gi_545778205_gb_U000_116

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:

1846.0

E-value:

0

From sequence:

3943703

To sequence:

3946606

Alignments:

                                                                                                                 NC
                               :::::{{{{,,,,,,{{{{{{{{{{-----{{{,,{{{{.{{{{{{,,,,,,,((((<<<________>>>,,,,,<<<<< CS
               RF02540       1 uauaucgcgcuauuAcgCcgcccgGuGGAUGGCUcGGCU.cGgGcGcCGAuGAaGGgcGuGgCAAGCUgCgAUAAGCccgG 80     
                               +  +U:::: + U A ::::C:CGGUGGAUG:C +GGC: :::G:G CGAUGA:GG:CGUG  AA CUGCGAUAAGC:::G
  gi_545778205_gb_U000 3943703 AGGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAgUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG 3943783
                               **************************************636789************************************* PP

                                                                                                                 NC
                               <---<<<_______>>>.------>>>>>>,,,)))),,,<<<____>>>,,,,,,,,,,,,,,....,<<<<<____... CS
               RF02540      81 GGgAGgcGCAuGcAgcC.uuuGAuCCcggGAUucCCuAAUgGGAauUCCcguuacuuuuuaaac....gcucccuauu... 153    
                               G  AGG:G  +  A:CC UU+ A+CC:::GAUU:CC:AAUGGG A  CCC+ U + UUU  A      +:::::+A U   
  gi_545778205_gb_U000 3943784 GUAAGGUGAUAUGAACCgUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACAcacuAUCAUUAACUgaa 3943864
                               *****************445689****************************888887777776689999999999988999 PP

                                                                                                                 NC
                               ..........>>>>>,,,,,,<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<____>>,,,<<<<<--- CS
               RF02540     154 ..........gggagcGGGAACcCcccGAAuuGAAaCAUCUuAGUAgggGgAGGAaaAGAAAcCAAuuGgGAUgcCgcuAG 224    
                                         ::::: G GAACC::::GAA UGAAACAUCU AGUA::::GAGGAAAAGAAA:CAA +G:GAU:CC:C AG
  gi_545778205_gb_U000 3943865 uccauagguuAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAG 3943945
                               9********9*********************************************************************** PP

                                                                                                                 NC
                               --<<_____>>---->>>>>,,[[[[,,,,~~~~~~,,,,,,,,,,((((------((((------------(((,,,<-< CS
               RF02540     225 UAgcGGCGAgcGAAAgcGgcauAGccCAAA*[34]*uGUugugggccggcuuuaaugcgccuaguuaaugaAgccGAAgUg 333    
                               UAGCGGCGAGCGAA G:GG:  AGCCCA A      UG  +               :: :   + U + ++AG::GAAG :
  gi_545778205_gb_U000 3943946 UAGCGGCGAGCGAACGGGGAGCAGCCCAGA*[ 3]*UGAAU---------------CAGUA--UGUGUGUUAGUGGAAG-C 3944005
                               ******************************...5..66554...............77777..667778899*******.* PP

                                                                                                                 NC
                               <<<______>>>>>,,<___>,<<<_______>>>,,,)))------------))))----)))),,,,,,,,,,,<<<<< CS
               RF02540     334 gccUGGAAuggcccgccauAgAGGGUGAuAGcCCCGUAggcguAaucuaaaaggcgcuugagccguuuccaGAGUAcCgcg 414    
                               G CUGGAA+G C:CGC:AUA:AGGGUGA AGCCCCGUA::C +AA +  A A : ::U  +     U   +GAGUA:: C 
  gi_545778205_gb_U000 3944006 GUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUAUUGUGAG----CUCGAUGAGUAGGGCG 3944082
                               *********************************************9999888877777666....8999************ PP

