gi_545778205_gb_U000_296

"structRNAfinder"

gi_545778205_gb_U000_296
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: 685.4	E-value: 1.1e-205
From sequence: 3941813	To sequence: 3943344
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 3941813 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU[30]AGUGGCGGA 3941916 *********************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 3941917 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 3941996 ***************9.9****************************************9969******* PP v v NC ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS RF02542 153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202 ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :A gi_545778205_gb_U000 3941997 agaccaaagagggggaccuucgggccucuugCCAUCAGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCA 3942077 ***************************************************************************** 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 3942078 CCUAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 3942157 *************.*********************************************************** 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 3942158 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 3942238 *************************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 3942239 A[54]ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 3942366 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 3942367 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 3942447 ************************************************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 3942448 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 3942528 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 3942529 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 3942609 ***************************************************************************** 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 3942610 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 3942685 ******************************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 3942686 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 3942765 ***************************************************.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 3942766 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG[34]CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 3942874 ******************************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 3942875 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 3942955 *********************************************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 3942956 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 3943034 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 3943035 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC[31]UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 3943140 *****************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 3943141 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 3943221 ***************************************************************************** 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 3943222 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 3943302 *********99877666655555569*************66666677899******************* PP NC >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS RF02542 1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312 CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA gi_545778205_gb_U000 3943303 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 3943344 **************************************** PP >>
RNAfold
>gi_545778205_gb_U000_296 AAAGCGGCACUGCUCUUUAACAAUUUAUCAGACAAUCUGUGUGGGCACUC GAAGAUACGGAUUCUUAACGUCGCAAGACGAAAAAUGAAUACCAAGUCUC AAGAGUGAACACGUAAUUCAUUACGAAGUUUAAUUCUUUGAGCAUCAAAC UUUUAAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGG CCUAACACAUGCAAGUCGAACGGUAACAGGAAACAGCUUGCUGUUUCGCU GACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGG GGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAA AGAGGGGGACCUUCGGGCCUCUUGCCAUCAGAUGUGCCCAGAUGGGAUUA 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 AAAGAAGCGUUCUUUGCAGUGCUCACACAGAUUGUCUGAUAGGAAGUGAA AAGCAAGGCGUCUUGCGAAGCAGACUGAUACGUCCCCUUCGUCUAGAGGC CCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGG G ..........((((.((((....((((((((((((((((((((((((((((((((.(((..(((((..((((....))))...(((((((((....((........))....)).))))))).....((((((((...((((((((((((((((......)))))))))))....)))))))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.....(((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).))))))).((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).))...((((.((((((.....)))))).(((((((.......)))))))........)))).(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).....((((..(((((((((((((....))))))))).....))))..))))....))))).))))))))).))))))))))))))))))))))))))...)))).)))).(((.(((.((((((..(((......)))..))))))..))).)))......((((((.......))))))...(((((.......)))))..... (-720.40)
Length sequence : 1851	Length match: 1530