gi_545778205_gb_U000_298

"structRNAfinder"

gi_545778205_gb_U000_298
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: 2.9e-205
From sequence: 4166664	To sequence: 4168195
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 4166664 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU[30]AGUGGCGGA 4166767 *********************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 4166768 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 4166847 ***************9.9****************************************9969******* PP v v NC ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS RF02542 153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202 ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :A gi_545778205_gb_U000 4166848 agaccaaagagggggaccuucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCA 4166928 ***************************************************************************** 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 4166929 CCUAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 4167008 *************.*********************************************************** 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 4167009 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 4167089 *************************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 4167090 A[54]ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 4167217 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 4167218 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 4167298 ************************************************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 4167299 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 4167379 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 4167380 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 4167460 ***************************************************************************** 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 4167461 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 4167536 ******************************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 4167537 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 4167616 ***************************************************.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 4167617 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG[34]CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 4167725 ******************************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 4167726 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 4167806 *********************************************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 4167807 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 4167885 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 4167886 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC[31]UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 4167991 *****************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 4167992 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 4168072 ***************************************************************************** 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 4168073 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 4168153 *********99877666655555569*************66666677899******************* PP NC >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS RF02542 1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312 CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA gi_545778205_gb_U000 4168154 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 4168195 **************************************** PP >>
RNAfold
>gi_545778205_gb_U000_298 GAAGCGGCACUGCUCUUUAACAAUUUAUCAGACAAUCUGUGUGGGCACUC GAAGAUACGGAUUCUUAACGUCGCAAGACGAAAAAUGAAUACCAAGUCUC AAGAGUGAACACGUAAUUCAUUACGAAGUUUAAUUCUUUGAGCGUCAAAC UUUUAAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGG CCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCU GACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGG GGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAA AGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUA 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 AAAGAAGCGUACUUUGUAGUGCUCACACAGAUUGUCUGAUAGAAAGUGAA AAGCAAGGCGUUUACGCGUUGGGAGUGAGGCUGAAGAGAAUAAGGCCGUU CGCUUUCUAUUAAUGAAAGCUCACCCUACACGAAAAUAUCACGCAACGCG U .(((((.(..((((.((((....(((((((((((((((((((((((((((((((.((((..(((((..((((....))))...(((((((((....((........))....)).))))))).....((((((((...((((((((((((((((......)))))))))))....)))))))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.(((((((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))...((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).)).)))))).((((((.....)))))).(((((((.......)))))))........((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).....((((..(((((((((((((....))))))))).....))))..))))....))))).))))))))).))))))))))))))))))))))))))...)))).)))).).)))))((((((((...((((((((...........))))((..((((((.......))))))..))..............)))).)))))))) (-710.60)
Length sequence : 1851	Length match: 1530