gi_545778205_gb_U000_297

"structRNAfinder"

gi_545778205_gb_U000_297
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: 683.9	E-value: 3e-205
From sequence: 4035536	To sequence: 4037067
Alignments: v v NC :::<<<<<_______>>>>>,{{{{{.{{{{{,{{{{{{{{[-----[[[-[[[,,<<.-<<<---~~~~~~->>>>>,,, CS RF02542 1 CACCAGGuUGAUUCUgCCUGAcgugg.acgCUagucuccgaGAUUaAGCCAUGCAuGc.ucgcGAA[10]AgcggCGaA 83 A AG UUGAU UG CU A::U: ACGCU G:::C:G: UAA: CAUGCA+G: :CG AG: :CG+A gi_545778205_gb_U000 4035536 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU[30]AGUGGCGGA 4035639 *********************99649*********8.79*********87888754...9..6889* PP v v v NC ,,,(((,,,,,,<<<<<<<<--<<---<<<<<<<--<<<----<<<<<<<____>>>>>>>----->>>............ CS RF02542 84 cgGCUCAGUAauccggccccuAucUaaucgccccaugcggAUAcCcgcgguAAaccgcgGguAAuAcgc............ 152 CGG U AGUAAU :::::: A:CU+ ::G::::A :GGAUA:C::C:G+AAAC:G::G:UAAUAC: gi_545778205_gb_U000 4035640 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 4035719 ***************9.9****************************************9969******* PP v v NC ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS RF02542 153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202 ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :A gi_545778205_gb_U000 4035720 agaccaaagagggguaccuucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCA 4035800 ***************************************************************************** PP v v v NC >>>>>>>----->>>>,,,<<<<<<<<____>>>>--->>>>))),<<<<<<__________>>>>>>,<<<<____>>>> CS RF02542 203 ccgaggCgAugAcgGgUaACGGggaAuuagggUucgAUuCCGGAGAGGgAGCCUGAGAGAUgGCUcCCAcgUCCAAGGAcg 283 CC:AGGCGA GA :::U A ::::U AG+G:::GA : A A: G:: CUGAGA A G ::C :AC::C+A GG::G gi_545778205_gb_U000 4035801 CCUAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 4035880 *************.*********************************************************** PP v NC ,,,]]]]]]-],,,,,<-<<<---<<<<<.___>>>>>->>>>,}}-}}}}}},,,,,,,,,,.....,,<<<<<<_____ CS RF02542 284 GCAGCAGGCGCGAAAcUUgCCcAAccccc.auugggggAGGcAGucAggagacGUaaauuuaa.....gacgggcguGUAA 358 GCAGCAG :G GAA +UUGC CAA::::C ++G::::A GCAG:CA:G:::CGU++AU +A + :GG::UGUAA gi_545778205_gb_U000 4035881 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 4035961 *************************9999*********************999998888665777777777777 PP v v v NC _~~~~~~>>>>>>,,,..,,<<<<<<-------<<<<-----<<____>>------->>>>>>>>>>,}}}}}}}}}},,, CS RF02542 359 A[ 3]cgcccggaa..aAcuGGAGGGCAAGuCuGGUGCCAGCAgCCGCGGUAAUaCCaGCUCCaggAGcguccaugaug 434 A ::CC: + A AA::: GGC A :::GUGCCAGCAGCCGCGGUAAUAC::: ::: AGCGU :A:: + gi_545778205_gb_U000 4035962 A[54]ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 4036089 6.....77777766667***6.699999********************************************** PP NC ,,,,,,,[[[,,,,,,,((((---(((------------------------------------------------------ CS RF02542 435 auUGcUGCggUUAAAAaGucCGUAgUcggauaauuuuauuuuuuauuaaaaguguuuuuuuaagguguauuauauuaugua 515 AUU CUG:G: UAAA G::CG AG:CGG+U++UU++ U + +U+U+AAA+ + +U+AA UG ++ U ++ +A gi_545778205_gb_U000 4036090 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 4036170 ************************************************99999999999666666665555555555 PP v v v v NC -..