CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
J00914.1/146-309     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
Y00131.1/944-1108    CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
M32270.1/371-535     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
J00645.1/51-213      CUGAC---------CACUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
K03128.1/241-77      CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
M32271.1/288-452     CUGAC---------CCCUGCGAUUUCCCAAAU--GCGG---GAAACUCG-
K02430.1/690-853     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
X12936.1/575-738     CUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-
V01266.1/1-168       CUGAC---------CCCUGCGAUUUCCUCCAAAUGCGG---GAAACUCG-
M14386.1/106-268     CUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-
V00590.1/1-162       CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
M14385.1/106-268     CUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-
DQ058356.1/1-168     UUGCU---------CCCG-CGAUUUCCCCGA---AUGA--GAAAACUCG-
M14586.1/106-268     CUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-
V00591.1/394-557     CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
DQ058357.1/1-164     CUGAC---------CCCUGUGGUUUUCUACAAAUGUGG---GAAACUUA-
M14587.1/106-268     CUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-
K00529.1/225-388     CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
M14585.1/106-268     CUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-
K00788.1/2-165       CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
M28012.1/108-271     CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
M28013.1/108-271     CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
J00318.1/433-596     CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
M14387.1/399-562     CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
M38483.1/1-164       CUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-
DQ092354.1/1778-1949 CUGACUCUGGGUUGACUG-CGAUUACCGCUAAC-GUCG--GUA-ACUCG-
X75936.1/1034-1195   CUGAA---------GCUUGCGAUUCCCUCAAAC-GUAG---GGAACUCG-
M27880.1/1-161       CUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-
X56629.1/421-582     CUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-
X01749.1/448-609     CUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-
X04994.1/620-781     CUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-
X04993.1/647-808     CUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-
L22246.1/3195-3356   CUGAC---------CAGUGUGGCAGACCCGAG--UUGGGAUUGG--CCA-
L22246.1/5535-5699   CUGAC---------CCGUGUGGCAGUCCCGAG--UUGGGAUUGG--CCA-
L22246.1/2071-2235   CUGAC---------CUGUGUGGCAGUCCCGAG--UUGGGAUUGG--CCA-
L22246.1/4551-4714   CUGAC---------CCGUGUGGCAGUCCCGAG--UUGGGAUUGG--CCA-
X51371.1/181-345     CUGAC---------CUGUGUGGCAGUCUCGAGU-UGAG--AUU-CGCCA-
M73768.1/361-517     UUGAA---------GCCUGCGACGGACUCUAA--UCGG--GUUCGCUCG-
L25914.1/1-159       UUGAA---------ACUCGCGACGAACCCUAA--UUGG--GCUCGCUCG-
L25915.1/1-159       UUGAA---------ACUCGCGACGAACCCUAA--UUGG--GUGCGCUCG-
L25921.1/1-159       UUGAA---------ACUCGCGACGAACCCUAA--UUGG--GUGCGCUCG-
L25916.1/1-159       UUGAA---------ACUCGCGACGAACCCUAA--UUGG--GUGCGCUCG-
L25917.1/1-158       UUGAA---------GCCUGCGACGAUCCCUAA--UUGG--GUGCGCUCG-
L25919.1/1-159       UUGAA---------ACUUGCGACGAACCCUAA--UUGG--GUGCGCUCG-
X13841.1/396-551     CCCCU---------UCUA-UGAUUG-CCUUC-----GG--GUA-ACUCA-
X13842.1/1-150       CUCCU---------UCUA-UGAUUG-CCUUC-----GG--GUA-ACUCA-
X70869.1/1-161       CCUUC---------CGCA-GUCGGCCCUUCG-----GG--UGU-CCGGC-
X06880.1/1-162       UA--G---------CGCUGUGUGCGGGGCAA---GUCC---UCGUUACA-
X69334.1/1-160       CCUGG---------CCCA-CCAUCUCCCCAA---GUGG---GAGAGUGG-
X69333.1/1-157       GCUGG---------CCUA-UCAUCUCCCCAA---GUGG---GAGAGUGA-
S72336.1/2-161       GUUGG---------CCCA-CCAUCUCCCCAA---GUGG---GAGAGUGG-
X69329.1/1-160       GUUGG---------CCCA-CCAUCUCCCCAA---GUGG---GAGAGUGG-
X69328.1/1-158       GUUGG---------CCUA-CCAUCUCCCCAA---GUGG---GAGAGUGG-
Z11883.1/2839-2998   GCCUA---------CCUA-AGGUCGGCUCAA---GUAG--UCG-AGCCU-
Z11883.1/1496-1656   GCCUU---------CCUA-AGGUCGACCCAA---GUGG--UCG-AGCCU-
Z11881.1/1515-1675   GCCUG---------CCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-
Z11881.1/315-475     GCCUG---------CCUA-AGGUCGACCCAA---GUGG--UCG-AGCCU-
Z11883.1/3441-3603   GCCUG---------CCUAAAGUCUG-CCCAA---GUGG--UCG-AGCCU-
Z11883.1/361-521     GCCUG---------CCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-
Z11881.1/2581-2742   GCCUG---------CCUA-AGGUCAGCCCAA---GUGG--UUG-AGCCU-
Z11882.1/353-512     GCCUG---------CCUA-AGGUCGACCUAA---GUGG--UCG-GGCCU-
X14414.1/152-312     GCCAA---------UCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-
X14417.1/177-340     GCUUG---------CCUA-AGGUCGACCCAA---GUGG--UUG-AGCCU-
X14415.1/175-335     GCCUA---------CCUA-AGAUCGGCCCAA---GUGG--CCG-AAUCU-
X14419.1/178-338     GCCCG---------CCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-
X14416.1/171-331     GCCCG---------CCUA-AGAUCAGCCCAA---GAGG--UUG-AGUCU-
X06809.1/232-392     GCCUU---------UCUA-AGGUCUGUCCAA---GUGA--CAG-AGCCU-
X06810.1/261-421     GCUUU---------CCUA-AGGUCUGCCCAA---GUGG--CAG-AGCCU-
J03563.1/352-512     GCUAC---------UCUA-AGGUCUGUCCAA---GUGA--UGG-AGCCU-
X15926.1/1-161       GCUUU---------CCUA-AGGUCUACCCAA---GUGG--UGG-AGCCU-
X15927.1/1-160       GCUAG---------CCUA-AGGUCUACCCAA---GUGG--UGG-AGCCU-
X15928.1/1-160       GCUUG---------CCUA-AGGUCUACCCAA---GUGG--UGG-AACCU-
AY222070.1/1-157     GCUAA---------CGCAAAGGU-CACCCCAA--GUGG---GAGAUCCU-
#=GC SS_cons         ..............>>>..<<<.<<.<<........>>...>>...>>>.
#=GC RF              xxxxx.........xxxx.xxxxxxxxxxxxx..xxxx...xx.xxxxx.

X58845.1/1-161       ACAGCACAAUUUCUGCUAG--GGGAGAC-GUGCACUU--A-GUGCUGUCU
X63783.1/2024-2186   ACAGCACAAUUUCUGCUAG--GGGAGAC-GUGCACUU--A-GUGCUGUCU
X63783.1/1394-1556   ACAGCACAAUUUCUGCUAG--GGGAGAC-GUGCACUU--A-GUGCUGUCU
X63783.1/596-756     ACAACAAAAUUUCUGAUUG--GAAAUAG--UCAUUAAACUAACUGGCUAU
M29062.1/238-387     GAUGCAUCAUUUUUGAGUU--CGU-----CCCUCAUU----UGGGGC---
AY198212.1/1-163     GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCC
AJ243001.2/347-509   GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCC
AY198211.1/1-163     GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCC
AY198213.1/1-163     GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCC
AY198214.1/1-163     GGUGUGUAAUUUUUGGUAG--CUGGGG--ACUGCGUU--CGCGCUAUCCC
K00787.1/2-165       UGCGUGUAAUUUUUGGUAG--CCGGGAA--UGGCGUU--CGCGCCG-UCC
X01725.1/69-233      UGCGUGUAAUUUUUGUUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCC
X53541.1/1195-1359   UGCGUGUAAUUUUUGUUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCC
X04257.1/1-164       UGCGUGUAAUUUUUGGUAG--CCGGGAA--UGGCGUU--CGCGCCG-UCC
J01156.1/9-172       UGCGUGUAAUUUUUGGUAG--CCGGGAA--UGGCGUU--CGCGCCG-UCC
X53543.1/383-547     UGCGUGUAAUUUUUGGUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCC
X53542.1/2592-2756   UGCGUGUAAUUUUUGUUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCC
X53544.1/117-281     UGCGCGUAAUUUUUGGUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCC
X53544.1/1653-1817   UGCGUGUAAUUUUUGGUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCC
X02585.1/923-1086    ACUGCAUAAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
X00549.1/150-313     ACUGCAUAAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
X02585.1/1513-1676   ACUGCAUAAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
M59827.1/771-934     ACUGUAUUAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
X01093.1/329-492     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
X01091.1/442-605     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
X01092.1/374-537     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
V00444.1/1-162       ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
J00914.1/146-309     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
Y00131.1/944-1108    A-UGCA-AAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
