gi_545778205_gb_U000_126

cmsearch-Rfam

Family :

LSU_rRNA_bacteria

Id:

RF02541

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea;

Ontology:

GO:0003735 structural constituent of ribosomeRF02541

Description:

not description

Score:

2889.3

E-value:

0

From sequence:

4210043

To sequence:

4212946

Alignments:

                                                                                                                 NC
                               {{{{{{{{,,,,,,{{{{{{{{{{-----{{{,,{{{{{{{{{{{[[,,,,,((((<<<________>>>,,,,,<<<<<< CS
               RF02541       1 ggucaagcuauuAAggGCgcgcGGuGGAUGCCUuGGcgccgggaggCGAuGAgGGaCGcGguaagCugCGAuAAGCcccGg 81     
                               GGU:AAGC A UAA::G::C:CGGUGGAUGCC UGGC:::::GAGGCGAUGA:GGACG:G UAA CU:CGAUAAGC::CGG
  gi_545778205_gb_U000 4210043 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGG 4210123
                               ********************************************************************************* PP

                                                                                                                 NC
                               <--<<<_______>>>----.->>>>>>>,,,)))),,,<<<____>>><<<<<<<______>>>>>>>,<<<<<<<<<__ CS
               RF02541      82 ggAGccGcaAacAggCuuuG.AccCgggGAUuuCCcAAUgGGGaAACCcgcccgggguaauacccgggcAcccccggccGA 161    
                               : AG::G +A  A::C UU  A:CCG::GAUUUCC:AAUGGGGAAACCC:::::G:  ++  :C:::::A:C:::::C:GA
  gi_545778205_gb_U000 4210124 UAAGGUGAUAUGAACCGUUAuAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGU--UUCGACACACUAUCAUUAACUGA 4210202
                               ****************88877***********************************..6778******************* PP

                                                                                                                 NC
                               _______>>>>>>>>>,]],,,<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<____>>,,{<<<<<-- CS
               RF02541     162 AuacAUAggccgggggaGcaAACccgGgGAAcUGaAACAuCUaAGUAcCcggAGGAAAAGAAAgcAAaagcgAuuCCccuA 242    
                               AU CAUA:G:::::G:+GC+AACC:GGGGAACUGAAACAUCUAAGUACCC:GAGGAAAAGAAA:CAA  G:GAUUCCCC A
  gi_545778205_gb_U000 4210203 AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCA 4210283
                               ********************************************************************************* PP

                                                                                                  v              NC
                               ---<<_____>>---->>>>>,,[[[[,,,,<<<<<<<________>>>>>>>,,,,,,(((-(((((-------(((((( CS
               RF02541     243 GUAGcGGCGAgCGAAaggGGaauaGcCcAAACcggggguuauuguucccccgGGGUugugGGacccccaaauuaagagccc 323    
                               GUAGCGGCGAGCGAA+GGGGA  AGCCCA                                  :::C +   +A+:AG: :
  gi_545778205_gb_U000 4210284 GUAGCGGCGAGCGAACGGGGAGCAGCCCA----------------------------------GAGCCUG--AAUCAGUGU 4210328
                               ***************************98..................................9999988..899****** PP

                                                                                                          v      NC
                               (((((((-(((,,,<<<<<______>>>>>,,<___>,<<<_______>>>,,,)))---)))))))))))))--)))))- CS
               RF02541     324 cccggcuAgccGAAcggccUGGAAaggccgaCCauAGagGGUGAuAGuCCcGUAggcgaAagccggggggcucuugggggu 404    
                               :::: :UAG::GAA::G:CUGGAAAG:C::+C:AUA:AGGGUGA AG+CCCGUA::C AAA: ::::: :CU:U  G:::+
  gi_545778205_gb_U000 4210329 GUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCG 4210409
                               ***************************************************************************999999 PP

                                                                                                                 NC
                               --))),,,,,<<<<<<<<<_______>>>>>>>>>,,,,,,<<<<<______>>>>>,,]]]],,},,}}-}}}}}}}-}} CS
               RF02541     405 auCCcgAGUAgggCggggcAcGuGaAgccccGcccGAAuaugggggGACCAccccccAAGgCuAAaUAcuccccggcgACC 485    
                               AU   GAGUA:G:C:GG::ACGUG  ::CC:G:C:GAAUAUGG:GGGACCA+CC:CCAAGGCUAAAUACUCC:::::GACC
  gi_545778205_gb_U000 4210410 AU---GAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACC 4210487
                               98...**************************************************************************** PP