-----------(((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>>>>>-->>,,,, CS RF02542 516 a..uuaagaauuuaggaccGcccggcGgccacggUAuucggcgGcgAgggGUGAAAcccgAuGACCcgccgagGAccaaCa 594 + U +A UU+:G: :::: G+:GG::::: AUUC::: AG::GUGAAA::CG +GA :::GAGGA :A C gi_545778205_gb_U000 4036171 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 4036251 5458999999******************************************************************* PP v v NC <--<<____>>>)))))))-))))))-)))---)))---)))),,,,<<<<<<---<<---<<<<_________>>>>--- CS RF02542 595 gAgGCGAAAGCgguggcCgagggCggauccGaugAucAAGgaCGuAaGCcgGaGgAuCGAAggcGAUUAGAuACCgccGUA 675 G GGCGAA GCG::::CC: :::: :C:GA G:UCA G::CG+AAGC::G:GGA:C AA:::GAUUAGAUACC:::GUA gi_545778205_gb_U000 4036252 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 4036332 ***************************************************************************** PP NC >>>>>>>>,,,,,,,,,,((((((,<<<<<<<<<<......____..>>>>>>>>>>,,<<____>>...,,)))----)) CS RF02542 676 GuuCcgGCaGUAAACgAUGCCcAcagggcggcgcc......uuua..ggcgccgcccaagaGAAAuc...uAgUgUauGGG 745 G::C::GC GUAAACGAUG:C:AC+ GG::G: : + : :C::CC +AG: AA :C +AGU: G: gi_545778205_gb_U000 4036333 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 4036408 ******************************9999975333.5799**************999999.... PP NC ),]]],<<<------<<<<____>>>>---->>>,,,,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{{{{{{{{{{,,, CS RF02542 746 CUccGGggguAGUAcccgcGCAAgcggGAAAcuuaAaGAAAUUGACgGAaggACACCACAAGgAgUGgAgUGuGCGGcUUA 826 C :C: :GG AGUAC:::CGCAAG::: AAACU:AAA AAUUGACGG :G::C: CACAAG::GUGGAG::UG:GG:UUA gi_545778205_gb_U000 4036409 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 4036488 ***************************************************.7********************** PP v v v NC ,<<<<________>>>>,,,,,,,,{{{{{{{,,,...<<<<<<-~~~~~~>>>>>>,,,[[-[[[[--[[[[[[[[[,,, CS RF02542 827 AuuuGACUCAACGCgggacAaCUUACCagggccga...ggccccu[20]ggggccgaggGUGGugCAUggCCGUUcuuA 918 A:::GA CAACGC:::++A CUUACC:GG:C+ C:C: :G:G + +GGUG UGCAUGGC:G ::U+A gi_545778205_gb_U000 4036489 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG[34]CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 4036597 ******************************9886443333332...4..444457999***************** PP NC ((((((<<<____>>>.,<<<<______>>>>,,)))))),,,,,((((,..............................< CS RF02542 919 AcgcgUgggGUGAccu.UccggUUAAaUccgguAAcgcgUGAGAuccccg..............................c 968 :C:CGUG::GUGA::U U::GGUUAA UCC:: AACG:G:G A+CC::+ : gi_545778205_gb_U000 4036598 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 4036678 *********************************************99999999999999999999999999999999 PP v NC <____>>,,<<<<<<<<.____>>>>>>>>,,,,,)))),,,,]]]]-]]]---]-]]]]]]],,,,,}}}}}}},,,}}- CS RF02542 969 cuuaaggGACccgcgcc.guaAggcgcggGAAGgaggggucaAgAACAGGuCaGuGAugCCCcuAGAUgcccuGGGCUgCA 1048 C +A G:GAC:::C::: +UAA:::G:::GAAGG ::GG+ A:: CA:GUCA U AUG CCCU A G:CC:GGGCU:CA gi_545778205_gb_U000 4036679 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 4036757 99999********99*****************************9.55***85.89*********** PP NC }}}}}}}}}},,,<<<<<<_____________~~~~~~>>>>>>..,,,,<---<<<<<<<<______..>>>>>>>>--- CS RF02542 1049 CGCgCAcUaCAaUggccgcuugaaauauaaua[ 8]gcggcc..aauuGGGAcuggccccUGUAAu..ggggccagGAA 1127 C:CG::CUACAAUG:C:::U+ AAA A AA :::G:C A+U :GGA:UGG:::CUG AA G:::CCA:GAA gi_545778205_gb_U000 4036758 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC[31]UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 4036863 *****************9888877766554...6..**999999*************888******* PP v v v NC >,,,,,}}}}},,,,,<<<<<<<<_______>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,,,<<-<<-<-<<<<<< CS RF02542 1128 CguGGAAuUcCUAGUAgucgcgcgUCAuuAAcgcgcgacGAAUguGUCCCUGUccuUuGUACACACCGcCCGUCGcuAuCu 1208 : GGAAU::CUAGUA: CG:G: UCA A :C:CG :GAAU+ GU CC:G::C: UGUACACACCGCCCGUC+C::: : gi_545778205_gb_U000 4036864 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 4036944 ***************************************************************************** PP v vvvv vvvv v v NC <<--<<<<<<<<<<<<<<<<<<<<____...................