gi_545778205_gb_U000_127

"structRNAfinder"

gi_545778205_gb_U000_127
cmsearch-Rfam
Family : LSU_rRNA_eukarya	Id: RF02543	Type: Gene; rRNA;
Taxonomy: Eukaryota; Bacteria; Viruses; Archaea;	Ontology: GO:0003735 structural constituent of ribosomeRF02543
Description: not description
Score: 1258.4	E-value: 0
From sequence: 225918	To sequence: 228644
Alignments: NC :::::::::::::::::::::::<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<____>>,,,<<<<<--- CS RF02543 1 ugacCUuaaaUcAgguaaGAuUAcCcgCuGAAuUUAAGCAUAUuAaUAaGcgGAgGAAAAGAAAcuAACaagGAUUcccuuAG 83 + CC UA+ U+A A+G ACC:G :GAA+U AA CAU U A UA: C:GAGGAAAAGAAA::AAC ::GAUUCCC: AG gi_545778205_gb_U000 225918 AAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAG 226000 ********************************************************************************* PP v NC --<<_____>>---->>>>>,,[[[[,,.<<<<<<<<<<<<<<<<_______>>>>>>>>>>>>>>>>,,,,((((((-(((( CS RF02543 84 UAgcGGCGAgcGAAgagggAAuAGCcCA.cgcugcaacuccgcccucuuuuugggcggaguugcagcgUauaggggccuccuc 165 UAGCGGCGAGCGAA :GGGA AGCCCA + G: :C: gi_545778205_gb_U000 226001 UAGCGGCGAGCGAACGGGGAGGAGCCCAg----------------------A----------------GCCUGAAUCA----- 226040 ************************2......................2................4444664444..... PP v vvvv vvvv v NC -(((((((-(((((((,,,<-<<<<______>>>>>,,<___>,,<<_______>>,,,,,)))))))--)))))))-----) CS RF02543 166 agccgcggcccccgccuAAgUccccUgGAAuggggcaccAuAgAGGGUGAgAguCCcGUauggcgggguaccgcggcuuuaug 248 G: :::G+ :: AAG C::CUGGAA G::GC C:AUA:AGGGUGA AG CCCGUA :: U C::: :CU gi_545778205_gb_U000 226041 -GUGUGUGUGUUAGUGGAAG-CGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUG---- 226117 .4444444233333445666.**********************************98655444444444444444.... PP v NC )))))))-)),,,,,,,,<<<<<<<___..._____>>>>>>>,,,,.,<<<<<________>>>>>,,]]]],,,,,,,,,, CS RF02543 249 aggggccuccaaaGAGUCGgGuugcUUG...ggAaUgcagCcCaAAg.UgGguGGUAaAuUuCauCcAAgGCUAAAUAuuagc 327 :G: :C A+GAGU :G : G: GG AU:C : C: AA+ UGGG:GG A + UC:UCCAAGGCUAAAUA+U + gi_545778205_gb_U000 226118 ---UGAGCUCGAUGAGUAGGGCGGGACAcguGGUAUCCUGUCUGAAUaUGGGGGG--ACCAUCCUCCAAGGCUAAAUACUCCU 226195 ...4444577999999999999998643111345678999999999845666665..45667999999*********** PP NC ,,,,,,,,,,,,,,,,,,,,,,,<<____>>,,,,,,,,,,,,,,,<<<<__.__>>>>,,,,,,,,,,,,,,,,,,,,,,,, CS RF02543 328 aaGAGACCGAUAGcgaACAAGUAccGUGAggGAAAGaUGAAAAGaACucuGA.AaagaGAGUUAAAuAGuAcgUGAAAuuGuU 409 A GACCGAUAG+GAAC AGUACCGUGAGGGAAAG GAAAAGAAC:C:G A:G:GAGU AAA AG AC UGAAA++GU gi_545778205_gb_U000 226196 GACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGcGAGGGGAGUGAAAAAGAACCUGAAACCGUG 226278 **********************************************87368999*********************9 PP v v v v v v NC ,,,,,,,,,,(~~~~~~~),,<<<<________>>>>{{{{{{,,,,(((((((((((((,,<<<--<<<<<<____>>>>>> CS RF02543 410 aAgAgGgAAgc[225]gACCCGUCUUGAAACACGGACCAAGGAGUccaacauguguGCgAGuguuugggucauuAgaccca 710 +A AAGC G CC U UUG A A GG::CA: GA U:::A::::: ::C+AG U+ :: A UA :: gi_545778205_gb_U000 226279 UACGUACAAGC[ 29]GUACCUU-UUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACC--GAAUA---GGG 226377 99988888876....7..4556644.78889899*****************************99765..33444...667 PP NC -->>>,,,<<____>>,,,,,,,~~~~~~~~~~~~,,,,))))))))))))),,[[-[---[[[[[[,,,((((((((((((, CS RF02543 711 uacgCGuAacgAAagugAauuaa[29]*[33]aaGAGCacacauguuggGACCCGAAAGauGGUGAACUAugCcugggcA 843 A CG A::GAAA::GA U ++ AG:: :::::U:::GACCCGAAA:::GGUGA C A::C:UG GCA gi_545778205_gb_U000 