M32270.1/371-535     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
J00645.1/51-213      ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--UGUGCUCUCCC
K03128.1/241-77      ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
M32271.1/288-452     ACUGCAUAAUUUGUGGUAG--UGGGGGA-GCUGCGUU--CGCGCGCCCCC
K02430.1/690-853     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
X12936.1/575-738     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCC
V01266.1/1-168       ACUGCAUAAUUUGUGGUAG--UGCGGGG--GACUGUU--CGCGCUC-CUC
M14386.1/106-268     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
V00590.1/1-162       ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
M14385.1/106-268     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
DQ058356.1/1-168     GCUGCAUAACUUGUGGUAG--UGGGGG--ACUGCUUU--UGCGCUUUUCU
M14586.1/106-268     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
V00591.1/394-557     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
DQ058357.1/1-164     AUUGCAUAAUUUGUGGUAG--UGGGGAC-U---AUGU--UGGUUCUCUCC
M14587.1/106-268     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
K00529.1/225-388     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUC--CGCGCUUUCCC
M14585.1/106-268     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
K00788.1/2-165       ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
M28012.1/108-271     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
M28013.1/108-271     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
J00318.1/433-596     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
M14387.1/399-562     ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
M38483.1/1-164       ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCC
DQ092354.1/1778-1949 ACCGUACACUUUCUGGCUG--UGGGGG--CCUGCGUU--GGCGCUCGCCC
X75936.1/1034-1195   GGCGUAUUAUUUAUGGUAG---CGGGGA-UCUGCGUU--CGCGCUAUCCC
M27880.1/1-161       GGCGUAUUAUUUAUGGUAG--CGGAGAU--CUGCGUU--CGCGCUA-UCU
X56629.1/421-582     GGCGUAUUAUUUAUGGUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUC
X01749.1/448-609     GGCGUACAAUUUAUGGUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUC
X04994.1/620-781     GGCGUACAAUUUAUGAUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUC
X04993.1/647-808     GGCGUACAAUUUAUGGUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUC
L22246.1/3195-3356   ACAGCAUAAUUUUUGCGUU---UGGGGA--CAGCGUU--CGCGCUU-CCC
L22246.1/5535-5699   ACAGCAUAAUUUUUGCGUU----UGGGG-ACAGCGUU--CGCGCUUCCCC
L22246.1/2071-2235   ACAGCAUAAUUUUUGCGUU----UGGGG-ACAGCGUU--CGCGCUUCCCC
L22246.1/4551-4714   ACAGCAUAAUUUUUGCGUU----UGGGG-ACAGCGUU--CGCGCUUCCCC
X51371.1/181-345     ACAGCUUAAUUUUUGCGUA--UCGGGG---CUGCGUG--CGCGCGG-CCC
M73768.1/361-517     GGUGCAUAGUUUUUGCCAG--UGGGGA-----GCCUU--CGGGC--GUCC
L25914.1/1-159       GACGCGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCC
L25915.1/1-159       GGCGUGUAGUUUUUGUCAG--UGGGGA---GGUCUCA--C-AGUCC-UCC
L25921.1/1-159       GGCGUGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCC
L25916.1/1-159       GGCGUGUAGUUUUUGUCAG--UGGGGA---GGUCUCA--C-AGUCA-UCC
L25917.1/1-158       GACGCGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCC
L25919.1/1-159       GACGCGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCC
X13841.1/396-551     ACGGCAUAAUUUGUGAUAG--CGUGGG---GUGCGCUU-GUCGCGC-CCU
X13842.1/1-150       ACGGCAUAAUUUGUGAUAG--CGUGGG---GUGCGCUU-GUCGCGC-CCU
X70869.1/1-161       AGGGCUAAAUUUUUGUUAG--GCUGAGGACCCGCGCUA-UGCGCGGCCUC
X06880.1/1-162       ACGGAAUAAUUUCUGGCAG--GCCGUUG-CACGCGCU--UGCGCGUCCUC
X69334.1/1-160       AUGUCAUAAUUUGUGGUAG---AGGGGG-UACGCGUU--CGCGCGGCCCC
X69333.1/1-157       ACGUCAUAAUUUGUGGUAG---AGGGGG-UACGCGUU--CGCGCGGCCCC
S72336.1/2-161       ACGUCAUAAUUUGUGCUAG---AGGGGG-UACGCGUU--CGCGCGGCCCC
X69329.1/1-160       ACGUCAUAAUUUGUGCUAG---AGGGGG-UACGCGUU--CGCGCGGCCCC
X69328.1/1-158       ACGUCGUAAUUUGUGGUAG---AGGGGG-UACGCGUU--CGCGCGGCCCC
Z11883.1/2839-2998   ACGUCAUAAUUUGUUGCAG----UGGG--CCUGCGUU--CGCGCGGCCCC
Z11883.1/1496-1656   AUGUCAUAAUUUGUUGCAG---UGGGGG-CCAGCGUU--CGCGCGGCCCC
Z11881.1/1515-1675   ACGUCAUAAUUUGUUACAG--CGGGGG--CCUGCGUU--CGCGCGGCCCU
Z11881.1/315-475     ACGUCAUAAUUUGUUGCUG--UGGGGG--CCUGCGUU--CGCGCGGCCCU
Z11883.1/3441-3603   ACACUAUAAUUUGUGAUAG---UGGGGG-CUUGCGUU--CGCGCAGCCCC
Z11883.1/361-521     ACGUCAUAAUUUGUUGCAG---UGGGGG-CCUGCGUU--CGCGCGGCCCC
Z11881.1/2581-2742   AUGUCAUAAUUUGUUGCAG---UGGGUG-CCUGUGUU--UGCGCACGCCC
Z11882.1/353-512     AUGUCAUAAUUUGUUGCUG--UGGGGG--CCUGCGUU--C-UGCGCGCCC
X14414.1/152-312     ACGUCAUAAUUUGUUGCUG--UGAGGG--CCUGUGUU--CGCGCGGCCCC
X14417.1/177-340     ACGUCAUAAUUUGUUGUUGCAGAGGGGG-CCUGUGUU--CGCGCAGCCCC
X14415.1/175-335     ACGUCAUAAUUUGUUGCUG---AGGGGG-CCUGCGUU--CGCGCGGCCCC
X14419.1/178-338     ACGUCAUAAUUUGUUGCUG---AGGGGG-CCUGCGUU--CGCGCGGCCCC
X14416.1/171-331     ACAUCAUAAUUUGUUGCUG---AGGGGG-CAUGCGUU--CGCGCAGCCCC
X06809.1/232-392     ACGUCAUAAUUUGUGGUAG--UGGGGG--CCUGCGUU--CGCGCGGCCCC
X06810.1/261-421     ACGUCAUAAUUUGUGGUAG--UGGGGG--CUUGCGUU--CGCGCAGCCCC
J03563.1/352-512     ACGUCAUAAUUUGUGGUAG--UGGGGG--CCUGCGUU--CGCGCGGCCCC
X15926.1/1-161       ACAUCAUAAUUUGUUGCCU--GAGGGGG-CCUGCGUU--CGCGCGGCCCC
X15927.1/1-160       ACAUCAUAAUUUGUUGCUG--UGGGGG--CCUGUGUU--CGCGCGGCCCC
X15928.1/1-160       ACAUCAUAAUUUGUUGCUG--UGGGGG--CCUGCGUU--CGCGCGGCCCU
AY222070.1/1-157     GCGUCAUUAUUUGUUGCCU---UGGGGG-CCUGCGUU--CGCGCAGCCCC
#=GC SS_cons         .>>>>.................<<<<<...<<<<<......>>>>>.>>>
#=GC RF              xxxxxxxxxxxxxxxxxxx..xxxxxx..xxxxxxxx..xxxxxxxxxxx

X58845.1/1-161       CCG
X63783.1/2024-2186   CCG
X63783.1/1394-1556   CCG
X63783.1/596-756     UUC
M29062.1/238-387     --A
AY198212.1/1-163     CUU
AJ243001.2/347-509   CUU
AY198211.1/1-163     CUU
AY198213.1/1-163     CUU
AY198214.1/1-163     CUU
K00787.1/2-165       CGA
X01725.1/69-233      GAC
X53541.1/1195-1359   GAC
X04257.1/1-164       CGA
J01156.1/9-172       CGA
X53543.1/383-547     GAC
X53542.1/2592-2756   GAC
X53544.1/117-281     GAC
X53544.1/1653-1817   GAC
X02585.1/923-1086    CUG
X00549.1/150-313     CUG
X02585.1/1513-1676   CUG
M59827.1/771-934     CUG
X01093.1/329-492     CUG
X01091.1/442-605     CUG
X01092.1/374-537     CUG
V00444.1/1-162       CUG
J00914.1/146-309     CUG
Y00131.1/944-1108    CUG
M32270.1/371-535     CUG
J00645.1/51-213      CUU
K03128.1/241-77      CUG
M32271.1/288-452     CUG
K02430.1/690-853     CUG
X12936.1/575-738     CUG
V01266.1/1-168       UCG
M14386.1/106-268     CUG
V00590.1/1-162       CUG
M14385.1/106-268     CUG
DQ058356.1/1-168     GUC
M14586.1/106-268     CUG
V00591.1/394-557     CUG
DQ058357.1/1-164     CCU
M14587.1/106-268     CUG
K00529.1/225-388     CUG
M14585.1/106-268     CUG
K00788.1/2-165       CUG
M28012.1/108-271     CUG
M28013.1/108-271     CUG
J00318.1/433-596     CUG
M14387.1/399-562     CUG
M38483.1/1-164       CUG
DQ092354.1/1778-1949 CUU
X75936.1/1034-1195   CUU
M27880.1/1-161       CCU
X56629.1/421-582     CUA
X01749.1/448-609     CUA
X04994.1/620-781     CUA
X04993.1/647-808     CUA
L22246.1/3195-3356   CGC
L22246.1/5535-5699   GCC
L22246.1/2071-2235   GCC
L22246.1/4551-4714   GCC
X51371.1/181-345     UGA
M73768.1/361-517     CUU
L25914.1/1-159       CUU
L25915.1/1-159       CUU
L25921.1/1-159       CUU
L25916.1/1-159       CUU
L25917.1/1-158       UU-
L25919.1/1-159       CUU
X13841.1/396-551     GCA
X13842.1/1-150       GCA
X70869.1/1-161       GGC
X06880.1/1-162       GGC
X69334.1/1-160       UGC
X69333.1/1-157       UGC
S72336.1/2-161       UGC
X69329.1/1-160       UGC
X69328.1/1-158       UAC
Z11883.1/2839-2998   UAC
Z11883.1/1496-1656   UAC
Z11881.1/1515-1675   ACC
Z11881.1/315-475     GCC
Z11883.1/3441-3603   UAG
Z11883.1/361-521     UAU
Z11881.1/2581-2742   UAC
Z11882.1/353-512     CUG
X14414.1/152-312     UGC
X14417.1/177-340     UAC
X14415.1/175-335     UGC
X14419.1/178-338     UGC
X14416.1/171-331     UGC
X06809.1/232-392     UUU
X06810.1/261-421     UUC
J03563.1/352-512     UUA
X15926.1/1-161       CAC
X15927.1/1-160       CUC
X15928.1/1-160       CUU
AY222070.1/1-157     CAC
#=GC SS_cons         >>.
