X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=utils%2Fjalviewjs%2Fsite-resources%2Fexamples%2FRF00031_folded.stk;fp=utils%2Fjalviewjs%2Fsite-resources%2Fexamples%2FRF00031_folded.stk;h=e7a76fba13840b9fa75d9b6dba6ec8b55e9e4dab;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=0000000000000000000000000000000000000000;hpb=056dad85a910551cc95e44d451a61f6b8c4dd35d;p=jalview.git diff --git a/utils/jalviewjs/site-resources/examples/RF00031_folded.stk b/utils/jalviewjs/site-resources/examples/RF00031_folded.stk new file mode 100644 index 0000000..e7a76fb --- /dev/null +++ b/utils/jalviewjs/site-resources/examples/RF00031_folded.stk @@ -0,0 +1,227 @@ +# STOCKHOLM 1.0 + +#=GF ID SECIS_1 +#=GF AC RF00031 +#=GF DE Selenocysteine insertion sequence 1 +#=GF AU Griffiths-Jones SR +#=GF GA 20.0 +#=GF NC 0.0 +#=GF TC 22.6 +#=GF PI SECIS +#=GF SE Gautheret D, PMID:12458087 +#=GF SS Published; PMID:12458087 +#=GF TP Cis-reg; +#=GF BM cmbuild -F CM SEED; cmcalibrate --mpi -s 1 CM +#=GF BM cmsearch -Z 169604 -E 1000 --toponly CM SEQDB +#=GF DR SO:1001274 SO:SECIS_element +#=GF DR GO:0001514 GO:selenocysteine incorporation +#=GF RN [1] +#=GF RM 8634917 +#=GF RT A novel RNA structural motif in the selenocysteine insertion element +#=GF RT of eukaryotic selenoprotein mRNAs. +#=GF RA Walczak R, Westhof E, Carbon P, Krol A; +#=GF RL RNA 1996;2:367-379. +#=GF RN [2] +#=GF RM 12458087 +#=GF RT A survey of metazoan selenocysteine insertion sequences. +#=GF RA Lambert A, Lescure A, Gautheret D; +#=GF RL Biochimie 2002;84:953-959. +#=GF CC The incorporation of selenocysteine into a protein sequence +#=GF CC is directed by an in-frame UGA codon (usually a stop codon) +#=GF CC within the coding region of the mRNA. Selenoprotein mRNAs +#=GF CC contain a conserved secondary structure in the 3' UTR that +#=GF CC is required for the distinction of UGA stop from UGA +#=GF CC selenocysteine. The selenocysteine insertion sequence +#=GF CC (SECIS) is around 60 nt in length and adopts a hairpin +#=GF CC structure which is sufficiently well-defined and conserved +#=GF CC to act as a computational screen for selenoprotein genes [2]. +#=GF WK http://en.wikipedia.org/wiki/SECIS_element +#=GF SQ 61 + +#=GS D.melanogaster.1 AC AY119185.1/838-902 +#=GS D.melanogaster.2 AC AC092237.1/57223-57161 +#=GS D.melanogaster.3 AC AY060611.1/560-627 +#=GS O.niloticus.1 AC Y11109.1/1272-1330 +#=GS O.niloticus.2 AC Y11109.1/927-987 +#=GS O.niloticus.3 AC Y11111.1/1260-1324 +#=GS D.rerio.1 AC AF322071.1/1577-1642 +#=GS X.laevis.1 AC L28111.1/1299-1365 +#=GS G.gallus.1 AC AF125575.1/5781-5843 +#=GS G.gallus.2 AC Y11110.1/1218-1277 +#=GS G.gallus.3 AC