gi_545778205_gb_U000_113

cmsearch-Rfam

Family :

LSU_rRNA_archaea

Id:

RF02540

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea;

Ontology:

GO:0003735 structural constituent of ribosomeRF02540

Description:

not description

Score:

1848.1

E-value:

0

From sequence:

225758

To sequence:

228661

Alignments:

                                                                                                                  NC
                              :::::{{{{,,,,,,{{{{{{{{{{-----{{{,,{{{{.{{{{{{,,,,,,,((((<<<________>>>,,,,,<<<<<<- CS
               RF02540      1 uauaucgcgcuauuAcgCcgcccgGuGGAUGGCUcGGCU.cGgGcGcCGAuGAaGGgcGuGgCAAGCUgCgAUAAGCccgGGG 82    
                              +  +U:::: + U A ::::C:CGGUGGAUG:C +GGC: :::G:G CGAUGA:GG:CGUG  AA CUGCGAUAAGC:::GG 
  gi_545778205_gb_U000 225758 AGGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAgUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGU 225840
                              **************************************636789*************************************** PP

                                                                                                                  NC
                              --<<<_______>>>.------>>>>>>,,,)))),,,<<<____>>>,,,,,,,,,,,,,,....,<<<<<____....... CS
               RF02540     83 gAGgcGCAuGcAgcC.uuuGAuCCcggGAUucCCuAAUgGGAauUCCcguuacuuuuuaaac....gcucccuauu....... 153   
                               AGG:G  +  A:CC UU+ A+CC:::GAUU:CC:AAUGGG A  CCC+ U + UUU  A      +:::::+A U       
  gi_545778205_gb_U000 225841 AAGGUGAUAUGAACCgUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACAcacuAUCAUUAACUgaaucca 225923
                              ***************445689****************************8888877777766899999999999889999*** PP

                                                                                                                  NC
                              ......>>>>>,,,,,,<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<____>>,,,<<<<<-----<<__ CS
               RF02540    154 ......gggagcGGGAACcCcccGAAuuGAAaCAUCUuAGUAgggGgAGGAaaAGAAAcCAAuuGgGAUgcCgcuAGUAgcGG 230   
                                    ::::: G GAACC::::GAA UGAAACAUCU AGUA::::GAGGAAAAGAAA:CAA +G:GAU:CC:C AGUAGCGG
  gi_545778205_gb_U000 225924 uagguuAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAGUAGCGG 226006
                              *****9***************************************************************************** PP

                                                                                                                  NC
                              ___>>---->>>>>,,[[[[,,,,~~~~~~,,,,,,,,,,((((------((((------------(((,,,<-<<<<_____ CS
               RF02540    231 CGAgcGAAAgcGgcauAGccCAAA*[34]*uGUugugggccggcuuuaaugcgccuaguuaaugaAgccGAAgUggccUGGAA 341   
                              CGAGCGAA G:GG: +AGCCCA A      UG  +               ::G    + U + ++AG::GAAG :G CUGGAA
  gi_545778205_gb_U000 226007 CGAGCGAACGGGGAGGAGCCCAGA*[ 3]*UGAAU---------------CAGUG--UGUGUGUUAGUGGAAG-CGUCUGGAA 226068
                              ************************...5..66554...............88888..77888899********.********* PP

                                                                                                                  NC
                              _>>>>>,,<___>,<<<_______>>>,,,)))------------))))----)))),,,,,,,,,,,<<<<<<<___...__ CS
               RF02540    342 uggcccgccauAgAGGGUGAuAGcCCCGUAggcguAaucuaaaaggcgcuugagccguuuccaGAGUAcCgcgggUUG...Ga 421   
                              +G C:CGC:AUA:AGGGUGA AGCCCCGUA::C +AA +  A A  C::U  +     U   +GAGUA:: C GG      G 
  gi_545778205_gb_U000 226069 AGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAG----CUCGAUGAGUAGGGCGGGACAcguGG 226147
                              ****************************************9999999998777....8999**************76422367 PP