#=GC RF              xxx
//
# STOCKHOLM 1.0
#=GF ID U2
#=GF AC RF00004
#=GF DE U2 spliceosomal RNA
#=GF AU Griffiths-Jones SR, Mifsud W
#=GF GA 46.2
#=GF NC 46.1
#=GF TC 46.2
#=GF SE The uRNA database, PMID:9016512; Griffiths-Jones SR
#=GF SS Published; PMID:2339054; Griffiths-Jones SR
#=GF TP Gene; snRNA; splicing;
#=GF BM cmbuild CM SEED
#=GF BM cmsearch -W 220 CM SEQDB
#=GF DR URL; http://psyche.uthct.edu/dbs/uRNADB/u2/u2.html;
#=GF RN [1]
#=GF RM 9016512
#=GF RT The uRNA database.
#=GF RA Zwieb C;
#=GF RL Nucleic Acids Res 1997;25:102-103.
#=GF RN [2]
#=GF RM 11424937
#=GF RT A conserved pseudouridine modification in eukaryotic U2 snRNA induces
#=GF RT a change in branch-site architecture.
#=GF RA Newby MI, Greenbaum NL;
#=GF RL RNA 2001;7:833-845.
#=GF RN [3]
#=GF RM 11350032
#=GF RT Crystal structure of a model branchpoint-U2 snRNA duplex containing
#=GF RT bulged adenosines.
#=GF RA Berglund JA, Rosbash M, Schultz SC;
#=GF RL RNA 2001;7:682-691.
#=GF RN [4]
#=GF RM 2339054
#=GF RT The spliceosomal snRNAs of Caenorhabditis elegans.
#=GF RA Thomas J, Lea K, Zucker-Aprison E, Blumenthal T;
#=GF RL Nucleic Acids Res 1990;18:2633-2642.
#=GF CC U2 is a small nuclear RNA (snRNA) component of the spliceosome
#=GF CC (involved in pre-mRNA splicing). Complementary binding between U2
#=GF CC snRNA (in an area lying towards the 5' end but 3' to hairpin I)
#=GF CC and the branchpoint sequence (BPS) of the intron results in 
#=GF CC the bulging out of an unpaired adenosine, on the BPS, which
#=GF CC initiates a nucleophilic attack at the intronic 5' splice site,
#=GF CC thus starting the first of two transesterification reactions that
#=GF CC mediate splicing.
#=GF SQ 77

X63784.1/412-602     AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X63786.1/1152-1341   AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X58842.1/1-191       AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X63786.1/549-738     AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
AY007785.1/849-1041  AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GNGUAGUAUCUGUUCU
AF095839.1/1586-1389 AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
AF326335.1/1-142     AUAUCU-UCU-CGGCUUUUU-AGCUAAGAUCAU-GUUUAUAAACUGUUCU
M58665.1/571-712     AUAUCU-UCU-CGGCUAUUU-AGCUAAGAUCAU-GUUUAUAAACUGUUCU
AY007788.1/537-679   AUAUCU-UCU-CGGCUAUUU-AGCUAAGAUCAU-GUUUAUAAACUGUUCU
X56455.1/161-312     AUAUCU-UCU-CGGCUUUUU-AGCUAAGAUCAU-GUUUUUAAAAUGUUCU
U23406.1/206-352     AUAUCU-UCU-CGGCUAUUU-AGCUAAGAUCAU-GUUUAUAAACUGUUCU
AF047722.1/3099-3243 AUAUCU-UCU-CGGCUAUUU-AGCUAAGAUCAA-GUUAUUAAACUGUUCU
M58666.1/571-715     AUAUCU-UCU-CGGCUAUUU-AGCUAAGAUCAA-GUUAUUAAACUGUUCU
X56458.1/91-238      AUAUCU-UCU-CGGCUAUUU-AGCUAAGAUCAA-GUUUUUAAACUGUUCU
X56457.1/243-390     AUAUCU-UCU-CGGCCAUUU-AGCUAAGAUCAA-GUUUUUAAACUGUUCU
AY205287.1/148-4     AUAUCU-UCU-GGGCUAUUU-AGCUAAGAUCAA-GUUUUUAAACUGUUCU
X56456.1/243-390     AUAUCU-UCU-CGGCCAUUU-AGCUAAGAUCAA-GUUUUCAAGCUGUUCU
M14625.1/332-488     AUC----UCU-UUGCCUUUU-GGCUUAGAUCAA-GUGUAGUAUCUGUUCU
M23361.1/1-186       AUUCUC-UCU-UUGCCUUUU-GGCUUAGAUCAA-GUGUAGUAUCUGUUCU
X55772.1/223-412     AUUCUC-UCU-UUGCCUUUU-GGCUUAGAUCAA-GUGUAGUAUCUGUUCU
AF053589.1/90-279    CCACCUCUCA-AAGCUCAU--AGCUUUGAUCAA-GUGUAGUAUCUGUUCU
X04247.1/87-278      AUCGCU-UCU-CGGCCUUAU-GGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X04241.1/85-276      AUCGCU-UCU-CGGCCUUAU-GGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X04244.1/85-276      AUCGCU-UCU-CGGCCUUAU-GGCUAACAUCAAAGUGUAGUAUCUGUUCU
X04256.1/85-275      AUCGCU-UCU-CGGCCUUAU-GGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X04243.1/69-260      AUCGCU-UCU-CGGCCUUAU-GGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X04246.1/87-278      AUCGCU-UCU-CGGCCUUAU-GGCUAAGAUCAAAGUGUAGUAUCUGUUCU
K02457.1/1-187       AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X00093.1/360-550     AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
M12856.1/361-551     AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X07913.1/1061-1251   AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X04212.1/1-187       AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X59360.1/1-185       AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUU--
M19204.1/1-187       AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
AF287992.1/4918-5108 AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X54113.1/230-415     AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAU-GUGUAGUAUCUGUUCU
M58447.1/507-698     AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAU-GUGUAGUAUCUGUUCU
S64589.1/1-189       AUCGCU-UCU-CGGCCUUUU-GGCUAAGAUCAU-GUGUAGUAUCUGUUCU
L22247.1/6321-6513   AUCGCU-UCU-CGGCCUAUU-GGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51380.1/303-493     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51381.1/239-429     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51372.1/210-400     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51378.1/335-525     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51374.1/284-474     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51379.1/254-444     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51375.1/389-580     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
X51376.1/309-499     AUCGCU-UCUUCGGCUUAUU-AGCUAAGAUCAAAGUGUAGUAUCUGUUCU
L25918.1/1-181       AUCGCU-UCU-CGGCUCUCUGAGCUAAGAUCAU-GUGUAGUAUCUGUUCU
X71483.1/1-191       AUACCUUUCU-CGGCCUUUU-GGCUCAGAUCAU-GUGUAGUAUCUGUUCU
AF106847.1/185-380   AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
AF106845.1/257-451   AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUGAUAUCUGUUCU
AF106845.1/1870-2065 AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X69326.1/1-193       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
S72337.1/1-193       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X69327.1/1-196       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X16459.1/280-475     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X56322.1/513-709     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X56321.1/284-479     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
M72889.1/1-196       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X55840.1/268-462     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
Z37972.1/1-174       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCA
M72891.1/1-196       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
M72890.1/1-196       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
M72888.1/1-195       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
M72887.1/1-195       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
Z37973.1/1-173       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCA
X56323.1/358-553     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X15930.1/1-195       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X15936.1/256-455     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X15929.1/1-194       AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X05084.1/1-191       AUACCU-UCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X06477.1/503-698     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X06475.1/589-783     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X06473.1/389-584     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X06474.1/512-707     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X06476.1/456-651     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
X52312.1/235-430     AUACCUUUCU-CGGCCUUUU-GGCUAAGAUCAA-GUGUAGUAUCUGUUCU
#=GC SS_cons         .......<<<..<<<<.....>>>>.>>>.....................