                                                                                                                 NC
                               ,,,,,,,,,,,,,,,<<____>>,,,,}},,,,,,,,,<<<<_____>>>>,,,,,,,,,,,,,}-----}}}}}}}}}}, CS
               RF02541     486 GAUAGuGaAcuAGUACCGUGAGGGAAAGGUGAAAAGaACCCcggugAgGGGAGUGAAAuAGaaCCUGAAACCgcgcGCccA 566    
                               GAUAGUGAAC AGUACCGUGAGGGAAAGG GAAAAGAACCCCGG+GAGGGGAGUGAAA AGAACCUGAAACCG:G::C::A
  gi_545778205_gb_U000 4210488 GAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUA 4210568
                               ********************************************************************************* PP

                                                                     v              v                            NC
                               ,,,,{,<<<<<<<<<<<________>>>>>>>>>>>,,<<<<________>>>>{{{{{{,,,,(((((((((((((,,<< CS
               RF02541     567 CAAgcaGucGcggcccgauuuuaaucgggccgCggCGUcCcUUUUGuAuAAgGggcCggCGAgUugccgcgcgcggCaAGg 647    
                               CAAGCAGU G:::C:CG   UUA+ CG:G:::C GCGU C:UUUUGUAUAA:G G:C:GCGA UU::: :::G::GCAAGG
  gi_545778205_gb_U000 4210569 CAAGCAGUGGGAGCACG--CUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGG 4210647
                               *****************..667777******************************************************** PP

                                                                                                                 NC
                               <<--<<<_____>>>-->>>>,,,<<____>>,<<<<<_____>>>>>,,,,))))))))))))),,[[-[---[[[[[[, CS
               RF02541     648 uUAAgccugauaggcGuAgcCGuAGcGAAAgCGcGuCcgAAuAgGgCgauuAGucgcgcgcggcaGACcCGAAACcggGuG 728    
                               UUAA:C  +AUA G:G+AGCCG+AG:GAAA:CG:GUC:+AA  :GGC:+U+AGU::C::: :::AGACCCGAAACC:GGUG
  gi_545778205_gb_U000 4210648 UUAACC-GAAUA-GGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUG 4210726
                               *****9.67777.99****************************************************************** PP

                                                                                                                 NC
                               ,,((((((((((((,<<<<---<<<<<<<____>>>>>>>---->>>>,,,<<<-<<<<<________>>>>>>>>,,)-) CS
               RF02541     729 AuCuaccCauggcCAGGguGAAgccgggcUAAagcccgguGGAGgcCCGAACccacgcccGUUGAAAAgggcgggGAUGAg 809    
                               AUC A:CCAUG :CAGG:UGAAG::: G:UAA+:C :::UGGAGG:CCGAACC:AC::::GUUGAAAA::::G:GGAUGA:
  gi_545778205_gb_U000 4210727 AUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGAC 4210807
                               ********************************************************************************* PP

                                                                                                                 NC
                               )))))))))),<<<_____>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<<-- CS
               RF02541     810 cuguGgguaGgGGcGAAAggCCAAUCaAaCccgGaGAUAGCUgGUUCUCccCGAAAugccuUuAGgggcaGCgucgggcga 890    
                                UGUGG:U GGGG:GAAAG:CCAAUCAAACC:GGAGAUAGCUGGUUCUCCCCGAAA::::UUUAGG::::GC:UCG:G:++
  gi_545778205_gb_U000 4210808 UUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAU 4210888
                               ********************************************************************************* PP

                                         v                                                              v        NC
                               <<<<<<<<<<<----<<<---<<<-<<<<---<<<<<<<____.>>>>>->>--->>>>->>>-->>->---->>>>>>>. CS
               RF02541     891 ucccccccggcGGUAgaGCACuggaugggcuAgGgggccuaaa.ggccuACcaAacccaaccaAACuccGAAUgccgggg. 969    
                               UC::C:CCGG GGUAGAGCACUG +U:GGC+AGGG:G:C + + G:C:UACCAA CC:A  CAAACU CGAAU CCGG:G 
  gi_545778205_gb_U000 4210889 UCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCcGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGa 4210969
                               ***************************************99989************************************9 PP

