gi_545778205_gb_U000_293

"structRNAfinder"

gi_545778205_gb_U000_293
cmsearch-Rfam
Family : SSU_rRNA_eukarya	Id: RF01960	Type: Gene; rRNA;
Taxonomy: Eukaryota; Bacteria; Viruses; Archaea; Viroids;	Ontology: GO:0003735 structural constituent of ribosomeRF01960
Description: not description
Score: 685.1	E-value: 1.3e-205
From sequence: 223776	To sequence: 225307
Alignments: v v NC :::<<<<<_______>>>>>,{{{{{.{{{{{,{{{{{{{{[-----[[[-[[[,,<<.-<<<---~~~~~~->>>>>,,,,, CS RF02542 1 CACCAGGuUGAUUCUgCCUGAcgugg.acgCUagucuccgaGAUUaAGCCAUGCAuGc.ucgcGAA[10]AgcggCGaAcg 85 A AG UUGAU UG CU A::U: ACGCU G:::C:G: UAA: CAUGCA+G: :CG AG: :CG+ACG gi_545778205_gb_U000 223776 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU[30]AGUGGCGGACG 223881 *********************99649*********8.79*********87888754...9..6889*** PP v v v NC ,(((,,,,,,<<<<<<<<--<<---<<<<<<<--<<<----<<<<<<<____>>>>>>>----->>>................ CS RF02542 86 GCUCAGUAauccggccccuAucUaaucgccccaugcggAUAcCcgcgguAAaccgcgGguAAuAcgc................ 152 G U AGUAAU :::::: A:CU+ ::G::::A :GGAUA:C::C:G+AAAC:G::G:UAAUAC: gi_545778205_gb_U000 223882 GGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgcaagac 223963 *************9.9****************************************9969*********** PP v v NC ...........................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>>>>>>>> CS RF02542 153 ...........................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUAccgagg 208 ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :ACC:AGG gi_545778205_gb_U000 223964 caaagagggggaccuucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGG 224046 ******************************************************************************* PP v v v NC >----->>>>,,,<<<<<<<<____>>>>--->>>>))),<<<<<<__________>>>>>>,<<<<____>>>>,,,]]]]] CS RF02542 209 CgAugAcgGgUaACGGggaAuuagggUucgAUuCCGGAGAGGgAGCCUGAGAGAUgGCUcCCAcgUCCAAGGAcgGCAGCAGG 291 CGA GA :::U A ::::U AG+G:::GA : A A: G:: CUGAGA A G ::C :AC::C+A GG::GGCAGCAG gi_545778205_gb_U000 224047 CGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGU 224128 *******.********************************************************************* PP v NC ]-],,,,,<-<<<---<<<<<.___>>>>>->>>>,}}-}}}}}},,,,,,,,,,.....,,<<<<<<______~~~~~~>>> CS RF02542 292 CGCGAAAcUUgCCcAAccccc.auugggggAGGcAGucAggagacGUaaauuuaa.....gacgggcguGUAAA[ 3]cgc 365 :G GAA +UUGC CAA::::C ++G::::A GCAG:CA:G:::CGU++AU +A + :GG::UGUAAA ::C gi_545778205_gb_U000 224129 GGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAAA[54]ACC 224259 *******************9999*********************9999988886657777777777776.....777 PP v v v NC >>>,,,..,,<<<<<<-------<<<<-----<<____>>------->>>>>>>>>>,}}}}}}}}}},,,,,,,,,,[[[,, CS RF02542 366 ccggaa..aAcuGGAGGGCAAGuCuGGUGCCAGCAgCCGCGGUAAUaCCaGCUCCaggAGcguccaugaugauUGcUGCggUU 446 C: + A AA::: GGC A :::GUGCCAGCAGCCGCGGUAAUAC::: ::: AGCGU :A:: +AUU CUG:G: U gi_545778205_gb_U000 224260 CGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGU 224341 77766667***6.699999********************************************************** PP NC ,,,,,((((---(((-------------------------------------------------------..----------- CS RF02542 447 AAAAaGucCGUAgUcggauaauuuuauuuuuuauuaaaaguguuuuuuuaagguguauuauauuauguaa..uuaagaauuua 527 AAA G::CG AG:CGG+U++UU++ U + +U+U+AAA+ + +U+AA UG ++ U ++ +A+ U +A UU+ gi_545778205_gb_U000 224342 AAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUacUGGCAAGCUUG 224424 ************************************999999999996666666655555555555458999999 PP v v v v NC (((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>>>>>-->>,,,,<--<<____>>>)))) CS RF02542 528 ggaccGcccggcGgccacggUAuucggcgGcgAgggGUGAAAcccgAuGACCcgccgagGAccaaCagAgGCGAAAGCggugg 610 :G: :::: G+:GG::::: AUUC::: AG::GUGAAA::CG +GA :::GAGGA :A C G GGCGAA GCG:::: gi_545778205_gb_U000 224425 AGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCC 224507 ******************************************************************************* PP v v NC )))-))))))-)))---)))---)))),,,,<<<<<<---<<---<<<<_________>>>>--->>>>>>>>,,,,,,,,,, CS RF02542 611 cCgagggCggauccGaugAucAAGgaCGuAaGCcgGaGgAuCGAAggcGAUUAGAuACCgccGUAGuuCcgGCaGUAAACgAU 693 CC: :::: :C:GA G:UCA G::CG+AAGC::G:GGA:C AA:::GAUUAGAUACC:::GUAG::C::GC GUAAACGAU gi_545778205_gb_U000 224508 CCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAU 224590 ******************************************************************************* PP NC ((((((,<<<<<<<<<<......____..>>>>>>>>>>,,<<____>>...,,)))----))),]]],<<<------<<<<_ CS RF02542 694 GCCcAcagggcggcgcc......uuua..ggcgccgcccaagaGAAAuc...uAgUgUauGGGCUccGGggguAGUAcccgcG 765 G:C:AC+ GG::G: : + : :C::CC +AG: AA :C +AGU: G:C :C: :GG AGUAC:::CG gi_545778205_gb_U000 224591 GUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GACCGCCUGGGGAGUACGGCCG 224668 ************9999975333.5799**************999999....******************** PP NC ___>>>>---->>>,,,,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{{{{{{{{{{,,,,<<<<________>>>>,,,,, CS RF02542 766 CAAgcggGAAAcuuaAaGAAAUUGACgGAaggACACCACAAGgAgUGgAgUGuGCGGcUUAAuuuGACUCAACGCgggacAaC 848 CAAG::: AAACU:AAA AAUUGACGG :G::C: CACAAG::GUGGAG::UG:GG:UUAA:::GA CAACGC:::++A C gi_545778205_gb_U000 224669 CAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACC 224750 *******************************.7******************************************** PP v v v v v NC ,,,{{{{{{{,,,.<<<<<<------~~~~~~-->>>>>>,,,[[-[[[[--[[[[[[[[[,,,((((((<<<____>>>.,< CS RF02542 849 UUACCagggccga.ggccccuugaGA[13]AuggggccgaggGUGGugCAUggCCGUUcuuAAcgcgUgggGUGAccu.Uc 936 UUACC:GG:C+ : : C: + A :G : :+ +GGUG UGCAUGGC:G ::U+A:C:CGUG::GUGA::U U: gi_545778205_gb_U000 224751 UUACCUGGUCUUGaCAUCCACA----[33]ACUGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUgUU 224856 ********887644444432.......5..4477777899************************************* PP NC <<<______>>>>,,)))))),,,,,((((,..............................<<____>>,,<<<<<<<<.___ CS RF02542 937 cggUUAAaUccgguAAcgcgUGAGAuccccg..............................ccuuaaggGACccgcgcc.gua 988 :GGUUAA UCC:: AACG:G:G A+CC::+ :C +A G:GAC:::C::: +UA gi_545778205_gb_U000 224857 GGGUUAAGUCCCGCAACGAGCGCAACCCUUAucuuuuguugccagcgguccggccgggaacUCAAAGGAGACUGCCAGUgAUA 224939 ***************************888888888888888888888888888888888888********99 PP v NC _>>>>>>>>,,,,,)))),,,,]]]]-]]]---]-]]]]]]],,,,,}}}}}}},,,}}-}}}}}}}}}},,,<<<<<<____ CS RF02542 989 AggcgcggGAAGgaggggucaAgAACAGGuCaGuGAugCCCcuAGAUgcccuGGGCUgCACGCgCAcUaCAaUggccgcuuga 1071 A:::G:::GAAGG ::GG+ A:: CA:GUCA U AUG CCCU A G:CC:GGGCU:CAC:CG::CUACAAUG:C:::U+ A gi_545778205_gb_U000 224940 AACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACA 225020 *****************************9.55***85.89*****************************9888 PP v NC _________~~~~~~>>>>>>..,,,,<---<<<<<<<<______..>>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<_ CS RF02542 1072 aauauaaua[ 8]gcggcc..aauuGGGAcuggccccUGUAAu..ggggccagGAACguGGAAuUcCUAGUAgucgcgcgU 1152 AA A AA :::G:C A+U :GGA:UGG:::CUG AA G:::CCA:GAA: GGAAU::CUAGUA: CG:G: U gi_545778205_gb_U000 225021 AAGAGAAGC[31]UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAU 225128 877766554...6..***999999*************888******************************** PP v v v vvvv NC ______>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,,,<<-<<-<-<<<<<<<<--<<<<<<<<<<<<<<<<<<<<___ CS RF02542 1153 CAuuAAcgcgcgacGAAUguGUCCCUGUccuUuGUACACACCGcCCGUCGcuAuCucAGAuggcugcccgggcgaagagcuua 1235 CA A :C:CG :GAAU+ GU CC:G::C: UGUACACACCGCCCGUC+C::: : :GA G ::::C::: G ::+UA gi_545778205_gb_U000 225129 CAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA 225211 *****************************************************************99877666655555 PP vvvv v v NC _...................