#=GC RF              xxxxxx.xxx.xxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxx

X63784.1/412-602     UAUCAGUGUGAAAACUGAUA--CUGUCCCU-ACUAGGGACAUGU-GGUUU
X63786.1/1152-1341   UAUCAGUGUGAAAACUGAUA--CUGUCCCU-AC-UGGGACAUGU-GGUUU
X58842.1/1-191       UAUCAGUGUGAAAACUGAUA--CUGUCCCU-ACUAGGGACAUGU-GGUUU
X63786.1/549-738     UAUCAGUGUGAAAACUGAUA--CUGUCCCU-AC-UGGGACAUGU-GGUUU
AY007785.1/849-1041  UAUCAGCUUAAUAUCUGAUA--CAGCACAC-UU-GUGUGUCGA--UGAGU
AF095839.1/1586-1389 UAUCAGCUUAAUUUCUGAUA--UAUCGGAC-ACUGUCCGAUUGA-GAAAU
AF326335.1/1-142     UAUCAGAGUAACUCCUGAUA---UUGCCU---UC-GGGCAAA---GGAAU
M58665.1/571-712     UAUCAGAGUAACUCCUGAUA--C-UGCCU---UC-GGGCA-AA--GGAAU
AY007788.1/537-679   UAUCAGAGUAACUCCUGAUA--C-UGCCU---UC-GGGCA-AA--GGAAU
X56455.1/161-312     UAUCAGAGUAACUCCUGAUA--UUUGCCU---UC-GGGCAAUUA-GGAAU
U23406.1/206-352     UAUCAGAGUAACUCCUGAUA---UUGCCU---UC-GGGCAAA---GGAAU
AF047722.1/3099-3243 UAUCAGAGUAACUCCUGAUA--C--GGGCC-UUUGGCCC--A---AGGAU
M58666.1/571-715     UAUCAGAGUAACUCCUGAUA----UGGGCC--UCGGCCCA-AG--GAUA-
X56458.1/91-238      UAUCAGAGUAAUUCCUGAUA---UGGGCU---UC-GUCCCA----GGAAU
X56457.1/243-390     UAUCAGAUUAAUUCCUGAUA---UGGGCU---UC-GUCCCA----GGAAU
AY205287.1/148-4     UAUCAGAGUAAUUCCUGAUA----UGGGNC-UUUGUCCCA-----GGAAU
X56456.1/243-390     UAUCAGAUUAAUUCCUGAUA---UGGGCU---UC-GUCCCA----GGAAU
M14625.1/332-488     UUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCA--------
M23361.1/1-186       UUUCAGUUUAAUCGCUGAAA--U-CACCUC-ACUGAGGUG-UU--CCGAU
X55772.1/223-412     UUUCAGUUUAAUCGCUGAAA---UCACCUC-ACUGAGGUGUUU--CCGAU
AF053589.1/90-279    UGUCAGUGUGACAGCUGACAAACUAGCUCC-UU-GGAGCUA----GAA--
X04247.1/87-278      UAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACAAAUGU
X04241.1/85-276      UAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACAAAUGU
X04244.1/85-276      UAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACAAAUGU
X04256.1/85-275      UAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGCAACA-AAUGU
X04243.1/69-260      UAUCAGCUUAACAUCUGAUA--AGUCCUCC-AUUGGAGGACAACAAAUGU
X04246.1/87-278      UAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACAAAUGU
K02457.1/1-187       UAUCAGUUUAAUAUCUGAUA--CGUCCCCU-AUCUGGGGACCA--UAUAU
X00093.1/360-550     UAUCAGUUUAAUAUCUGAUA--CGUCCCCU-AUCUGGGGACCA--UAUAU
M12856.1/361-551     UAUCAGUUUAAUAUCUGAUA--CGUCCUCG-AUGAGAGGACUU--UAUAU
X07913.1/1061-1251   UAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA--UAUAU
X04212.1/1-187       UAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA--UAUAU
X59360.1/1-185       CAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA--UAUAU
M19204.1/1-187       UAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA--UAUAU
AF287992.1/4918-5108 UAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA--UAUAU
X54113.1/230-415     UUUCAGAAUAAUAUCUGAAA--UGCUGCUC-AUCGAGCAGCAAG-UAUAU
M58447.1/507-698     UUUCAGCUUAAUAUCUGAAA--CGCGACUC-ACCGAGUCGCUUG-UAUAU
S64589.1/1-189       UUUCAGCUUAAUAUCUGAAA--CGCGACUC-ACCGAGUCGCUUG-UAUAU
L22247.1/6321-6513   UAUCAGCUUAAUCUCUGAUA--UGUGAUCA-AC-CGAUCACUUC-GAGAU
X51380.1/303-493     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51381.1/239-429     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51372.1/210-400     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51378.1/335-525     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51374.1/284-474     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51379.1/254-444     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51375.1/389-580     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
X51376.1/309-499     UAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUAAAGGU
L25918.1/1-181       UUGCAGUGUAAUUU-UGCAA-CGGGUCUCUAAACUGAGACCAA--UAAAU
X71483.1/1-191       UAUAAGCUUAAUCGCUUAUA--UGGUUCUC-AUUGAGAACCU---GCGAU
AF106847.1/185-380   UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGCUCACUAC-GAUAU
AF106845.1/257-451   UAUCAGUUUAAUAUCUGAUA--UGUGG-CC-AUGUGCCCACUUU-GAUAU
AF106845.1/1870-2065 UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGUCUACUUU-GAUAU
X69326.1/1-193       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGUCCACAAC-GAUAU
S72337.1/1-193       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGUCCACAAC-GAUAU
X69327.1/1-196       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGCCCACAAC-GAUAU
X16459.1/280-475     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGUCCACUUC-GAUAU
X56322.1/513-709     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUUGGUCCACAU--GAUAU
X56321.1/284-479     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUUGGUCCACAC--GAUAU
M72889.1/1-196       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUUGGUCCACAC--GAUAU
X55840.1/268-462     UAUCAGUUUAAUAUCUGAUA--UGUGAGUC-AUCGACUCACAC--GAUAU
Z37972.1/1-174       UAUCAGUAUAUUACAUUAUACUG---------------------------
M72891.1/1-196       UAUCAGUUUAAUAUCUGAUA--UGUGAACC-AUCGGUUCACAC--GAUAU
M72890.1/1-196       UAUCAGUUUAAUAUCUGAUA--UGUGGACC-AUCGGUUCACAC--GAUAU
M72888.1/1-195       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUUGGUCCACAC--GAUAU
M72887.1/1-195       UAUCAGUUUAAUAUCUGAUA--UGUGAGUU-AUUGACUCACAC--GAUAU
Z37973.1/1-173       UAUUAGUAUAUUACAUUAUACU----------------------------
X56323.1/358-553     UAUCAGUUUAAUAUCUGAUA--UGUGAGUC-AUCGACUCACAC--GAUAU
X15930.1/1-195       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUUGGUCCACAC--GAUAU
X15936.1/256-455     UAUCAGUUUAAUAUCUGAUA--UGUGAGCC-AAUGGUUCACAC--GAUAU
X15929.1/1-194       UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AAUGGUCCACAC--GAUAU
X05084.1/1-191       UAUUAGUUUAAUAUCUGAUA--UGUGGGCC-AAUGGCCCACAC--GAUAU
X06477.1/503-698     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCCCACAC--GAUAU
X06475.1/589-783     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCCCACAC--GAUAU
X06473.1/389-584     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCUCACAC--GAUAU
X06474.1/512-707     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCCCACAC--GAUAU
X06476.1/456-651     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCCCACAC--GAUAU
X52312.1/235-430     UAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCCCACAC--GAUAU
#=GC SS_cons         <<<<<<........>>>>>>...<<<<<<<....>>>>>>>.........
#=GC RF              xxxxxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxxxxxxxx..xxxxx

X63784.1/412-602     CACAUU-AAUUUUUCACAGGG-GUCG-GA--UUCA-CUAGUGGCUU----
X63786.1/1152-1341   CACAUU-AAUUUUUCAAGGG--GUCG-GACAAACUA--GU-GGCUU----
X58842.1/1-191       CACAUU-AAUUUUUCACAGGG-GUCG-GA--UUUA-CUAGUGGCUU----
X63786.1/549-738     CACAUU-AAUUUUUCAAGGG--GUCG-GAUA-UAU-UAGU-GGCUU----
AY007785.1/849-1041  UGAUGUGAAUUUUUCACGGGG-GUGGCGGGUAGCU-CUGA-GGCAA----
AF095839.1/1586-1389 UAAACU-AAUUUUUUGAUGGG-GGCAAGGGGUUCCCCUCG-UGCUU----
AF326335.1/1-142     A---CA-AA----UGAUCGCA-----------CUAG--------------
M58665.1/571-712     AGAAAU-UAUAUCUCAAG--------------------------------
AY007788.1/537-679   AGAAAU-UAUAACUCAAG--------------------------------
X56455.1/161-312     --ACGA-AAUCUUUGAUCAC------------------------------
U23406.1/206-352     A---GA-AAUCAUGGUACUA------------------------------
AF047722.1/3099-3243 CA---A-AACUGUUG-CCUGU-----------------------------
M58666.1/571-715     ----GU-AACUGUUGAGGCG------------------------------
X56458.1/91-238      A---GA-AACCGCUGAUCUC-------------UCA--------------