                                                                                                                 NC
                               <<___..._____>>>>>>>,,,,,,<<<<<_______>>>>>,,]]]],,,,,}}-}}}}.}}-}},,,,,,,,,,,,,, CS
               RF02540     415 ggUUG...GaauUcccgcGgGAAuaugGggGgcAucaaCccCcAAggCUAAAUACguCcCg.AGACCGAUAGcGaAcuAGU 491    
                               GG      G ++UCC G ::GAAUAUGG:GGG A CA CC:CCAAGGCUAAAUAC: C::: :GACCGAUAG+GAAC AGU
  gi_545778205_gb_U000 3944083 GGACAcguGGUAUCCUGUCUGAAUAUGGGGGG-ACCAUCCUCCAAGGCUAAAUACUCCUGAcUGACCGAUAGUGAACCAGU 3944162
                               **76422367788****************997.89999*******************987636****************** PP

                                                                                                            vv   NC
                               ,<<____>>,,,,}}--------------.-----------.--------}-----}}}}}}}}}},,,,,,,<<<<<<<< CS
               RF02540     492 AccGUGAggGAAAGCUGAAAAGuAcCccu.gaaGGGggGUG.AAAAGaGCCUGAAACcgggcgGcgAuagaauggcgcggC 570    
                               ACCGUGAGGGAAAG: GAAAAG+ACCCC+   AGGGG GUG AAAAGA CCUGAAACCG:G:::: A+A   +G  G  GC
  gi_545778205_gb_U000 3944163 ACCGUGAGGGAAAGGCGAAAAGAACCCCGgCGAGGGGAGUGaAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC 3944243
                               *****************************8889999999998899************************************ PP

                                            vv      v v          v v                                 v       v   NC
                               <<-~~~~~~>>>>>>>>>>,,<<<<________>>>>{{{{{{,,,,(((((((((((((,,<<<<--<<<<_____>>>> CS
               RF02540     571 ccg*[61]*ggGucgcgccgUcCGUuUuGAAaaACGggCCgGGGAGUucgcggccguGgCGAGccUAAgggguuuAacccc 706    
                               :CG      G:GU  C  CGU C UUUUG A AA G G:C:G GA UU:::::C:G :GC AG::UAA:: :    A: ::
  gi_545778205_gb_U000 3944244 ACG*[ 7]*GUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGA----AUAGG 3944321
                               *97...8..9***********************************************************954....4669* PP

                                                                                                                 NC
                               -->>>>,,,<<____>>,,,,,~~~~~~~~~~~~,,,,))))))))))))),,[[-[---[[[[[[,,,(((((((((((( CS
               RF02540     707 GaAggCGuAGgGAAAcCGAuaa*[26]**[16]*uggAGuCacggccgcgaGACCaGAAaCCgggCGAUCUaggCccggGC 817    
                               G A::CG+AGGGAAACCGA               U++AGU: C:G:::::AGACC+GAAACC:GG:GAUC AG:C::: GC
  gi_545778205_gb_U000 3944322 GGAGCCGAAGGGAAACCGAG--*[ 7]**[ 6]*UUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGC 3944401
                               ******************96.....9.....*..9********************************************** PP

                                             v    v                     v                  v                     NC
                               ,<<<<---<<<<<<<____>>>>>>>---->>>>,,,,<<<<-<<-<<________>>>>>>>>,,)-))))))))))),< CS
               RF02540     818 AGGgcGAAgccgggcgaAAgcccgguGGAGgcCCGauAggggUgcUGaugUGCAAauCgcccccgUGACccggGccuAGGG 898    
                               AGG::GAAG::::G  AA  C::::UGGAG::CCGA A::G  :: ::  UG AAA:::: C::+UGAC :::G:CU GGG
  gi_545778205_gb_U000 3944402 AGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGA-ACCGACUA-AUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGG 3944480
                               ************************************.*****999.9********************************** PP