                                                                                                                 NC
                               >>>-->>>>>>>>->,,,<<<<<<<<<<______>>>>>>>>>>,,,,<<<______>>>,,,((((-(((---(((---- CS
               RF02541     970 gggaaagcccggcAGucAgaccgcgggcGaUAAgguccgcggucgAgAGGGaAAcAaCCCAGAcCgcCagcUAAGGuCCCu 1050   
                               ::G++A:C:CGG:AG+CA:AC::CGGG:G+UAA :UCCG::GU:+AGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCC+
  gi_545778205_gb_U000 4210970 AUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCA 4211050
                               9******************************************************************************** PP

                                                             vv                                                  NC
                               --(-((((((-----------(((-((((((((((-------(((((,<<<--<<<_________>>>-->>><___><-- CS
               RF02541    1051 AAgugcggGcUAAGUGggAAAGGcuGuggggccgCuaAgACAaCcaGGAgGUUGGCUUAGAAGCAGCCAUCcUuuAAaGAg 1131   
                               AAGU:::GG:UAAGUGGGAAA:G:UGU:GG  ::C  AGACA:CCAGGA:GUUGGCUUAGAAGCAGCCAUC:UUUAAAGA+
  gi_545778205_gb_U000 4211051 AAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAA 4211131
                               ********************************************************************************* PP

                                                        vv                                                       NC
                               -<<______>>->,)))))---)))))))))))))--------------------))))))))))---)))))))<<<<<< CS
               RF02541    1132 uGCGUAAuAGCUCACugGuCaAGcggccccgCgCCGAaAAUguaaCGGGGCUcAAgCccgccaCCGAAgcugcGggcucgc 1212   
                               +GCGUAAUAGCUCACUGG:C+AG::  CC:GC:C:GAA AUGUAACGGGGCU AA:CC:::CACCGAAGCUGCGG:: C :
  gi_545778205_gb_U000 4211132 AGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCU-AAACCAUGCACCGAAGCUGCGGCAGCGA 4211211
                               ****************************************************.**************************** PP

                                                                vv                                    vv         NC
                               <<._____>>>>>>>>,,,,]]]]]]<-<<<<<<<.<<<------<<<<<<<<____>>>>>>>>--->>>>>>>>>>--> CS
               RF02541    1213 gg.uuuaaccgcgagcGGUAGggGAGCguuccgcc.cgcgguGAAggcgccccGuaAggggcgccGGAgcgggcggaaGuG 1291   
                               :G UU++ C:: G ::GGUAGGGGAGCGUUC:G   ::C+G GAA:G: ::C:GU+A:G:: :C:GGAG::  C:GAAGUG
  gi_545778205_gb_U000 4211212 CGcUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAaGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUG 4211292
                               **888899*************************9999******************************************** PP

                                                                                                                 NC
                               ,,,,,}}}}}}{{-----{{,,,,,<<<<<<_______>>>>>>{{{{,,,,{{{{,,{{,,,<<<<<<---<<_____>> CS
               RF02541    1292 AgaAUGccGgcacgAGUAgCGAuAAgggggGUGAGAAuCcccccCGCCGaAAgcCcAAGGuUUCCuggguAAgGuUaaUCc 1372   
                                GAAUGC:G:CA:+AGUA:CGAUAA:G:GGGUGA AA CCC:C:CGCCG AAG:CCAAGG UUCCUG :+AA:GUUAAUC:
  gi_545778205_gb_U000 4211293 CGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCG 4211373
                               ********************************************************************************* PP

                                               v                                                                 NC
                               ->>>>>>,,,,,,[[[[,<<---<<<-<-<<<____>>>->->>>--->>,,,<<<<<________>>>>>,,(((((((( CS
               RF02541    1373 gcccaGGGUuAGuCGggaCCUAAGgcGaGGccGAaAggCGuAgcCGAUGGaaAgcgGGUuAAuAuUCCcgcaCcgcccggg 1453   
                               G: CAGGGU AGUCG: +CCUAAG:CGAGGCCGAAAGGCGUAG:CGAUGG+AA:C:GGUUAAUAUUCC:G:AC::: :G::
  gi_545778205_gb_U000 4211374 GGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUU 4211454
                               ********************************************************************************* PP

