gi_545778205_gb_U000_133

cmsearch-Rfam

Family :

LSU_rRNA_eukarya

Id:

RF02543

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea;

Ontology:

GO:0003735 structural constituent of ribosomeRF02543

Description:

not description

Score:

1260.5

E-value:

0

From sequence:

4210202

To sequence:

4212928

Alignments:

                                                                                                                 NC
                               :::::::::::::::::::::::<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<____>>,,,<<<<<- CS
               RF02543       1 ugacCUuaaaUcAgguaaGAuUAcCcgCuGAAuUUAAGCAUAUuAaUAaGcgGAgGAAAAGAAAcuAACaagGAUUcccuu 81     
                                + CC UA+ U+A   A+G   ACC:G :GAA+U AA CAU U A UA: C:GAGGAAAAGAAA::AAC ::GAUUCCC: 
  gi_545778205_gb_U000 4210202 AAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC 4210282
                               ********************************************************************************* PP

                                                                                                           v     NC
                               ----<<_____>>---->>>>>,,[[[[,,.<<<<<<<<<<<<<<<<_______>>>>>>>>>>>>>>>>,,,,((((((- CS
               RF02543      82 AGUAgcGGCGAgcGAAgagggAAuAGCcCA.cgcugcaacuccgcccucuuuuugggcggaguugcagcgUauaggggccu 161    
                               AGUAGCGGCGAGCGAA :GGGA  AGCCCA                       +                    G: :C: 
  gi_545778205_gb_U000 4210283 AGUAGCGGCGAGCGAACGGGGAGCAGCCCAg----------------------A----------------GCCUGAAUCA- 4210324
                               ******************************2......................2................4444664444. PP

                                            v  vvvv                                             vvvv  v          NC
                               ((((-(((((((-(((((((,,,<-<<<<______>>>>>,,<___>,,<<_______>>,,,,,)))))))--))))))) CS
               RF02543     162 ccucagccgcggcccccgccuAAgUccccUgGAAuggggcaccAuAgAGGGUGAgAguCCcGUauggcgggguaccgcggc 242    
                                    G: :::G+ ::     AAG C::CUGGAA G::GC C:AUA:AGGGUGA AG CCCGUA     :: U C::: :C
  gi_545778205_gb_U000 4210325 -----GUGUGUGUGUUAGUGGAAG-CGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGC 4210399
                               .....4444444233333445666.**************************************986554444444444444 PP

                                           v                                                                     NC
                               -----))))))))-)),,,,,,,,<<<<<<<___..._____>>>>>>>,,,,.,<<<<<________>>>>>,,]]]],, CS
               RF02543     243 uuuaugaggggccuccaaaGAGUCGgGuugcUUG...ggAaUgcagCcCaAAg.UgGguGGUAaAuUuCauCcAAgGCUAA 319    
                               U        :G:  :C A+GAGU :G : G:      GG AU:C : C: AA+ UGGG:GG  A + UC:UCCAAGGCUAA
  gi_545778205_gb_U000 4210400 UG-------UGAGCUCGAUGAGUAGGGCGGGACAcguGGUAUCCUGUCUGAAUaUGGGGGG--ACCAUCCUCCAAGGCUAA 4210471
                               44.......4444577999999999999998643111345678999999999845666665..45667999999******* PP

                                                                                                                 NC
                               ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<____>>,,,,,,,,,,,,,,,<<<<__.__>>>>,,,,,,,,,,,,,, CS
               RF02543     320 AUAuuagcaaGAGACCGAUAGcgaACAAGUAccGUGAggGAAAGaUGAAAAGaACucuGA.AaagaGAGUUAAAuAGuAcg 399    
                               AUA+U  + A  GACCGAUAG+GAAC AGUACCGUGAGGGAAAG  GAAAAGAAC:C:G   A:G:GAGU AAA AG AC 
  gi_545778205_gb_U000 4210472 AUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGcGAGGGGAGUGAAAAAGAACC 4210552
                               **********************************************************87368999*************** PP