                                                                                                                  NC
                              ___>>>>>>>,,,,,,<<<<<_______>>>>>,,]]]],,,,,}}-}}}}.}}-}},,,,,,,,,,,,,,,<<____>>,,, CS
               RF02540    422 auUcccgcGgGAAuaugGggGgcAucaaCccCcAAggCUAAAUACguCcCg.AGACCGAUAGcGaAcuAGUAccGUGAggGAA 503   
                              ++UCC G ::GAAUAUGG:GGG A CA CC:CCAAGGCUAAAUAC: C::: :GACCGAUAG+GAAC AGUACCGUGAGGGAA
  gi_545778205_gb_U000 226148 UAUCCUGUCUGAAUAUGGGGGG-ACCAUCCUCCAAGGCUAAAUACUCCUGAcUGACCGAUAGUGAACCAGUACCGUGAGGGAA 226229
                              788****************997.89999*******************987636****************************** PP

                                                                                               vv               v NC
                              ,}}--------------.-----------.--------}-----}}}}}}}}}},,,,,,,<<<<<<<<<<-~~~~~~>>>>> CS
               RF02540    504 AGCUGAAAAGuAcCccu.gaaGGGggGUG.AAAAGaGCCUGAAACcgggcgGcgAuagaauggcgcggCccg*[61]*ggGuc 639   
                              AG: GAAAAG+ACCCC+   AGGGG GUG AAAAGA CCUGAAACCG:G:::: A+A   +G  G  GC::G      ::GU 
  gi_545778205_gb_U000 226230 AGGCGAAAAGAACCCCGgCGAGGGGAGUGaAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCAUG*[ 7]*GUGUG 226313
                              *****************8889999999998899************************************986...9..89*** PP

                              v      v v          v v                                 v       v                   NC
                              >>>>>,,<<<<________>>>>{{{{{{,,,,(((((((((((((,,<<<<--<<<<_____>>>>-->>>>,,,<<____> CS
               RF02540    640 gcgccgUcCGUuUuGAAaaACGggCCgGGGAGUucgcggccguGgCGAGccUAAgggguuuAaccccGaAggCGuAGgGAAAc 722   
                               C  CGU C UUUUG A AA G G:C:G GA UU:::::C:G :GC AG::UAA:: :    A: ::G A::CG+AGGGAAAC
  gi_545778205_gb_U000 226314 ACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGA----AUAGGGGAGCCGAAGGGAAAC 226392
                              *******************************************************954....4669***************** PP

                                                                                                             v    NC
                              >,,,,,~~~~~~~~~~~~,,,,))))))))))))),,[[-[---[[[[[[,,,((((((((((((,<<<<---<<<<<<<___ CS
               RF02540    723 CGAuaa*[26]**[16]*uggAGuCacggccgcgaGACCaGAAaCCgggCGAUCUaggCccggGCAGGgcGAAgccgggcgaA 835   
                              CGA               U++AGU: C:G:::::AGACC+GAAACC:GG:GAUC AG:C::: GCAGG::GAAG::::G  AA
  gi_545778205_gb_U000 226393 CGAG--*[ 7]**[ 6]*UUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAA 226474
                              **96.....9.....*..9**************************************************************** PP

                               v                     v                  v                                         NC
                              _>>>>>>>---->>>>,,,,<<<<-<<-<<________>>>>>>>>,,)-))))))))))),<<<_____>>>,,,,,,]]]] CS
               RF02540    836 AgcccgguGGAGgcCCGauAggggUgcUGaugUGCAAauCgcccccgUGACccggGccuAGGGGcgAAAGgCCAAUCuAGccc 918   
                                C::::UGGAG::CCGA A::G  :: ::  UG AAA:::: C::+UGAC :::G:CU GGGG:GAAAG:CCAAUC A:CC:
  gi_545778205_gb_U000 226475 CACUAACUGGAGGACCGA-ACCGACUA-AUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCG 226555
                              ******************.*****999.9****************************************************** PP