226378 GAGCCGAAGGGAAACCGAGU---[ 8][ 4]UUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCA 226457 99**************974......8.......9********************************************* PP v v v v NC <<<<---<<<<<<<____>>>>>>>---->>>>,,,<<<<-<<-<<________>>>>>>>>,,)-))))))))))),<<<__ CS RF02543 844 GggcGAAGccAGgGGAAACcCUggUGGAGgccCGuAgcgaUuCUGACGUGCAAAUCGaucgucagAccuggGuaUAGGgGcGA 926 GG::GAAG::: G AA C :::UGGAG::CCG+A:CG U: : UG AAA ::A CG: +GAC UG:G::U GG:G GA gi_545778205_gb_U000 226458 GGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUA-AUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGA 226539 *************99****************9887.777788898888899******************** PP v NC ___>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,,(((((((,,,,,,,,,<<<<<<<<--- CS RF02543 927 AAGaCuAAUCGAACCauCUAGUAGCUGGUUcCcuCCGAAGuuUCCCUCAGGAuaGCuggagcuuuuuuuuAGUcuuAuccGGU 1009 AAG C:AAUC AACC::: UAGCUGGUUC:C:CCGAA ::U:: U ::A::GC: ::::: U +A UCU:::: GGU gi_545778205_gb_U000 226540 AAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAACU---CA-UCUCCGGGGGU 226618 *****************************************************999999333...33.******* PP v vv v v v v vv v v NC -<<<----<<<<<<<<<<--<<<<<<-<_____>->>>>>>.>>>>>>>>>>-->>->---->>>>>>>>,<<<<<<<<<___ CS RF02543 1010 AAAGCgAAUGAuUAgaGGcuucggGgacgaAAugucCucga.CCuaUUcUCAAACUUUAAAUgggUaagAagccccgguuaCU 1091 A:AGC A UG :::: C+ : G:G+C + +G+C:U : +C:::: CAAACU : AAU ::::AGAA gi_545778205_gb_U000 226619 AGAGC-ACUGUUUCGG--CAAGGGGGUCAUCCCGACUUACCaACCCGAUGCAAACUGCGAAUACCGGAGAA------------ 226686 *8.789887776..889999999*9999995543567777889*****************6............ PP NC ______>>>>>>>>>,,,,,,,,,,,))))))),,,,,<<<<<<<<<<_.____>>>>>>>>>>,,,,<<<______>>>,,, CS RF02543 1092 UaauUGaaccggggcauuuaAuauaaagcuccaAGUGGGCCAcUUuUGG.UAAGCAgAAgUGGCGAUGcGGGAUGAACCgAAc 1173 UG U A::::: :AG C: :: G UAA :: :G A :GG A AACC:A gi_545778205_gb_U000 226687 ----UG-----------------UUAUCACGGGAGACACACGGCGGGUGcUAACGUCCGUCGUGAAGAGGGAAACAACCCAGA 226748 ....22.................33399999999987766666666665599966666666666666677777889999 PP v vv NC (((.((-(---(((------(-(--(((------------------(((-((((((((((-------(((((,<<<--<<<__ CS RF02543 1174 Gcc.ggGuUAAGGuGCcuaAgUgcacgCUcAUcuAGAuaCCAuAAAaGGUGUuggUucaUauaGACAGCaGgAcGGUGgccAU 1255 C: ::G:UAAGGU CC+AAGU:++:G:U A G AAA:G UGU GG : : AGACA C::G ::GU ::C U gi_545778205_gb_U000 226749 CCGcCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG-------AAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUU 226824 999459******************99997666.......799********************************* PP vv v NC _______>>>-->>><___><---<<______>>->,)))))---)))))))))))))-------------------)))--) CS RF02543 1256 GGAAGUCggaAUCCgCUAAGGAGUGUGUAACAACUCAcCuGCCGAAugaAccaGCCCuGAAAAUGGAUGGCGCUuAAGcguac 1338 GAAG G::AUC:::UAA:GA G:GUAA A:CUCAC::G CGA: : CC GC C:GAA AUG A G G UAA:C:++: gi_545778205_gb_U000 226825 AGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUG 226907 *************************************************************9887777777999* PP vv NC ))))---)-)))))<<<<<<<<<_________>>>>>>>>>,,,,]]]]]]<-<<<<<<<<.<<------<<----<<<____ CS RF02543 1339 caCCuAUaCccggCCgucggggcAaauuuaaugccccgacGAGUAGGagGgcGuggcGgcu.gcguuGAAgcuuugggcGUgA 1420 CACC A :C:::G C: C:::GC +AUGC:::G :G GUAGG:G:GCGU:::G : :C UGAAG:U U :: GUGA gi_545778205_gb_U000 226908 CACCGAAGCUGCGGCAGCGACGCU-----UAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAgCCUGUGAAGGUGU-ACUGUGA 226984 *******************5.....566*************************99999999999766.