gi_545778205_gb_U000_287

"structRNAfinder"

gi_545778205_gb_U000_287
cmsearch-Rfam
Family : SSU_rRNA_bacteria	Id: RF00177	Type: Gene; rRNA;
Taxonomy: Eukaryota; Bacteria; Viruses; Archaea; Viroids;	Ontology: GO:0003735 structural constituent of ribosomeRF00177
Description: not description
Score: 1578.9	E-value: 0
From sequence: 2731157	To sequence: 2729616
Alignments: NC ::::::::<<<<<_______>>>>>,{{{{-{{{{{{,{{{{{{{{{----{{{-{{{,,<<<--<<<<<-....<<<<<< CS RF00177 1 uuuauggAGaGuuUGAUCcUggCuCAGggcGaaCGCuGGCGGcgcGcuUaAcaCAuGCAAGuCGagcccca....cggggc 77 ++++UG+AGAGUUUGAUC UGGCUCAG:::GAACGCUGGCGGC::GC+UAACACAUGCAAGUCGA:C:::A :::G:: gi_545778205_gb_U000 2731157 AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAacagGAAGCA 2731077 ********************************************************************999**** PP v v v NC <____>>>>>>>...->>->>>>>>,,,,,,[[[,,,,,,((((((((--((---(((((((,<<<<----<<<<<<<___ CS RF00177 78 cuuaaggccccg...agggggcGgCGaAcGGGuGAGUAAcgCGcgggcAAccUacCcccgggugcgGgAUAccccccgGAA 155 : U++:::C::: +::G:G:GGCG ACGGGUGAGUAA+::::GGG A CU+CC :::GG+G GGGAUA C::C:GGAA gi_545778205_gb_U000 2731076 GCUUGCUGCUUCgcuGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGA-AGCUGCCUGAUGGAGGGGGAUAACUACUGGAA 2730997 ********9999***************************9.9*************************** PP v v NC _>>>>>>>----->>>>,,,,,<<<<<<<<<<____>>>>>>>>>>,,,,<<<..........._____>>>,)))))))- CS RF00177 156 AcggggggUAAUACcgcAUaaugccccggcccguaugggccggggcuAAAGgc...........auuuagcCGcccgggGA 225 AC:G::G UAAUACC CAUAAU ::CG+A+G:: AAA::: ++:::GCC::: GA gi_545778205_gb_U000 2730996 ACGGUAGCUAAUACCGCAUAAU-------GUCGCAAGAC-------CAAAGAGggggaccuucgGGCCUCUUGCCAUCGGA 2730930 ******************.......9****9.......**9999877655556******** PP v NC -))))))))))<<<--<-<<<--<<<<<<<<_______>>>>>>>>>>>----->>>>,,<<<<<<<<____>>>>--->> CS RF00177 226 ugggcccgCGccccAUcAGcuAGuuGGuggGGUAAuGGCccaCCaaggCgAuGAggggUAGccGgccuGAGAgggcGauCg 306 UG CCC:::::::AU:AGCU GUUGGUG:GGUAA GGC:CACCAAGGCGA+GA::::UAGC:G::CUGAGAGG::GA C: gi_545778205_gb_U000 2730929 UGUGCCCAGAUGGGAUUAGCUUGUUGGUGGGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCA 2730849 ***************************************************************************** PP NC >>]]],<<<<<<__________>>>>>>,<<<<____>>>>,,,}}}}}}-},,,,,<-<<<---<<<<<____>>>>>-> CS RF00177 307 gCCaCAcuGGgaCUGAGAcACGgcCCagACuCCUACGGGaGGCAGCaGugggGAAUauUgcgCAAugGgcGaAAgcCugAc 387 GCCACACUGG:ACUGAGACACGG:CCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGC:CAAUGGGCG AAGCCUGA: gi_545778205_gb_U000 2730848 GCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAU 2730768 ***************************************************************************** PP v NC >>>,}}-}}}}}},,<<<<------<<<<____>>>>----->>>>,,,<<<<<<<---<-----<<<___........