                                                                                                     vv        v NC
                               <<_____>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<---<<<-<<<<<<<< CS
               RF02540     899 GcgAAAGgCCAAUCuAGcccGGuaAuAGCUGGUUCCcgcCGAAacggccCgcAggccgacCccggcgGAGgcuGgcggcgg 979    
                               G:GAAAG:CCAAUC A:CC:GG +AUAGCUGGUUC:C:CCGAAA:::::  + :::::+CC:CG::   : C+::::::G 
  gi_545778205_gb_U000 3944481 GUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAA-UUCAUCUCCGGG 3944560
                               *****************************************************************964.55679******* PP

                                            v    vvv        vvv    v             v       vv                      NC
                               ----<<<----<<<<<<<<<<--~~~~~~>>>>>>>>>>--->>->---->>>>>>>>>>>------>>>>>>->,,,<<< CS
               RF02540     980 gGUAGaGCACugaccGggggguu*[18]*cccccCggucaAACuCCGAAcccgccgcCgcCGuAGAagccggGAgucgGgc 1072   
                               GGUAGAGCACUG  ::GG    +      ++ CC::  CAAACU CGAA+ C::::::  :    A+::CG:GAG C+ :C
  gi_545778205_gb_U000 3944561 GGUAGAGCACUGUUUCGGC---A*[21]*AACCCGAUGCAAACUGCGAAUACCGGAGA--AUGUUAUCACGGGAGACACAC 3944651
                               ****************993...2...3..34599********************9987..45566889************* PP

                                                                                                                 NC
                               <<<<<<__._____>>>>>>>>>,,,,<<<______>>>,,,((((.(((---(((------(-((((((----------- CS
               RF02540    1073 gcccgggG.UAAGcccgggcgcCGaGAGGGgaACAACCCAGAccgg.GGUUAAGGuCCCuAAgUgccGGcUAAGUGucAau 1151   
                               G C:G: G UAA  :C:G CG:  AGAGGG+AACAACCCAGACCG: :G:UAAGGUCCC AAGU:::GG:UAAGUG     
  gi_545778205_gb_U000 3944652 GGCGGGUGcUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCcAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG--- 3944729
                               ****9977478888*******************************55*****************************95... PP

                                      v      vv                                                                  NC
                               -----(((-((((((((((-------(((((,<<<--<<<_________>>>-->>><___><---<<______>>->,)) CS
               RF02540    1152 cuaAAGgguGuccccggcCuaAGACAgCggGgaGGUagGCUuAGAAGCAGCcAUCCucUAAgGAgUGCGUAAcAGCUCACc 1232   
                                 AAA:G UGU ::  G C  AGACA:C::GGA GU GGCUUAGAAGCAGCCAUC U:UAA:GA  GCGUAA AGCUCAC:
  gi_545778205_gb_U000 3944730 --AAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACU 3944808
                               ..568**************************************************************************** PP

                                        vv     v                                                                 NC
                               )))---)))))))))))))--------.-----------))))))))))---)))))))<<<<<<<________>>>>>-- CS
               RF02540    1233 cGcCGAGgccgggggCccCgAAAAUGg.aCGGGGCUuAAgCCggccaCCGAuACCccggggcgcgcuuauuaaagcgcgAu 1312   
                               :G:CGAG C  :: GC C:GAA AUG  ACGGGGCU AA:CC:::CACCGA :C::CGG:: : :C  +U+++ G: :   
  gi_545778205_gb_U000 3944809 GGUCGAGUCGGCCUGCGCGGAAGAUGUaACGGGGCU-AAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGU-- 3944886
                               **************************9788888888.89**********************655555555555555555.. PP

                                                    v                                   v                        NC
                               >>,,,,]]]]]]<-<<<<<.<<<<<------<<<<<<<<____>>>>>>>>--->>>>>>>>>>-->,,,,,}}}}}},,, CS
               RF02540    1313 ccgGUAGgcgGGCGucccg.cccGGguaGAAgccgGgccGuGAggcCcgguGGACCgggcgggaauGaaaAUCCcGGcggu 1392   
                               ::GGUAGG:G:GCGU:C:G :   :   GAAG:  :GC:GUGA:GC:  :UGGA:   :C:G:A UG++AAU C:G:C+  
  gi_545778205_gb_U000 3944887 UGGGUAGGGGAGCGUUCUGuAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUA 3944967
                               *******************445688889***************************************************** PP