X56457.1/243-390     A---GA-AACCGCUGAUCUC-------------UCA--------------
AY205287.1/148-4     A---GA-AACCGUUGAUCUC-------------UCA--------------
X56456.1/243-390     A---GA-AACCGCUGAUCUC-------------UCA--------------
M14625.1/332-488     -----U-UACCUUUUAAUUU--GUUACAAUACACAU--------------
M23361.1/1-186       UAAUCU-UGUUUUUGGUUUGA-GUUG-GAAAGC---CUCU-GGCUU----
X55772.1/223-412     UAAUCU-UGUUUUUGGUUUGA-GUUG-GAAAGC---CUCU-GGCUU----
AF053589.1/90-279    ----UA-UGCUGGUG-UGUGU-GUGG-AUGC-UUU-GACA-GGCUU----
X04247.1/87-278      UAAACU-CAUUUUUGGAAUCA-GACG-GAGU-GCUA--GG-GGCUU----
X04241.1/85-276      UAAACU-GAUUUUUGGAAUCA-GACG-GAGU-GCUA--GG-AGCUU----
X04244.1/85-276      UAAACU-GAUUUUUGGAAUCA-GACG-GAGU-GCUA--GG-ACCUU----
X04256.1/85-275      UAAACU-GAUUUUUGGAAUCA-GACG-GAGU-GCUA--GG-AGCUU----
X04243.1/69-260      UAAACU-GAUUUUUGGAAUCA-GACG-GAGU-GCUA--GG-AGCUU----
X04246.1/87-278      UAAACU-GAUUUUUGGAAUCA-GACG-GAGU-GCUA--GG-GGCUU----
K02457.1/1-187       UAAAUG-GAUUUUUGGAACAG-GGAGUUGGA--AGA--AG-AGCUU----
X00093.1/360-550     UAAAUG-GAUUUUUGGAACAG-GGAGAUGGA--AGA--AG-AGCUU----
M12856.1/361-551     UAAACG-GAUUUUUGGGCGCG-GGAGUUGGA--CCC--GG-AGCUU----
X07913.1/1061-1251   UAAAUG-GAUUUUUGGAAGUA-GGAGUUGGA--AUA--GG-AGCUU----
X04212.1/1-187       UAAAUG-GAUUUUUGGAACUA-GGAGUUGGA--AUA--GG-AGCUU----
X59360.1/1-185       UAAAUG-GAUUUUUGGAGCAG-GGAGAUGGA--AUA--GG-AGCUU----
M19204.1/1-187       UAAAUG-GAUUUUUGGAGCAG-GGAGAUGGA--AUA--GG-AGCUU----
AF287992.1/4918-5108 UAAAUG-GAUUUUUGGAGCAG-GGAGAUGGA--AUA--GG-AGCUU----
X54113.1/230-415     UAAUCU-GAUUUUUGGAUGAUCGGCCAUGGA-AUAG---G-GGCUU----
M58447.1/507-698     UAAACU-GAUUUUUGAACCUA-GGCCAUGGA--AUA--GG-GGCUU----
S64589.1/1-189       UAAACU-GAUUUUUGAACUUA-GGCCAUGGA--AUA--GG-GGCUU----
L22247.1/6321-6513   UAAUCU-AUUUUUGCAACCUU-GGAA-GG--UUCG-UAGG-GGCUU----
X51380.1/303-493     U-AUAU-GAUUUUUGGAACCCAGGGA-AGACUC-----GG-GGCUU----
X51381.1/239-429     U-AUAU-GAUUUUUGGAAACUAGGGA-AGACUC-----GG-GGCUU----
X51372.1/210-400     U-AUAU-GAUUUUUGGAACCUAGGGA-AGACUC-----GG-GGCUU----
X51378.1/335-525     U-AUAU-GAUUUUUGGAACCUAGGGA-AGACUC-----GG-GGCUU----
X51374.1/284-474     U-AUAU-GAUUUUUGGAACCUAGGGA-AGACUC-----GG-GGCUU----
X51379.1/254-444     U-AUAU-GAUUUUUGGAUCCUAGGAA-AGACUC-----GG-GGCUU----
X51375.1/389-580     U-AUAU-GAUUUUUGGAACCUAGGGA-AGACUC-----GG-GGCUU----
X51376.1/309-499     U-AUAU-GAUUUUUGGAACCUAGGGA-AGACUC-----GG-GGCUU----
L25918.1/1-181       UACCUG-UAUUUUUCACCUC-CGGAC-GGGU-U------G-AGCUU----
X71483.1/1-191       UAACUU-UAAUAUUUUAGGGG-GUCA-AGGCAAUG-GGGG-CGCUU----
AF106847.1/185-380   UAAAUU-UAUUUUUUGUGGG--GAGG-GUCCACCA-CAGU-GGCUU----
AF106845.1/257-451   UAAAUU-UAUUUUUUGUGGGG-GAGG-GUCCACCA-UAGU-GGCUU----
AF106845.1/1870-2065 UAAAUU-UAUUUUUCGUGGGG-GAGA-GUCCACCA-UAGU-GGCUU----
X69326.1/1-193       UAAAUU-UAUUUUUUGUGGG--GAGG-GUCCACCA-CAGU-GGCUU----
S72337.1/1-193       UAAAUU-UAUUUUUUGUGGG--GUGG-GUCCACCA-CAGU-AGCUU----
X69327.1/1-196       UAAAUU-UAUUUUUUAUGGGG-GAGG-GCCCACCA-CAGU-AGCUU----
X16459.1/280-475     UAAAUU-AAUUUUUUGUGGGG-AAAG-GUCCACUA-CAGU-GGCUU----
X56322.1/513-709     UAACUC-AAUUUUUUAAGGGG-AAGA-GUCUGUUA-AGGUUAGCUU----
X56321.1/284-479     UAACUC-AAUUUUUUAAGGGG-AAGA-GUCCAUUA-AGGU-AGCUU----
M72889.1/1-196       UAACUC-AAUUUUUUAAGGGG-AAGA-GUCCAUUA-AGGU-AGCUU----
X55840.1/268-462     UAACUC-UAUUUUUUGAGGG--GAGG-GUCUAUCA-CGGU-AGCUU----
Z37972.1/1-174       --ACUC-UAUUUUUUAGG----GGAU-GUCC-AUA-CGGU-AGCUU----
M72891.1/1-196       UAACUC-AAUUUUUUAAGGGG-GAAG-ACCCAUCA-AAGU-AGCUU----
M72890.1/1-196       UAACUC-AAUUUUUUAAGGGG-AAGA-GUCCAUUA-AGGU-AGCUU----
M72888.1/1-195       UAACUC-AAUUUUGUAAGGGG-AAGA-GUCCAUUA-AGGU-AGCUU----
M72887.1/1-195       UAACUU-AAUUUUUUAGGGG--GAAG-GUCAAUUA-GAGU-AGCUU----
Z37973.1/1-173       -AACUC-UAUUUUUGAGG----GGAU-GUCC-AUA-CGGU--GCUU----
X56323.1/358-553     UAACUC-UAUUUUUUGAGGGG-GAAG-GUCCACCA-CGGU-AGCUU----
X15930.1/1-195       UAAAUU-UAUUUCUUGAGGGG-AAGA-GUCCACCA-CAAU-AGCUU----
X15936.1/256-455     UAAAUU-UAUCUCUUGAGGGG-GAGA-GUCCACUA-CAAU-AGCUUGCUA
X15929.1/1-194       UAAAUU-UAUUUCUUGAGGGG-GAGA-GUCA-CCA-CAGU-AGCUU----
X05084.1/1-191       UAAAUU-UAUUUCUUGAGGGG-AAGA-GGCCACCA-CAGU-AGCUU----
X06477.1/503-698     UAACUC-UAUUUUUUAAGGGA-GAAA-ACCCACUA-AGGU-AGCUU----
X06475.1/589-783     UAACUC-UAUUUUUUAAGGGA-GAAA-GCCCACUA-AGAU-AGCUU----
X06473.1/389-584     UAACUC-UAUCUUUUAAGGGA-GAAA-GCCCGCUA-UGAU-AGCUU----
X06474.1/512-707     UAACUC-UAUUUUUUAAGGGA-GAAA-GCCCACUA-AGAU-AGCUU----
X06476.1/456-651     UAACUC-UAUUUUUUAAGGGA-GGAA-GCCCGUUU-AGAU-AGCUU----
X52312.1/235-430     UAACUC-UAUUUUUUGAGGGA-GAAA-GCCCACUA-AGAU-AGCUU----
#=GC SS_cons         ......................<<<<.<<<<.......<<.<<<......
#=GC RF              xxxxxx.xxxxxxxxxxxxxx.xxxx.xxxx.xxx...xx.xxxxx....

X63784.1/412-602     GCCCUAG--------U--CC-CGACGC-----GGUUGC--CCUUGG-CCU
X63786.1/1152-1341   GCCAC---------UGGUCC-CGACGC-----UGUUGC--CCUUAG-CAU
X58842.1/1-191       GCCCUAG--------U--CC-CGACGC-----GGUUGC--CCUUGG-CAU
X63786.1/549-738     GCCACUG-------GU--CC-CGACGC-----UGUUGC--CCUUAG-CAU
AY007785.1/849-1041  ACUCAGA-------GU--CCGCCACAC-----GUGUUGC-CCUGGA-GCU
AF095839.1/1586-1389 GCGCGAG-------UC-CCU-UGCCAC-----GGGUUGC-CCUGCU-AUU
AF326335.1/1-142     -------------------------GU-----UGUUUC--CCUGGA-GUU
M58665.1/571-712     -------------------------GU-----UGUUUC--CCUGGA-GUU
AY007788.1/537-679   -------------------------GU-----UGUUUC--CCUGGA-GUU
X56455.1/161-312     -------------------------GCG----AGUUUU--CCUGGA-GUU
U23406.1/206-352     -------------------------GG-----UUGUUUC-UCUGGA-GUU
AF047722.1/3099-3243 -------------------------CCCG---CGUUCU--UCCGGG-GUU
M58666.1/571-715     -------------------------CCG----GCGUCCU-CCCGGA-GUU
X56458.1/91-238      -------------------------AG-----CGUUCU--UCCGGA-GUU
X56457.1/243-390     -------------------------AG-----UGUUCC--UCCGGA-GUU
AY205287.1/148-4     -------------------------AG-----CGUUCU--UCCGGA-GUU
X56456.1/243-390     -------------------------AG-----UGUUCC--UCCGGA-GUU
M14625.1/332-488     --------------UU--UU-UGGCACC----CAAAAU--AAUAAA--AU
M23361.1/1-186       GCUAUGC-------UU--UC-CGACACU----GGUGUU--CUUGCU-AUU
X55772.1/223-412     GCUAUGC-------UU--UC-CGACACU----GGUGUU--CUUGCU-AUU
AF053589.1/90-279    GCUUGUA----GGGGC-CAU-GCACACACCAGGCAGACUCCCGGAA-GUU
X04247.1/87-278      GCUCC--------ACC--UC-UGUCAC-----GGGUUGG-CCCGGU-AUU
X04241.1/85-276      GCUCC--------ACC--UC-UGUCGC-----GGGUUGG-CCCGGU-AUU
X04244.1/85-276      GCUCC--------ACC--UC-UGUCGC-----GGGUUGG-CCCGGU-AUU
X04256.1/85-275      GCUCC--------ACC--UC-UGUCGC-----GGGUUGG-CCCGGU-AUU
X04243.1/69-260      GCUCC--------GCC--UC-UGUCGC-----GGGUUGG-CCCGGU-AUU
X04246.1/87-278      GCUCC--------ACC--UC-UGUCAC-----GGGUUGG-CCCGGU-AUU
K02457.1/1-187       GCUCU--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
X00093.1/360-550     GCUCU--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
M12856.1/361-551     GCUCC--------CUC--CG-CUCCGC-----GCAUCGU-CCCGGU-AUG
X07913.1/1061-1251   GCUCC--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
X04212.1/1-187       GCUCC--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
X59360.1/1-185       GCUCC--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
M19204.1/1-187       GCUCC--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
AF287992.1/4918-5108 GCUCC--------GUC--CA-CUCCAC-----GCAUCGA-CCUGGU-AUU
X54113.1/230-415     GCCG----------UC--CU-GGCCACG----GGUUGG--CCCGGU--UU
M58447.1/507-698     GCUCC--------GUC--CU-GGCCAC-----GGGUUGG-CCCGGU-AUU