                                                                                vv        v             v    vvv  NC
                              ]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<---<<<-<<<<<<<<----<<<----<<<<<<<<<<- CS
               RF02540    919 GGuaAuAGCUGGUUCCcgcCGAAacggccCgcAggccgacCccggcgGAGgcuGgcggcgggGUAGaGCACugaccGgggggu 1001  
                              GG +AUAGCUGGUUC:C:CCGAAA:::::  + :::::+CC:CG::   :  +::::::G GGUAGAGCACUG  ::GG    
  gi_545778205_gb_U000 226556 GGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAA-CUCAUCUCCGGGGGUAGAGCACUGUUUCGGC--- 226634
                              *********************************************975.7789************************993... PP

                                     vvv    v             v       vv                                              NC
                              -~~~~~~>>>>>>>>>>--->>->---->>>>>>>>>>>------>>>>>>->,,,<<<<<<<<<__._____>>>>>>>>>, CS
               RF02540   1002 u*[18]*cccccCggucaAACuCCGAAcccgccgcCgcCGuAGAagccggGAgucgGgcgcccgggG.UAAGcccgggcgcCG 1095  
                              +      ++ CC::  CAAACU CGAA+ C::::::  : U  A+::CG:GAG C+ :CG C:G: G UAA  :C:G CG:  
  gi_545778205_gb_U000 226635 A*[21]*AACCCGAUGCAAACUGCGAAUACCGGAGAAUGUU--AUCACGGGAGACACACGGCGGGUGcUAACGUCCGUCGUGA 226730
                              2...3..34599************************87766..56******************9977478888********** PP

                                                                                              v      vv           NC
                              ,,,<<<______>>>,,,((((.(((---(((------(-((((((----------------(((-((((((((((------- CS
               RF02540   1096 aGAGGGgaACAACCCAGAccgg.GGUUAAGGuCCCuAAgUgccGGcUAAGUGucAaucuaAAGgguGuccccggcCuaAGACA 1177  
                              AGAGGG+AACAACCCAGACCG: :G:UAAGGUCCC AAGU:::GG:UAAGUG       AAA:G UGU ::  G C  AGACA
  gi_545778205_gb_U000 226731 AGAGGGAAACAACCCAGACCGCcAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG-----AAACGAUGUGGGAAGGCCCAGACA 226808
                              *********************55*****************************95.....568********************* PP

                                                                                              vv     v            NC
                              (((((,<<<--<<<_________>>>-->>><___><---<<______>>->,)))))---)))))))))))))--------. CS
               RF02540   1178 gCggGgaGGUagGCUuAGAAGCAGCcAUCCucUAAgGAgUGCGUAAcAGCUCACccGcCGAGgccgggggCccCgAAAAUGg. 1259  
                              :C::GGA GU GGCUUAGAAGCAGCCAUC U:UAA:GA  GCGUAA AGCUCAC::G:CGAG C  :: GC C:GAA AUG  
  gi_545778205_gb_U000 226809 GCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUa 226891
                              *********************************************************************************97 PP

                                                                                                        v         NC
                              -----------))))))))))---)))))))<<<<<<<________>>>>>-->>,,,,]]]]]]<-<<<<<.<<<<<----- CS
               RF02540   1260 aCGGGGCUuAAgCCggccaCCGAuACCccggggcgcgcuuauuaaagcgcgAuccgGUAGgcgGGCGucccg.cccGGguaGA 1341  
                              ACGGGGCU AA:CC:::CACCGA :C::CGG:: : :C  +U+++ G: :   ::GGUAGG:G:GCGU:C:G :   :   GA
  gi_545778205_gb_U000 226892 ACGGGGCU-AAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGU--UGGGUAGGGGAGCGUUCUGuAAGCCUGUGA 226971
                              88888888.89**********************655555555555555555..*******************445688899** PP