                                                                v          v                                v    NC
                               ,,,,,,,,,,,,,,,,,,,,(~~~~~~~),,<<<<________>>>>{{{{{{,,,,(((((((((((((,,<<<--<<<< CS
               RF02543     400 UGAAAuuGuUaAgAgGgAAgc*[225]*gACCCGUCUUGAAACACGGACCAAGGAGUccaacauguguGCgAGuguuuggg 698    
                               UGAAA++GU +A     AAGC       G  CC U UUG A  A GG::CA: GA U:::A::::: ::C+AG  U+ :: 
  gi_545778205_gb_U000 4210553 UGAAACCGUGUACGUACAAGC*[ 29]*GUACCUU-UUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACC- 4210653
                               *********999999888876....6..4556644.788888899******************************99765. PP

                                v    v    v                                                                      NC
                               <<____>>>>>>-->>>,,,<<____>>,,,,,,,~~~~~~~~~~~~,,,,))))))))))))),,[[-[---[[[[[[,, CS
               RF02543     699 ucauuAgacccauacgCGuAacgAAagugAauuaa*[29]**[33]*aaGAGCacacauguuggGACCCGAAAGauGGUGA 829    
                                 A UA   ::  A  CG A::GAAA::GA U               ++ AG:: :::::U:::GACCCGAAA:::GGUGA
  gi_545778205_gb_U000 4210654 -GAAUA---GGGGAGCCGAAGGGAAACCGAGU---*[ 8]**[ 4]*UUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGA 4210727
                               .33444...66799***************974......8.....*..9********************************* PP

                                                          v    v                    v                  v         NC
                               ,((((((((((((,<<<<---<<<<<<<____>>>>>>>---->>>>,,,<<<<-<<-<<________>>>>>>>>,,)-) CS
               RF02543     830 ACUAugCcugggcAGggcGAAGccAGgGGAAACcCUggUGGAGgccCGuAgcgaUuCUGACGUGCAAAUCGaucgucagAc 910    
                                C A::C:UG GCAGG::GAAG::: G  AA  C :::UGGAG::CCG+A:CG  U: :   UG AAA ::A CG: +GAC
  gi_545778205_gb_U000 4210728 UCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUA-AUGUUGAAAAAUUAGCGGAUGAC 4210807
                               *******************************99********************9887.777788898888899******** PP

                                                                                                                 NC
                               )))))))))),<<<_____>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,,(((((((,, CS
               RF02543     911 cuggGuaUAGGgGcGAAAGaCuAAUCGAACCauCUAGUAGCUGGUUcCcuCCGAAGuuUCCCUCAGGAuaGCuggagcuuu 991    
                                UG:G::U GG:G GAAAG C:AAUC AACC:::   UAGCUGGUUC:C:CCGAA ::U:: U  ::A::GC: ::::: U
  gi_545778205_gb_U000 4210808 UUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAU 4210888
                               *************************************************************************99999933 PP

                                             v              v    vv  v v               v v vv    v             v NC
                               ,,,,,,,<<<<<<<<----<<<----<<<<<<<<<<--<<<<<<-<_____>->>>>>>.>>>>>>>>>>-->>->----> CS
               RF02543     992 uuuuuAGUcuuAuccGGUAAAGCgAAUGAuUAgaGGcuucggGgacgaAAugucCucga.CCuaUUcUCAAACUUUAAAUg 1071   
                               U   +A UCU:::: GGUA:AGC A UG  ::::  C+ : G:G+C +  +G+C:U :  +C::::  CAAACU : AAU 
  gi_545778205_gb_U000 4210889 U---CA-UCUCCGGGGGUAGAGC-ACUGUUUCGG--CAAGGGGGUCAUCCCGACUUACCaACCCGAUGCAAACUGCGAAUA 4210962
                               2...22.***************8.78*9887776..889999999***99**99995543567777889************ PP

                                                                                                                 NC
                               >>>>>>>,<<<<<<<<<_________>>>>>>>>>,,,,,,,,,,,))))))),,,,,<<<<<<<<<<_.____>>>>>>> CS
               RF02543    1072 ggUaagAagccccgguuaCUUaauUGaaccggggcauuuaAuauaaagcuccaAGUGGGCCAcUUuUGG.UAAGCAgAAgU 1151   
                               ::::AGAA                UG                 U A::::: :AG     C: ::   G UAA    :: :
  gi_545778205_gb_U000 4210963 CCGGAGAA----------------UG-----------------UUAUCACGGGAGACACACGGCGGGUGcUAACGUCCGUC 4211010
                               *******6................22.................33399999999987766666666665599966666666 PP