                                                v                                                                NC
                               (((-----((--((((((---((((--(((--(((((<<<<<<__________>>>>>><<--<<<<---<<<.-<<<<<< CS
               RF02541    1454 gccuuuaagcgacGgggcGACgcagaaggcuaggcgcgcgggcuguuGGaagugcccgcccaagcccuuaggc.ugggggg 1533   
                               :C:     GCGA:G:GG GACG:AGAAGGCUA:G::::C:GG: G+ GG++GU:CC:G:::AA:C::+UA:GC + :::::
  gi_545778205_gb_U000 4211455 ACU-----GCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCuGGUUUUC 4211530
                               ***.....*****************************************************************99999999 PP

                                                                     vv              vv                          NC
                               <-<<_____>>>>>>>>>---.>>>--->>>>--->>,<<<<<<<____>>>>>>>,,)))))---)))---))))----- CS
               RF02541    1534 cAGguAAAucCgccccccaau.gccgaggggcgaugggccgccgcuuaagcggcggaggcgccgaagccaugcugcCaaGA 1613   
                               CAGG+AAAUCCG:::::  A+ GC:GAG::G:GAU::    :C:CU+ +G:G:   AG:::C:+A+GCC UGCU:CCA GA
  gi_545778205_gb_U000 4211531 CAGGCAAAUCCGGAAAAUCAAgGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGA 4211611
                               9**********99999998888*********************************************************** PP

                                  v                        v                                                     NC
                               ---))))))--))---.)))))))))))]]]],,}},,,,,<<______>>,}}}},<<<<_____>>>>,,}}}},,{{{ CS
               RF02541    1614 AAAgcccCgaagcuaa.ggccccgggcgccCGUACCguAAACCGACACAGGUgGgcagGgaGAGaAucCcaAGGCGcucGg 1693   
                               AAA CC:C:AAGC++  :G:::C: ::: :CGUACC +AAACCGACACAGGUGG:CAGG:AGAGAAU:CCAAGGCGCU:G:
  gi_545778205_gb_U000 4211612 AAAGCCUCUAAGCAUCaGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGA 4211692
                               **************989**************************************************************** PP

                                                                                                      vvvv       NC
                               {----{{{{{{{{-{{{,,,,,,,,,,,,,,<<<<<---<<____>>---->>>>><<<<<<.........<<<<<<____ CS
               RF02541    1694 GagAAcccuggucAAGgAACUCGGCAAAaUagcccCGUAccUUcGggAgAAGgggcgCCccc.........ccgggcguaa 1765   
                               GAGAAC:C:GGU:AAGGAACU GGCAAAAU+G::CCGUA:CUUCGG:AGAAGG::C:C::::             ::GU  
  gi_545778205_gb_U000 4211693 GAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUauguaggug----AGGUCC 4211769
                               **************************************************************998885443....333333 PP

                                 vvvv                                                                            NC
                               >>>>>>............>>>>>><___>,,,,,,,[[[[[[[[[,,<<<_________>>>,,<<<<<<<<<--<<<<__ CS
               RF02541    1766 gcccgg............gggGGccGCAgagAauaGGcccgggCGACUGuUUAccAAAAaCACAggccucugCuAagucGu 1834   
                               ::C  G            ::::G:CG AGA A  AG::::: :C:ACUGUUUA++AAAAACACAG::CU:UGC+AA::CG+
  gi_545778205_gb_U000 4211770 CUCGCGgauggagcugaaAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGA 4211850
                               333333555555677778*************************************************************** PP

                                                                             vv vv                       vv vv   NC
                               __>>>>-->-->>>>>>>>,,((((,<<<--<<<<<<<--<<<---<<-<<<<<<<--<<____>>--->>>>>>>->>-- CS
               RF02541    1835 AAgacgAuGUAuaggggcuGAcGCCUGCCCGGUgCcgGAAGGuUAAgggccgggGuuAgcGcaAgcgAAgCcccggAccgA 1915   
                               AAG::GA+GUAUA:GG::UGACGCCUGCCCGGUGCCGGAAGGUUAA  G  :G:GUUAGCGCAAGCGAAGC:C:  A  GA
  gi_545778205_gb_U000 4211851 AAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGA 4211931
                               ********************************************************************************* PP