                                                         v                                                        NC
                              -<<<<<<<<____>>>>>>>>--->>>>>>>>>>-->,,,,,}}}}}},,,,,,,,,,,,,,,<<<<<<_______>>>>>>{ CS
               RF02540   1342 AgccgGgccGuGAggcCcgguGGACCgggcgggaauGaaaAUCCcGGcgguAGUAgCAGCaaAGuggGGUGAGAAUCCccaCc 1424  
                              AG:  ::C:GUGA:G::  :UGGA:   :C:G:A UG++AAU C:G:C+  AGUA+C G  AA:::GGGUGA AA CCC:::C
  gi_545778205_gb_U000 226972 AGGUGUACUGUGAGGUAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAAC-GAUAAAGCGGGUGAAAAGCCCGCUC 227053
                              *******************************************************99.66799******************** PP

                                                                                            v v            v v    NC
                              {{{,,,,{{{{,,{{,,,<<<<<<---<<_____>>->>>>>>,,,,,,[[[,<<.---<<<<<<<<<_____>>>->>>>>> CS
               RF02540   1425 GCCGaAaGgGCaAGGGUUccccGGCAAuGuUcGUCaGCCggggGUUAGuCGGUCC.UAAggcgggccguAAcucggacccgcc 1506  
                              GCCG AAG::CAAGGGUUCC:: :CAA:GUU +UC:G: ::GGGU AGUCG: CC UAAG:C :G:C: AA  :G:  : G:C
  gi_545778205_gb_U000 227054 GCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCcUAAGGCGAGGCCGAAA-GGCG-UAGUC 227134
                              ****************************************************76539999999988888777.9995.67899 PP

                                                                                                    vv v          NC
                              ---->>,,,<<<<<________>>>>>,,((((((((-------------------------(((---(((((((((--(((( CS
               RF02540   1507 GAAaGGGAAgcgGGUUAAUAUUCCcgcgCcgcgggggUaggugcgguAacgcaagccuaauucccGACgccucggGgUAggcc 1589  
                              GA +GGGAA:C:GGUUAAUAUUCC:G:+C::: :G::  +G+G               AA   ::GAC:   : GG:UA:G::
  gi_545778205_gb_U000 227135 GA-UGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCG---------------AAGGGGGGACGGAGAAGGCUAUGUU 227201
                              85.799*******************************544422...............3345888****************** PP

                                                                    v v   v v         v v   v v                   NC
                              (<<<<<<..________>>>>>>,.,,<<<<-----<<<<<<<<<-<<<_____>>>->>>>>>>.>>----->>>>,,,,,, CS
               RF02540   1590 gggcggg..gcuguCgucccgccu.AAgcgcuuAAgcccggcgagagcCGUAAUGgcGcgagccg.ggugAAggcgcgAuugG 1668  
                              G::CGGG  +C GU GUCCCG::U AA:CG: UA GC: G :::   ::  AAU:: G ::: C  :G+  AG:CG:GAU++ 
  gi_545778205_gb_U000 227202 GGCCGGGcgACGGUUGUCCCGGUUuAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAaGGCUGAGGCGUGAUGAC 227284
                              ******99556666666999998627788888888887666666666666678888666666666435677778888888887 PP

                                                             v vv                                                 NC
                              ,,,,,<____..>,,,,,,,)))))---)))))))))---------.))).------------)))))))),]]],,}},,,, CS
               RF02540   1669 cuuuccgUaa..ggagagUUcggccgAucCccggggcCCaUGAAAA.ggg.auugggaaugAucccccgcguCCGUACCgAGA 1747  
                                  C: UA   :G +++  C::C:+AU:CC :   :CCA GAAAA ::   ++G +   G U::C: :::+:CGUACC   A
  gi_545778205_gb_U000 227285 GAGGCACUACggUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAgCCUcUAAGCAUCAGGUAACAUCAAAUCGUACCCCAA 227367
                              77777666655588899999*********9988777777778887744444666667778889******************** PP