                                                                                                     v      vv   NC
                               >>>,,,,<<<______>>>,,,(((.((-(---(((------(-(--(((------------------(((-((((((((( CS
               RF02543    1152 GGCGAUGcGGGAUGAACCgAAcGcc.ggGuUAAGGuGCcuaAgUgcacgCUcAUcuAGAuaCCAuAAAaGGUGUuggUuca 1231   
                               G   A  :GG A  AACC:A   C: ::G:UAAGGU CC+AAGU:++:G:U A    G       AAA:G UGU GG  : 
  gi_545778205_gb_U000 4211011 GUGAAGAGGGAAACAACCCAGACCGcCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG-------AAACGAUGUGGGAAGG 4211084
                               6666666777778899****99999459**********************99997666.......799************* PP

                                                                                                       vv     v  NC
                               (-------(((((,<<<--<<<_________>>>-->>><___><---<<______>>->,)))))---)))))))))))) CS
               RF02543    1232 UauaGACAGCaGgAcGGUGgccAUGGAAGUCggaAUCCgCUAAGGAGUGUGUAACAACUCAcCuGCCGAAugaAccaGCCC 1312   
                               :  AGACA C::G ::GU ::C U GAAG  G::AUC:::UAA:GA  G:GUAA A:CUCAC::G CGA: :  CC GC C
  gi_545778205_gb_U000 4211085 CCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGC 4211165
                               ********************************************************************************* PP

                                                                                                                 NC
                               )-------------------)))--)))))---)-)))))<<<<<<<<<_________>>>>>>>>>,,,,]]]]]]<-<< CS
               RF02543    1313 uGAAAAUGGAUGGCGCUuAAGcguaccaCCuAUaCccggCCgucggggcAaauuuaaugccccgacGAGUAGGagGgcGug 1393   
                               :GAA AUG A  G G  UAA:C:++:CACC A :C:::G C: C:::GC      +AUGC:::G :G GUAGG:G:GCGU:
  gi_545778205_gb_U000 4211166 GGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCU-----UAUGCGUUGUUGGGUAGGGGAGCGUU 4211241
                               ********9887777777999****************************5.....566*********************** PP

                                  vv                                     vv                                      NC
                               <<<<<<.<<------<<----<<<____>>>--->>--->>>>>>>>>>-->,,,,,}}}}}},,,,,,,,,,,,,,<<<< CS
               RF02543    1394 gcGgcu.gcguuGAAgcuuugggcGUgAgccuggguGGAgcagcCgccaGUgCAGAUCUUGGUGGUAGUAGCAAAUAcUCa 1473   
                               ::G  : :C   GAAG:U U G: GUGA :C  G:UGGAG::  C:::AGUGC  AU :UG::   AGUA C A  A::C:
  gi_545778205_gb_U000 4211242 CUGUAAgCCUGCGAAGGUGU-GCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCG 4211321
                               ******99999999999766.************************************************************ PP

                                                                                                                 NC
                               <<_______>>>>>>{{{{,,,,,{{{{,,{{,,,<<<<<<---<<_____>>->>>>>>,,,,,,{{{,((.---((    CS
               RF02543    1474 AaUGAGAaCuUuGAggACuGAAGUGGaGAAGGGUUcCgugugAACaGuAgUuGaacacGgGUuAGUCGgUCC.UAAGg    1550   
                               ::UGA AA :::G::::C:G A  G:::AAGGGUUCC:: : AAC: UA+U:G+: ::GGGU AGUCG: CC UAA  
  gi_545778205_gb_U000 4211322 GGUGAAAAGCCCGCUCGCCGGA-AGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCcUAA--    4211396
                               ********************98.5*********************************************8763666..    PP