Y11273.1/1139-1211 +#=GS M.musculus.1 AC AF195142.1/461-524 +#=GS M.musculus.2 AC AF021345.1/10097-10160 +#=GS M.musculus.3 AC X03920.1/1172-1235 +#=GS M.musculus.4 AC AF096875.1/5504-5568 +#=GS M.musculus.5 AC AF241527.2/359-424 +#=GS M.musculus.6 AC AF136399.1/1808-1868 +#=GS M.musculus.7 AC X84742.1/5239-5302 +#=GS M.musculus.8 AC AF288740.1/1291-1357 +#=GS M.musculus.9 AC AF274027.1/835-900 +#=GS M.musculus.10 AC AB030643.1/4176-4241 +#=GS M.musculus.11 AC AL645723.11/192421-192359 +#=GS M.musculus.12 AC AC002327.1/156204-156268 +#=GS M.musculus.13 AC AF333036.1/2190-2249 +#=GS M.musculus.14 AC U43285.1/2009-2075 +#=GS R.norvegicus.1 AC X57999.1/1526-1586 +#=GS R.norvegicus.2 AC M63574.1/1465-1528 +#=GS R.norvegicus.3 AC AF390544.1/1076-1142 +#=GS R.norvegicus.4 AC AF072865.1/1887-1947 +#=GS R.norvegicus.5 AC X12367.1/703-764 +#=GS R.norvegicus.6 AC U25264.1/366-432 +#=GS R.norvegicus.7 AC L24896.1/600-665 +#=GS H.sapiens.1 AC AF201385.1/3055-3117 +#=GS H.sapiens.2 AC AL049837.4/130674-130738 +#=GS H.sapiens.3 AC U67171.1/375-442 +#=GS H.sapiens.4 AC AF195141.1/689-759 +#=GS H.sapiens.5 AC X53463.1/847-903 +#=GS H.sapiens.6 AC AF093774.1/5851-5916 +#=GS H.sapiens.7 AC X58295.1/1384-1453 +#=GS H.sapiens.8 AC AL833145.1/1479-1545 +#=GS H.sapiens.9 AC S48220.1/1731-1788 +#=GS H.sapiens.10 AC X71973.1/730-791 +#=GS H.sapiens.11 AC AF166127.1/1919-1981 +#=GS H.sapiens.12 AC U43286.1/2054-2120 +#=GS H.sapiens.13 AC BC003127.1/865-928 +#=GS H.sapiens.14 AC S79854.1/1605-1666 +#=GS H.sapiens.15 AC X13710.1/946-1008 +#=GS B.taurus.1 AC D88033.3/5711-5774 +#=GS B.taurus.2 AC D25220.1/1493-1556 +#=GS B.taurus.3 AC AB017534.1/661-726 +#=GS B.taurus.4 AC AB032826.1/1401-1464 +#=GS B.taurus.5 AC AB022283.1/1669-1729 +#=GS B.taurus.6 AC AF053984.1/1951-2017 +#=GS B.taurus.7 AC X13684.1/700-760 +#=GS O.aries.1 AC U67853.1/375-442 +#=GS S.scrofa.1 AC AF380118.1/366-433 +#=GS S.scrofa.2 AC L12743.1/694-758 +#=GS S.scrofa.3 AC AF532927.1/678-740 +#=GS S.scrofa.4 AC X76008.1/2709-2772 +#=GS C.elegans.1 AC U61947.2/4246-4309 +#=GS S.mansoni.1 AC L37762.1/2940-3006 + +D.melanogaster.1 G.AGCC.CU...AUGAUCGAUGAUUGG.CAAA.UCCUCUC..GAGG..A.......ACCGAUC.G.U.UGAGAA..CCCCU.....UUGCCUU +#=GR D.melanogaster.1 SS ................(((((((((((......((((......)))..)........)))))).).).)))...................... +D.melanogaster.2 C.AUUCAACU.UAUGAGGAUUAUUUCU.UAAA.GGCCUCU...GGC..U.......CGGAAAU.A.G.UCUGAA...CCU........UAUUG +#=GR D.melanogaster.2 SS ................(((((((((((......((((......)))..)........)))))).).).)))...................... +D.melanogaster.3 G.UGGCGCU..UAUGACGCAGUUGUCU.UAAA.CUCGAAC..UCGA.GC........GGGCAA.U.U.GCUGAU...UACG...AUUAACCAC +#=GR D.melanogaster.3 SS (.