*** PP vv NC >>>--->>--->>>>>>>>>>-->,,,,,}}}}}},,,,,,,,,,,,,,<<<<<<_______>>>>>>{{{{,,,,,{{{{,, CS RF02543 1421 gccuggguGGAgcagcCgccaGUgCAGAUCUUGGUGGUAGUAGCAAAUAcUCaAaUGAGAaCuUuGAggACuGAAGUGGaGAA 1503 :: G:UGGAG:: C:::AGUGC AU :UG:: AGUA C A A::C:::UGA AA :::G::::C:G A G:::AA gi_545778205_gb_U000 226985 GGUAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGA-AGACCAA 227066 *********************************************************************98.5**** PP NC {{,,,<<<<<<---<<_____>>->>>>>>,,,,,,{{{,((.---((~~~~~~~~~~~~,,,,,))----)),,,<<<<<__ CS RF02543 1504 GGGUUcCgugugAACaGuAgUuGaacacGgGUuAGUCGgUCC.UAAGg[17][21]auuuacCGAAAGGGAAgcgGGUU 1611 GGGUUCC:: : AAC: UA+U:G+: ::GGGU AGUCG: CC UAA GGGAA:C:GGUU gi_545778205_gb_U000 227067 GGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCcUAA--[13][11]----------UGGGAAACAGGUU 227149 *************************************8763666.....6.....6............3******** PP v v v NC ______>>>>>,,[[[[-[[[[[[[,,,,<<<<____>>>>,,,,,,((((((---((((-(((((((-(((<<<<<<.____ CS RF02543 1612 AAuAUUCCcgcACcuggacguggauuuuaugcgGuAAcgcaAaugAacucggaGAcgccggcgggggccccgggaaGa.GUUu 1693 AAUAUUCC:G:AC:UG GU:::U A ::G:GACG :G :GG :: ::GG:::G: G gi_545778205_gb_U000 227150 AAUAUUCCUGUACUUGGU-GUUACUGCG--------A----------AGGGGGGACGGAGAAGGCUAUGUUGGCCGGGcGACG 227213 ***********994.776655433........2..........357899*******************9977777 PP vvv v v v v v v v v vvv vv NC _____>>>>>>,,,<<<<<-----<<<<<<<<<<<<<_____>>>>>>>>>>>>>----->>>>>,,,,,,<<<<<<<_____ CS RF02543 1694 UCUUUuCuucuUAAcggccuauuuaCCcugcAaccgguUuauccggaGguagGGuuuaauggccgGaAgAGcgccgcauuuuu 1776 U U:C:::UU A: : ++ :: : ::: C GG AUCC G ::: : :: + : :GA GA ::::U gi_545778205_gb_U000 227214 GUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACG- 227295 8888999999988765555444447767777777789999999977777766655555555555688888888899999888. PP vv v v v NC >>>>>>>,,)))---)))))))-))))---------)))))),,,,,,,,,,,]]-]]]]]]]]],}}},,}},,,,,<<___ CS RF02543 1777 ugcggcgUCcggUgugcccccgacggcCCUUGAAAAuccgagGgAaggaauaaauuccacgccaggcCGUACCcAUAaCCGCA 1859 :::: C:: + :: CC: C: CC AAA :C:: A+ + A: ::AC+ CA:+:CGUACCC AACCG gi_545778205_gb_U000 227296 GUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUA--AGCAUC---AGGUAACAUCAAAUCGUACCCCAAACCGAC 227373 9999999**************99888777777776543..333333...4456777899**************** PP NC ___>>,}}}},<<<<_____>>>>,,}}}},,{{{{----{{{{{{{{-{{{,,,,,,,,,,,,,,<<<<<---<<____>>- CS RF02543 1860 uCAGGUCuCCAAGGugAauAgCCUCUaGUcgAUAGAAuAAgGUAGgUAAGGGAAGUCGGCAAAaUAGAUCCGUAaCUUcGGgA 1942 CAGGU:::CA:G :GA +A: C: :G:: U:::A AA: ::GGU:A:GGAA U GGCAAAAU :: CCGUAACUUCGGGA gi_545778205_gb_U000 227374 ACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGA 227456 ********************************************************************************* PP NC --->>>>><<<<<<<<<~~~~~~~-->>>>>>>>><___>,,,,,,,[[[[[[[[[,,<<<_________>>>,,<<<<<<<< CS RF02543 1943 aAAGGAUUGGCUCUgAg[146]AAcUcAGAACUGGuACGGACaAGgGGAAUCcGACUGUuUAAUUAAAACAuAGcAUugcG 2164 AAGG ::G CUGA: AA:UCAG U:G+A: AC AG: G: C:ACUGUUUA U AAAACA AGCA: G:: gi_545778205_gb_U000 227457 GAAGGCACG---CUGAU[ 31]AAAUCAG---UCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUG 227557 ******9...66776....9..5667766...9********************************************** PP v v v v NC -<-<<<<_____>>>>->--->>>>>>>>,,((((,<<<--<<<<<<-<--<<<----~~~~~~--->>>>>>>>-->>>>>< CS RF02543 2165 AcGgcccgaAaggggcGgUGACgcaAUgUGAuUuCUGCCCAGUGCUcUGAAuGuCAAa[15]cAAgCgCgGGUAAACGGCG 2256 + C:CGAAA G:G A::C :UGUGA: :CUGCCC GUGC:: GAA:GU AA AAGC:C::GUAAACGGCG gi_545778205_gb_U000 227558 CAAACACGAAA-GUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCG-GAAGGUUAAU[32]GAAGCCCCGGUAAACGGCG 227664 *********.