gi_545778205_gb_U000_125

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:

2889.8

E-value:

0

From sequence:

4168641

To sequence:

4171544

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 4168641 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGG 4168721
                               ********************************************************************************* 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 4168722 UAAGGUGAUAUGAACCGUUAuAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGU--UUCGACACACUAUCAUUAACUGA 4168800
                               ****************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 4168801 AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCA 4168881
                               ********************************************************************************* PP

                                                                                                  v              NC
                               ---<<_____>>---->>>>>,,[[[[,,,,<<<<<<<________>>>>>>>,,,,,,(((-(((((-------(((((( CS
               RF02541     243 GUAGcGGCGAgCGAAaggGGaauaGcCcAAACcggggguuauuguucccccgGGGUugugGGacccccaaauuaagagccc 323    
                               GUAGCGGCGAGCGAA+GGGGA  AGCCCA                                  :::C +   +A+:AG: :
  gi_545778205_gb_U000 4168882 GUAGCGGCGAGCGAACGGGGAGCAGCCCA----------------------------------GAGCCUG--AAUCAGUGU 4168926
                               ***************************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 4168927 GUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCG 4169007
                               ***************************************************************************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 4169008 AU---GAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACC 4169085
                               98...**************************************************************************** PP

                                                                                                                 NC
                               ,,,,,,,,,,,,,,,<<____>>,,,,}},,,,,,,,,<<<<_____>>>>,,,,,,,,,,,,,}-----}}}}}}}}}}, CS
               RF02541     486 GAUAGuGaAcuAGUACCGUGAGGGAAAGGUGAAAAGaACCCcggugAgGGGAGUGAAAuAGaaCCUGAAACCgcgcGCccA 566    
                               GAUAGUGAAC AGUACCGUGAGGGAAAGG GAAAAGAACCCCGG+GAGGGGAGUGAAA AGAACCUGAAACCG:G::C::A
  gi_545778205_gb_U000 4169086 GAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUA 4169166
                               ********************************************************************************* 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 4169167 CAAGCAGUGGGAGCACG--CUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGG 4169245
                               *****************..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 4169246 UUAACC-GAAUA-GGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUG 4169324
                               *****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 4169325 AUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGAC 4169405
                               ********************************************************************************* PP

                                                                                                                 NC
                               )))))))))),<<<_____>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<<-- CS
               RF02541     810 cuguGgguaGgGGcGAAAggCCAAUCaAaCccgGaGAUAGCUgGUUCUCccCGAAAugccuUuAGgggcaGCgucgggcga 890    
                                UGUGG:U GGGG:GAAAG:CCAAUCAAACC:GGAGAUAGCUGGUUCUCCCCGAAA::::UUUAGG::::GC:UCG:G:++
  gi_545778205_gb_U000 4169406 UUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAU 4169486
                               ********************************************************************************* 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 4169487 UCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCcGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGa 4169567
                               ***************************************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 4169568 AUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCA 4169648
                               9******************************************************************************** PP

                                                             vv                                                  NC
                               --(-((((((-----------(((-((((((((((-------(((((,<<<--<<<_________>>>-->>><___><-- CS
               RF02541    1051 AAgugcggGcUAAGUGggAAAGGcuGuggggccgCuaAgACAaCcaGGAgGUUGGCUUAGAAGCAGCCAUCcUuuAAaGAg 1131   
                               AAGU:::GG:UAAGUGGGAAA:G:UGU:GG  ::C  AGACA:CCAGGA:GUUGGCUUAGAAGCAGCCAUC:UUUAAAGA+
  gi_545778205_gb_U000 4169649 AAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAA 4169729
                               ********************************************************************************* PP

                                                        vv                                                       NC
                               -<<______>>->,)))))---)))))))))))))--------------------))))))))))---)))))))<<<<<< CS
               RF02541    1132 uGCGUAAuAGCUCACugGuCaAGcggccccgCgCCGAaAAUguaaCGGGGCUcAAgCccgccaCCGAAgcugcGggcucgc 1212   
                               +GCGUAAUAGCUCACUGG:C+AG::  CC:GC:C:GAA AUGUAACGGGGCU AA:CC:::CACCGAAGCUGCGG:: C :
  gi_545778205_gb_U000 4169730 AGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCU-AAACCAUGCACCGAAGCUGCGGCAGCGA 4169809
                               ****************************************************.**************************** 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 4169810 CGcUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAaGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUG 4169890
                               **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 4169891 CGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCG 4169971
                               ********************************************************************************* PP

