gi_545778205_gb_U000_296

cmsearch-Rfam

Family :

SSU_rRNA_eukarya

Id:

RF01960

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea; Viroids;

Ontology:

GO:0003735 structural constituent of ribosomeRF01960

Description:

not description

Score:

685.4

E-value:

1.1e-205

From sequence:

3941813

To sequence:

3943344

Alignments:

                                                                                           v              v      NC
                               :::<<<<<_______>>>>>,{{{{{.{{{{{,{{{{{{{{[-----[[[-[[[,,<<.-<<<---~~~~~~->>>>>,,, CS
               RF02542       1 CACCAGGuUGAUUCUgCCUGAcgugg.acgCUagucuccgaGAUUaAGCCAUGCAuGc.ucgcGAA*[10]*AgcggCGaA 83     
                                A  AG UUGAU  UG CU A::U:  ACGCU G:::C:G:   UAA: CAUGCA+G:   :CG        AG: :CG+A
  gi_545778205_gb_U000 3941813 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU*[30]*AGUGGCGGA 3941916
                               ***********************99649*************8.79*************87888754...9..6889***** PP

                                                  v                v                               v             NC
                               ,,,(((,,,,,,<<<<<<<<--<<---<<<<<<<--<<<----<<<<<<<____>>>>>>>----->>>............ CS
               RF02542      84 cgGCUCAGUAauccggccccuAucUaaucgccccaugcggAUAcCcgcgguAAaccgcgGguAAuAcgc............ 152    
                               CGG U AGUAAU ::::::  A:CU+ ::G::::A  :GGAUA:C::C:G+AAAC:G::G:UAAUAC:             
  gi_545778205_gb_U000 3941917 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 3941996
                               *******************9.9********************************************9969*********** PP

                                                                         v            v                          NC
                               ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS
               RF02542     153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202    
                                                              ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :A
  gi_545778205_gb_U000 3941997 agaccaaagagggggaccuucgggccucuugCCAUCAGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCA 3942077
                               ********************************************************************************* PP

                                           v                                      v          v                   NC
                               >>>>>>>----->>>>,,,<<<<<<<<____>>>>--->>>>))),<<<<<<__________>>>>>>,<<<<____>>>> CS
               RF02542     203 ccgaggCgAugAcgGgUaACGGggaAuuagggUucgAUuCCGGAGAGGgAGCCUGAGAGAUgGCUcCCAcgUCCAAGGAcg 283    
                               CC:AGGCGA GA :::U A   ::::U AG+G:::GA :    A A: G:: CUGAGA A G ::C :AC::C+A GG::G
  gi_545778205_gb_U000 3942078 CCUAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 3942157
                               *****************.*************************************************************** PP

                                                                                                     v           NC
                               ,,,]]]]]]-],,,,,<-<<<---<<<<<.___>>>>>->>>>,}}-}}}}}},,,,,,,,,,.....,,<<<<<<_____ CS
               RF02542     284 GCAGCAGGCGCGAAAcUUgCCcAAccccc.auugggggAGGcAGucAggagacGUaaauuuaa.....gacgggcguGUAA 358    
                               GCAGCAG :G GAA +UUGC CAA::::C  ++G::::A GCAG:CA:G:::CGU++AU +A       + :GG::UGUAA
  gi_545778205_gb_U000 3942158 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 3942238
                               *****************************9999************************999998888665777777777777 PP

                                           v           v                                     v                   NC
                               _~~~~~~>>>>>>,,,..,,<<<<<<-------<<<<-----<<____>>------->>>>>>>>>>,}}}}}}}}}},,, CS
               RF02542     359 A*[ 3]*cgcccggaa..aAcuGGAGGGCAAGuCuGGUGCCAGCAgCCGCGGUAAUaCCaGCUCCaggAGcguccaugaug 434    
                               A      ::CC: + A  AA:::   GGC A  :::GUGCCAGCAGCCGCGGUAAUAC:::   ::: AGCGU :A::  +
  gi_545778205_gb_U000 3942239 A*[54]*ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 3942366
                               6...*..77777766667*****6.699999************************************************** PP

                                                                                                                 NC
                               ,,,,,,,[[[,,,,,,,((((---(((------------------------------------------------------ CS
               RF02542     435 auUGcUGCggUUAAAAaGucCGUAgUcggauaauuuuauuuuuuauuaaaaguguuuuuuuaagguguauuauauuaugua 515    
                               AUU CUG:G: UAAA  G::CG AG:CGG+U++UU++ U + +U+U+AAA+   +   +U+AA  UG  ++ U  ++  +A
  gi_545778205_gb_U000 3942367 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 3942447
                               ****************************************************99999999999666666665555555555 PP