                                                                                                                 NC
                               ,,,,,,,,,,,,<<<<<<_______>>>>>>{{{{,,,,{{{{,,{{,,,<<<<<<---<<_____>>->>>>>>,,,,,, CS
               RF02540    1393 AGUAgCAGCaaAGuggGGUGAGAAUCCccaCcGCCGaAaGgGCaAGGGUUccccGGCAAuGuUcGUCaGCCggggGUUAGu 1473   
                               AGUA+C G  AA:::GGGUGA AA CCC:::CGCCG AAG::CAAGGGUUCC:: :CAA:GUU +UC:G: ::GGGU AGU
  gi_545778205_gb_U000 3944968 AGUAAC-GAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGU 3945047
                               ****99.66799********************************************************************* PP

                                            v v            v v                                                   NC
                               [[[,<<.---<<<<<<<<<_____>>>->>>>>>---->>,,,<<<<<________>>>>>,,((((((((---------- CS
               RF02540    1474 CGGUCC.UAAggcgggccguAAcucggacccgccGAAaGGGAAgcgGGUUAAUAUUCCcgcgCcgcgggggUaggugcggu 1553   
                               CG: CC UAAG:C :G:C: AA  :G:  : G:CGA +GGGAA:C:GGUUAAUAUUCC:G:+C::: :G::  +G+G    
  gi_545778205_gb_U000 3945048 CGACCCcUAAGGCGAGGCCGAAA-GGCG-UAGUCGA-UGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCG---- 3945121
                               ***76539999999988888777.9995.6789985.799*******************************544422.... PP

                                                      vv v                                               v v   v NC
                               ---------------(((---(((((((((--(((((<<<<<<..________>>>>>>,.,,<<<<-----<<<<<<<<< CS
               RF02540    1554 AacgcaagccuaauucccGACgccucggGgUAggccgggcggg..gcuguCgucccgccu.AAgcgcuuAAgcccggcgag 1631   
                                          AA   ::GAC:   : GG:UA:G::G::CGGG  +C GU GUCCCG::U AA:CG: UA GC: G ::: 
  gi_545778205_gb_U000 3945122 -----------AAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGcgACGGUUGUCCCGGUUuAAGCGUGUAGGCUGGUUUUC 3945191
                               ...........3345888************************995566666669999986277888888888876666666 PP

                                v         v v   v v                                                 v vv         NC
                               -<<<_____>>>->>>>>>>.>>----->>>>,,,,,,,,,,,<____..>,,,,,,,)))))---)))))))))------ CS
               RF02540    1632 agcCGUAAUGgcGcgagccg.ggugAAggcgcgAuugGcuuuccgUaa..ggagagUUcggccgAucCccggggcCCaUGA 1709   
                                 ::  AAU:: G ::: C  :G+  AG:CG:GAU++     C: UA   :G +++  C::C:+AU:CC :   :CCA GA
  gi_545778205_gb_U000 3945192 CAGGCAAAUCCGGAAAAUCAaGGCUGAGGCGUGAUGACGAGGCACUACggUGCUGAAGCAACAAAUGCCCUGCUUCCAGGA 3945272
                               6666667888866666666643567777888888888777777666655588899999*********99887777777788 PP

                                                                                        v             v          NC
                               ---.))).------------)))))))),]]],,}},,,,,<<______>>,}}}},<<<<_______>>>>,}}}},,,{ CS
               RF02540    1710 AAA.ggg.auugggaaugAucccccgcguCCGUACCgAGAaCCGACACAGGUGCcCcugGcUGAGaAGgCcaAGGCgUaUc 1788   
                               AAA ::   ++G +   G U::C: :::+:CGUACC   AACCGACACAGGUG::C  GG: GAGAA :CCAAGGCG + :
  gi_545778205_gb_U000 3945273 AAAgCCUcUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCA-GGUAGAGAAUACCAAGGCGCU-U 3945351
                               87744444666667778889************************************7.*******************86.9 PP