                                                                                    v                            NC
                               ~~~~~~~~~~~~,,,,,))----)),,,<<<<<________>>>>>,,[[[[-[[[[[[[,,,,<<<<____>>>>,,,,, CS
               RF02543    1551 *[17]**[21]*auuuacCGAAAGGGAAgcgGGUUAAuAUUCCcgcACcuggacguggauuuuaugcgGuAAcgcaAaugA 1657   
                                                      GGGAA:C:GGUUAAUAUUCC:G:AC:UG   GU:::U           A         
  gi_545778205_gb_U000 4211397 *[11]**[13]*----------UGGGAAACAGGUUAAUAUUCCUGUACUUGGU-GUUACUGCG--------A--------- 4211461
                               ...6.....6............3***************************994.776655433........2......... PP

                                v                v                                 vvv        v v   v v          NC
                               ,((((((---((((-(((((((-(((<<<<<<._________>>>>>>,,,<<<<<-----<<<<<<<<<<<<<_____>> CS
               RF02543    1658 acucggaGAcgccggcgggggccccgggaaGa.GUUuUCUUUuCuucuUAAcggccuauuuaCCcugcAaccgguUuaucc 1737   
                                  ::G:GACG :G :GG  :: ::GG:::G: G     U U:C:::UU A:   : ++  :: : ::: C GG   AUCC
  gi_545778205_gb_U000 4211462 -AGGGGGGACGGAGAAGGCUAUGUUGGCCGGGcGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCC 4211541
                               .357899***********************997777788889999999887655554444477677777777899999999 PP

                               v v   v v        vvv       vv               vv           v                      v NC
                               >>>>>>>>>>>----->>>>>,,,,,,<<<<<<<_____>>>>>>>,,)))---)))))))-))))---------)))))) CS
               RF02543    1738 ggaGguagGGuuuaauggccgGaAgAGcgccgcauuuuuugcggcgUCcggUgugcccccgacggcCCUUGAAAAuccgag 1818   
                                G ::: : ::  +  :   :GA GA    ::::U    ::::     C:: + ::  CC: C: CC    AAA :C::  
  gi_545778205_gb_U000 4211542 GGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACG-GUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUA 4211621
                               77777766655555555555688888888899999888.9999999******************99888777777776543 PP

                                                 v                                                               NC
                               ,,,,,,,,,,,]]-]]]]]]]]],}}},,}},,,,,<<______>>,}}}},<<<<_____>>>>,,}}}},,{{{{---- CS
               RF02543    1819 GgAaggaauaaauuccacgccaggcCGUACCcAUAaCCGCAuCAGGUCuCCAAGGugAauAgCCUCUaGUcgAUAGAAuAA 1899   
                                 A+ +     A: ::AC+ CA:+:CGUACCC  AACCG   CAGGU:::CA:G :GA +A: C:  :G::  U:::A AA
  gi_545778205_gb_U000 4211622 --AGCAUC---AGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAA 4211697
                               ..333333...4456777899************************************************************ PP

                                                                                           vv  v                 NC
                               {{{{{{{{-{{{,,,,,,,,,,,,,,<<<<<---<<____>>---->>>>><<<<<<<<<<<<<<-<<<<~~~~~~~>>>> CS
               RF02543    1900 gGUAGgUAAGGGAAGUCGGCAAAaUAGAUCCGUAaCUUcGGgAaAAGGAUUGGCUCUgAggGcugggccc*[121]*gggc 2094   
                               : ::GGU:A:GGAA U GGCAAAAU :: CCGUAACUUCGGGA AAGG ::G   CUGA:  :: GG:::       :::C
  gi_545778205_gb_U000 4211698 CUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACG---CUGAUAUGUAGGUGA*[  6]*UCGC 4211774
                               ***************************************************9...888886665555555....7..5555 PP

                                     v  vv                                                            v v        NC
                               ------>>>>>-->>>>>>>>><___>,,,,,,,[[[[[[[[[,,<<<_________>>>,,<<<<<<<<-<-<<<<____ CS
               RF02543    2095 aauuAAcagCcAAcUcAGAACUGGuACGGACaAGgGGAAUCcGACUGUuUAAUUAAAACAuAGcAUugcGAcGgcccgaAa 2175   
                               +  U   ::  AA:UCAG   U:G+A:  AC AG: G:   C:ACUGUUUA U AAAACA AGCA: G::  + C:CGAAA
  gi_545778205_gb_U000 4211775 GGAUGGAGCUGAAAUCAG---UCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAA 4211852
                               555555555667888888...9*********************************************************** PP

