gi_545778205_gb_U000_295

"structRNAfinder"

gi_545778205_gb_U000_295
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: 684.3	E-value: 2.2e-205
From sequence: 3428757	To sequence: 3427226
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 3428757 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU[30]AGUGGCGGA 3428654 *********************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 3428653 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 3428574 ***************9.9****************************************9969******* PP v v NC ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS RF02542 153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202 ::::C::AUG: :::::: :::AU AGCU+GU:GGU: GGUAA GGC :A gi_545778205_gb_U000 3428573 agaccaaagagggggacccucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUUGUUGGUGGGGUAACGGCUCA 3428493 ***************************************************************************** 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 3428492 CCAAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 3428413 *************.*********************************************************** 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 3428412 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 3428332 *************************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 3428331 A[54]ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 3428204 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 3428203 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 3428123 ************************************************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 3428122 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 3428042 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 3428041 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 3427961 ***************************************************************************** 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 3427960 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 3427885 ******************************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 3427884 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 3427805 ***************************************************.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 3427804 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG[34]CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 3427696 ******************************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 3427695 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 3427615 *********************************************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 3427614 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 3427536 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 3427535 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC[31]UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 3427430 *****************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 3427429 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 3427349 ***************************************************************************** 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 3427348 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 3427268 *********99877666655555569*************66666677899******************* PP NC >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS RF02542 1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312 CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA gi_545778205_gb_U000 3427267 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 3427226 **************************************** PP >>
RNAfold
