gi_545778205_gb_U000_117

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:

1846.5

E-value:

0

From sequence:

4037518

To sequence:

4040422

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 4037518 AGGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAgUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG 4037598
                               **************************************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 4037599 GUAAGGUGAUAUGAACCgUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACAcacuAUCAUUAACUgaa 4037679
                               *****************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 4037680 uccauagguuAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAG 4037760
                               9********9*********************************************************************** PP

                                                                                                                 NC
                               --<<_____>>---->>>>>,,[[[[,,,,~~~~~~,,,,,,,,,,((((------((((------------(((,,,<-< CS
               RF02540     225 UAgcGGCGAgcGAAAgcGgcauAGccCAAA*[34]*uGUugugggccggcuuuaaugcgccuaguuaaugaAgccGAAgUg 333    
                               UAGCGGCGAGCGAA G:GG:  AGCCCA A      UG  +               ::G    + U + ++AG::GAA  :
  gi_545778205_gb_U000 4037761 UAGCGGCGAGCGAACGGGGAGCAGCCCAGA*[ 3]*UGAAU---------------CAGUG--UGUGUGUUAGUGGAAG-C 4037820
                               ******************************...5..66554...............88888..778888999*****99.* PP

                                                                                                                 NC
                               <<<______>>>>>,,<___>,<<<_______>>>,,,)))------------))))----)))),,,,,,,,,,,<<<<< CS
               RF02540     334 gccUGGAAuggcccgccauAgAGGGUGAuAGcCCCGUAggcguAaucuaaaaggcgcuugagccguuuccaGAGUAcCgcg 414    
                               G CUGGAA+G C: GC:AUA:AGGGUGA AGCCCCGUA::C +AA +  A A  C::U  +     U   +GAGUA:: C 
  gi_545778205_gb_U000 4037821 GUCUGGAAAGGCGUGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAG----CUCGAUGAGUAGGGCG 4037897
                               ************************************************9999999998777....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 4037898 GGACAcguGGUAUCCUGUCUGAAUAUGGGGGG-ACCAUCCUCCAAGGCUAAAUACUCCUGAcUGACCGAUAGUGAACCAGU 4037977
                               **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 4037978 ACCGUGAGGGAAAGGCGAAAAGAACCCCGgCGAGGGGAGUGaAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC 4038058
                               *****************************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 4038059 ACG*[ 7]*GUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGA----AUAGG 4038136
                               *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 4038137 GGAGCCGAAGGGAAACCGAG--*[ 7]**[ 6]*UUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGC 4038216
                               ******************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 4038217 AGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGA-ACCGACUA-AUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGG 4038295
                               ************************************.*****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 4038296 GUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAA-UUCAUCUCCGGG 4038375
                               *****************************************************************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 4038376 GGUAGAGCACUGUUUCGGC---A*[21]*AACCCGAUGCAAACUGCGAAUACCGGAGA--AUGUUAUCACGGGAGACACAC 4038466
                               ****************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 4038467 GGCGGGUGcUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCcAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG--- 4038544
                               ****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 4038545 --AAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACU 4038623
                               ..568**************************************************************************** PP

                                        vv     v                                            v                v   NC
                               )))---)))))))))))))--------.-----------))))))))))---)))))))<<<<<<<________>>>>>-- CS
               RF02540    1233 cGcCGAGgccgggggCccCgAAAAUGg.aCGGGGCUuAAgCCggccaCCGAuACCccggggcgcgcuuauuaaagcgcgAu 1312   
                               :G:CGAG C  :: GC C:GAA AUG  ACGGGGCU AA:CC:::CACCGA :C::CGG:: : :C+ ++U+  G: :  U
  gi_545778205_gb_U000 4038624 GGUCGAGUCGGCCUGCGCGGAAGAUGUaACGGGGCU-AAACCAUGCACCGAAGCUGCGGCAGCGACACUAUG-UGUUG--U 4038700
                               **************************9788888888.89*********************944444433333.34444..4 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 4038701 UGGGUAGGGGAGCGUUCUGuAAGCCUGUGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUA 4038781
                               9******************445688899***************************************************** 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 4038782 AGUAAC-GAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGU 4038861
                               ****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 4038862 CGACCCcUAAGGCGAGGCCGAAA-GGCG-UAGUCGA-UGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCG---- 4038935
                               ***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 4038936 -----------AAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGcgACGGUUGUCCCGGUUuAAGCGUGUAGGCUGGUUUUC 4039005
                               ...........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 4039006 CAGGCAAAUCCGGAAAAUCAaGGCUGAGGCGUGAUGACGAGGCACUACggUGCUGAAGCAACAAAUGCCCUGCUUCCAGGA 4039086
                               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 4039087 AAAgCCUcUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCA-GGUAGAGAAUACCAAGGCGCU-U 4039165
                               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 4039166 GAG-AGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGuAGGUGAAgcgac 4039245
                               ***.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 4039246 uugcucguggagcuGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAA 4039326
                               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 4039327 AGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAU*[33]*CGAAGCCCCGGUAAACGGCGGCCGUAACU 4039434
                               ********************************************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 4039435 AUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUC 4039515
                               ********************************************************************************* 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 4039516 CACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUA 4039596
                               ********************************************************************************* 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 4039597 CUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGA 4039677
                               ********************************************************************************* PP