                                   v v                                                                           NC
                               _>>>>->--->>>>>>>>,,((((,<<<--<<<<<<-<--<<<----~~~~~~--->>>>>>>>-->>>>><<<<<<____ CS
               RF02543    2176 ggggcGgUGACgcaAUgUGAuUuCUGCCCAGUGCUcUGAAuGuCAAa*[15]*cAAgCgCgGGUAAACGGCGGGAGUAACU 2265   
                                G:G     A::C :UGUGA: :CUGCCC GUGC:: GAA:GU AA        AAGC:C::GUAAACGGCGG  GUAACU
  gi_545778205_gb_U000 4211853 -GUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCG-GAAGGUUAAU*[32]*GAAGCCCCGGUAAACGGCGGCCGUAACU 4211957
                               .***********************************.********98...9..689************************* PP

                                                                                                                 NC
                               ___>>>>>><___>,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]],,,,}}}- CS
               RF02543    2266 AUGACUCUCuUAAgGUAGCCAAAUGCCUCGUCAucUAAUUagUGACGCGCAUGAAUGgAuUAACgAGAUUCCcACUGUCCC 2346   
                               AU AC  UC:UAA:GUAGC AAAU CCU GUC:: UAA U ::GAC  GCA GAAUG: :UAA:GA   :C : CUGUC:C
  gi_545778205_gb_U000 4211958 AUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUC 4212038
                               ********************************************************************************* PP

                                                                                                                 NC
                               }}}}}}}}-}}}},,,,,,,,,,,.,<<<<<________>>>>>,,{{{{{{{{-{{{-{{,,,,,,{{{{-{{{{{{{,[ CS
               RF02543    2347 UAcCUACcAUCUAGCGAAACCACA.GcCAAGGGAACGGGCUUGgaAccaucAGcGGGGAAAGAAGACCCUgUUGAGCUUGA 2426   
                               :ACC:: :A:::AG GAAA    A  C   G GAA   GC   G+ACC: C:G: :G: :: AAGACCC:GU :A CUU A
  gi_545778205_gb_U000 4212039 CACCCGAGACUCAGUGAAAUUGAAcUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUA 4212119
                               *******************9977735******************************************************* PP

                                       v                 v    v                                                  NC
                               [[[---[[[[[[[,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<______........................ CS
               RF02543    2427 CUCUAGucuGgcaUUGugaagcgacauggggGgUGUAGaAUAaGUGGGAGcuuuuag........................ 2483   
                               CU UAG:: G:CA UG:::A:::A : :::: :UGUAG AUA:GUGGGAG:+UUU++                        
  gi_545778205_gb_U000 4212120 CUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAaguguggacgccagucugcaugga 4212200
                               ******************************************************997************************ PP

                                                    v    v                  v      v            v                NC
                               .>>------------>>>>>>>>>>>>>->>>>>>>>>>,,,((((~~~~~~)))),,,,,]]]]]]]----]]]],,<<< CS
               RF02543    2484 .gCGccagUGAAAUACCACuaCccccauugucgcuucaCUUAcucc*[68]*ggagGACAuugcCaggUGGGGAGUUUGgC 2625   
                                :CG+C  UGAAAUACCAC:: :::: :  U:::U:::CU AC::        ::GGACA UG:C ::UGGG AGUUUG:C
  gi_545778205_gb_U000 4212201 gCCGACCUUGAAAUACCACCCUUUAAUG-UUUGAUGUUCUAACGUU*[16]*UGCGGACAGUGUCUGGUGGGUAGUUUGAC 4212290
                               ****************************.89************975...7..589************************** PP