__ CS RF00177 388 gcaGCgAcgCCGCGUGgggGAuGAAggccUUcGggccGUAAAcccCUuUcccggGgGAagAaaaaccgaua........uu 460 GCAGC:A:GCCGCGUG:::GA+GAA::CCUUCGGG::GUAAA:::CUUUC ::GGGGA GAA ::G++A gi_545778205_gb_U000 2730767 GCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAG-GGAGUAAaguuaauaCC 2730688 ********************************************************998.78888888999887544 PP v NC ____>>>----->---->>>>>>--->,,<<<<<------<<<<<-----<<____>>------->>>>>>>>>>,}}}}} CS RF00177 461 uuaucgguuuGAcggUAcCccgggAagAAGcccCGGCUAAcuccGUGCCAGCAGCCGCGGUAAuACggagGgggCaaGCGu 541 UU+ C::+UUGACG UACCC:: GAAGAAGC:CCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGG:GCAAGCGU gi_545778205_gb_U000 2730687 UUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGU 2730607 45558999********************************************************************* PP v v v NC }}}}},,,,,,,,,,{{{-----{,[[[[-[-[[[,<<<<<<<-<<<<<<<<<<<----<<<<<<<_____>>>>>>>--> CS RF00177 542 ugccCGGAaUuAuUGGGcGUAAAGgGcgcGcAgGcGGcccggcAaGucgggcgcgAAAucccgcgGCUcAACcgcgggauc 622 U:::CGGAAUUA+UGGGCGUAAAG GC:CG AGGCGG:::G::AAGUC:G::G::AAAU CC: GGCUCAACC :GG A+: gi_545778205_gb_U000 2730606 UAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACU 2730526 ***************************************************************************** PP v NC >>>>>>>>-->>>>>>>>>,,,(((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>>>>> CS RF00177 623 gcgcccgaaACugccgggCUuGaGuccggccGAgGggggcggAAcucccgguGUAGcgGUGAAAugCGUAGAuaucgggag 703 :C::C:GA+ACU::C:::CUUGAGU ::G::GAGGGGGG::GAA:UCC:GGUGUAGCGGUGAAAUGCGUAGA AUC:GGA: gi_545778205_gb_U000 2730525 GCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG 2730445 ***************************************************************************** PP v v v v NC -->>,,,,<--<<____>>>)))))))-))))))-))),,,]]]]--]]]],,,,<<<<<<---<<---<<<<________ CS RF00177 704 GAacACCacugGCGAAGGCggccccCuGggccgguaCuGACgCugAggcgCGAAAGCguGGGgAgCaAAcgGGAUUAGAUA 784 GAA:ACC+ UGGCGAAGGC :CCCCCUG::C:: ACUGACGCU AGG:GCGAAAGCGUGGGGAGCAAAC:GGAUUAGAUA gi_545778205_gb_U000 2730444 GAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUA 2730364 ***************************************************************************** PP NC _>>>>--->>>>>>>>,,,,,,,,,,((((((,,<<<<<<<<<<<<_____>>>>>>>>>>>>,,,<<____>>,,,,,)) CS RF00177 785 CCCcgGUAGuCCacGCcgUAAACGAUGggcgCUAGgcgccggggggauuaaccccccggcgcCgaAGcuAAcgCauUAAGc 865 CCC:GGUAGUCCACGCCGUAAACGAUG::::CU GG::: : G:: UU A::C : :::CCG AGCUAACGC+UUAAG: gi_545778205_gb_U000 2730363 CCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGU 2730283 ***************************************************************************** PP NC ))))}}}},<<<------<<<<____>>>>---->>>,,,,,,,,{{{{{-{{{{{{{-{{,,{{{{{{{{{{{{{{{{{, CS RF00177 866 gccCCgCCUGgGGAgUACggcCGCAAGgcugAAACuCAAAGGAAUuGaCgGgGgCCCGCaCAAGCGguGgagcauGuGGuU 946 :::CCGCCUGGGGAGUACG:CCGCAAGG:U+AAACUCAAA GAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUU gi_545778205_gb_U000 2730282 CGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUU 2730202 ***************************************************************************** PP v v NC ,,,<<<<________>>>>,,,,,,,,{{{{{{{,,,,,((((((((,,<<<<<<<____>>>>>>>,<<<<____>>>>) CS RF00177 947 UAAuuCGAuGcaAcgCGaaGAACCUUACCcgggcUUGAcgugccgggaaccccccgGAaAcgggggguccccuuaaggggc 1027 UAAUUCGAUGCAACGCGAAGAACCUUACC:GG:CUUGAC:U:C::GGAA ::::C:GA A:G:::: +: CCUU +GG :C gi_545778205_gb_U000 2730201 UAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAAC 2730121 ***************************************************************************** PP NC ))))-))),[[-[[[[--[[[[[[[[[,,,((((((<<<____>>>,,<<<<______>>>>,,)))))),,,,,((((,< CS RF00177 1028 ccggacacAGGUGcugCAuGgcuGuCGUCAGCuCGuguCGUGAGauGUcgGGUUAAGUCCcgcAaCGaGCGCAACCCccgc 1108 C::GA:A:AGGUGCUGCAUGGCUGUCGUCAGCUCGUGU:GUGA:AUGU:GGGUUAAGUCCC:CAACGAGCGCAACCC::+: gi_545778205_gb_U000 2730120 CGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAU 2730040 ***************************************************************************** PP NC <<<<<<---<<--<<<______>>>>>---->>>>>>>,,<<<<<<<<_____>>>>>>>>,,,,,)))),,,,]]]]-]] CS RF00177 1109 cccuagUUgCcAucgguuuauuccggGcACUcuaggggGACcgCCggcGauAAgccGGagGAAGGuggGGAuGACGuCAag 1189 CC:U:GUUGCCA+CGG U ++CCGGG+ACUC:A:GG:GAC:GCC:G:GAUAA:C:GGA:GAAGGU::GGAUGACGUCAAG gi_545778205_gb_U000 2730039 CCUUUGUUGCCAGCGG-UCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAG 2729960 ************.88899******************************************************* PP NC ]---]]]]]]]],,,,}}}}}}},,,}}-}}}}}}}}}},,,<<<<<<<-----<<<--<<---<<<____>>>--->>-- CS RF00177 1190 uCauCauggCCCUUAugcccgGGGCuaCACaCgugcuaCAAUGgccggcACAaaggGuaGCaAagccGcGAggcggAGCuA 1270 UCAUCAUGGCCCUUA+G:CC:GGGCUACACACGUGCUACAAUG:C::::ACAAAG:G+AGC+A ::CGCGAG:: +AGC gi_545778205_gb_U000 2729959 UCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGG 2729879 ***************************************************************************** PP NC -->>>----->>>>>>>,,,,,,<---<<<<<<<<________>>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<___ CS RF00177 1271 AUCccauAAAgccggcCucAGUUCGGAcuGgaGgCUGcAAcUCGcCucCagGAAGuuGGAauCGCUAGUAaucGcggcUCA 1351 A C:CAUAAA::::G:C +AGU CGGA:UGGAG:CUGCAACUCG:CUCCA:GAAGU+GGAAUCGCUAGUAAUCG:GG:UCA gi_545778205_gb_U000 2729878 ACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCA 2729798 ***************************************************************************** PP NC ____>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,<-<<-<<---<<<<<<<<--<<<<<<<<<<<<----<<<<<<- CS RF00177 1352 GcAugccgCgguGAAUACGuUCcCGGGcCuuGuACaCACCGcCCGUCAcgcCacggaAgccggccccgcCcGAAGccgccg 1432 G AU:CC:CGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAC:CCA::G+A::::::::C::: GAAG:::::+ gi_545778205_gb_U000 2729797 GAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA 2729717 ***************************************************************************** PP NC <<<<--<<____>>->>>>>>>>>>--->>>>>>>>>>>>-->>>>>>>>---->>-->>-->,<<<<<<<<<<____>>> CS RF00177 1433 cgccAAccuuaaggaggcgggcggCuAaGgcggggccggcgAccggGgcgAAGUCGUAaCAAGGuagCcguaccGGAAggu 1513 ::::AACCUU GGA:::::::::C A :::G::::::::GAC::GGG:GAAGUCGUAACAAGGUA:CCGUA::GGAA::U gi_545778205_gb_U000 2729716 GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCU 2729636 ***************************************************************************** PP NC >>>>>>>::::::::::::: CS RF00177 1514 gcgGcugGAUcAccUcCUUu 1533 GCGG:UGGAUCACCUCCUU gi_545778205_gb_U000 2729635 GCGGUUGGAUCACCUCCUUA 2729616 ****************** PP >>
RNAfold