                                               v                                                                 NC
                               ->>>>>>,,,,,,[[[[,<<---<<<-<-<<<____>>>->->>>--->>,,,<<<<<________>>>>>,,(((((((( CS
               RF02541    1373 gcccaGGGUuAGuCGggaCCUAAGgcGaGGccGAaAggCGuAgcCGAUGGaaAgcgGGUuAAuAuUCCcgcaCcgcccggg 1453   
                               G: CAGGGU AGUCG: +CCUAAG:CGAGGCCGAAAGGCGUAG:CGAUGG+AA:C:GGUUAAUAUUCC:G:AC::: :G::
  gi_545778205_gb_U000 4169972 GGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUU 4170052
                               ********************************************************************************* 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 4170053 ACU-----GCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCuGGUUUUC 4170128
                               ***.....*****************************************************************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 4170129 CAGGCAAAUCCGGAAAAUCAAgGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGA 4170209
                               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 4170210 AAAGCCUCUAAGCAUCaGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGA 4170290
                               **************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 4170291 GAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUauguaggug----AGGUCC 4170367
                               **************************************************************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 4170368 CUCGCGgauggagcugaaAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGA 4170448
                               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 4170449 AAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGA 4170529
                               ********************************************************************************* PP

                                                                                                                 NC
                               ->>>>>>>>-->>>>><<<<<<_______>>>>>><___>,,,,,<---------<<<<<<_____>>>>>>>,,,,,,,, CS
               RF02541    1916 AgCCCcgGuAAACGGCGgCCGUAACUAUAACGGuCCUAAGGUAGCGAAAUUCCUUGuCGGgUAAGUuCCGaCCuGCACGAA 1996   
                               AGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAA
  gi_545778205_gb_U000 4170530 AGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAA 4170610
                               ********************************************************************************* 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 4170611 UGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCA 4170691
                               ********************************************************************************* PP

                                                                                   v                             NC
                               {{{-{{,,,,,,{{{{-{{{{{{{,((((---(((((((,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<<--- CS
               RF02541    2078 gGACgGAAAGACCCCGUGgAcCUUUACUguAgccuggcauUGgcccccggcgcggcccGUguAGgAUAgGuGGGAGgCuuu 2158   
                               :GACGGAAAGACCCCGUG:ACCUUUACU:UAGC::G:CA UG::C::::: : :: ::GUGUAGGAUAGGUGGGAGGCUUU
  gi_545778205_gb_U000 4170692 AGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUU 4170772
                               ********************************************************************************* PP

                                                                                   v                             NC
                               ---<<<<<<<<____>>>>>>>>--->>>------------>>>>>>>>>>>>>>>>>>>>>>>,,,<<<-<<<<<<____ CS
               RF02541    2159 GAAgccggggcgcuAgccccggcGGAGcCaacguUGAaAUACCaCcCgggccgcgccgggggcCUAACccagccccguaAu 2239   
                               GAA:::::G:CGC+AG:C:::::GGAGCC+AC UUGAAAUACCACCC:: :: : :::::G::CUAAC::+ :CCCGUAAU
  gi_545778205_gb_U000 4170773 GAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAU 4170853
                               ********************************************************************************* PP

                                                                                                                 NC
                               _>>>>>>>>>,,,,,)))))))----)))),,<<<<_____>>>><<<<<<___________>>>>>>{,[[,,,,((((( CS
               RF02541    2240 ccggggcggGGACagugccagguGGGcAGUUUGaCuGGGGCgGuCgCCUCCuAAAgaGUAACGGAGGcGcgCaAAGGuucc 2320   
                               CCGGG: ::GGACAGUG:C::GUGGG:AGUUUGACUGGGGCGGUC:CCUCCUAAAGAGUAACGGAGG:GC:C+AAGGUU::
  gi_545778205_gb_U000 4170854 CCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGG 4170934
                               ********************************************************************************* 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 4170935 CUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCG 4171015
                               ********************************************************************************* PP

                                                                                                                 NC
                               ___>>>,]],,,,,,,,,,<<<<<<<-<<________>>>>>>>>>,,,,,},,,,,,}}}}}--}}}}}},,,,,,,,<< CS
               RF02541    2402 AAAGccGGccuUAGUGAUCCggcGGcuccgagUGGaAgggCCgucGCUCAACGGAUAAAAGgUACcCCGGGGAUAACAGGC 2482   
                               AAAGC:GG:C+UAGUGAUCCGG:GG:UC:GA+UGGAA:G:CC:UCGCUCAACGGAUAAAAGGUAC:CCGGGGAUAACAGGC
  gi_545778205_gb_U000 4171016 AAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGC 4171096
                               ********************************************************************************* PP

                                                                                                                 NC
                               <-<<<<<<<<---<<_______>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<-<<<<<<______>>> CS
               RF02541    2483 ugAucccccCCAAGaGUuCAuAuCGACGggggggUUUgGCACCUCGAUGUCgGCUCauCgCAUCCUGGGgCuGgAGuAgGu 2563   
                               UGAU:CC:CCCAAGAGUUCAUAUCGACGG:GG:GUUUGGCACCUCGAUGUCGGCUCAUC:CAUCCUGGGGCUG+AGUAGGU
  gi_545778205_gb_U000 4171097 UGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGU 4171177
                               ********************************************************************************* PP

                                                                                                                 NC
                               >>>--->>,<<<<<_____>>>>>,,,,,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}} CS
               RF02541    2564 CCCAAGGGUucGGCUGUUCGCCgaUUAAAGcGguACGuGAGCuGGGUUcAGaaCGUCGUGAGACAGuuCGGUCCcUAUCcg 2644   
                               CCCAAGGGU::GGCUGUUCGCC::UUAAAG:GGUACG+GAGCUGGGUU+AGAACGUCGUGAGACAGUUCGGUCCCUAUC:G
  gi_545778205_gb_U000 4171178 CCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUG 4171258
                               ********************************************************************************* 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 4171259 CCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUC 4171339
                               ********************************************************************************* 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 4171340 AUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUG 4171420
                               ********************************************************************************* PP