                                                                                                                 NC
                               <_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((((<<-<<<<<<_______>>>>>>--->><<____ CS
               RF02543    2626 uGGGGCgGcACAuCuGuuAAAuaAUAACgCaGgUGUCCUAAGGcgaGCUCAgcGaGgACAGAAAcCuCgcGUaGAgcAAAA 2706   
                               UGGGGCGG: C :CU::UAAA A UAAC::AG: G  C AAGG:::GCU:A:C :G: C GA A:C: G:G  :AG:  AA
  gi_545778205_gb_U000 4212291 UGGGGCGGU-CUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAA 4212370
                               *********.*********************************************************************** PP

                                                      v             v                                     v      NC
                               __>>,,,,)))))),,,,<<<<<<<<<_______>>>>>>>>>,<<<____>>>,]],,,,,,,,,,<<<<<<--<<<<__ CS
               RF02543    2707 GGgcAAAAGCucgCUUGAUuuccauucUCAGUAugaauggaaAccgcGAAAgcgUGGCCUAUCGAUCCUuuaguucuucaa 2787   
                                G:CA AAGC:::CUUGA:U:C: :::U A    ::: :G:A: :GCGAAAGC: G C UA  GAUCC  U:GU  :::+A
  gi_545778205_gb_U000 4212371 UGGCAUAAGCCAGCUUGACUGCGAGCGUGA-CGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGU--UCUGA 4212448
                               ***************************998.5679**************************************5..67788 PP

                                       v                                                                         NC
                               _____>>>>>>>>>>,,,,,,,...,,}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<_______>>--->>>> CS
               RF02543    2788 AaUUUgaagcuagAGGUGUCAG...AAAAGUUACCAcAGGGAUAACUGGcuUGUGGCgGCCAAGCGUUCAUAGCGACGUcG 2865   
                               A    :::GC:A  G U    G   AAAAG UAC: C:GGGAUAAC G::U : ::CG CCAAG:GUUCAUA:CGACG CG
  gi_545778205_gb_U000 4212449 AUGGAAGGGCCAUCGCUCAACGgauAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCG 4212529
                               888888899999999887654422267****************************************************** PP

                                                                                                                 NC
                               >>>-->>>>,,,,,,,,,,(((((((((((,,<<-<<<<<<______>>>>>>--->>,<<<<<_____>>>>>,,,,,)) CS
               RF02543    2866 CUUUUUgaUCCUUCGAUGUCGGCUCUUCCUAUCaUuguGAaGCAGAAuUCacaAAGuGUuGGaUUGUUCAcCCaCuAAUAG 2946   
                               :: UU:G:: C UCGAUGUCGGCUC UC :AUC:U:G: : G AG A : :C:AAG:GU::G::UGUUC::C::+UAA : 
  gi_545778205_gb_U000 4212530 GUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGU 4212610
                               ********************************************************************************* PP

                                                                                                           v     NC
                               )))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}}}}},.,,((((((((--((((,<<<<< CS
               RF02543    2947 GGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUaCUgaugga.augucguugcaAcaGcAaucca 3026   
                               GG ACG GAGCUGGGUUUA:A CGUCGUGAGACAG U: GU ::  :C::C:G :GG   UG::G::::+A::G:  :  :
  gi_545778205_gb_U000 4212611 GGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCgCUGGAGAACUGAGGGGGGCUGC 4212691
                               **********************************************************9899999999************* PP

                                                        v                    v                v                  NC
                               <<<_______________>>>>>>>><<<<<---<<<----<<<<<<<<<<<.____.>>>>>>-->>>>>--->>>-->> CS
               RF02543    3027 gccuAGUACGAGAGGAACggcugguucggAuAaUUggUuuucGcggcuGgcu.GAaa.agcCagUGccgCgAAGcuAcCaU 3105   
                               :CCUAGUACGAGAGGA CGG::  : CG:AU A UGGU U :::GG UG:C: G  A :G:CA UGCC::: AGCUA  AU
  gi_545778205_gb_U000 4212692 UCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGU-UCGGGUUGUCAuGCCAaUGGCACUGCCCGGUAGCUA-AAU 4212770
                               ****************************************.8888888877637777457788888888899*****.*** PP