                                                                                                v v              NC
                               {{{-----{{{{{{{{-{{{,,,,,,,,,,,,,,<<<<<---<<____>>---->>>>><<<<<<<<<._______..... CS
               RF02540    1789 GGguauAAcccgggcgAGGgAAuUCGGCAAAuUagccCCGUAccUUcGggAgAAGGggugCCuGcggc.uuggaaa..... 1863   
                               G:G A AAC:CGGG:GA:GGAA+U GGCAAA U+:::CCGUA:CUUCGG:AGAAGG:::GC:::: :    G +AA     
  gi_545778205_gb_U000 3945352 GAG-AGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGuAGGUGAAgcgac 3945431
                               ***.99*********************************************************998876555555578888 PP

                                             v v                                                         v       NC
                               ..............>>>>>>>>><___>,,,,,,,[[[[[[[[[,,<<<_________>>>,,<<<<<<<<<--<<<<___ CS
               RF02540    1864 ..............gccgCaGGuCGCAGUGACuAGGGggccCcgACUGUUUAauAAAAACAuAggcccCcGCuAgcCCGaA 1930   
                                              : ::::GUCG AG  AC AG::GGC: C:ACUGUUUA UAAAAACA A:::C :::C+A C:CGAA
  gi_545778205_gb_U000 3945432 uugcucguggagcuGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAA 3945512
                               8888888888888878899************************************************************** PP

                                   v                                                                             NC
                               _>>>>-->-->>>>>>>>,,((((,<<<--<<<<<<<--<<<----~~~~~~---->>>>>>>>-->>>>><<<<<<____ CS
               RF02540    1931 AGGgcguGUACgGgggccGAcuCCUGcCCAgugccGGUAccuGAAa*[16]*cgAAgggCCgguaAacGgCGgGgGUAACU 2021   
                               AG:G   GUA::: G:::GAC:CCUGCCC GUGCCGG A::U AA       CGAAG::CCGGUAAACGGCGG::GUAACU
  gi_545778205_gb_U000 3945513 AGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAU*[31]*CGAAGCCCCGGUAAACGGCGGCCGUAACU 3945618
                               ********************************************99...9..689************************** PP

                                                                                                                 NC
                               ___>>>>>><___>,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]],,,,}}}- CS
               RF02540    2022 aUGACcCuCuUAAgGUAGCgaAAUaCCUuGcCGgcUaAgUgcCGgCuuGcAUGAAuGGaguAAcgAGggccCCACUGuCCc 2102   
                               AU AC::UC:UAA:GUAGCGAAAU+CCUUG:CGG:UAAGU:CCG:C UGCA GAAUGG:GUAA:GA :GCC:: CUGUC:C
  gi_545778205_gb_U000 3945619 AUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUC 3945699
                               ********************************************************************************* PP

                                                                                                                 NC
                               }}}}}}}}-}}}},,,,,,,,,,,,,<<<<<________>>>>>,,{{{{{{{{-{{{-{{,,,,,,{{{{-{{{{{{{,( CS
               RF02540    2103 cgcccgggacCCggUGAAcuuacugugccgGuGcAcAguCcggcgacccCcggcggGgAGcGAAGACCCcgUgGAgCUUUA 2183   
                               C:CCCG:GAC:C:GUGAA+UU ++ U: C:GUG A+A  C:G : ACCC CGGC+:G: G: AAGACCCCGUG:A:CUUUA
  gi_545778205_gb_U000 3945700 CACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUA 3945780
                               ********************************************************************************* PP