(((...(....((((((((((((((......((((......))).).........)))))).).).)).).)...)).....)....)))) +O.niloticus.1 G.UUUCUCA...GUGAAGGCUACAGAU.UAAA..CCUCU....GGC...........CUCUGG.A.G.CCAGAU..GCAUU.......GAAAC +#=GR O.niloticus.1 SS ......(((...(((..(((((.((..........)).)....)))...........)((((.......))))....)))).......))... +O.niloticus.2 U.GUUUAUU..AAUGACGGCUACAGAU.UAAA..CCUUU....AGC...........CUCUGG.A.G.CCAGAU..GCAUU......CAAACA +#=GR O.niloticus.2 SS ..((((.....((((..(((((.((..........)).)....)))...........)((((.......))))....)))).......)))). +O.niloticus.3 G.UGUCUCU...GUGAAGUUCGGUUUU.UAAA.AGGGUCA...UCC..A.......GAAAACC.G.ACACUGAU..GUUUC......CGACAC +#=GR O.niloticus.3 SS (.((((..........(((((((((((.(......((.......))..........))))))).).).))).................))))) +D.rerio.1 A.UGUGGUCUUUAUGAAGGCAGGUGCA.GAAA.CUAUGCA...CUA.GU........GGUGUC.U.G.UCUGAU..GUUUG.......GCCAU +#=GR D.rerio.1 SS ...((((((.......(((((((..(.....(.(((........)).)).........)..)).).).))).........).......))))) +X.laevis.1 G.UGUUUGCA.AAUGACGACCGAUUUU.GAAA.UGGUCUCACGGCC..A.......AAAACUC.GUG.UCCGAC...AUC........AACCC +#=GR X.laevis.1 SS .................((((((.(((......(((((....))))..)........))).)).).).))....................... +G.gallus.1 G.UGUGUUU...AUGAAGAGCACUAAC.AAAA.GAGUAAU.UGACU..C.......AGUUGGU.G.U.UCAGAU..GCU.........CUCAC +#=GR G.gallus.1 SS (.((.(..(...((...((((((((((......((((......)))..)........)))))).).).))..))..)...........).))) +G.gallus.2 U.AUUUGUC...AUGACAGUCACAGCA.UAAA..GCGCA....GAC...........GGCUGU.G.A.CCUGAU..UUUAG......AAAAUA +#=GR G.gallus.2 SS ................((((((((((................................))))).).)..)))..................... +G.gallus.3 U.AUUUCUU..UGUGAUGACCGAUUUU.GAAA.UGGGUUU...CUC..UAAUGCCAGGAAAUC.GUG.UCUGAU...GUUG.....UCAAGUA +#=GR G.gallus.3 SS ......(((...(..((((((((((((......((((((..........))).))).)))))).).).)).......)).......).))).. +M.musculus.1 G.UCACCGA...AUGAUCUGCUCUGGU.CAAA.UCCUUCU...AUG..C......CAGCCAGG.G.U.GGUGAU..GACCC.......GUGAC +#=GR M.musculus.1 SS (.((((.(....((.(((.((((((((..............................)))))).).).))).)).....)........))))) +M.musculus.2 G.UUACAUU..AAUGAGAACAGAAACA.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU..AGCUU.......GUAAU +#=GR M.musculus.2 SS (.(((((..........(((((((((........(((......)))............))))).).).))..........).......))))) +M.musculus.3 G.GUUCUUC..CAUGAUGGUGUUUCCUCUAAA..UUUGC....ACG...........GAGAAA.C.A.CCUGAU.UUCCAG.....GAAAAUC +#=GR M.musculus.3 SS (.(((.(((..(..((.((((((((.(((................)...........)))))).).).))......))..).....))))))) +M.musculus.4 G.UGUGCGA...AUGAUAACUACUGAC.GAAA.GAGCUGU.CUGCU..C.......AGUCUGU.G.G.UUGGAU...GUAG......UCACAC +#=GR M.musculus.4 SS (.