                                                                                                                 NC
                               ->>>>>>>>-->>>>><<<<<<_______>>>>>><___>,,,,,<---------<<<<<<_____>>>>>>>,,,,,,,, CS
               RF02541    1916 AgCCCcgGuAAACGGCGgCCGUAACUAUAACGGuCCUAAGGUAGCGAAAUUCCUUGuCGGgUAAGUuCCGaCCuGCACGAA 1996   
                               AGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAA
  gi_545778205_gb_U000 4211932 AGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAA 4212012
                               ********************************************************************************* PP

                                                                                                                 NC
                               ,)))),,,]]-]]]]]]],,,,}}}-}}}}}}}}-}}}}}}----}}},,,,<<<<<________>>>>>,,{{{{{{{{- CS
               RF02541    1997 uGGCgUAACGAcccgggCgCUGuCUCgaccagggaCcCgGcGAAAguguAgUgccgGUgAAGAUGCcggcUaCcCgCggcu 2077   
                               UGGCGUAA:GA: :::::GCUGUCUC:ACC:G:GAC:C:G:GAAA:UG+A U: C:GUGAAGAUGC:G :UACCC:CGGC+
  gi_545778205_gb_U000 4212013 UGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCA 4212093
                               ********************************************************************************* PP

                                                                                   v                             NC
                               {{{-{{,,,,,,{{{{-{{{{{{{,((((---(((((((,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<<--- CS
               RF02541    2078 gGACgGAAAGACCCCGUGgAcCUUUACUguAgccuggcauUGgcccccggcgcggcccGUguAGgAUAgGuGGGAGgCuuu 2158   
                               :GACGGAAAGACCCCGUG:ACCUUUACU:UAGC::G:CA UG::C::::: : :: ::GUGUAGGAUAGGUGGGAGGCUUU
  gi_545778205_gb_U000 4212094 AGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUU 4212174
                               ********************************************************************************* PP

                                                                                   v                             NC
                               ---<<<<<<<<____>>>>>>>>--->>>------------>>>>>>>>>>>>>>>>>>>>>>>,,,<<<-<<<<<<____ CS
               RF02541    2159 GAAgccggggcgcuAgccccggcGGAGcCaacguUGAaAUACCaCcCgggccgcgccgggggcCUAACccagccccguaAu 2239   
                               GAA:::::G:CGC+AG:C:::::GGAGCC+AC UUGAAAUACCACCC:: :: : :::::G::CUAAC::+ :CCCGUAAU
  gi_545778205_gb_U000 4212175 GAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAU 4212255
                               ********************************************************************************* PP

                                                                                                                 NC
                               _>>>>>>>>>,,,,,)))))))----)))),,<<<<_____>>>><<<<<<___________>>>>>>{,[[,,,,((((( CS
               RF02541    2240 ccggggcggGGACagugccagguGGGcAGUUUGaCuGGGGCgGuCgCCUCCuAAAgaGUAACGGAGGcGcgCaAAGGuucc 2320   
                               CCGGG: ::GGACAGUG:C::GUGGG:AGUUUGACUGGGGCGGUC:CCUCCUAAAGAGUAACGGAGG:GC:C+AAGGUU::
  gi_545778205_gb_U000 4212256 CCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGG 4212336
                               ********************************************************************************* PP

                                                                                                                 NC
                               (<<-<<<<<<_______>>>>>>--->><<______>>,,,,)))))),,,,<<<<<<<<<______>>>>>>>>>,<<<_ CS
               RF02541    2321 CUCAgcgcGguuGGaAAcCgcgcguaGAGcGcAAaggCAuAAGggagCuUgACuGcccGacugACAaguCgggCaGaggCG 2401   
                               CU:A:C::G:U+GGA A:C::G:G +:AG:GCAA+G:CAUAAG::AGCUUGACUGC::G::UGAC  ::C::GCAG+:GCG
  gi_545778205_gb_U000 4212337 CUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCG 4212417
                               ********************************************************************************* PP

