gi_545778205_gb_U000_297

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:

683.9

E-value:

3e-205

From sequence:

4035536

To sequence:

4037067

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 4035536 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU*[30]*AGUGGCGGA 4035639
                               ***********************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 4035640 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 4035719
                               *******************9.9********************************************9969*********** PP

                                                                         v            v                          NC
                               ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS
               RF02542     153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202    
                                                              ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :A
  gi_545778205_gb_U000 4035720 agaccaaagagggguaccuucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCA 4035800
                               ********************************************************************************* 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 4035801 CCUAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 4035880
                               *****************.*************************************************************** 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 4035881 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 4035961
                               *****************************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 4035962 A*[54]*ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 4036089
                               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 4036090 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 4036170
                               ****************************************************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 4036171 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 4036251
                               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 4036252 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 4036332
                               ********************************************************************************* 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 4036333 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 4036408
                               **********************************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 4036409 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 4036488
                               *******************************************************.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 4036489 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG*[34]*CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 4036597
                               ********************************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 4036598 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 4036678
                               *************************************************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 4036679 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 4036757
                               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 4036758 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC*[31]*UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 4036863
                               *******************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 4036864 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 4036944
                               ********************************************************************************* 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 4036945 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 4037025
                               *************99877666655555569*****************66666677899*********************** PP

                                                                          NC
                               >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS
               RF02542    1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312   
                               CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA   
  gi_545778205_gb_U000 4037026 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 4037067
                               ****************************************** PP

>>

RNAfold

>gi_545778205_gb_U000_297
GAAGCGGCACUGCUCUUUAACAAUUUAUCAGACAAUCUGUGUGGGCACUC
GAAGAUACGGAUUCUUAACGUCGCAAGACGAAAAAUGAAUACCAAGUCUC
AAGAGUGAACACGUAAUUCAUUACGAAGUUUAAUUCUUUGAGCGUCAAAC
UUUUAAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGG
CCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCU
GACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGG
GGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAA
AGAGGGGUACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUA
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
AAAGAAGCGUUCUUUGAAGUGCUCACACAGAUUGUCUGAUGAAAAUGAGC
AGUAAAACCUCUACAGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGA
UAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCUACCAAAUUUGCAC
G
....(((((((((((.((.....((((((((((((((((((((((((((((((((.(((..(((((..((((....))))...(((((((((....((........))....)).))))))).....((((((((...((((((((((((((((......)))))))))))....)))))))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.(((((((((((((((((....((((((....))))))....((((.(.....(((....)))......).))))((....)))))))).)))))...((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).)).)))))).((((((.....)))))).(((((((.......)))))))........((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).....((((..(((((((((((((....))))))))).....))))..))))....))))).))))))))).)))))))))))))))))))))))))))).))))))........(((((....))))).(((((.(((........))))))))....(((.((((((((((.......)))))..)))))))).....))).)) (-716.40)

Length sequence

: 1851

Length match:

1530