S64589.1/1-189       GCUCC--------GUC--CU-GGCCAC-----GGGUUGG-CCCGGU-AUU
L22247.1/6321-6513   GCUCCUC----------GCC-UUCCGC-----GGGUCGA-CCCGGU-AUU
X51380.1/303-493     GCUCC---------GA--CU-UCCCAA-----GGGUCGUCCUGGCG--UU
X51381.1/239-429     GCUCC---------GU--CU-UUCCAA-----GGGUCGUCCCGGCG--UU
X51372.1/210-400     GCUCC---------GA--CU-UCCCAA-----GGGUCGUCCUGGCG--UU
X51378.1/335-525     GCUCC---------GA--CU-UCCCAA-----GGGUCGUCCUGGCG--UU
X51374.1/284-474     GAUCC---------GA--CU-UCCCAA-----GGGUCGUCCUGGCG--UU
X51379.1/254-444     GCUCC---------GA--CU-UUCCGC-----GGGUCGUACUGGCG--UU
X51375.1/389-580     GCUCUC--------GA--NU-UCCCAA-----GGGUCGUCCUGGCG--UU
X51376.1/309-499     GCUCC---------GA--CU-UCCCAA-----GGGUCGUCCUGGCG--UU
L25918.1/1-181       GCUC---------AAC--CC-GUCCAC-----GGGUCGG-CCUCGU-AUU
X71483.1/1-191       GCGUCCC-------GC--CG-CGACAG-----CUUGGCA-GGAGGC--UU
AF106847.1/185-380   GCCACUG-------GG--GC-CCUCAC-----GCGUUGCCCAGGCG--UU
AF106845.1/257-451   GCCACUA-------GG--GC-CUUCGU-----GUGUCGCCUAGGCG--UU
AF106845.1/1870-2065 GCCACUA-------GG--GC-CCUCAU-----GUGUCGCCUAGGCG--UU
X69326.1/1-193       GCCACUG-------GG--GC-CCUCAC-----GUGUUC--CCUGGACGUU
S72337.1/1-193       GCUAUUG-------GG--GC-CCACAU-----GCGUCGCCUGGGCG--UU
X69327.1/1-196       GCUGCUG-------GG--GC-CCUUGC-----GUGUCGCCCAGGCG--UU
X16459.1/280-475     GC-AUUG-------GG--UC-CCUUAU-----GUGUCGCUCUAGCG--UU
X56322.1/513-709     GCUACCU-------GG--GU-UCUUGU-----GCGUCGCCCAUGCG--UU
X56321.1/284-479     GCUGCCU-------GG--GC-UCUUGC-----GCGUCGCCCAUGCG--UU
M72889.1/1-196       GCUACCU-------GG--GC-UCUUGC-----GCGUCGCCCAUGCG--UU
X55840.1/268-462     GCUAUCG-------GG--AC-CUUUAA-----GCAUCGCCUUGGUG--CU
Z37972.1/1-174       GCUAUUGGGAUUCAGG--AC-CUUCAA-----GCGUCCU-CUGGCA--UU
M72891.1/1-196       GCUACUU-------GG--GU-CUUCAC-----GCGUCGCCUGGGCG--UU
M72890.1/1-196       GCUACCU-------GG--GC-UCUUGC-----UCGUCGCCCAUGUG--UU
M72888.1/1-195       GCUACCU-------GG--GC-UCUUGG-----GCGUCGC-CAUGCG--UU
M72887.1/1-195       GCUACUU-------GG--GU-CUUCGU-----GUGUCGCCUAGGUG--UU
Z37973.1/1-173       GCUAUUGUGAUUCAGG--AC-CUUCAA-----GCGUCCU-CUGGCG--UU
X56323.1/358-553     GCUAUCG-------AG--AC-CUUCAA-----GUCUCGCCUAGGUG--UU
X15930.1/1-195       GCUAUUC-------GG--UC-UCUUGU-----GUGUCGCUUUUGCG--UU
X15936.1/256-455     GCUAUUG-------GG--UC-UCUCAA-----GUGUUGCUUUUGCG--UU
X15929.1/1-194       GCUAUUG-------GG--UC-UCUCGC-----GUGUCGCUCUUGCG--UU
X05084.1/1-191       GCUAUUG-------GG--UC-UCUUAC-----GUGUCGCUCUUGCG--UU
X06477.1/503-698     GCUAUCU-------GG--GU-UUUCAC-----GAGUCGCCCAUGCG--UU
X06475.1/589-783     GCUAUCU-------GG--GC-UUUCAA-----GAGUCGCCCAUGCG--UU
X06473.1/389-584     GCUAUCU-------GG--GC-UUCCAC-----GAGUCGCCCAUGCG--UU
X06474.1/512-707     GCUAUCU-------GG--GC-UUUCAC-----GAGUCGCCCAUGCG--UU
X06476.1/456-651     GCUAUCU-------GG--GC-UUUCAC-----GAGUCUCCCAUGCG--UU
X52312.1/235-430     GCUAUCU-------GG--GC-UUUCAA-----GAGUCGCCUAUGCG--UU
#=GC SS_cons         >>>>>.........>>..>>.>>>>.......<<<<<<..<<<<<<....
#=GC RF              xxxxx.........xx..xx.xxxxxx.....xxxxxxx.xxxxxx..xx

X63784.1/412-602     GCA-CGCU-ACUAAGG---AGCGGCUACCCCUG
X63786.1/1152-1341   GCA-CGUA-ACUAAGG---AGUGGCUAACCCUA
X58842.1/1-191       GCA-CGCU-ACUAAGG---AGCGGCUACCCCUG
X63786.1/549-738     GCA-CGUA-ACUAAGG---AGUGGCUAACCCUA
AY007785.1/849-1041  GCA-CUAC-A-UCAGGAG-UUGGCACACCC---
AF095839.1/1586-1389 GCA-CUAC-CGGCAGG--CGCGGCCCAACCCAC
AF326335.1/1-142     CCA-CCUU--UCCAGG----GGAGCAACU----
M58665.1/571-712     CCA-CGUU--UCCAGG-----GAGCAACUC---
AY007788.1/537-679   CCA-CGUU--UCCAGG----GGAGCAACUC---
X56455.1/161-312     CCA-CUCU-UUCCAGG---CGAAGCUCGCCCUU
U23406.1/206-352     CCA-CCUU--UCCAGG---GGAGCAGCUACCUU
AF047722.1/3099-3243 CCA-CUUG--UCCGGA---CGGAGCGCGAC---
M58666.1/571-715     CCA-CGUG--UCCGGU--UGGGGCGCCGCC---
X56458.1/91-238      CCA-CGUG--UCCGGA---UGGAGCGCUUCCUU
X56457.1/243-390     UCG-CGUG--UCCGGA---UGGAGCGCUUCCUU
AY205287.1/148-4     CCA-CGUG--UCCGGA---UGGAGCGUCA----
X56456.1/243-390     UCG-CGUG--UCCGGA---UGGAGCGCUUCCUU
M14625.1/332-488     GGA-CGGG--AAGAGA---CUUUUUAAGC----
M23361.1/1-186       GCA-CUUACUGGCAAG---CGACGCCGAA----
X55772.1/223-412     GCA-CUAC-UGGCAAG---CGACGCCGAAUCUU
AF053589.1/90-279    G----UUCCG-UCCGG---AG-CUGCACUUUUU
X04247.1/87-278      GCA-GUAC-CGCCGGGAUUUCGGCCCAAC----
X04241.1/85-276      GCA-GUAC-CGCCGGGAUUUUGGCCCAAC----
X04244.1/85-276      GCA-GUAC-CGCCGGGAUUUUGGCCCAAC----
X04256.1/85-275      GCA-GUAC-CGCCGGGAUUUUGGCCCAAC----
X04243.1/69-260      GCA-GUACCC-CCGGGAUUUCGGCCCAAC----
X04246.1/87-278      GCA-GUAC-CGCCGGGAUUUCGGCCCAAC----
K02457.1/1-187       GCA-GUACCU-CCAGG--ACCGGUGCACU----
X00093.1/360-550     GCA-GUACCU-CCAGG--ACCGGUGCACUUCUC
M12856.1/361-551     GCA-GUACCU-CCGGG--CACGGUGCACCUCCC
X07913.1/1061-1251   GCA-GUACCU-CCAGG--AACGGUGCACCCCCU
X04212.1/1-187       GCA-GUACCU-CCAGG--AACGGUGCACC----
X59360.1/1-185       GCA-GUACCU-CCAGG--AACGGUGCACC----
M19204.1/1-187       GCA-GUACCU-CCAGG--AACGGUGCACC----
AF287992.1/4918-5108 GCA-GUACCU-CCAGG--AACGGUGCACUUCCC
X54113.1/230-415     GCA-CUAC-UGCCGGG---AUCGGCCACAC---
M58447.1/507-698     GCA-GUACUU-CCGGG--AUCGGCCCACCCCUC
S64589.1/1-189       GCA-GUACCU-CCGGG--AUCGGCCCACCC---
L22247.1/6321-6513   GCACCUACCU-CCGGG--AACGCCCACGCCCCC
X51380.1/303-493     GCA-CUGC--UGCCGGG-CUCGGCCCAGUCCCC
X51381.1/239-429     GCA-CUGC--UGCCGGG-CUCGGCCCAGUCCCC
X51372.1/210-400     GCA-CUGC--UGCCGGG-CUCGGCCCAGUCCCC
X51378.1/335-525     GCA-CUGC--UGCCGGG-CUCGGCCCAGUGCCC
X51374.1/284-474     GCA-CUGC--UGUCGGG-CUCGGCCCAGUCCCC
X51379.1/254-444     GCA-CUGC--UGCCGGG-CUCGGCCCAGUCCCC
X51375.1/389-580     GCA-CUGC--UGCCGGNN-UCGGCCCANNCCCC
X51376.1/309-499     GCA-CUGC--UGCCGGNN-UCGNNCCAGUCCCG
L25918.1/1-181       GCA-UUGCCU-CGAGG---UUGGCUCA------
X71483.1/1-191       ACA-CUAC--CUCUCU---UGCCGAGCACCCCA
AF106847.1/185-380   GCA-CUGC--UGCCCGGGCCUGGCGCACCCCAA
AF106845.1/257-451   GCA-CUAC--AGCCUUGG-CUGGCGCACCCCAA
AF106845.1/1870-2065 GCA-CUAC--AGCCUUGG-CUGGUGCACCCCAU
X69326.1/1-193       GCA-CUACUGUCCAGG--UGUGGCGCACCC---
S72337.1/1-193       GCA-CUGC--UGCCCUGGCCCGGCGCACCC---
X69327.1/1-196       GCA-CUGC--UGCCUGGG-CCGGCGCACCCCAC
X16459.1/280-475     GCA-CUAU--UGCUUGAGCCUGGCGCACCCCAA
X56322.1/513-709     GCA-CUAC--UGCACGGGCCUGGCGCACCCCAC
X56321.1/284-479     GCA-CUAC--UGCACGGGCCUGGCGCACCCCAC
M72889.1/1-196       GCA-CUAC--UGCAUGGGCCUGGCGCACCCCAC
X55840.1/268-462     GCA-CUAU--AACCUUGGCCUGGUGCACCGUAC
Z37972.1/1-174       GCA-CUAC--UGUCUUGGCUUGACGCACCCCCA
M72891.1/1-196       GCA-CUAC--AGCCCAGGCCUGGCACACCCCAC
M72890.1/1-196       GCA-CUAC--UGCACGGGCCUGGCGUACCCCAC
M72888.1/1-195       GCA-CUAC--UGCAUGGUCCUGGCGCACCCCAC
M72887.1/1-195       GCA-CUAU--AGCCUUGGCCUGGAGCACCCCAC
Z37973.1/1-173       GCA-CUAC--UGUCUUGACUUGACGCACCCCCA
X56323.1/358-553     GCA-CUAC--UGCCUUGGCCUGGCACACCCCAC
X15930.1/1-195       GCA-CUAU--AGCAAUUG-CUGGCGCACCCCAC
X15936.1/256-455     GCA-CUAU--AGCAAUAGCCCGACACACCCCAC
X15929.1/1-194       GCA-CUAU--AGCAAUUG-CUGGCGCACCCCAC
X05084.1/1-191       GCA-CUAU--AGCAAUUG-CUGGCGCACCC---
X06477.1/503-698     GCA-CUAC--UGCACGGGCCUGGCUCAUCCCGC
X06475.1/589-783     GCA-CUAC--UGCAAGGG-CUGGCUCAACCCGC
X06473.1/389-584     GCA-CUAC--UGCACGGGCCUGGCUCAACCCGC
X06474.1/512-707     GCA-CUAC--UGCACGGGCCUGGCUCAACCCGC
X06476.1/456-651     GCA-CUAU--UGCGAGGGCUUGGCUCAACCCGC
X52312.1/235-430     GCA-CUAC--UGCACAGGCUUGGCUCAACCCGC
#=GC SS_cons         ..........>>>>>>....>>>>>>.......