                                                                                                                 NC
                               ___>>>,]],,,,,,,,,,<<<<<<<-<<________>>>>>>>>>,,,,,},,,,,,}}}}}--}}}}}},,,,,,,,<< CS
               RF02541    2402 AAAGccGGccuUAGUGAUCCggcGGcuccgagUGGaAgggCCgucGCUCAACGGAUAAAAGgUACcCCGGGGAUAACAGGC 2482   
                               AAAGC:GG:C+UAGUGAUCCGG:GG:UC:GA+UGGAA:G:CC:UCGCUCAACGGAUAAAAGGUAC:CCGGGGAUAACAGGC
  gi_545778205_gb_U000 4212418 AAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGC 4212498
                               ********************************************************************************* PP

                                                                                                                 NC
                               <-<<<<<<<<---<<_______>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<-<<<<<<______>>> CS
               RF02541    2483 ugAucccccCCAAGaGUuCAuAuCGACGggggggUUUgGCACCUCGAUGUCgGCUCauCgCAUCCUGGGgCuGgAGuAgGu 2563   
                               UGAU:CC:CCCAAGAGUUCAUAUCGACGG:GG:GUUUGGCACCUCGAUGUCGGCUCAUC:CAUCCUGGGGCUG+AGUAGGU
  gi_545778205_gb_U000 4212499 UGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGU 4212579
                               ********************************************************************************* PP

                                                                                                                 NC
                               >>>--->>,<<<<<_____>>>>>,,,,,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}} CS
               RF02541    2564 CCCAAGGGUucGGCUGUUCGCCgaUUAAAGcGguACGuGAGCuGGGUUcAGaaCGUCGUGAGACAGuuCGGUCCcUAUCcg 2644   
                               CCCAAGGGU::GGCUGUUCGCC::UUAAAG:GGUACG+GAGCUGGGUU+AGAACGUCGUGAGACAGUUCGGUCCCUAUC:G
  gi_545778205_gb_U000 4212580 CCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUG 4212660
                               ********************************************************************************* PP

                                                                                                                 NC
                               }}}}}}},,,,((((((((--((((,,<<<<<<<_______________>>>>>>><<<<<<---<<<----<<<<<<<<< CS
               RF02541    2645 ccGcGgGcGuaGGaggccUGAggGgauccgccccUAGUACGAGAGGACCggggcgggCggaCCucugGUGuacCgGuuGuc 2725   
                               CCG:GGGCG +GGAG::CUGAGGGG +C::C:CCUAGUACGAGAGGACCGG:G::G:CG:A:C+CU:GUGU C:GGUUGUC
  gi_545778205_gb_U000 4212661 CCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUC 4212741
                               ********************************************************************************* PP

                                                                                                                 NC
                               <<____>>>>>>-->>>>>---->>>->>>>>>,,<<<----<<<<<___________>>>>>---->>>,))))------ CS
               RF02541    2726 gcGCcAgcggCauugCcGgGUAGCcauGuccGcaaggGAUAAcCGCUGAAaGCAUCUAAGCGgGAAgCccacCccAAGAua 2806   
                               ::GCCA::GGCA UGCC:GGUAGC:A+:U:CG:AA :GAUAA::GCUGAAAGCAUCUAAGC::GAA+C:  CCCC AGAU 
  gi_545778205_gb_U000 4212742 AUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUG 4212822
                               ********************************************************************************* PP

                                                               vv                             vv                 NC
                               )))))))),,<<<...._____>>>.,(--((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<____> CS
               RF02541    2807 AggccuCCcucgg....uaaauccg.uuaAGgccccuggaAGAcuAccaggUuGAuaGgccggcgGUGcAAgcgcgGuAAc 2882   
                               AG::CUCCCU:::    U A +::: U AAGG  C:U:GAAGAC AC:A:GUUGAUAGGCCGG  GUG:AA:CGC:G+ A:
  gi_545778205_gb_U000 4212823 AGUUCUCCCUGACuccuUGAGAGUCcUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAU 4212903
                               *************988656677999789***************************************************** PP

                                        vv             vv                  NC
                               >>>>>--->>>->>>>>->>>,,,))))-),,,}}}}}}}}:: CS
               RF02541    2883 gcgcguAGCcgAccgguACuaAUaggcCgauaggcuugaccuu 2925   
                               GCG:: AGC  ACCGGUACUAAU   CCG  AGGCUU:ACCUU
  gi_545778205_gb_U000 4212904 GCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU 4212946
                               ******************************************* PP