(((((.........(((((((.(((......((((......)))..)........))).)).).).))).........).......))))) +M.musculus.5 G.CCGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUUA...GAC..C.....UGUGGUCUU.U.C.CUCGAU..GUUCC......UGCGGC +#=GR M.musculus.5 SS (.((((..(...((...((((((((((.(.....(((......)))..........))))))).).).))..))..)...........))))) +M.musculus.6 G.UCAGAUG...AUGAUGGCCUGGGCA.GAAA.CCCCAUG..UGGG..C........CGCCCA.G.G.UUUGAA...CCC........CUGGC +#=GR M.musculus.6 SS (.((((...........(((((((((..(.....(((......)))..).........))))).).).))..................))))) +M.musculus.7 G.UGUCUCU...AUGAAGGAGGGGCCC.GAAG.CCCUUGU...GGG..C........GGGCCU.C.C.CCUGAG...CCCG....UCUGUGGU +#=GR M.musculus.7 SS ................(((.(((((((....(.(((.......)))..)........)))))).)...)))..(...(((........).))) +M.musculus.8 U.UUGCAUU..AAUGAGGAUUACACAG.AAAA.CCUUUGU..UAAG.GA.......CUUGUGU.AGA.UCUGAU..AAUUG.......GCAAA +#=GR M.musculus.8 SS ..((((......((.(((.((((((((......((((......))).).........)))))).))..))).))..............)))). +M.musculus.9 C.CGGCACU..CAUGAAGGUCUGCUUG.AAAA.CCAGCCU..GCUG.GU........GGGGCA.G.U.CCUGAG.GACCUG.......GCGUG +#=GR M.musculus.9 SS (.(((..((..((....((.((((((.....(.((((......))).)).........))))).)...))))))...)).).......).... +M.musculus.10 C.CGGCACU..CAUGAAGGUCUGCCUG.AAAA.CCAGCCU..GCUG.GU........GGGGCA.G.U.CCUGAG.GACCUG.......GCGUG +#=GR M.musculus.10 SS (.(((..((..((....((.((((((.....(.((((......))).)).........))))).)...))))))...)).).......).... +M.musculus.11 U.AUUUGUG..UAUGAUGGUCACAGUG.UAAA..GUUCC....CAC...........AGCUGU.G.A.CUUGAU..UUUUA....AAAAUGUC +#=GR M.musculus.11 SS (.((((...........((((((((((.(...............))...........).)))).).).))................))))).. +M.musculus.12 C.UCAGCAG..GAUGAUGAGAAGGGCU.GAAA.UGCUGCC..AAAC..C.......AGGUCCU.U.U.UCUGAU..GGUGG.......CUGGG +#=GR M.musculus.12 SS (.(((((..........((((((((((......((....)..)..............)))))).).).))..........).......))))) +M.musculus.13 C.AUGCGUC..CAUGAAGUCACUGGCC.UCAA.GCCCAA....GUG.GU........GGGCAG.U.G.ACAGAA...GA.........GCUGC +#=GR M.musculus.13 SS (.(((......))))..(((((((.((......(((.........).))........)).))).).).))....................... +M.musculus.14 C.UCUGAUA...AUGAUGUCUCUCCCU.CUAA.CUCCCAGUAAGGA..C........UGGGAG.A.G.GCUGAACAAACCU.......CAGAG +#=GR M.musculus.14 SS (.(((((.........(((.((..(((.(.....(((((((....)..)........)))))).).).)..)))))....).......))))) +R.norvegicus.1 A.UAUUUGUU.UAUGAUGGUCACAGUG.UAAA..GUUCA....CAC...........AGCUGU.G.A.CUUGAU..UUUUA.......AAAAU +#=GR R.norvegicus.1 SS ....((((.........((((((((((.(...............))...........).)))).).).)).........)).......))