>gi_545778205_gb_U000_287 AAGGAGGUGAUCCAACCGCAGGUUCCCCUACGGUUACCUUGUUACGACUU CACCCCAGUCAUGAAUCACAAAGUGGUAAGCGCCCUCCCGAAGGUUAAGC UACCUACUUCUUUUGCAACCCACUCCCAUGGUGUGACGGGCGGUGUGUAC AAGGCCCGGGAACGUAUUCACCGUGGCAUUCUGAUCCACGAUUACUAGCG AUUCCGACUUCAUGGAGUCGAGUUGCAGACUCCAAUCCGGACUACGACGC ACUUUAUGAGGUCCGCUUGCUCUCGCGAGGUCGCUUCUCUUUGUAUGCGC CAUUGUAGCACGUGUGUAGCCCUGGUCGUAAGGGCCAUGAUGACUUGACG UCAUCCCCACCUUCCUCCAGUUUAUCACUGGCAGUCUCCUUUGAGUUCCC GGCCGGACCGCUGGCAACAAAGGAUAAGGGUUGCGCUCGUUGCGGGACUU AACCCAACAUUUCACAACACGAGCUGACGACAGCCAUGCAGCACCUGUCU CACGGUUCCCGAAGGCACAUUCUCAUCUCUGAAAACUUCCGUGGAUGUCA AGACCAGGUAAGGUUCUUCGCGUUGCAUCGAAUUAAACCACAUGCUCCAC CGCUUGUGCGGGCCCCCGUCAAUUCAUUUGAGUUUUAACCUUGCGGCCGU ACUCCCCAGGCGGUCGACUUAACGCGUUAGCUCCGGAAGCCACGCCUCAA GGGCACAACCUCCAAGUCGACAUCGUUUACGGCGUGGACUACCAGGGUAU CUAAUCCUGUUUGCUCCCCACGCUUUCGCACCUGAGCGUCAGUCUUCGUC CAGGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCAUUUCA CCGCUACACCUGGAAUUCUACCCCCCUCUACGAGACUCAAGCUUGCCAGU AUCAGAUGCAGUUCCCAGGUUGAGCCCGGGGAUUUCACAUCUGACUUAAC AAACCGCCUGCGUGCGCUUUACGCCCAGUAAUUCCGAUUAACGCUUGCAC CCUCCGUAUUACCGCGGCUGCUGGCACGGAGUUAGCCGGUGCUUCUUCUG CGGGUAACGUCAAUGAGCAAAGGUAUUAACUUUACUCCCUUCCUCCCCGC UGAAAGUACUUUACAACCCGAAGGCCUUCUUCAUACACGCGGCAUGGCUG CAUCAGGCUUGCGCCCAUUGUGCAAUAUUCCCCACUGCUGCCUCCCGUAG GAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCUGGUCAUCCUCUCAGACC AGCUAGGGAUCGUCGCCUUGGUGAGCCGUUACCCCACCAACAAGCUAAUC CCAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAAGGUCCCCCUCUUUGGU CUUGCGACAUUAUGCGGUAUUAGCUACCGUUUCCAGUAGUUAUCCCCCUC CAUCAGGCAGCUUCCCAGACAUUACUCACCCGUCCGCCACUCGUCAGCGA AGCAGCAAGCUGCUUCCUGUUACCGUUCGACUUGCAUGUGUUAGGCCUGC CGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAAUUU .(((((.(((((.(((((.(((....))).)))))......(((.((((.......)))).))).......(((((...(((.........((((......))))........)))...)))))....(((((.((((((.(((((((((((((((((((((....))).))).)))....(((((...)))))..((((((.(.(((((((((((((.(.((((.((..(((.....))))).)))).)))))))))))))).)(((((....)))))))))))....))))))))))))......(((((.((((((((((((((.....))))).((((((.....)))))).........(((((((.....))))).))..(((((((.....(((((......)))))...)))))))...))))))))).)).)))(((......)))............((((((((((.((((((((((((((.(.((((...((((....((((((.......(((((.((........)).)))))....((((......))))(((((.((((.............((((.((......)).))))(((....)))((((.....))))............(((((((.((....)))))))))......((.((((((((((..(((((((((...(((......)))....((.(((...))).))))))))).))..((((((.....))))))..........((((((........)))))).(((((.(((..(((((((((..........)))......(((((.....((.((........))))...))))).......))))))..))))))))......(((((((((((((((.(((((((.(((...))).)))))))...)))))))...........((..((((.((..((((.....))))...))....))))..)).....((((......)))).))))))))))))))))))))((((((..((.(((((..........(((.((((.......)))).)))........))))).))))))))....)))).))))))))))).....)).)).)))).))))))))..)))((((((.....))))))...(((..(((.((((.....)))).)))..)))...)))))))))))..)))(((((((((.........)))))))))(((((....((.((((((...........))))))...))..))))).((((((.....(((((((...((((((.(((((......)))))))))))((........))((...(((((((........)))))))...))..))))).))......)))))).........))))))))))).....(((.(((((((....)))))))))).....(((((..(((.((((....((....))....)))).)))..)))))...)))))..)))))...... (-496.10)
Length sequence : 1541	Length match: 1540