#=GC RF              xxx.xxxx..xxxxxx...xxxxxxxxxxxxxx
//
# STOCKHOLM 1.0
#=GF ID U3
#=GF AC RF00012
#=GF DE Small nucleolar RNA U3
#=GF AU Griffiths-Jones SR, Mifsud W
#=GF GA 55.3
#=GF NC 55.1
#=GF TC 55.3
#=GF SE Zwieb C, The uRNA database, PMID:9016512
#=GF SS Published; PMID:10199569
#=GF TP Gene; snRNA; guide; CD-box;
#=GF BM cmbuild CM SEED
#=GF BM cmsearch -W 350 CM SEQDB
#=GF DR URL; http://psyche.uthct.edu/dbs/uRNADB/u3/u3.html;
#=GF RN [1]
#=GF RM 9016512
#=GF RT The uRNA database.
#=GF RA Zwieb C;
#=GF RL Nucleic Acids Res 1997;25:102-103.
#=GF RN [2]
#=GF RM 10567566
#=GF RT Nuclear retention elements of U3 small nucleolar RNA.
#=GF RA Speckmann W, Narayanan A, Terns R, Terns MP;
#=GF RL Mol Cell Biol 1999;19:8412-8421.
#=GF CC Small nucleolar RNAs (snoRNAs) are involved in the processing and
#=GF CC modification of rRNA in the nucleolus. There are two main classes
#=GF CC of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA
#=GF CC is a member of the box C/D class. Indeed, the box C/D element is
#=GF CC a subset of the six short sequence elements found in all U3
#=GF CC snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA
#=GF CC secondary structure is characterised by a small 5' domain (with
#=GF CC boxes A and A'), and a larger 3' domain (with boxes B, C, C', and
#=GF CC D), the two domains being linked by a single-stranded
#=GF CC hinge. Boxes B and C form the B/C motif, which appears to be
#=GF CC exclusive to U3 snoRNAs, and boxes C' and D form the C'/D
#=GF CC motif. The latter is functionally similar to the C/D motifs found
#=GF CC in other snoRNAs.
#=GF CC The 5' domain and the hinge region act as a pre-rRNA-binding
#=GF CC domain. The 3' domain has conserved protein-binding sites. Both
#=GF CC the box B/C and box C'/D motifs are sufficient for nuclear
#=GF CC retention of U3 snoRNA. The box C'/D motif is also necessary for
#=GF CC nucleolar localisation, stability and hyper-methylation of
#=GF CC U3 snoRNA. Both box B/C and C'/D motifs are involved in specific
#=GF CC protein interactions and are necessary for the rRNA processing
#=GF CC functions of U3 snoRNA.
#=GF SQ 21

U27297.1/2-180         AGACUGUACUCCACAAGGAUCAUUUCUUGAGGAAGUAUCAGUCCGAUUCA
AF277396.1/3-126       GACCGUACUCUGAACAGAAUCGUUUUAUGAGUACAACCUCUUAAUUGAAA
L32919.1/393-532       GACCGUACUCUGAACAGAAUCGUUUUAUGAGUAUAACCUCUUAAUGGAAA
X05498.1/324-651       AACACAUUCAACAGUAGGAUCAUUUCUAUAUUAAUCGUCACUCUUUGACU
X05499.1/124-451       AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACU
M18578.1/158-485       AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACU
M26649.1/1-332         GUCGACGUACUUCAUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACU
AL121770.1/10682-10430 UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUU
X13850.1/317-568       GUAUCGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCUUCUUGGGUU
Z12613.1/694-912       AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUGUACCUGGUGAAAUGU
X07318.1/1-219         AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUGUACCUGGUGAAAUGU
X07319.1/1-197         AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUUUACCUGGUGAGAUGU
J01884.1/1-214         AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUU
V01267.1/2-213         GUGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUU
X14945.1/538-753       AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUU
V00190.1/62-269        AUGACCAAAC-UCUUAGGAUCAUUUCUAGAGUAUCGUCUAUUAAAAUUAU
X79685.1/140-354       CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCGUUGCAUCC
X63065.1/859-1073      CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCGCUGCAUCC
Z29641.1/760-980       CGACCUUACUUGAACAGGAUCUGUUCUAUAGGAU-CGUACUGUUGCAUCU
X52629.1/326-541       CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCC
X52630.1/530-744       CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCC
#=GC SS_cons           ......<<<<<<<<.<<<..<<<<<<..<<<<.....>>>>..>>>>>>.
#=GC RF                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

U27297.1/2-180         CAGAGAACACUACAAUCUUCAA----CAGCCACGAUGAUGACUGG--CA-
AF277396.1/3-126       AAAAACCGAGUUUCAAAUCCUG------------AUGAUGACGG--UUG-
L32919.1/393-532       AGAAACCGAGUUUCAAAUCCUG------------AUGAAGACGG--UUG-
X05498.1/324-651       CUUCAAAAGAGCCACUGAAUCC-----AACUUGGUUGAUGAGCC-C-CA-
X05499.1/124-451       CUUCAAAAGAGCCACUGAAUCC-----AACUUGGUUGAUGAGUC-C-CA-
M18578.1/158-485       CUUCAAAAGAGCCACUGAAUCC-----AACUUGGUUGAUGAGUC-C-CA-
M26649.1/1-332         CUUCAAAAGAGCCACUGAAUCC-----AACUUGGUUGAUGAGUC-C-CA-
AL121770.1/10682-10430 UCCUAACCUAGCCACAGAACUC-----AACACGGAUGAUGAUAG------
X13850.1/317-568       UCCUAACCUAGCCACAGAAGUG-----AACACGGAUGAUGAUAG------
Z12613.1/694-912       GCUCGAAAGUGUCUGAACUCAC----AAACCACGAGGAAGAGCGU--CA-
X07318.1/1-219         GCUCGAAAGUGUCUGAACUCAC----AAACCACGAGGAAGAGCGU--CA-
X07319.1/1-197         GCUCUAAAGUGUCUGAACUCAC----AAACCACGAGGAAGAGCGU--CA-
J01884.1/1-214         CUCUGACUGUGUAGAGCACCCG----AAACCACGAGGAGGAGACG--UA-
V01267.1/2-213         CUCUGACUGUGUAGAGCCCACG----AAACCACGAGGACGAGACA--UA-
X14945.1/538-753       CUCUGAACGUGUAGAGCACCGA----AAACCACGAGGAAGAGAGG--UA-
V00190.1/62-269        UCAUCAAUAAUUUUUCCUCUUUCA--CAGCUAGGAUGAUGAUACA--CA-
X79685.1/140-354       UUGACUAAUAAGGAGGCAAGCAC-UUAAGCUUGGUUGAUGACGC---AUG
X63065.1/859-1073      UUUACCAAUAAGGAGGCAAGCAC-UUCAGUCUGGUUGAUGCAUC----UG
Z29641.1/760-980       UUGAUUAAUAAGAAGGCAAGUAC-UUAAACCUGGUUGAUGAGAAU--UUG
X52629.1/326-541       UUGAUUUCUCAAGAGACAGGCCC-UUAACCCUGGUUGAUGAACC---AUG
X52630.1/530-744       UUGAUUUCUCAAGAGACAGGCCU-UAAACCCUGGUUGAUGAACC---AUG
#=GC SS_cons           .>>>>>>>>>>>.................<<<<.................
#=GC RF                xxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx...xx.