... +R.norvegicus.2 G.UUACAUU..GAUGAGAACAGAAACA.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU..AGCUC.......GUAAU +#=GR R.norvegicus.2 SS ............((((((((((((((........(((......)))............))))).).).))........))).......))... +R.norvegicus.3 U.UUGCAUU..AAUGAGGAUUACACAG.AAAA.CCUUUGU..UAAGGGU........UUGUGUCG.A.UCUGCU..AAUUG.......GCAAA +#=GR R.norvegicus.3 SS ..((((..........(((((((((((.(....((((......)))).)........)))))).).).))).................)))). +R.norvegicus.4 G.UCAGAUG...AUGACGGCCUGUGCA.GAAA.CCCCCAC.GUGGG..C........UGC.CA.G.G.UUUGAA...CCC........CUGGC +#=GR R.norvegicus.4 SS (.(((........)))).(((..((...(.......)..).)..))..).........((.((.(.(............)........))))) +R.norvegicus.5 G.UUUUUCC...AUGACGGUGUUUCCUCUAAA..UUUAC....AUG...........GAGAAA.C.A.CCUGAU.UUCCAG......AAAAAU +#=GR R.norvegicus.5 SS (.((((((......(((((((((((.((((..............))...........)))))).).).)).).).)....)......)))))) +R.norvegicus.6 G.CCGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUCA.AAGAC..C.....UGUGGUCUU.U.C.UUCGAU..GUUCU.......GCGGC +#=GR R.norvegicus.6 SS (.((((..(...((((..(((((((((.(.....(((......)))..........))))))).).).))).))..)...........))))) +R.norvegicus.7 C.CGGCACU..CAUGACGGUCUGCCUG.AAAA.CCAGCCC..GCUG.GU........GGGGCA.G.U.CCCGAG.GACCUG.......GCGUG +#=GR R.norvegicus.7 SS (.(((..((..(.....((.((((((.....(.((((......))).)).........))))).)...)).)))...)).).......).... +H.sapiens.1 G.CCAGAUG...AUGACGACCUGGGUG.GAAA.CCUACCC.UGUGG..G........CACCCA.U.G.UCCGAG...CCCC.......CUGGC +#=GR H.sapiens.1 SS (.((((...........(((.((((((......(((((....))))..)........))))))...).))..................))))) +H.sapiens.2 G.UGUGCGG...AUGAUAACUACUGAC.GAAA.GAGUCAU.CGACU..C.......AGUUAGU.G.G.UUGGAU...GUAG......UCACAU +#=GR H.sapiens.2 SS (.(((((.........(((((((((((......(((((....))))..)........)))))).).).))).........).......))))) +H.sapiens.3 G.ACGCUUC...AUGAUAGGAAGGACU.GAAA.AGUCUUG.UGGAC..A.....CCUGGUCUU.U.C.CCUGAU..GUUCU......CGUGGC +#=GR H.sapiens.3 SS ..(((...(...((.(..(((((((((.......(((......)))...........)))))).).).).).))..)..........)))... +H.sapiens.4 G.ACUGACAU.UAUGAAGGCCUGUACU.GAAG.ACAGCAA..GCUG..U.......UAGUACA.G.A.CCAGAU..GCUUU..CUUGGCAGGC +#=GR H.sapiens.4 SS ...(((.((.....(((((((((((((....(.((((......)))..).......))))))).)...........)))))..).)).))).. +H.sapiens.5 U.UCACAGA...AUGAUGGCACCUUCC.UAA...ACCCU....CAU...........GGGUGG.U.G.UCUGAG..AGGC........GUGAA +#=GR H.sapiens.5 SS ..((((...........((((((...........((((...................)))))).).).))..................)))). +H.sapiens.6 G.UGUGCGG...AUGAUAACUACUGAC.GAAAGAGUCAUC...GAC..C.....UCAGUUAGU.G.G.UUGGAU...GUAG......UCACAU +#=GR H.sapiens.6 SS (.(((((.........(((((((((((....