                                                v    v          v                                         v      NC
                               -..-----------(((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>>>>>-->>,,,, CS
               RF02542     516 a..uuaagaauuuaggaccGcccggcGgccacggUAuucggcgGcgAgggGUGAAAcccgAuGACCcgccgagGAccaaCa 594    
                               +  U   +A  UU+:G: :::: G+:GG:::::  AUUC:::    AG::GUGAAA::CG +GA   :::GAGGA :A C 
  gi_545778205_gb_U000 3942448 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 3942528
                               5458999999*********************************************************************** PP

                                                   v    v                                                        NC
                               <--<<____>>>)))))))-))))))-)))---)))---)))),,,,<<<<<<---<<---<<<<_________>>>>--- CS
               RF02542     595 gAgGCGAAAGCgguggcCgagggCggauccGaugAucAAGgaCGuAaGCcgGaGgAuCGAAggcGAUUAGAuACCgccGUA 675    
                               G GGCGAA GCG::::CC:  ::::  :C:GA G:UCA G::CG+AAGC::G:GGA:C AA:::GAUUAGAUACC:::GUA
  gi_545778205_gb_U000 3942529 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 3942609
                               ********************************************************************************* PP

                                                                                                                 NC
                               >>>>>>>>,,,,,,,,,,((((((,<<<<<<<<<<......____..>>>>>>>>>>,,<<____>>...,,)))----)) CS
               RF02542     676 GuuCcgGCaGUAAACgAUGCCcAcagggcggcgcc......uuua..ggcgccgcccaagaGAAAuc...uAgUgUauGGG 745    
                               G::C::GC GUAAACGAUG:C:AC+ GG::G:  :       +    :  :C::CC +AG: AA :C   +AGU:    G:
  gi_545778205_gb_U000 3942610 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 3942685
                               **********************************9999975333.5799******************99999**9....** PP

                                                                                                                 NC
                               ),]]],<<<------<<<<____>>>>---->>>,,,,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{{{{{{{{{{,,, CS
               RF02542     746 CUccGGggguAGUAcccgcGCAAgcggGAAAcuuaAaGAAAUUGACgGAaggACACCACAAGgAgUGgAgUGuGCGGcUUA 826    
                               C :C: :GG AGUAC:::CGCAAG::: AAACU:AAA  AAUUGACGG :G::C: CACAAG::GUGGAG::UG:GG:UUA
  gi_545778205_gb_U000 3942686 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 3942765
                               *******************************************************.7************************ PP

                                                                      v               v                   v      NC
                               ,<<<<________>>>>,,,,,,,,{{{{{{{,,,...<<<<<<-~~~~~~>>>>>>,,,[[-[[[[--[[[[[[[[[,,, CS
               RF02542     827 AuuuGACUCAACGCgggacAaCUUACCagggccga...ggccccu*[20]*ggggccgaggGUGGugCAUggCCGUUcuuA 918    
                               A:::GA  CAACGC:::++A CUUACC:GG:C+       C:C:       :G:G  + +GGUG UGCAUGGC:G ::U+A
  gi_545778205_gb_U000 3942766 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG*[34]*CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 3942874
                               ********************************9886443333332...4..444457999********************* PP

                                                                                                                 NC
                               ((((((<<<____>>>.,<<<<______>>>>,,)))))),,,,,((((,..............................< CS
               RF02542     919 AcgcgUgggGUGAccu.UccggUUAAaUccgguAAcgcgUGAGAuccccg..............................c 968    
                               :C:CGUG::GUGA::U U::GGUUAA UCC:: AACG:G:G  A+CC::+                              :
  gi_545778205_gb_U000 3942875 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 3942955
                               *************************************************99999999999999999999999999999999 PP

                                                                            v                                    NC
                               <____>>,,<<<<<<<<.____>>>>>>>>,,,,,)))),,,,]]]]-]]]---]-]]]]]]],,,,,}}}}}}},,,}}- CS
               RF02542     969 cuuaaggGACccgcgcc.guaAggcgcggGAAGgaggggucaAgAACAGGuCaGuGAugCCCcuAGAUgcccuGGGCUgCA 1048   
                               C +A G:GAC:::C::: +UAA:::G:::GAAGG ::GG+  A:: CA:GUCA U AUG CCCU  A G:CC:GGGCU:CA
  gi_545778205_gb_U000 3942956 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 3943034
                               99999************99*********************************9.55*******85.89************* PP