                                                                                                       v       v NC
                               >>>,..<<<----<<<<<___________>>>>>---->>>,))))--..--.)))))))),,,,,,<<<<<<~~~~~~~> CS
               RF02543    3106 ccgu..uggAUuAuggCUGAAcGCCUCUAAGccaGAAuccaugCugga..Aa.gcaacgacuuuuuccccccc*[115]*g 3289   
                               :CG    :GAU+A::GCUGAA GC UCUAAGC::GAA C:  :C::GA     ::::C::C  U +C:CC::         
  gi_545778205_gb_U000 4212771 GCGGaaGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAgaU-gAGUUCUCC-CUGACUCCUUG*[  8]*G 4212850
                               ***93345579************************************9744.599999999.55555555553....5..3 PP

                                                                    vv v   v                                     NC
                               >>>>>,,,(((((<<<<<_______>>>>>,,,,<<<<<<<<<-<<--<--<<<<-<<<<<<<<______>>>>>>>>>>> CS
               RF02543    3290 gggggguugaAucccccGuAGACGACggggaUauccgaccgGGUgcUGuAAgcgguacaGcagccUuuuUgcugCgguccg 3370   
                               ::GG:        C:: G AGACGAC ::G+U +::G  C GG  :UGUAA:CG:             +U        :CG
  gi_545778205_gb_U000 4212851 AAGGAA-------CGUUGAAGACGACGACGUUGAUAGGCC-GGGUGUGUAAGCGCA---------GCGAU--------GCG 4212906
                               555554.......*******************87777655.55568********95.........45666........9** PP

                                     v      v  vv              NC
                               >>--->>---->>>->>>>>>,,,))))):: CS
               RF02543    3371 cuGAGgcUuAgCCcuggucggauagaUucgu 3401   
                               :UGAG:   A CC  G  C::AU      G 
  gi_545778205_gb_U000 4212907 UUGAGCU--AACCG-GUACUAAU------GA 4212928
                               *****75..55776.55566676......** PP