((.(((......)))..).....)..)))))).).).))).........).......))))) +H.sapiens.7 U.GGCGUCUU.CAUGAGGGAGGGGCCC..AAA.GCCCUUG..UGGG..C........GGACCU.C.C.CCUGAG...CCUGUCUGAGGGGCCA +#=GR H.sapiens.7 SS ..(((.((((.((...((((((((.........((((......)))..)...............).).)))......)))...))))))))). +H.sapiens.8 U.UUGCUUU..AAUGAGAAUAGAAACG.UAAA..CUAUGA.CCUAG.G.........GGUUUC.U.G.UUGGAU.AAUUAG.....CAGUUUA +#=GR H.sapiens.8 SS ..(((((..........(((((((((........(((......)))............))))).).).)).........)).....))).... +H.sapiens.9 U.AUUUGUU..UAUGAUGGCCACAGCC.UAAA..GUACA....CAC...........GGCUGU.G.A.CUUGAU...UCA........AAAGA +#=GR H.sapiens.9 SS .............(((.((.(((((((..............................)))))).)...)).......)))............. +H.sapiens.10 C.CGGCACU..CAUGACGGCCUGCCUG.CAAA..CCUGC....UGG..U........GGGGCA.G.A.CCCGAA.AAUCCA.......GCGUG +#=GR H.sapiens.10 SS ...((((....(......)..))))............((....(((..(........(((........))))......))).......))... +H.sapiens.11 G.CCGGAUG...AUGACGACCUGGGUG.GAAA.CCUACCC.UGUGG..G........CACCCA.U.G.UCCGAG...CCCC.......CUGGC +#=GR H.sapiens.11 SS (.((((...........(((.((((((......(((((....))))..)........))))))...).))..................))))) +H.sapiens.12 C.UCUGUUA...AUGACGUCUCUCCCUCUAAA.CCCCAUU.AAGGA..C........UGGGAG.A.G.GCAGAGCAAGCCU.......CAGAG +#=GR H.sapiens.12 SS (.((((.......((..(((((((((.......((........)).............))))).).).))....))............))))) +H.sapiens.13 G.UCACUGC...AUGAUCCGCUCUGGU.CAAA.CCCUUCC...AGG..C......CAGCCAGA.G.U.GGGGAU..GGUCU.......GUGAC +#=GR H.sapiens.13 SS (.((((.((.......(((((((((((......((.........))...........)))))).).).)))......)).........))))) +H.sapiens.14 C.ACUGCUG...AUGACGAACUAUCUC.UAAC.UGGUCUU..GACC..A.......CGAGCUA.G.U.UCUGAA...UU.G.......CAGGG +#=GR H.sapiens.14 SS ...((((.(...((...((((((.(((......((((......)))..)........))).)).).).))...)...)).).......))).. +H.sapiens.15 U.UUUCAUC..UAUGAGGGUGUUUCCUCUAAA..CCUACG...AGG...........GAGGAA.C.A.CCUGAU...CUUA.....CAGAAAA +#=GR H.sapiens.15 SS .......((..(.((((((((((.(((((................)...........)))))).).).)).......))))......)))... +B.taurus.1 C.UUGCGUU..AAUGAGAACAGAAACG.UAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAAC +#=GR B.taurus.1 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))... +B.taurus.2 C.UUGCGUU..AAUGAGAACAGAAACG.AAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAAC +#=GR B.taurus.2 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))... +B.taurus.3 C.CCGGUGCC.UAUGACGGUCUGUCUG.AAAA.CCAGCCC...CUG.GU........GGGGCA.G.A.CCUGAG.AACCUG.......GCGUG +#=GR B.taurus.3 SS (.(.(((..(.(.....(((((((((.....(.((((......))).)).........))))).).).))..))