>gi_545778205_gb_U000_295 GUGCAAAUUUGGUAGGCCUGAGUGGACUUGAACCACCGACCUCACCCUUA UCAGGGGUGCGCUCUAACCACCUGAGCUACAAGCCUGUAGAGGUUUUACU GCUCAUUUUCAUCAGACAAUCUGUGUGAGCACUGCAAAGUACGCUUCUUU AAGGUAAGGAGGUGAUCCAACCGCAGGUUCCCCUACGGUUACCUUGUUAC GACUUCACCCCAGUCAUGAAUCACAAAGUGGUAAGCGCCCUCCCGAAGGU UAAGCUACCUACUUCUUUUGCAACCCACUCCCAUGGUGUGACGGGCGGUG UGUACAAGGCCCGGGAACGUAUUCACCGUGGCAUUCUGAUCCACGAUUAC UAGCGAUUCCGACUUCAUGGAGUCGAGUUGCAGACUCCAAUCCGGACUAC GACGCACUUUAUGAGGUCCGCUUGCUCUCGCGAGGUCGCUUCUCUUUGUA UGCGCCAUUGUAGCACGUGUGUAGCCCUGGUCGUAAGGGCCAUGAUGACU UGACGUCAUCCCCACCUUCCUCCAGUUUAUCACUGGCAGUCUCCUUUGAG UUCCCGGCCGGACCGCUGGCAACAAAGGAUAAGGGUUGCGCUCGUUGCGG GACUUAACCCAACAUUUCACAACACGAGCUGACGACAGCCAUGCAGCACC UGUCUCACGGUUCCCGAAGGCACAUUCUCAUCUCUGAAAACUUCCGUGGA UGUCAAGACCAGGUAAGGUUCUUCGCGUUGCAUCGAAUUAAACCACAUGC UCCACCGCUUGUGCGGGCCCCCGUCAAUUCAUUUGAGUUUUAACCUUGCG GCCGUACUCCCCAGGCGGUCGACUUAACGCGUUAGCUCCGGAAGCCACGC CUCAAGGGCACAACCUCCAAGUCGACAUCGUUUACGGCGUGGACUACCAG GGUAUCUAAUCCUGUUUGCUCCCCACGCUUUCGCACCUGAGCGUCAGUCU UCGUCCAGGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCA UUUCACCGCUACACCUGGAAUUCUACCCCCCUCUACGAGACUCAAGCUUG CCAGUAUCAGAUGCAGUUCCCAGGUUGAGCCCGGGGAUUUCACAUCUGAC UUAACAAACCGCCUGCGUGCGCUUUACGCCCAGUAAUUCCGAUUAACGCU UGCACCCUCCGUAUUACCGCGGCUGCUGGCACGGAGUUAGCCGGUGCUUC UUCUGCGGGUAACGUCAAUGAGCAAAGGUAUUAACUUUACUCCCUUCCUC CCCGCUGAAAGUACUUUACAACCCGAAGGCCUUCUUCAUACACGCGGCAU GGCUGCAUCAGGCUUGCGCCCAUUGUGCAAUAUUCCCCACUGCUGCCUCC CGUAGGAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCUGGUCAUCCUCUC AGACCAGCUAGGGAUCGUCGCCUUGGUGAGCCGUUACCCCACCAACAAGC UAAUCCCAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAGGGUCCCCCUCU UUGGUCUUGCGACGUUAUGCGGUAUUAGCUACCGUUUCCAGUAGUUAUCC CCCUCCAUCAGGCAGUUUCCCAGACAUUACUCACCCGUCCGCCACUCGUC AGCGAAACAGCAAGCUGUUUCCUGUUACCGUUCGACUUGCAUGUGUUAGG CCUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAAUUUAAAA GUUUGAUGCUCAAAGAAUUAAACUUCGUAAUGAAUUACGUGUUCACUCUU GAGACUUGGUAUUCAUUUUUCGUCUUGCGACGUUAAGAAUCCGUAUCUUC GAGUGCCCACACAGAUUGUCUGAUAAAUUGUUAAAGAGCAGUUGCGACGC G ((((((....((((((..((.((((.......)))))).))).)))....((((((((........))).))))).....((((((....))))))..((((((.((..((((((((((((((((((.(((((..((.(((((.(((((....((((.((((((.....((((.(((....))).)))))))))).))))((((.......))))((((((..((((((((...(((.........((((......))))........)))...)))))....(((((.((((((.(((((((((((((((((((((....))).))).)))....(((((...)))))..((((((.(.(((((((((((((.(.((((.((..(((.....))))).)))).)))))))))))))).)(((((....)))))))))))....))))))))))))......(((((.((((((((((((((.....))))).((((((.....)))))).........(((((((.....))))).))..(((((((.....(((((......)))))...)))))))...))))))))).)).)))(((......)))............((((((((((.((((((((((((((.(.((((...((((....((((((.......(((((.((........)).)))))....((((......))))(((((.((((.............((((.((......)).))))(((....)))((((.....))))............(((((((.((....)))))))))......((.((((((((((..(((((((((...(((......)))....((.(((...))).))))))))).))..((((((.....))))))..........((((((........)))))).(((((.(((..(((((((((..........)))......(((((.....((.((........))))...))))).......))))))..))))))))......(((((((((((((((.(((((((.(((...))).)))))))...)))))))...........((..((((.((..((((.....))))...))....))))..)).....((((......)))).))))))))))))))))))))((((((..((.(((((..........(((.((((.......)))).)))........))))).))))))))....)))).))))))))))).....)).)).)))).))))))))..)))((((((.....))))))...(((..(((.((((.....)))).)))..)))...)))))))))))..)))(((((((((.........)))))))))(((((....((.((((((...........))))))...))..))))).((((((.((..(((((((...((((((.(((((...)))))...))))))((........))((...(((((((........)))))))...))..))))).))..))..)))))).........))))))))))).....(((.(((((((....)))))))))).....(((((..(((.((((....((....))....)))).)))..)))))....((((((((.((......)).)))))))).(((((.((....(((..(((((....))))).)))...)))))))..)))..))))))....((((....))))..)))))..))))).))..))))).)))))))))))))))).....))..)).)))))))))).))... (-608.70)
Length sequence : 1851	Length match: 1530