                                       v                 v                                                       NC
                               (((---(((((((,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<<---------<<<<<____>>>>>------ CS
               RF02540    2184 CuGCAGcCugccguUGgggcgcggccgcgggcgcguAGuGUAGguGGGAGccguugaagcccccccuccggggggggugGA 2264   
                               CU: AGC: G:C: UG:::::::: C :::::G+GUAG  UAGGUGGGAG:C UUGAAG+   ::C CC+G::    UGGA
  gi_545778205_gb_U000 3945781 CUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGA 3945861
                               ********************************************************************************* PP

                                                         v                                               v       NC
                               >>>------------>>>>>>>>>>>>>>>>>>>>>>>,,,<<<<._____..........>>>>,,,,,)))))))---- CS
               RF02540    2265 ggCgacaaUGaaACACCacCcgcccgcggccgcgcccCUaACccc.uaaaa..........gggGGACAucggcaGgUGGG 2334   
                               G:CGAC  UGAAA ACCACCC::::: G ::::::::CUAAC::                  ::GGACA :G:C :GUGGG
  gi_545778205_gb_U000 3945862 GCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUGgACCCGugauccggguUGCGGACAGUGUCUGGUGGG 3945942
                               ********************************************985555457788888889******************* PP

                                                                                                                 NC
                               )))),,<<<<_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((((<<-<<<<<<_______>>>>>>-- CS
               RF02540    2335 CaGUUuGGcuGGGGCggCACgCccccGAAAAgaUAuCggggGcGCCCaAAGgucggCUCAggcGGguCAGAAacCCgccGu 2415   
                               :AGUUUG:CUGGGGCGG: C:CC:CC AAA  +UA+CGG:GG:GC:C AAGGU:GGCU A::C G:UC GA A:C G::G 
  gi_545778205_gb_U000 3945943 UAGUUUGACUGGGGCGGU-CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGG 3946022
                               ******************.************************************************************** PP

                                                              vv               vv                                NC
                               ->><<______>>,,,,)))))),,,,<<<<<<<<<_________>>>>>>>>>,<-<____>->,]],,,,,,,,,,<<< CS
               RF02540    2416 AGAGcGcAAGGgCAAAAGccggccUGACugggccccuaAaagcaaggggcccaGaggcGAAAgccgGGcCUAGCGAACccc 2496   
                                 AG:GCAA G:CA AAGCC:GC+UGACUG:  :C:U A+ G   :G:  :CAG :GCGAAAGC:GG:C UAG GA CC: 
  gi_545778205_gb_U000 3946023 UUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGG---CGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGG 3946100
                               ************************************988765...************************************ PP

                                                                                                                 NC
                               <<-<<<<<_______>>>>>>>>>>,,,,,...,,,,}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<______ CS
               RF02540    2497 cguGcCcccuuggUGggGgCcggggAuGAC...AGAAAAGcUACCccgGGGAUAACaGagucgucgCgGGCgAGAGcuCau 2574   
                               :G G  C:    G  :G  CC: :G U A    A AAAAG:UAC:CCGGGGAUAACAG::U :U::CG: C+AGAG+UCAU
  gi_545778205_gb_U000 3946101 UG-GUUCUGAAUGGAAGGGCCAUCGCUCAAcggAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAU 3946180
                               **.999999999999**********987753337789******************************************** PP

                                                                              v            v                     NC
                               _>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<--<<<<<______>>>>>---->>,<<<<<_____>> CS
               RF02540    2575 AUCGACCCcGcgguUugcuACcUCGAUGUCgGcucuccCcAUCCUGGcgguGCAGcAgccgCCAAGGGUcgGGcUGuUCgC 2655   
                               AUCGAC :CG::GUU:G::ACCUCGAUGUCGGCUC::C CAUCCUGG  :UG AG AG:  CCAAGGGU::GGCUGUUCGC
  gi_545778205_gb_U000 3946181 AUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGAGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGC 3946261
                               ********************************************************************************* PP