                                                         v                 v                v            v       NC
                               >>>------------>>>>>>>>>>>>>>>>>>>>>>>,,,<<<<._____..........>>>>,,,,,)))))))---- CS
               RF02540    2265 ggCgacaaUGaaACACCacCcgcccgcggccgcgcccCUaACccc.uaaaa..........gggGGACAucggcaGgUGGG 2334   
                               G:CGAC  UGAAA ACCACCC::::: G ::::::::CUAAC::                  ::GGACA :G:C :GUGGG
  gi_545778205_gb_U000 4039678 GCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUgACCCGuaauccggguUGCGGACAGUGUCUGGUGGG 4039758
                               *******************************************99755444567888888899****************** 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 4039759 UAGUUUGACUGGGGCGGU-CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGG 4039838
                               ******************.************************************************************** 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 4039839 UUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGG---CGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGG 4039916
                               ************************************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 4039917 UG-GUUCUGAAUGGAAGGGCCAUCGCUCAAcggAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAU 4039996
                               **.999999999999**********987753337789******************************************** PP

                                                                                                                 NC
                               _>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<--<<<<<______>>>>>---->>,<<<<<_____>> CS
               RF02540    2575 AUCGACCCcGcgguUugcuACcUCGAUGUCgGcucuccCcAUCCUGGcgguGCAGcAgccgCCAAGGGUcgGGcUGuUCgC 2655   
                               AUCGAC :CG::GUU:G::ACCUCGAUGUCGGCUC::C CAUCCUGG: :UG AG AG: :CCAAGGGU::GGCUGUUCGC
  gi_545778205_gb_U000 4039997 AUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGC 4040077
                               ********************************************************************************* 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 4040078 CAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGA 4040158
                               ********************************************************************************* 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 4040159 GGGGGG-CUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAuGCCAaUGGCACUGCCCGG 4040238
                               ****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 4040239 UAGCUAAAUGCGGAaGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCugacuccuuga 4040319
                               ***********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 4040320 gagucCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCA--G------CGAUGCGUUGAGCUAA 4040392
                               *****999***********************************************9..9......9*************** PP

                                           vv                 NC
                               >>>>>->>>,,,)))),,,,,}}}}::::: CS
               RF02540    2961 CcgccaCcAAuagcCcgAaugcgcgauauu 2990   
                               CCG::AC:AAU   CCG  +G::::A+  U
  gi_545778205_gb_U000 4040393 CCGGUACUAAUGAACCGUGAGGCUUAACCU 4040422
                               ****************************** PP