                                                               vv                             vv                 NC
                               )))))))),,<<<...._____>>>.,(--((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<____> CS
               RF02541    2807 AggccuCCcucgg....uaaauccg.uuaAGgccccuggaAGAcuAccaggUuGAuaGgccggcgGUGcAAgcgcgGuAAc 2882   
                               AG::CUCCCU:::    UAA  ::: U AAGG  C:U:GAAGAC AC:A:GUUGAUAGGCCGG  GUG:AA:CGC:G+ A:
  gi_545778205_gb_U000 4171421 AGUUCUCCCUGACccuuUAAGGGUCcUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAU 4171501
                               ***********99998655666999789***************************************************** PP

                                        vv             vv                  NC
                               >>>>>--->>>->>>>>->>>,,,))))-),,,}}}}}}}}:: CS
               RF02541    2883 gcgcguAGCcgAccgguACuaAUaggcCgauaggcuugaccuu 2925   
                               GCG:: AGC  ACCGGUACUAAU   CCG  AGGCUU:ACCUU
  gi_545778205_gb_U000 4171502 GCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU 4171544
                               ******************************************* PP

>>

RNAfold

>gi_545778205_gb_U000_125
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
GACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGC
CGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGAACCG
UGAGGCUUAACCUUACAACGCCGAA
((((((((((((((((((.....(((((.((((((((((((((((.....))).)))......((((.(((......))).....(((((((..(((.......)))......))))))).(((((...((((....))))((((((....))))))..(((((((((.........))))))))).......(((((..(((..........))).))))).)))))...((((......))))..((((((.(((((.(..(((.((.((((((((..((((......(((((((((((((.(((...((((((....))))))....(((.((((....)))).))))))...)))))))))))))...))))(((((((.((((((((.((...)).)))))))).....((((((......))))))..........(((((((((((((((((((.((((....((((((((((.............((((.....))))............(((...(((...((((((..(((.((((..((((((....))))))..))))(((((((((((....((((((.......(((((((((((((..((((..((.....))..)))).........((.(((....))).))......)))))))))))))))))))...((((((..((((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))))(((.....)))......))))))......((((((((((((((...((.((((...((((((((((((...(((((((((.......(((.(((.((((...(((((((.....))))).))...)))).)))...))).....)))))).)))...))))).......(((((((((((....)))))))))))....(((......))).(((((((......(((.(((......))).....((((..(((((.((((....)))).........((((.(((((.......))))).))))...((..(((......)))..))((((((.(((.(((((.(.((.(((((..(((.((........)).)))...((((..(((((((((....))))))))).))))....((((((((...((((.(...((((((((....))))))))).))))..))))).)))...((((......)))).......(((((((.....))))))).((.(((..(((...)))))).))...)))))..)).).))))).))).))))))((((.(((.(.(((....))).).)))..))))..(((((........)))))..(((((((((((((..((((((((.(.((..(((..((((((((((((((...))).))))))....((((.(((.((((((((((.((.....)))))))))).)).)))..)))).....(..(((((....)))))...))))))...))))).).)))........)))))..))....))))))))))))))))..)))).)))......))))))).((((.....)))).)))))))))))))...))))).))..))))))))))))).))))).((..((((....))))..)))))..))))))))).))))))))))))).....((((...(((((((((..((((.(((((..(((.(((((.........((((.(..(((((...(((....)))...))))).).)))).(((..((((((((((((..((((..(((((((((((.((....))..))))))..))))))))))))))).((((.((((((.......)))))).(((((..........)))))(((((.....)))))((((((((...(((.(((((.(((.(((((((((((.....))))).((((((........))))))......(((.(((....))).)))..((((.......)))).............))))))...)))..))))).)))....))))))))...(((((..((((((...((((((((....))))))))))))))............)))))..((((((((.((...)).)))))))).))))...)))))).)))))))))))))))).)))).)))))))))..))))(((((((...........)))))))......)))).))).)))..))))))...)))))))(((.((((....)))).)))(((((((.((((..((((....))))..)))).(((....)))(((((...)))))((((((((((.......)))))))))).((..((((..........))))..))...)))))))((((((((...((.......))...)))))))).(((((......))))))))))))..(((((((((((......)))))).)))))..)))))))).)).)))....).)).)))..))))))....(((((((....))).)))).))))..)))))))))).)))))((((((((.(..(((((((((((..((.(....).)).))))))).(((((...((((..((((((((((((....))))))..))))))..)))).)))))...(((....(((((...........)))))....))).))))....).))))))))..((((((...)))))).........(((((....)))))(((((.(((((((((..((...((((((....))))))..))...))))).)).)).)).)))...))))))))))))))).))).. (-1104.10)

Length sequence

: 2925

Length match:

2902