                                                                                                                 NC
                               >>>,,,,,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}}}}},,,,((((((((-- CS
               RF02540    2656 CcgUUAAAgGggaaCgUGagCuGGGUUuAGacCGuCGuGAGaCAGguCGGuugCUacCcgccgGgggUGuugGccGcCUGA 2736   
                               C::UUAAAG G::ACG GAGCUGGGUUUAGA:CGUCGUGAGACAG:UCGGU :CUA:C:GCCG GGG G UGG::::CUGA
  gi_545778205_gb_U000 3946262 CAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGA 3946342
                               ********************************************************************************* PP

                                     v                             v                                             NC
                               ((((,,<<<<<<<<_______________>>>>>>>><<<<<---<<<----<<<<<<<<<<.____.>>>>>-->>>>>- CS
               RF02540    2737 gGGgAAGgcgccccUAGUACGAGAGGAACggggcgcCgggGCCuCugGUgUAcCGGuuGuCc.Gaua.gGgCaaugCCGgG 2815   
                               GGGG   :: C:CCUAGUACGAGAGGA CGG:G ::+:G:::C+CU:GUGU C:GGUUGUC: G +A :GGCA UGCC:GG
  gi_545778205_gb_U000 3946343 GGGGGG-CUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAuGCCAaUGGCACUGCCCGG 3946422
                               ****86.******************************************************85655558************ PP

                                                                                                                 NC
                               --->>>->>>>>,,.<<<----<<<<<___________>>>>>---->>>,))))------)))))))),........... CS
               RF02540    2816 cAGCcacGCcccaa.gggaUAAggGCUGAAaGCAUCUAAGCccGAAacccucCCcGAAAAgAGgCggCcu........... 2884   
                               +AGC:A :::C: A  :GAUAAG:GCUGAAAGCAUCUAAGC:CGAAAC:  CCCCGA A GAG::::CC            
  gi_545778205_gb_U000 3946423 UAGCUAAAUGCGGAaGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCugacuccuuga 3946503
                               ***********98889***************************************************************** PP

                                           vv                             vv                                 vv  NC
                               .....,,,,,((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<--<______>-->>>>>>--->>>- CS
               RF02540    2885 .....gauuAgGgcccccgUAgAAGAcggggUuGAUgGggcgGgGGUGuAAgccccgAGguuaauCGAggggcuuAGCCcg 2960   
                                     + +AGG  C:: G AGA GAC ::GUUGAU:G::CGG  GUGUAA:C:C:  G      CGA:G:G:U AGC  +
  gi_545778205_gb_U000 3946504 gagucCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCA--G------CGAUGCGUUGAGCUAA 3946576
                               *****999***********************************************9..9......9*************** PP

                                           vv                 NC
                               >>>>>->>>,,,)))),,,,,}}}}::::: CS
               RF02540    2961 CcgccaCcAAuagcCcgAaugcgcgauauu 2990   
                               CCG::AC:AAU   CCG  +G::::A+  U
  gi_545778205_gb_U000 3946577 CCGGUACUAAUGAACCGUGAGGCUUAACCU 3946606
                               ****************************** PP