>>

RNAfold

>gi_545778205_gb_U000_117
CGCAACACGAUGAUGAAUCGAAAGAAACAUCUUCGGGUUGUGAGGUUAAG
CGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGAC
GUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCG
GCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAAC
UGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUA
CCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAAC
GGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUG
GAAAGGCGUGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGC
UGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGG
GGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCA
GUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGA
ACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGAC
UGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUU
AACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGU
UGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAG
GUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAG
CGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCU
GGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGG
GGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUG
CAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGC
UAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCC
AAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGA
UGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGG
UCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAG
CUGCGGCAGCGACACUAUGUGUUGUUGGGUAGGGGAGCGUUCUGUAAGCC
UGUGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCU
GACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAA
GGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCG
AGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGG
UGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUU
GUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCA
AGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCC
UGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCA
AACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUC
GGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGC
UGAUAUGUAGGUGAAGCGACUUGCUCGUGGAGCUGAAAUCAGUCGAAGAU
ACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGA
AAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGA
UGGGGUUAGCCGCAAGGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCG
GCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUU
CCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGAC
UCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACG
GAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUU
GAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUG
GAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGAC
CCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGG
UCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUC
GGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGU
GACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGA
AUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGC
UGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGU
CGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUC
GCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUC
GGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGU
ACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAA
UGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCU
AAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCC
UGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCA
GCGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUUAC
AACGCCGAAGGUGUUUUGGCGGAUUGAGAGAAGAUUUUCA
(((....((((.....))))...((((((((((((((((((((((((((((.....(((((.((((((((((((((((.....))).)))......((((.(((......))).....(((((((..(((.......)))......))))))).(((((...((((....))))((((((....))))))..(((((((((.........))))))))).......(((((..(((..........))).))))).)))))...((((......))))..((((((.(((((.(..(((.((.((((((((..((((......(((((((((((((.(((...((((((....))))))....(((.((((....)))).))))))...)))))))))))))...))))(((((((.((((((((.((...)).)))))))).....((((((......))))))..........(((((((((((((((((((.((((....(((((.((...(((((.......((((.....)))).((........)).....(((((((((((.......((((..((((((....))))))..))))......((((((((.((((((.......(((((((((((((..((((..((.....))..)))).........((.(((....))).))......)))))))))))))))))))...((((((..((((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))))(((.....)))......))))))...((((((((((((((((...(((((....)))))..(((((((...(((((((((.......(((.(((.((((...(((((((.....))))).))...)))).)))...))).....)))))).)))...))))))).....(((((((((((....)))))))))))....(((......)))...((((..((.....(((((....(((.(((........))).))))))))(((((..(((.(((((((((.(((((.......))))).)))).......(((......)))..)))))...)))))))))))))).........))))).....(((((..((((((.(((((((.((..(((((.(((.(((((...((((.(((...((...(((((.......(((((..(((((.(.(((((((((.((....(((...((((......))))........((((((.....))))))((((.(..(.((((((....(((((((..((.....)))))))))((......))(((...(((.(.(((....))).).)))...)))..(((((........))))).)))))).)..).)))).((((.((((..(..(((((...)))))...)..).))).)))).(((...((((.(((.((((((((((.((.....)))))))))).)).)))..))))...)))..(((((....)))))...))).....))...))))))))).)...)))))..)))))))))).....))...))).))))...)))))))).)))))..((((.....))))....((((((((....))))))))................)).))))))).)))))).....((((((((..(((....))).))))...))))))))).((((....))))...))).))))))))((((....(((((.....)))))))))..))))))))(((....))).)))))))))))....)))))(((...((((((..((((..(((((((((((.(((....)))..))))))..)))))))))))))))...)))((((((.......))))))..((((..........))))((((((.....))))))(((((.(..((((.........))))..).(((((.....))))).((((((........))))))......)))))....))))))).............((((((.((.....(((((.(((.(((((((((((((((((.((((.(.((.((((....((..((((((...((((((((....))))))))))))))..)).....)).)))).).)))).))))))))))....(((.((((((.....)))))))))..))))))).)))..))))))).)).))))((..(((((((...........)))))))..))..)))).))).)))..))))))...)))))))(((.((((....)))).)))(((((((.((((..((((....))))..)))).(((....)))(((((...)))))((((((((((.......)))))))))).((..((((..........))))..))...)))))))((((((((...((.......))...)))))))).(((((......))))))))))))..(((((((((((......)))))).)))))..)))))))).)).)))....).)).)))..))))))....(((((((....))).)))).))))..)))))))))).)))))((((((((.(..(((((((((((..((.(....).)).))))))).(((((...((((..((((((((((((....))))))..))))))..)))).)))))...(((....(((((...........)))))....))).))))....).)))))))).....(((((.((....)).))))).(((((....)))))(((((.(((((((((..((...((((((....))))))..))...))))).)).)).)).)))...))))))))))))))).))))))))))))).)))...(((((......))))) (-1119.60)

Length sequence

: 2990

Length match:

2903