*******************************.****98...9..689************ PP NC <<<<<_______>>>>>><___>,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]], CS RF02543 2257 GGAGUAACUAUGACUCUCuUAAgGUAGCCAAAUGCCUCGUCAucUAAUUagUGACGCGCAUGAAUGgAuUAACgAGAUUCCcA 2339 G GUAACUAU AC UC:UAA:GUAGC AAAU CCU GUC:: UAA U ::GAC GCA GAAUG: :UAA:GA :C : gi_545778205_gb_U000 227665 GCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGG 227747 ******************************************************************************* PP NC ,,,}}}-}}}}}}}}-}}}},,,,,,,,,,,.,<<<<<________>>>>>,,{{{{{{{{-{{{-{{,,,,,,{{{{-{{{{ CS RF02543 2340 CUGUCCCUAcCUACcAUCUAGCGAAACCACA.GcCAAGGGAACGGGCUUGgaAccaucAGcGGGGAAAGAAGACCCUgUUGAG 2421 CUGUC:C:ACC:: :A:::AG GAAA A C G GAA GC G+ACC: C:G: :G: :: AAGACCC:GU :A gi_545778205_gb_U000 227748 CUGUCUCCACCCGAGACUCAGUGAAAUUGAAcUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAAC 227830 **********************9977735********************************************** PP v v v NC {{{,[[[[---[[[[[[[,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<______..................... CS RF02543 2422 CUUGACUCUAGucuGgcaUUGugaagcgacauggggGgUGUAGaAUAaGUGGGAGcuuuuag..................... 2483 CUU ACU UAG:: G:CA UG:::A:::A : :::: :UGUAG AUA:GUGGGAG:+UUU++ gi_545778205_gb_U000 227831 CUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAaguguggacgccagucugcau 227913 *******************************************************997******************* PP v v v v v NC ....>>------------>>>>>>>>>>>>>->>>>>>>>>>,,,((((~~~~~~)))),,,,,]]]]]]]----]]]],,<< CS RF02543 2484 ....gCGccagUGAAAUACCACuaCccccauugucgcuucaCUUAcucc[68]ggagGACAuugcCaggUGGGGAGUUUGg 2624 :CG+C UGAAAUACCAC:: :::: : U:::U:::CU AC:: ::GGACA UG:C ::UGGG AGUUUG: gi_545778205_gb_U000 227914 ggagCCGACCUUGAAAUACCACCCUUUAAUG-UUUGAUGUUCUAACGUU[16]UGCGGACAGUGUCUGGUGGGUAGUUUGA 228005 *****************************.89********975...7..589********************* PP NC <<_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((((<<-<<<<<<_______>>>>>>--->><<_____ CS RF02543 2625 CuGGGGCgGcACAuCuGuuAAAuaAUAACgCaGgUGUCCUAAGGcgaGCUCAgcGaGgACAGAAAcCuCgcGUaGAgcAAAAG 2707 CUGGGGCGG: C :CU::UAAA A UAAC::AG: G C AAGG:::GCU:A:C :G: C GA A:C: G:G :AG: AA gi_545778205_gb_U000 228006 CUGGGGCGGU-CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAU 228087 ******.******************************************************************** PP v v v NC _>>,,,,)))))),,,,<<<<<<<<<_______>>>>>>>>>,<<<____>>>,]],,,,,,,,,,<<<<<<--<<<<_____ CS RF02543 2708 GgcAAAAGCucgCUUGAUuuccauucUCAGUAugaauggaaAccgcGAAAgcgUGGCCUAUCGAUCCUuuaguucuucaaAaU 2790 G:CA AAGC:::CUUGA:U:C: :::U A ::: :G:A: :GCGAAAGC: G C UA GAUCC U:GU :::+AA gi_545778205_gb_U000 228088 GGCAUAAGCCAGCUUGACUGCGAGCGUGA-CGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGU--UCUGAAUG 228167 **********************998.5679**********************************5..67788888 PP v NC __>>>>>>>>>>,,,,,,,...,,}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<_______>>--->>>>>>>-- CS RF02543 2791 UUgaagcuagAGGUGUCAG...AAAAGUUACCAcAGGGAUAACUGGcuUGUGGCgGCCAAGCGUUCAUAGCGACGUcGCUUUU 2870 :::GC:A G U G