                                               v             v                                                    NC
                              ,<<______>>,}}}},<<<<_______>>>>,}}}},,,{{{{-----{{{{{{{{-{{{,,,,,,,,,,,,,,<<<<<--- CS
               RF02540   1748 aCCGACACAGGUGCcCcugGcUGAGaAGgCcaAGGCgUaUcGGguauAAcccgggcgAGGgAAuUCGGCAAAuUagccCCGUA 1830  
                              ACCGACACAGGUG::C  GG: GAGAA :CCAAGGCG + :G:G A AAC:CGGG:GA:GGAA+U GGCAAA U+:::CCGUA
  gi_545778205_gb_U000 227368 ACCGACACAGGUGGUCA-GGUAGAGAAUACCAAGGCGCU-UGAG-AGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUA 227447
                              ****************7.*******************86.9***.99************************************ PP

                                                     v v                           v v                            NC
                              <<____>>---->>>>><<<<<<<<<._______...................>>>>>>>>><___>,,,,,,,[[[[[[[[[ CS
               RF02540   1831 ccUUcGggAgAAGGggugCCuGcggc.uuggaaa...................gccgCaGGuCGCAGUGACuAGGGggccCcg 1893  
                              :CUUCGG:AGAAGG:::GC:::: :    G +AA                    : ::::GUCG AG  AC AG::GGC: C:
  gi_545778205_gb_U000 227448 ACUUCGGGAGAAGGCACGCUGAUAUGuAGGUGAAgcgacuugcucguggagcuGAAAUCAGUCGAAGAUACCAGCUGGCUGCA 227530
                              *********************9988765555555788888888888888888878899************************* PP

                                                            v          v                                          NC
                              ,,<<<_________>>>,,<<<<<<<<<--<<<<____>>>>-->-->>>>>>>>,,((((,<<<--<<<<<<<--<<<---- CS
               RF02540   1894 ACUGUUUAauAAAAACAuAggcccCcGCuAgcCCGaAAGGgcguGUACgGgggccGAcuCCUGcCCAgugccGGUAccuGAAa 1976  
                              ACUGUUUA UAAAAACA A:::C :::C+A C:CGAAAG:G   GUA::: G:::GAC:CCUGCCC GUGCCGG A::U AA 
  gi_545778205_gb_U000 227531 ACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAU 227613
                              *********************************************************************************99 PP

                                                                                                                  NC
                              ~~~~~~---->>>>>>>>-->>>>><<<<<<_______>>>>>><___>,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,, CS
               RF02540   1977 *[16]*cgAAgggCCgguaAacGgCGgGgGUAACUaUGACcCuCuUAAgGUAGCgaAAUaCCUuGcCGgcUaAgUgcCGgCuu 2069  
                                    CGAAG::CCGGUAAACGGCGG::GUAACUAU AC::UC:UAA:GUAGCGAAAU+CCUUG:CGG:UAAGU:CCG:C U
  gi_545778205_gb_U000 227614 *[31]*CGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCU 227721
                              ...9..689************************************************************************** PP

                                                                                                                  NC
                              ,,,,,,,,)))),,,]]-]]]]]]],,,,}}}-}}}}}}}}-}}}},,,,,,,,,,,,,<<<<<________>>>>>,,{{{{ CS
               RF02540   2070 GcAUGAAuGGaguAAcgAGggccCCACUGuCCccgcccgggacCCggUGAAcuuacugugccgGuGcAcAguCcggcgacccC 2152  
                              GCA GAAUGG:GUAA:GA :GCC:: CUGUC:CC:CCCG:GAC:C:GUGAA+UU ++ U: C:GUG A+A  C:G : ACCC 
  gi_545778205_gb_U000 227722 GCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCG 227804
                              *********************************************************************************** PP

                                                                     v                 v                          NC
                              {{{{-{{{-{{,,,,,,{{{{-{{{{{{{,((((---(((((((,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<< CS
               RF02540   2153 cggcggGgAGcGAAGACCCcgUgGAgCUUUACuGCAGcCugccguUGgggcgcggccgcgggcgcguAGuGUAGguGGGAGcc 2235  
                              CGGC+:G: G: AAGACCCCGUG:A:CUUUACU: AGC: G:C: UG:::::::: C :::::G+GUAG  UAGGUGGGAG:C
  gi_545778205_gb_U000 227805 CGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGC 227887
                              *********************************************************************************** PP