>>>>>>>>>>>>>>>>>>>>-->>>>>>>>-->- CS RF02542 1209 cAGAuggcugcccgggcgaagagcuuaa...................gcucugagcccgggcagcuaGAUgaGaUagAAGU 1270 :GA G ::::C::: G ::+UA :: A :::G:::: C GA: : :::GAAGU gi_545778205_gb_U000 4036945 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 4037025 *********99877666655555569*************66666677899******************* PP NC >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS RF02542 1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312 CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA gi_545778205_gb_U000 4037026 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 4037067 **************************************** PP >>
RNAfold
>gi_545778205_gb_U000_297 GAAGCGGCACUGCUCUUUAACAAUUUAUCAGACAAUCUGUGUGGGCACUC GAAGAUACGGAUUCUUAACGUCGCAAGACGAAAAAUGAAUACCAAGUCUC AAGAGUGAACACGUAAUUCAUUACGAAGUUUAAUUCUUUGAGCGUCAAAC UUUUAAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGG CCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCU GACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGG GGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAA AGAGGGGUACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUA GCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCU GAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACG GGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCC AUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGG GAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAA GAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCA AGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAA GUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGG CAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAA UGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGA AGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACC CUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAG GCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGC CGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGA GCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACA UCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACA GGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUC CCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAA CUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCA AGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCA UACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUC GUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUA GUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACA CACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUA ACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUC GUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUACCUU AAAGAAGCGUUCUUUGAAGUGCUCACACAGAUUGUCUGAUGAAAAUGAGC AGUAAAACCUCUACAGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGA UAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCUACCAAAUUUGCAC G ....(((((((((((.((.....((((((((((((((((((((((((((((((((.(((..(((((..((((....))))...(((((((((....((........))....)).))))))).....((((((((...((((((((((((((((......)))))))))))....)))))))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.(((((((((((((((((....((((((....))))))....((((.(.....(((....)))......).))))((....)))))))).)))))...((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).)).)))))).((((((.....)))))).(((((((.......)))))))........((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).....((((..(((((((((((((....))))))))).....))))..))))....))))).))))))))).)))))))))))))))))))))))))))).))))))........(((((....))))).(((((.(((........))))))))....(((.((((((((((.......)))))..)))))))).....))).)) (-716.40)
Length sequence : 1851	Length match: 1530