AAAAG UAC: C:GGGAUAAC G::U : ::CG CCAAG:GUUCAUA:CGACG CG:: UU gi_545778205_gb_U000 228168 GAAGGGCCAUCGCUCAACGgauAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUU 228250 888899999999887654422267******************************************************* PP NC >>>>,,,,,,,,,,(((((((((((,,<<-<<<<<<______>>>>>>--->>,<<<<<_____>>>>>,,,,,)))))--)- CS RF02543 2871 UgaUCCUUCGAUGUCGGCUCUUCCUAUCaUuguGAaGCAGAAuUCacaAAGuGUuGGaUUGUUCAcCCaCuAAUAGGGAACGU 2953 :G:: C UCGAUGUCGGCUC UC :AUC:U:G: : G AG A : :C:AAG:GU::G::UGUUC::C::+UAA : GG ACG gi_545778205_gb_U000 228251 UGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGC 228333 ******************************************************************************* PP v NC -))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}}}}},.,,((((((((--((((,<<<<<<<<______ CS RF02543 2954 GAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUaCUgaugga.augucguugcaAcaGcAauccagccuAGUAC 3035 GAGCUGGGUUUA:A CGUCGUGAGACAG U: GU :: :C::C:G :GG UG::G::::+A::G: : ::CCUAGUAC gi_545778205_gb_U000 228334 GAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCgCUGGAGAACUGAGGGGGGCUGCUCCUAGUAC 228416 ***********************************************9899999999****************** PP v v v NC _________>>>>>>>><<<<<---<<<----<<<<<<<<<<<.____.>>>>>>-->>>>>--->>>-->>>>>,..<<<-- CS RF02543 3036 GAGAGGAACggcugguucggAuAaUUggUuuucGcggcuGgcu.GAaa.agcCagUGccgCgAAGcuAcCaUccgu..uggAU 3114 GAGAGGA CGG:: : CG:AU A UGGU U :::GG UG:C: G A :G:CA UGCC::: AGCUA AU:CG :GAU gi_545778205_gb_U000 228417 GAGAGGACCGGAGUGGACGCAUCACUGGUGU-UCGGGUUGUCAuGCCAaUGGCACUGCCCGGUAGCUA-AAUGCGGaaGAGAU 228497 ***************************.8888888877637777457788888888899*.***93345579 PP v v NC --<<<<<___________>>>>>---->>>,))))--..--.)))))))),,,,,,<<<<<<~~~~~~~>>>>>>,,,((((( CS RF02543 3115 uAuggCUGAAcGCCUCUAAGccaGAAuccaugCugga..Aa.gcaacgacuuuuuccccccc[115]ggggggguugaAuc 3302 +A::GCUGAA GC UCUAAGC::GAA C: :C::GA ::::C::C U +C:CC:: ::GG: gi_545778205_gb_U000 228498 AAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAgaU-gAGUUCUCC-CUGACUCCUUG[ 8]GAAGGAA------- 228572 *********************************9744.599999999.55555555553....5..3555554....... PP vv v v v v NC <<<<<_______>>>>>,,,,<<<<<<<<<-<<--<--<<<<-<<<<<<<<______>>>>>>>>>>>>>--->>---->>>- CS RF02543 3303 ccccGuAGACGACggggaUauccgaccgGGUgcUGuAAgcgguacaGcagccUuuuUgcugCgguccgcuGAGgcUuAgCCcu 3385 C:: G AGACGAC ::G+U +::G C GG :UGUAA:CG: +U :CG:UGAG: A CC gi_545778205_gb_U000 228573 CGUUGAAGACGACGACGUUGAUAGGCC-GGGUGUGUAAGCGCA---------GCGAU--------GCGUUGAGCU--AACCG- 228634 ***************87777655.55568****95.........45666........9***75..55776. PP vv NC >>>>>>,,,))))).:: CS RF02543 3386 ggucggauagaUuc.gu 3401 G C::A G gi_545778205_gb_U000 228635 GUACUAA-------uGA 228644 5556667.......0 PP >>
RNAfold
>gi_545778205_gb_U000_127 UAGUGGUUAAAUAAAAAAUACUUCAGAGUGUACCUGCAAAGGUUCACUGC GAAGUUUUGCUCUUUAAAAAUCUGGAUCAAGCUGAAAAUUGAAACACUGA ACAAUGAAAGUUGUUCGUGAGUCUCUCAAAUUUUCGCAACACGAUGAUGG AUCGCAAGAAACAUCUUCGGGUUGUGAGGUUAAGCGACUAAGCGUACACG GUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUA AGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGG GAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAA UGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAA UCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAACGGGGAGGAGCCCAGAG CCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUAC AGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGU AGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAA GGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAG GCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUAC GUACAAGCAGUGGGAGCAUGCUUAGGCGUGUGACUGCGUACCUUUUGUAU AAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGC CGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCC GAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAAC UGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCU GGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGC UAUUUAGGUAGCGCCUCGUGAACUCAUCUCCGGGGGUAGAGCACUGUUUC GGCAAGGGGGUCAUCCCGACUUACCAACCCGAUGCAAACUGCGAAUACCG GAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAA GAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGU GGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCA GCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGC GGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCU UAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGUGAAGGUGUACUG UGAGGUAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAU AAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAAC GUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUA GUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGG GGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCG UGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAU GACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAG CCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGG UCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAG GCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAA GCGACUUGCUCGUGGAGCUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAA CUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACG GUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAG CGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGU CCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGG CGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUC GCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACC UUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUG GGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUA CCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCG GACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUA ACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAG UGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUG CGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCU CAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGU UCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUG GGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUAC GCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUG GGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUG GACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGC UAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCC CGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCCUGAAGGAACGUUGAAGA CGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAA CCGGUACUAAUGAACCGUGAGGCUUAACCUUACAACGCCGAAGCUGUUUU GGCGGAUUGAGAGAAGAUUUUCAGCCUGAUACAGAUUAAAUCAGAACGCA GAAGCGGUCUGAUAAAACAGAAUUUGCCUGGCGGCCGUAGCGCGGUGGUC CCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGG UAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAUCAAAUU AAGCAGUAAGCCGGUCAUAAAACCGGUGGUUGUAAAAGAAUUCGGUGGAG CGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGG 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Length sequence : 3400	Length match: 2725