                                                                                     v                 v          NC
                              ---------<<<<<____>>>>>------>>>------------>>>>>>>>>>>>>>>>>>>>>>>,,,<<<<._____... CS
               RF02540   2236 guugaagcccccccuccggggggggugGAggCgacaaUGaaACACCacCcgcccgcggccgcgcccCUaACccc.uaaaa... 2314  
                               UUGAAG+   ::C CC+G::    UGGAG:CGAC  UGAAA ACCACCC::::: G ::::::::CUAAC::          
  gi_545778205_gb_U000 227888 UUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUgACCCGuaa 227970
                              ************************************************************************99755444567 PP

                                     v            v                                                               NC
                              .......>>>>,,,,,)))))))----)))),,<<<<_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((( CS
               RF02540   2315 .......gggGGACAucggcaGgUGGGCaGUUuGGcuGGGGCggCACgCccccGAAAAgaUAuCggggGcGCCCaAAGgucgg 2390  
                                      ::GGACA :G:C :GUGGG:AGUUUG:CUGGGGCGG: C:CC:CC AAA  +UA+CGG:GG:GC:C AAGGU:GG
  gi_545778205_gb_U000 227971 uccggguUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGU-CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGG 228052
                              888888899************************************.************************************* PP

                                                                                      vv               vv         NC
                              (<<-<<<<<<_______>>>>>>--->><<______>>,,,,)))))),,,,<<<<<<<<<_________>>>>>>>>>,<-< CS
               RF02540   2391 CUCAggcGGguCAGAAacCCgccGuAGAGcGcAAGGgCAAAAGccggccUGACugggccccuaAaagcaaggggcccaGaggc 2473  
                              CU A::C G:UC GA A:C G::G   AG:GCAA G:CA AAGCC:GC+UGACUG:  :C:U A+ G   :G:  :CAG :GC
  gi_545778205_gb_U000 228053 CUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGG---CGCGAGCAGGUGC 228132
                              *************************************************************988765...************* PP

                                                                                                                  NC
                              ____>->,]],,,,,,,,,,<<<<<-<<<<<_______>>>>>>>>>>,,,,,...,,,,}}}}}--}}}}}},,,,,,,,<< CS
               RF02540   2474 GAAAgccgGGcCUAGCGAACccccguGcCcccuuggUGggGgCcggggAuGAC...AGAAAAGcUACCccgGGGAUAACaGag 2553  
                              GAAAGC:GG:C UAG GA CC: :G G  C:    G  :G  CC: :G U A    A AAAAG:UAC:CCGGGGAUAACAG::
  gi_545778205_gb_U000 228133 GAAAGCAGGUCAUAGUGAUCCGGUG-GUUCUGAAUGGAAGGGCCAUCGCUCAAcggAUAAAAGGUACUCCGGGGAUAACAGGC 228214
                              *************************.999999999999**********987753337789*********************** PP

                                                                                                                  NC
                              <-<<<<<<<<---<<_______>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<--<<<<<______>>>>> CS
               RF02540   2554 ucgucgCgGGCgAGAGcuCauAUCGACCCcGcgguUugcuACcUCGAUGUCgGcucuccCcAUCCUGGcgguGCAGcAgccgC 2636  
                              U :U::CG: C+AGAG+UCAUAUCGAC :CG::GUU:G::ACCUCGAUGUCGGCUC::C CAUCCUGG: :UG AG AG: :C
  gi_545778205_gb_U000 228215 UGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCC 228297
                              *********************************************************************************** PP