>>

RNAfold

>gi_545778205_gb_U000_133
UGAAAGUCACCUGCCUUAAUAUCUCAAAACUCAUCUUCGGGUGAUGUUUG
AGAUAUUUGCUCUUUAAAAAUCUGGAUCAAGCUGAAAAUUGAAACACUGA
ACAACGAAAGUUGUUCGUGAGUCUCUCAAAUUUUCGCAACACGAUGAUGA
AUCGUAAGAAACAUCUUCGGGUUGUGAGGUUAAGCGACUAAGCGUACACG
GUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUA
AGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGG
GAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAA
UGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAA
UCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAG
CCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUAC
AGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGU
AGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAA
GGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAG
GCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUAC
GUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGCGUACCUUUUGUAU
AAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGC
CGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCC
GAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAAC
UGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCU
GGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGC
UAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUC
GGCAAGGGGGUCAUCCCGACUUACCAACCCGAUGCAAACUGCGAAUACCG
GAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAA
GAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGU
GGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCA
GCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGC
GGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCU
UAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUG
UGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAU
AAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAAC
GUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUA
GUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGG
GGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCG
UGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAU
GACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAG
CCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGG
UCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAG
GCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAG
GUCCCUCGCGGAUGGAGCUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAA
CUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACG
GUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAG
CGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGU
CCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGG
CGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUC
GCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACC
UUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUG
GGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUA
CCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCG
GACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUA
ACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAG
UGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUG
CGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCU
CAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGU
UCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUG
GGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUAC
GCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUG
GGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUG
GACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGC
UAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCC
CGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCCUGAAGGAACGUUGAAGA
CGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAA
CCGGUACUAAUGAACCGUGAGGCUUAACCUUACAACGCCGAAGGUGUUUU
GGCGGAUUGAGAGAAGAUUUUCAGCCUGAUACAGAUUAAAUCAGAACGCA
GAAGCGGUCUGAUAAAACAGAAUUUGCCUGGCGGCAGUAGCGCGGUGGUC
CCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGG
UAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAUCAAAUU
AGAAAAACCCCGGUCCAUAAGGCCGGGGUUUUUUGCAUAUCAAUUAUUUG
CAUGAUGAAGGGAAUCUCAUGUCAGUUCUGUAUAUCCAAAUUCGUCGUAA
.(((........((...(((((((((((..(((((....)))))..))))))))))).))........((((((..(((.((((((((((....(((.(((((((....))))))))))..((((((((...(((((...(((((.....)))))..((((((((((((((((((((((((((((.....(((((.((((((((((((((((.....))).)))......((((.(((......))).....(((((((..(((.......)))......))))))).(((((...((((....))))((((((....))))))..(((((((((.........))))))))).......(((((..(((..........))).))))).)))))...((((......))))..((((((.(((((.(..(((.((.((((((((..((((......(((((((((((((.(((...((((((....))))))....(((.((((....)))).))))))...)))))))))))))...))))(((((((.((((((((.((...)).)))))))).....((((((......))))))..........(((((((((((((((((((.((((....((((((((((.............((((.....))))............(((...(((...((((((..(((.((((..((((((....))))))..))))(((((((((((....((((((.......(((((((((((((..((((..((.....))..)))).........((.(((....))).))......)))))))))))))))))))...((((((..((((((((((((((((((...((((((......))))))....))))...(((.(((((........)))))))).)).))))))))))))(((.....)))......))))))......((((((((((((((...((.((((...((((((((((((...(((((((((.......(((.(((.((((...(((((((.....))))).))...)))).)))...))).....)))))).)))...))))).......(((((((((((....)))))))))))....(((......))).(((((((......(((.(((......))).....((((..(((((.((((....)))).........((((.(((((.......))))).))))...((..(((......)))..))((((((.(((.(((((.(.((.(((((..(((.((........)).)))...((((..(((((((((....))))))))).))))....((((((((...((((.(...((((((((....))))))))).))))..))))).)))...((((......)))).......(((((((.....))))))).((.(((..(((...)))))).))...)))))..)).).))))).))).))))))((((.(((.(.(((....))).).)))..))))..(((((........)))))..(((((((((((((..((((((((.(.((..(((..((((((((((((((...))).))))))....((((.(((.((((((((((.((.....)))))))))).)).)))..)))).....(..(((((....)))))...))))))...))))).).)))........)))))..))....))))))))))))))))..)))).)))......))))))).((((.....)))).)))))))))))))...))))).))..))))))))))))).))))).((..((((....))))..)))))..))))))))).))))))))))))).....((((...(((((((((..((((.(((((..(((.(((((.........((((.(..(((((...(((....)))...))))).).)))).(((..((((((((((((..((((..(((((((((((.((....))..))))))..))))))))))))))).((((.((((((.......)))))).(((((..........)))))(((((.....)))))((((((((...(((.(((((.(((.(((((((((((.....))))).((((((........))))))......(((.(((....))).)))..((((.......)))).............))))))...)))..))))).)))....))))))))...(((((..((((((...((((((((....))))))))))))))............)))))..((((((((.((...)).)))))))).))))...)))))).)))))))))))))))).)))).)))))))))..))))(((((((...........)))))))......)))).))).)))..))))))...)))))))(((.((((....)))).)))(((((((.((((..((((....))))..)))).(((....)))(((((...)))))((((((((((.......)))))))))).((..((((..........))))..))...)))))))((((((((...((.......))...)))))))).(((((......))))))))))))..(((((((((((......)))))).)))))..)))))))).)).)))....).)).)))..))))))....(((((((....))).)))).))))..)))))))))).)))))((((((((.(..(((((((((((..((.(....).)).))))))).(((((...((((..((((((((((((....))))))..))))))..)))).)))))...(((....(((((...........)))))....))).))))....).)))))))).....(((((.((....)).))))).(((((....)))))(((((.(((((((((..((...((((((....))))))..))...))))).)).)).)).)))...))))))))))))))).))))))))))))).))))))))))))).)))))))))).)))..))))))..((((((.(((....))).))))))...((((((((((((((((((.........((((....)))).((((((((((...((.((...(((..((...))..)))...)))).))))))))))..(((.(((....))))))..))))))))))........((((((((((((((.....))))))))))))))...............((((((.((......)))))))).)))))))).........)))....... (-1281.30)

Length sequence

: 3400

Length match:

2725