                                                                                                                 NC
                               }}}}}}}}}},,,<<<<<<_____________~~~~~~>>>>>>..,,,,<---<<<<<<<<______..>>>>>>>>--- CS
               RF02542    1049 CGCgCAcUaCAaUggccgcuugaaauauaaua*[ 8]*gcggcc..aauuGGGAcuggccccUGUAAu..ggggccagGAA 1127   
                               C:CG::CUACAAUG:C:::U+ AAA A AA        :::G:C  A+U :GGA:UGG:::CUG AA   G:::CCA:GAA
  gi_545778205_gb_U000 3943035 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC*[31]*UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 3943140
                               *******************9888877766554...6..******999999*****************888*********** PP

                                                      v       v                                               v  NC
                               >,,,,,}}}}},,,,,<<<<<<<<_______>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,,,<<-<<-<-<<<<<< CS
               RF02542    1128 CguGGAAuUcCUAGUAgucgcgcgUCAuuAAcgcgcgacGAAUguGUCCCUGUccuUuGUACACACCGcCCGUCGcuAuCu 1208   
                               :  GGAAU::CUAGUA: CG:G: UCA  A  :C:CG :GAAU+ GU CC:G::C: UGUACACACCGCCCGUC+C::: :
  gi_545778205_gb_U000 3943141 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 3943221
                               ********************************************************************************* PP

                                               v vvvv                           vvvv v                 v         NC
                               <<--<<<<<<<<<<<<<<<<<<<<____...................>>>>>>>>>>>>>>>>>>>>-->>>>>>>>-->- CS
               RF02542    1209 cAGAuggcugcccgggcgaagagcuuaa...................gcucugagcccgggcagcuaGAUgaGaUagAAGU 1270   
                                :GA  G ::::C::: G    ::+UA                    ::    A :::G:::: C  GA: : :::GAAGU
  gi_545778205_gb_U000 3943222 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 3943302
                               *************99877666655555569*****************66666677899*********************** PP

                                                                          NC
                               >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS
               RF02542    1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312   
                               CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA   
  gi_545778205_gb_U000 3943303 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 3943344
                               ****************************************** PP

>>

RNAfold

>gi_545778205_gb_U000_296
AAAGCGGCACUGCUCUUUAACAAUUUAUCAGACAAUCUGUGUGGGCACUC
GAAGAUACGGAUUCUUAACGUCGCAAGACGAAAAAUGAAUACCAAGUCUC
AAGAGUGAACACGUAAUUCAUUACGAAGUUUAAUUCUUUGAGCAUCAAAC
UUUUAAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGG
CCUAACACAUGCAAGUCGAACGGUAACAGGAAACAGCUUGCUGUUUCGCU
GACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGG
GGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAA
AGAGGGGGACCUUCGGGCCUCUUGCCAUCAGAUGUGCCCAGAUGGGAUUA
GCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCU
GAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACG
GGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCC
AUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGG
GAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAA
GAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCA
AGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAA
GUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGG
CAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAA
UGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGA
AGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACC
CUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAG
GCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGC
CGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGA
GCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACA
UCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACA
GGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUC
CCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAA
CUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCA
AGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCA
UACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUC
GUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUA
GUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACA
CACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUA
ACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUC
GUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUACCUU
AAAGAAGCGUUCUUUGCAGUGCUCACACAGAUUGUCUGAUAGGAAGUGAA
AAGCAAGGCGUCUUGCGAAGCAGACUGAUACGUCCCCUUCGUCUAGAGGC
CCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGG
G
..........((((.((((....((((((((((((((((((((((((((((((((.(((..(((((..((((....))))...(((((((((....((........))....)).))))))).....((((((((...((((((((((((((((......)))))))))))....)))))))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.....(((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).))))))).((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).))...((((.((((((.....)))))).(((((((.......)))))))........)))).(((((((((.....(((..((...(((....)))...))....))).....)))))))))..(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).....((((..(((((((((((((....))))))))).....))))..))))....))))).))))))))).))))))))))))))))))))))))))...)))).)))).(((.(((.((((((..(((......)))..))))))..))).)))......((((((.......))))))...(((((.......)))))..... (-720.40)

Length sequence

: 1851

Length match:

1530