                                                                                                                  NC
                              ---->>,<<<<<_____>>>>>,,,,,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}} CS
               RF02540   2637 CAAGGGUcgGGcUGuUCgCCcgUUAAAgGggaaCgUGagCuGGGUUuAGacCGuCGuGAGaCAGguCGGuugCUacCcgccgG 2719  
                              CAAGGGU::GGCUGUUCGCC::UUAAAG G::ACG GAGCUGGGUUUAGA:CGUCGUGAGACAG:UCGGU :CUA:C:GCCG 
  gi_545778205_gb_U000 228298 CAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGU 228380
                              *********************************************************************************** PP

                                                     v                             v                              NC
                              }}},,,,((((((((--((((,,<<<<<<<<_______________>>>>>>>><<<<<---<<<----<<<<<<<<<<.___ CS
               RF02540   2720 gggUGuugGccGcCUGAgGGgAAGgcgccccUAGUACGAGAGGAACggggcgcCgggGCCuCugGUgUAcCGGuuGuCc.Gau 2801  
                              GGG G UGG::::CUGAGGGG   :: C:CCUAGUACGAGAGGA CGG:G ::+:G:::C+CU:GUGU C:GGUUGUC: G +
  gi_545778205_gb_U000 228381 GGGCGCUGGAGAACUGAGGGGGG-CUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAuGCC 228462
                              *********************86.******************************************************85655 PP

                                                                                                                  NC
                              _.>>>>>-->>>>>---->>>->>>>>,,.<<<----<<<<<___________>>>>>---->>>,))))------))))))) CS
               RF02540   2802 a.gGgCaaugCCGgGcAGCcacGCcccaa.gggaUAAggGCUGAAaGCAUCUAAGCccGAAacccucCCcGAAAAgAGgCggC 2882  
                              A :GGCA UGCC:GG+AGC:A :::C: A  :GAUAAG:GCUGAAAGCAUCUAAGC:CGAAAC:  CCCCGA A GAG::::C
  gi_545778205_gb_U000 228463 AaUGGCACUGCCCGGUAGCUAAAUGCGGAaGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUC 228545
                              558***********************98889**************************************************** PP

                                                       vv                             vv                          NC
                              ),................,,,,,((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<--<______>-->> CS
               RF02540   2883 cu................gauuAgGgcccccgUAgAAGAcggggUuGAUgGggcgGgGGUGuAAgccccgAGguuaauCGAgg 2949  
                              C                  + +AGG  C:: G AGA GAC ::GUUGAU:G::CGG  GUGUAA:C:C:  G      CGA:G
  gi_545778205_gb_U000 228546 CCugacuccuugagagucCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCA--G------CGAUG 228620
                              ******************999***********************************************9..9......9**** PP

                                      vv             vv                 NC
                              >>>>--->>>->>>>>->>>,,,)))),,,,,}}}}::::: CS
               RF02540   2950 ggcuuAGCCcgCcgccaCcAAuagcCcgAaugcgcgauauu 2990  
                              :G:U AGC  +CCG::AC:AAU   CCG  +G::::A+  U
  gi_545778205_gb_U000 228621 CGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCU 228661
                              ***************************************** PP