..))).).......).... +B.taurus.4 ACUUGCGUU..AAUGAGAACAGAAACG.UAAA..CUAUAA.CCUAG.G.........GGUUUC.U.G.UUGGAU..GGUUG.......GCAA. +#=GR B.taurus.4 SS ......(((..(((.(.(((((((((........(((......)))............))))).).).))...)...)))).......))... +B.taurus.5 G.CCAGAUG...AUGAGGACCUGUGCG.GAAA.CCCCCCG..CGGG..C........UGCCCA.U.G.UCUGAG...CCC........CUGGC +#=GR B.taurus.5 SS (.((((((....(((.((.((((((.(.(.......))))..)))).............)))).).).)))).)...)............... +B.taurus.6 G.AUGCGUC..CAUGAAGUCACCAGCC.CCAA.GCCCCUC...GUG.GU........GGGUGG.U.G.AUGGAA.CCGUCA.....AAGCAGU +#=GR B.taurus.6 SS (.(((..((..((.....((((((.((.(((.............)).).........)).))).).).)))))...))))............. +B.taurus.7 U.UUUGCCC...AUGAAGGUGUUCCCUCUAAA..CCUAC....GUG...........GAGGAA.U.G.CCUGAU.GUCCAG.......GAAAA +#=GR B.taurus.7 SS (.((((..(...((..(((((((((.((((..............))...........)))))).).).))).)).)..))).......))... +O.aries.1 G.ACGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUCU.UGGAC.GC......CUGGUCCU.U.C.CUUGAU..GUUCU......CACGGC +#=GR O.aries.1 SS (.(.((.((...(....((((((((((.(....((((......))).)........))))))).).).)))))...))..)......)..... +S.scrofa.1 G.ACGCUUC...AUGACAGGAAGGACU.GAAA.UGUCUUG.UGGAC.GC......CUGGUCCU.U.C.CCUGAU..GUUCU......CAUGGC +#=GR S.scrofa.1 SS .......((...(((((((((((((((.(....((((......))).)........))))))).)...))))........)......))))). +S.scrofa.2 C.UGGCACC..CAUGACAGUCUGCCUA.AAAA.CCAGCCC...CUG.GU........GGGGCA.G.A.CUCGAG.AACCUG.......GCGUG +#=GR S.scrofa.2 SS .....((((..((.(.((((((((((.....(.((((......))).)).........))))).).).)).).....).)).......).))) +S.scrofa.3 A.UUUUAUC..CAUGAAAGUGUUUCCUCUAAA..CCUAU....GUG...........GAGGAA.C.A.CCUGAU.GUCCAG......GAAAAU +#=GR S.scrofa.3 SS ...........(((....))).((((((((..............))...........)))))).....((((......)))......)..... +S.scrofa.4 C.UGGCACC..CAUGACAGUCUGCCUA.AAAA.CCAGCC....CUG.GU........GGGGCA.G.A.CUCGAG.AACCUG.......GCGUG +#=GR S.scrofa.4 SS .....((((..((.(.((((((((((.....(.(((........)).)).........))))).).).)).).....).)).......).))) +C.elegans.1 G.AGGCAGCUUUGUGACGACCUUUGGC.UAAA.CUCCAUC..GUGA.GC........GCCUCU.G.G.UCUGAU...GC.........GCCUC +#=GR C.elegans.1 SS (.((((.((...((.(.((((...(((......(((........)).).........)))....).).))).))...)).........))))) +S.mansoni.1 C.UCGCUAU...AUGACGAUGGCAAUC.UCAA..AUGUU....CAU..U........GGUUGC.C.A.UUUGAU..GAAAUCAGUUUUGUGUG +#=GR S.mansoni.1 SS ...(((.((...(.(((((((((((((..............................)))))).).).)).............))).)))))) +#=GC SS_cons <-<<<<-----------<<<<<<<<<<-------<<<______>>>----------->>>>>>->->->>------------------>>>>> +#=GC RF g.ucucauu..uAUGAuGgccucuccc.uAAA.ucccuuu...ggg..c........gggaga.g.g.cCuGAU..gcuug.......gagac +//