>>>>>>>>>>>>>>>>>>>>-->>>>>>>>-->->>-->>,,,,<<<<<<<<<<____>>>>> CS RF02542 1236 a...................gcucugagcccgggcagcuaGAUgaGaUagAAGUCGUAaCAAGGcugCugucGGaGAACCggc 1299 :: A :::G:::: C GA: : :::GAAGUCGUAACAAGG:::C:GU:GG GAACC:GC gi_545778205_gb_U000 225212 GcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGC 225294 569*************66666677899************************************************ PP NC >>>>>:::::::: CS RF02542 1300 aGcagGAUCAuua 1312 :G:::GAUCA gi_545778205_gb_U000 225295 GGUUGGAUCACCU 225307 *********** PP >>
RNAfold
>gi_545778205_gb_U000_293 GCGUCGCAACUGCUCUUUAACAAUUUAUCAGACAAUCUGUGUGGGCACUC GAAGAUACGGAUUCUUAACGUCGCAAGACGAAAAAUGAAUACCAAGUCUC AAGAGUGAACACGUAAUUCAUUACAAAGUUUAAUUCUUUGAGCAUCAAAC UUUUAAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGG CCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCU GACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGG GGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAA AGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUA GCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCU GAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACG GGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCC AUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGG GAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAA GAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCA AGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAA GUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGG CAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAA UGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGA AGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACC CUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAG GCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGC CGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGA GCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACA UCCACAGAACUUUCCAGAGAUGGAUUGGUGCCUUCGGGAACUGUGAGACA GGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUC CCGCAACGAGCGCAACCCUUAUCUUUUGUUGCCAGCGGUCCGGCCGGGAA CUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCA AGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCA UACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUC GUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUA GUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACA CACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUA ACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUC GUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUACCUU AAAGAAGCGUACUUUGCAGUGCUCACACAGAUUGUCUGAUGAAAAUGAGC AGUAAAACCUCUACAGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGA UAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCUACCAAAUUUGCAC G .(((.((((((((((.((.....(((((((((((((((((((((((((((((((.((((..(((((..((((....))))...(((((((((....((........))....)).))))))).....((((((((...((((((((((((((((......)))))))))))....)))))))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.....(((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).))))))).((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.((((.((((((..((.(((.((((....))))..)))..))...)))..)))))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....))))))...........(((((.(((((((((((......(((....))).((.(((((.....))))).))........((((((.....)))))).(((((((.......)))))))....((.(((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))).))...(((((((........)))))))....))))).)))))).)))))(((((.........))))).........))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).....((((..(((((((((((((....))))))))).....))))..))))....))))).))))))))).)))))))))))))))))))))))))))).))))))).......(((((....))))).(((((.(((........))))))))....(((.((((((((((.......)))))..)))))))).....)))))) (-715.20)
Length sequence : 1851	Length match: 1530