>>

RNAfold

>gi_545778205_gb_U000_116
CGCAACACGAUGAUGAAUCGAAAGAAACAUCUUCGGGUUGUGAGGUUAAG
CGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGAC
GUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCG
GCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAAC
UGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUA
CCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAAC
GGGGAGCAGCCCAGAGCCUGAAUCAGUAUGUGUGUUAGUGGAAGCGUCUG
GAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUAU
UGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGG
GGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCA
GUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGA
ACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGAC
UGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUU
AACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGU
UGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAG
GUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAG
CGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCU
GGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGG
GGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUG
CAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGC
UAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCC
AAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGA
UGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGG
UCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAG
CUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGC
CUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGC
UGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCA
AGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGC
GAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUG
GUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGU
UGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUC
AAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCC
CUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCC
AAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACU
CGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACG
CUGAUAUGUAGGUGAAGCGACUUGCUCGUGGAGCUGAAAUCAGUCGAAGA
UACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACG
AAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUG
AUGGGGUCAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGG
CCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUC
CGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACU
CAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGG
AAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUG
AUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGG
AGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUGGACC
CGUGAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGU
CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCG
GACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUG
ACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAA
UGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCU
GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUC
GGCUCAUCACAUCCUGGAGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCG
CCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCG
GUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUA
CGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAU
GGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUA
AGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCCU
GAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAG
CGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUUACA
ACGCCGAAGAUGUUUUGGCGGAUGAGAGAAGAUUUUCAG
(((....((((.....))))...((((((((((((((((((((((((((((.....(((((.((((((((((((((((.....))).)))......((((.(((......))).....(((((((..(((.......)))......))))))).(((((...((((....))))((((((....))))))..(((((((((.........))))))))).......(((((..(((..........))).))))).)))))...((((......))))..((((((.(((((.(..(((.((.((((((((...(((((....(((((((((((((.(((...((((((....))))))....(((.((((....)))).))))))...)))))))))))))...((((...)))).((((((((.((...)).)))))))).....((((((......))))))))))).....(((((((((((((((((((.((((....(((((.((...(((((.......((((.....)))).((........)).....(((((((((((.((....((((..((((((....))))))..))))(((((((((((....((((((.......(((((((((((((..((((..((.....))..)))).........((.(((....))).))......)))))))))))))))))))...((((((..((((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))))(((.....)))......))))))......((((((((((((((...((.((((...((((((((((((...(((((((((.......(((.(((.((((...(((((((.....))))).))...)))).)))...))).....)))))).)))...))))).......(((((((((((....)))))))))))....(((......))).(((((((......(((.(((......))).....((((..(((((.((((....)))).........((((.(((((.......))))).))))...((..(((......)))..))((((((.(((.(((((.(.((.(((((..(((.((........)).)))...((((..(((((((((....))))))))).))))....((((((((...((((.(...((((((((....))))))))).))))..))))).)))...((((......)))).......(((((((.....))))))).((.(((..(((...)))))).))...)))))..)).).))))).))).))))))((((.(((.(.(((....))).).)))..))))..(((((........)))))..(((((((((((((..((((((((.(.((..(((..((((((((((((((...))).))))))....((((.(((.((((((((((.((.....)))))))))).)).)))..)))).....(..(((((....)))))...))))))...))))).).)))........)))))..))....))))))))))))))))..)))).)))......))))))).((((.....)))).)))))))))))))...))))).))..))))))))))))).)))))(((..((((....))))..))).......((((((......))))))(((((.(((((..(((.......)))..))))).((((....(((((.....)))))))))..........)))))...)).)))))))))))....)))))(((...((((((..((((..((((((((((..((....))...)))))..)))))))))))))))...)))((((((.......))))))..((((..........))))((((((.....))))))(((((.(..((((.........))))..).(((((.....))))).((((((........))))))......)))))....))))))).............((((((.((.....(((((.(((.(((((((((((((((((.((((.(.((.((((....((..((((((...((((((((....))))))))))))))..)).....)).)))).).)))).))))))))))....((((.(((((.....)))))))))..))))))).)))..))))))).)).))))((..(((((((...........)))))))..))..)))).))).)))..))))))...)))))))(((.((((....)))).)))(((((((.((((..((((....))))..)))).(((....)))(((((...)))))((((((((((.......)))))))))).((..((((..........))))..))...)))))))((((((((...((.......))...))))))))((((.((((.....(((((((...........)))))))...)))).))))......)))))))).)).)))....).)).)))..))))))....(((((((....))).)))).))))..)))))))))).)))))((((((((.(..(((((((((((..((.(....).)).))))))).(((((...((((..((((((((((((....))))))..))))))..)))).)))))...(((....(((((...........)))))....))).))))....).)))))))).....(((((.((....)).))))).(((((....)))))(((((.(((((((((..((...((((((....))))))..))...))))).)).)).)).)))...))))))))))))))).))))))))))))).)))..(((((......))))). (-1113.60)

Length sequence

: 2989

Length match:

2902