U27297.1/2-180         --GCUUUCCUCUCGGA-GCGUGAGGCAGCG--------------------
AF277396.1/3-126       ---CUUUCUCCGCCC--GGAGAGCGUUUC---------------------
L32919.1/393-532       ---CUUUCUUCGCCC--GGAGAGCGCUUC---------------------
X05498.1/324-651       -UAACCUUUGUACCCCAGAGUGAGGAAAUGAAAUCGAAUUUAAAUUAGCU
X05499.1/124-451       -UAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCU
M18578.1/158-485       -UAACCUUUGUACCCCAGAGUGAGAAACCGAAAU-GAAUCUAAAUUAGCU
M26649.1/1-332         -UAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCU
AL121770.1/10682-10430 -GAGGCACCGUUGCCCUCAGAGUGAGGACU--------UUUAA-------
X13850.1/317-568       -GAGGCACCGUUGCCU-CAGAGUGAGGACU--------UUUAA-------
Z12613.1/694-912       ---GUGUUCUCUCCU--GAGCGUGAAGUGA--------------------
X07318.1/1-219         ---GUGUUUUCUCCU--GAGCGUGAAGUGA--------------------
X07319.1/1-197         ---GUGUCUUCUCCU--GAGCGUGAAGUGA--------------------
J01884.1/1-214         ---GCGUUCUCUCCU--GAGCGUGAAGCCG--------------------
V01267.1/2-213         ---GCGUCCCCUCCU--GAGCGUGAAGCCG--------------------
X14945.1/538-753       ---GCGUUUUCUCCU--GAGCGUGAAGCCG--------------------
V00190.1/62-269        -----CUCACUAUACGAAAGCGUGAAACCG--------------------
X79685.1/140-354       A----CCUGUGGGCCA-GAGCGUGAUU-AA--------------------
X63065.1/859-1073      A----CCUCUGGGCCA-GAGCGUGAUU-AA--------------------
Z29641.1/760-980       A----CCUGUGGGCCA-GAGCGUGAUUUAA--------------------
X52629.1/326-541       A----CCGUGCGGCUA-GAGCGUGAUU-GA--------------------
X52630.1/530-744       A----CCGUGCGGCUA-GAGCGUGAUU-GA--------------------
#=GC SS_cons           ...<<<<<<<<<<<<..............<....................
#=GC RF                ...xxxxxxxxxxxx..xxxxxxxxxxxxx....................

U27297.1/2-180         --------------------------------------------------
AF277396.1/3-126       --------------------------------------------------
L32919.1/393-532       --------------------------------------------------
X05498.1/324-651       UGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAUUU
X05499.1/124-451       UGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUU
M18578.1/158-485       UGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUU
M26649.1/1-332         UGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUU
AL121770.1/10682-10430 --------------------------------------------------
X13850.1/317-568       --------------------------------------------------
Z12613.1/694-912       --------------------------------------------------
X07318.1/1-219         --------------------------------------------------
X07319.1/1-197         --------------------------------------------------
J01884.1/1-214         --------------------------------------------------
V01267.1/2-213         --------------------------------------------------
X14945.1/538-753       --------------------------------------------------
V00190.1/62-269        --------------------------------------------------
X79685.1/140-354       --------------------------------------------------
X63065.1/859-1073      --------------------------------------------------
Z29641.1/760-980       --------------------------------------------------
X52629.1/326-541       --------------------------------------------------
X52630.1/530-744       --------------------------------------------------
#=GC SS_cons           ..................................................
#=GC RF                ..................................................

U27297.1/2-180         --------------AGCGACCUCGGUCGCAUCGCAUCGAUGAUCGCA---
AF277396.1/3-126       --------------------------------------------------
L32919.1/393-532       --------------------------------------------------
X05498.1/324-651       UG-CUUUGCCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGAUA
X05499.1/124-451       UU-CUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUA
M18578.1/158-485       UUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUA
M26649.1/1-332         UUGCUUUGGCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUA
AL121770.1/10682-10430 -UUCUUUGAAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGC
X13850.1/317-568       -UUCUUUGAAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGC
Z12613.1/694-912       -------------GCUC-ACAGU-GCUGCUUCA-UUGUGGCUGCUGUUUG
X07318.1/1-219         -------------GCUC-ACAGU-GCUGCUUCA-UUGUGGCUGCUGUUUG
X07319.1/1-197         -------------GCUC-UCAGU-GCUGCUUCA-UUGUGGCUGCUGUUUG
J01884.1/1-214         -------------GCUC-UUAGU-GUUGCUUCC-GUGCAACUGCUAUUGG
V01267.1/2-213         -------------GCUC-UAGGU-GCUGCUUC--UGCCUCUUGCCAUUGG
X14945.1/538-753       -------------GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAG
V00190.1/62-269        ------------UUAUUAUCAAAUGAUUCAUUUAUUUGUUAUUAACAUU-
X79685.1/140-354       ---------CGGCC-GGAUCACUGGCUGAUUU--GAUC--CCACGGCUGU
X63065.1/859-1073      ---------CGGCCAGGAUUCCCUUAUGGGGGCAAUCCACG----GCUGU
Z29641.1/760-980       ---------CGGCCAGGACUUUG-CCUUGGUGC-AUUGUC-UGGAGCUGC
X52629.1/326-541       ---------CGGCUACGAU-CGUCCUCGGACGC-AUCCAGU----GCUGU
X52630.1/530-744       ---------CGGCUACGAU-CGUCCUUGGAUGC-AUCCGGU----GCUGU
#=GC SS_cons           .............<<...<<<<<.<<<<<.......>>>>>.>>>>>..>
#=GC RF                .............xxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxx

U27297.1/2-180         -------------GAUGAGAGG---------------UCAGCAAUUUGAG
AF277396.1/3-126       -------------GAUGAACGG-------------CA-------------
L32919.1/393-532       -------------GAUGAACGG-----------CAGAAGAAAGUUCCAGA
X05498.1/324-651       UUUAAUGG--CGCGAUGAUCUUGACCCAUCCUAUGUGCUUCCAUUUUGGA
X05499.1/124-451       UUUUAUGG--CGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAA
M18578.1/158-485       UUUUAUGG--CGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAA
M26649.1/1-332         UUUUAUGG--CGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAA
AL121770.1/10682-10430 UGUCUUUCUAUGCGAUGAUCUC---UUACAUGAUAUGUUUCCUUUUGGU-
X13850.1/317-568       UGUCAGAGUAUGCGAUGAUCUC---UUACAUGAUAUGUUUCCUUUUGGU-
Z12613.1/694-912       CUAUU--------GAUGAACGU------UCUG-CUCCCCUUUA-UUAUUG
X07318.1/1-219         CUAUU--------GAUGAACGU------UCUG-CUCCCCUUUA-UUAUUG
X07319.1/1-197         CUAUU--------GAUGAACGU------UCUACUUCCCCUUUA-UUAUUG
J01884.1/1-214         CCAUU--------GAUGAUCGU------UCUCGGUCCUCU-------CUG
V01267.1/2-213         CAGCU--------GAUGAUCG-------UCUUCUCUCCUU-------CGG
X14945.1/538-753       CCAUU--------GAUGAUCGU------UCUUCUCUCCGUA------UUG
V00190.1/62-269        -------------GAUGACCGU------------CUAAUUCA----GGGA
X79685.1/140-354       A------------GAGGAUCGU------UUCU--UGCCGGGCC-UCGCCU
X63065.1/859-1073      A------------GAGGAUCGU------UCCUG--CCUUGCUC--AUGCU
Z29641.1/760-980       A------------GAUGAUCGU------UCUUG-GCCAGGCUU-AAUGUC
X52629.1/326-541       A------------GAGGAUCGU------UACUC-GGCUCGGUUUCUACCU
X52630.1/530-744       A------------GAGGAUCGU------UACUC-GGCUCGGUU-CUACCU
#=GC SS_cons           >>..........................<<<..<<<<<<..........>
#=GC RF                x............xxxxxxxxx......xxxxx.xxxxxxxxx.xxxxxx

U27297.1/2-180         UGG----------------U-------------------------
AF277396.1/3-126       -GGA----------------G------------------------
L32919.1/393-532       AGGAU----------------------------------------
X05498.1/324-651       AGG-AUAGGGAUUCAUGGGUGGGUAC-AAAUGGCAGUCUGAC---
X05499.1/124-451       GGG-AUAGGGCUCUAUGGGUGGGUAC-AAAUGGCAGUCUGAC---
M18578.1/158-485       GGG-AUAGGGCUCUAUGGGUGGGUAC-AAAUGGCAGUCUGAC---
M26649.1/1-332         GGG-AUAGGGCUCUAUGGGUGGGUAC-AAAUGGCAGUCUGACAAG
AL121770.1/10682-10430 -CGUAUUAUGU---A----GGGCAGCUGGUGUUUU--CUGACGUG
X13850.1/317-568       -CGUAUUAUGU-------AGGGCAGCUGGUGUUUU--CUGACGUG
Z12613.1/694-912       GGGAGAUGGA----------GGGAGA-GAACACA-GGCUGAGUGG
X07318.1/1-219         GGGAGAUAGA----------GGGAGA-GAACACA-AGCUGAGUGG
X07319.1/1-197         GGGAGAUGGA-----------------------------------
J01884.1/1-214         AGGGGCGAGA----------GGGAGA-GAACGCA-GUCUGAGUGG
V01267.1/2-213         GGGGGUAAGA----------GGGAGG-GAACGCA-GUCUGAGUGG
X14945.1/538-753       GGGAGUGAGA----------GGGAGA-GAACGCG-GUCUGAGUGG
V00190.1/62-269        UGAA----------UUGGUUGUAUGG-UGGGAU---UCGUACUGG
X79685.1/140-354       GGCC--AGGA---------UGGCUCU-CAGGUU--GUCUGACAGG
X63065.1/859-1073      UGUG-CAGGG---------UGGCCCA-GAGGUU--GUCUGACAGA
Z29641.1/760-980       UGGC-UAGGG---------UGGCCUA-CAGGCU--GUUUGACAGG
X52629.1/326-541       UGCC-GGGG----------UGGUCGC-ACGGCG--GUCUGACAGG
X52630.1/530-744       UGUC-GGGG----------UGGUCGC-ACGGCG--GUCUGACAGG
#=GC SS_cons           >>>>>..>>>..........>>>>>>.>>>>>>........>>>>
#=GC RF                xxxx.xxxxx..........xxxxxx.xxxxxx..xxxxxxxxxx
//