>>

RNAfold

>gi_545778205_gb_U000_126
CGGGUUGUGAGGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGU
CAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAU
AUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUC
GACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGA
ACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGU
GUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUA
CACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGU
AUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGAC
UGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGC
GAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUA
UAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC
UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAG
CCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGAC
UAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAU
CAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCC
GACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGG
AGACACACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGA
CCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAA
GGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAA
GCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAG
GGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGU
AUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCC
CGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGU
GAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGU
UAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCA
GGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUG
CUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUA
ACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCA
AGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAA
CUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACAC
AGCACUGUGCAAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGG
UGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAA
GCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUU
CCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGC
UGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACA
CUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUG
GACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUG
AUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGU
AGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGG
UUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGU
GAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUAC
UCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUG
UUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCC
AAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAA
CGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUU
CGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUA
AGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCU
GACUCCUUGAGAGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGC
CGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGAACCG
UGAGGCUUAACCUUACAACGCCGAA
((((((((((((((((((.....(((((.((((((((((((((((.....))).)))......((((.(((......))).....(((((((..(((.......)))......))))))).(((((...((((....))))((((((....))))))..(((((((((.........))))))))).......(((((..(((..........))).))))).)))))...((((......))))..((((((.(((((.(..(((.((.((((((((..((((......(((((((((((((.(((...((((((....))))))....(((.((((....)))).))))))...)))))))))))))...))))(((((((.((((((((.((...)).)))))))).....((((((......))))))..........(((((((((((((((((((.((((....((((((((((.............((((.....))))............(((...(((...((((((..(((.((((..((((((....))))))..))))(((((((((((....((((((.......(((((((((((((..((((..((.....))..)))).........((.(((....))).))......)))))))))))))))))))...((((((..((((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))))(((.....)))......))))))......((((((((((((((...((.((((...((((((((((((...(((((((((.......(((.(((.((((...(((((((.....))))).))...)))).)))...))).....)))))).)))...))))).......(((((((((((....)))))))))))....(((......))).(((((((......(((.(((......))).....((((..(((((.((((....)))).........((((.(((((.......))))).))))...((..(((......)))..))((((((.(((.(((((.(.((.(((((..(((.((........)).)))...((((..(((((((((....))))))))).))))....((((((((...((((.(...((((((((....))))))))).))))..))))).)))...((((......)))).......(((((((.....))))))).((.(((..(((...)))))).))...)))))..)).).))))).))).))))))((((.(((.(.(((....))).).)))..))))..(((((........)))))..(((((((((((((..((((((((.(.((..(((..((((((((((((((...))).))))))....((((.(((.((((((((((.((.....)))))))))).)).)))..)))).....(..(((((....)))))...))))))...))))).).)))........)))))..))....))))))))))))))))..)))).)))......))))))).((((.....)))).)))))))))))))...))))).))..))))))))))))).))))).((..((((....))))..)))))..))))))))).))))))))))))).....((((...(((((((((..((((.(((((..(((.(((((.........((((.(..(((((...(((....)))...))))).).)))).(((..((((((((((((..((((..(((((((((((.((....))..))))))..))))))))))))))).((((.((((((.......)))))).(((((..........)))))(((((.....)))))((((((((...(((.(((((.(((.(((((((((((.....))))).((((((........))))))......(((.(((....))).)))..((((.......)))).............))))))...)))..))))).)))....))))))))...(((((..((((((...((((((((....))))))))))))))............)))))..((((((((.((...)).)))))))).))))...)))))).)))))))))))))))).)))).)))))))))..))))(((((((...........)))))))......)))).))).)))..))))))...)))))))(((.((((....)))).)))(((((((.((((..((((....))))..)))).(((....)))(((((...)))))((((((((((.......)))))))))).((..((((..........))))..))...)))))))((((((((...((.......))...)))))))).(((((......))))))))))))..(((((((((((......)))))).)))))..)))))))).)).)))....).)).)))..))))))....(((((((....))).)))).))))..)))))))))).)))))((((((((.(..(((((((((((..((.(....).)).))))))).(((((...((((..((((((((((((....))))))..))))))..)))).)))))...(((....(((((...........)))))....))).))))....).)))))))).....(((((.((....)).))))).(((((....)))))(((((.(((((((((..((...((((((....))))))..))...))))).)).)).)).)))...))))))))))))))).))).. (-1103.30)

Length sequence

: 2925

Length match:

2902