>>

RNAfold

>gi_545778205_gb_U000_113
CGCAACACGAUGAUGGAUCGCAAGAAACAUCUUCGGGUUGUGAGGUUAAG
CGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGAC
GUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCG
GCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAAC
UGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUA
CCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAAC
GGGGAGGAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUG
GAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGC
UGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGG
GGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCA
GUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGA
ACCUGAAACCGUGUACGUACAAGCAGUGGGAGCAUGCUUAGGCGUGUGAC
UGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUU
AACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGU
UGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAG
GUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAG
CGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCU
GGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAACUCAUCUCCGGG
GGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUG
CAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGC
UAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCC
AAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGA
UGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGG
UCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAG
CUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGC
CUGUGAAGGUGUACUGUGAGGUAUGCUGGAGGUAUCAGAAGUGCGAAUGC
UGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCA
AGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGC
GAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUG
GUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGU
UGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUC
AAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCC
CUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCC
AAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACU
CGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACG
CUGAUAUGUAGGUGAAGCGACUUGCUCGUGGAGCUGAAAUCAGUCGAAGA
UACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACG
AAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUG
AUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGG
CCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUC
CGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACU
CAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGG
AAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUG
AUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGG
AGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACC
CGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGU
CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCG
GACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUG
ACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAA
UGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCU
GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUC
GGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCG
CCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCG
GUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUA
CGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAU
GGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUA
AGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCCU
GAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAG
CGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUUACA
ACGCCGAAGCUGUUUUGGCGGAUUGAGAGAAGAUUUUCA
(((....((((.....))))...((((((.(((((((((((((((((((((.....(((((.((((((((((((((((.....))).)))......((((.(((......))).....(((((((..(((.......)))......))))))).(((((...((((....))))((((((....))))))..(((((((((.........))))))))).......(((((..(((..........))).))))).)))))...((((......))))..((((((.(((..((((..(((..((((.(((...(((((....(((((((((((((.(((...((((((....))))))....(((.((((....)))).))))))...)))))))))))))...((((...)))).((((((((.((...)).)))))))).....((((((......))))))))))).....(((((((((((((((((((.((((....(((((.((...(((((.......((((.....)))).((........)).....(((((((((((.((....((((..((((((....))))))..))))(((((((((((....((((((.......(((((((((((((..((((..((.....))..)))).........((.(((....))).))......)))))))))))))))))))...((((((..((((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))))(((.....)))......))))))......((((((((((((((...((.((((...((((((((((((...(((((((((.......(((.(((.((((...(((((((.....))))).))...)))).)))...))).....)))))).)))...))))).......(((((((((((....)))))))))))....(((......))).(((((((......(((.(((......))).....((((..(((((.((((....)))).........((((.(((((.......))))).))))...((..(((......)))..))((((((.(((.(((((.(.((.(((((..(((.((........)).)))...((((..(((((((((....))))))))).))))....((((((((...((((.....((((((((....))))))))..))))..))))).)))...((((......)))).......(((((((.....))))))).((.(((..(((...)))))).))...)))))..)).).))))).))).))))))((((.(((.(.(((....))).).)))..))))..(((((........)))))..(((((((((((((..((((((((.(.((..(((..((((((((((((((...))).))))))....((((.(((.((((((((((.((.....)))))))))).)).)))..)))).....(..(((((....)))))...))))))...))))).).)))........)))))..))....))))))))))))))))..)))).)))......))))))).((((.....)))).)))))))))))))...))))).))..))))))))))))).)))))(((..((((....))))..))).......((((((......))))))(((((.(((((..(((.......)))..))))).((((....(((((.....)))))))))..........)))))...)).)))))))))))....)))))(((...((((((..((((..(((((((((((.((....))..))))))..)))))))))))))))...)))((((((.......))))))..((((..........))))((((((.....))))))(((((.(..((((.........))))..).(((((.....))))).((((((........))))))......)))))....))))))).............((((((.((.....(((((.(((.(((((((((((((((((.((((.(.((.((((....((..((((((...((((((((....))))))))))))))..)).....)).)))).).)))).))))))))))....(((.((((((.....)))))))))..))))))).)))..))))))).)).))))((..(((((((...........)))))))..))..)))).))).)))..))))))...)))))))(((.((((....)))).)))(((((((.((((..((((....))))..)))).(((....)))(((((...)))))((((((((((.......)))))))))).((..((((..........))))..))...)))))))((((((((...((.......))...))))))))..))).))))..)))..))))((((((((((((((((......)))))).)))))(((((.....))))).....))))).)))..))))))....(((((((....))).)))).))))..)))))))))).)))))((((((((.(..(((((((((((..((.(....).)).))))))).(((((...((((..((((((((((((....))))))..))))))..)))).)))))...(((....(((((...........)))))....))).))))....).)))))))).....(((((.((....)).))))).(((((....)))))(((((.(((((((((..((...((((((....))))))..))...))))).)).)).)).)))...))))))))))))))).)))))).)))))).)))...(((((......))))) (-1108.50)

Length sequence

: 2989

Length match:

2902