gi_545778205_gb_U000_295

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:

684.3

E-value:

2.2e-205

From sequence:

3428757

To sequence:

3427226

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 3428757 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU*[30]*AGUGGCGGA 3428654
                               ***********************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 3428653 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 3428574
                               *******************9.9********************************************9969*********** PP

                                                                         v            v                          NC
                               ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS
               RF02542     153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202    
                                                              ::::C::AUG: :::::: :::AU AGCU+GU:GGU: GGUAA GGC :A
  gi_545778205_gb_U000 3428573 agaccaaagagggggacccucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUUGUUGGUGGGGUAACGGCUCA 3428493
                               ********************************************************************************* 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 3428492 CCAAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 3428413
                               *****************.*************************************************************** 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 3428412 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 3428332
                               *****************************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 3428331 A*[54]*ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 3428204
                               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 3428203 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 3428123
                               ****************************************************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 3428122 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 3428042
                               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 3428041 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 3427961
                               ********************************************************************************* 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 3427960 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 3427885
                               **********************************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 3427884 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 3427805
                               *******************************************************.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 3427804 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG*[34]*CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 3427696
                               ********************************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 3427695 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 3427615
                               *************************************************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 3427614 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 3427536
                               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 3427535 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC*[31]*UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 3427430
                               *******************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 3427429 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 3427349
                               ********************************************************************************* 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 3427348 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 3427268
                               *************99877666655555569*****************66666677899*********************** PP

                                                                          NC
                               >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS
               RF02542    1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312   
                               CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA   
  gi_545778205_gb_U000 3427267 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 3427226
                               ****************************************** PP

>>

RNAfold

>gi_545778205_gb_U000_295
GUGCAAAUUUGGUAGGCCUGAGUGGACUUGAACCACCGACCUCACCCUUA
UCAGGGGUGCGCUCUAACCACCUGAGCUACAAGCCUGUAGAGGUUUUACU
GCUCAUUUUCAUCAGACAAUCUGUGUGAGCACUGCAAAGUACGCUUCUUU
AAGGUAAGGAGGUGAUCCAACCGCAGGUUCCCCUACGGUUACCUUGUUAC
GACUUCACCCCAGUCAUGAAUCACAAAGUGGUAAGCGCCCUCCCGAAGGU
UAAGCUACCUACUUCUUUUGCAACCCACUCCCAUGGUGUGACGGGCGGUG
UGUACAAGGCCCGGGAACGUAUUCACCGUGGCAUUCUGAUCCACGAUUAC
UAGCGAUUCCGACUUCAUGGAGUCGAGUUGCAGACUCCAAUCCGGACUAC
GACGCACUUUAUGAGGUCCGCUUGCUCUCGCGAGGUCGCUUCUCUUUGUA
UGCGCCAUUGUAGCACGUGUGUAGCCCUGGUCGUAAGGGCCAUGAUGACU
UGACGUCAUCCCCACCUUCCUCCAGUUUAUCACUGGCAGUCUCCUUUGAG
UUCCCGGCCGGACCGCUGGCAACAAAGGAUAAGGGUUGCGCUCGUUGCGG
GACUUAACCCAACAUUUCACAACACGAGCUGACGACAGCCAUGCAGCACC
UGUCUCACGGUUCCCGAAGGCACAUUCUCAUCUCUGAAAACUUCCGUGGA
UGUCAAGACCAGGUAAGGUUCUUCGCGUUGCAUCGAAUUAAACCACAUGC
UCCACCGCUUGUGCGGGCCCCCGUCAAUUCAUUUGAGUUUUAACCUUGCG
GCCGUACUCCCCAGGCGGUCGACUUAACGCGUUAGCUCCGGAAGCCACGC
CUCAAGGGCACAACCUCCAAGUCGACAUCGUUUACGGCGUGGACUACCAG
GGUAUCUAAUCCUGUUUGCUCCCCACGCUUUCGCACCUGAGCGUCAGUCU
UCGUCCAGGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCA
UUUCACCGCUACACCUGGAAUUCUACCCCCCUCUACGAGACUCAAGCUUG
CCAGUAUCAGAUGCAGUUCCCAGGUUGAGCCCGGGGAUUUCACAUCUGAC
UUAACAAACCGCCUGCGUGCGCUUUACGCCCAGUAAUUCCGAUUAACGCU
UGCACCCUCCGUAUUACCGCGGCUGCUGGCACGGAGUUAGCCGGUGCUUC
UUCUGCGGGUAACGUCAAUGAGCAAAGGUAUUAACUUUACUCCCUUCCUC
CCCGCUGAAAGUACUUUACAACCCGAAGGCCUUCUUCAUACACGCGGCAU
GGCUGCAUCAGGCUUGCGCCCAUUGUGCAAUAUUCCCCACUGCUGCCUCC
CGUAGGAGUCUGGACCGUGUCUCAGUUCCAGUGUGGCUGGUCAUCCUCUC
AGACCAGCUAGGGAUCGUCGCCUUGGUGAGCCGUUACCCCACCAACAAGC
UAAUCCCAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAGGGUCCCCCUCU
UUGGUCUUGCGACGUUAUGCGGUAUUAGCUACCGUUUCCAGUAGUUAUCC
CCCUCCAUCAGGCAGUUUCCCAGACAUUACUCACCCGUCCGCCACUCGUC
AGCGAAACAGCAAGCUGUUUCCUGUUACCGUUCGACUUGCAUGUGUUAGG
CCUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAAUUUAAAA
GUUUGAUGCUCAAAGAAUUAAACUUCGUAAUGAAUUACGUGUUCACUCUU
GAGACUUGGUAUUCAUUUUUCGUCUUGCGACGUUAAGAAUCCGUAUCUUC
GAGUGCCCACACAGAUUGUCUGAUAAAUUGUUAAAGAGCAGUUGCGACGC
G
((((((....((((((..((.((((.......)))))).))).)))....((((((((........))).))))).....((((((....))))))..((((((.((..((((((((((((((((((.(((((..((.(((((.(((((....((((.((((((.....((((.(((....))).)))))))))).))))((((.......))))((((((..((((((((...(((.........((((......))))........)))...)))))....(((((.((((((.(((((((((((((((((((((....))).))).)))....(((((...)))))..((((((.(.(((((((((((((.(.((((.((..(((.....))))).)))).)))))))))))))).)(((((....)))))))))))....))))))))))))......(((((.((((((((((((((.....))))).((((((.....)))))).........(((((((.....))))).))..(((((((.....(((((......)))))...)))))))...))))))))).)).)))(((......)))............((((((((((.((((((((((((((.(.((((...((((....((((((.......(((((.((........)).)))))....((((......))))(((((.((((.............((((.((......)).))))(((....)))((((.....))))............(((((((.((....)))))))))......((.((((((((((..(((((((((...(((......)))....((.(((...))).))))))))).))..((((((.....))))))..........((((((........)))))).(((((.(((..(((((((((..........)))......(((((.....((.((........))))...))))).......))))))..))))))))......(((((((((((((((.(((((((.(((...))).)))))))...)))))))...........((..((((.((..((((.....))))...))....))))..)).....((((......)))).))))))))))))))))))))((((((..((.(((((..........(((.((((.......)))).)))........))))).))))))))....)))).))))))))))).....)).)).)))).))))))))..)))((((((.....))))))...(((..(((.((((.....)))).)))..)))...)))))))))))..)))(((((((((.........)))))))))(((((....((.((((((...........))))))...))..))))).((((((.((..(((((((...((((((.(((((...)))))...))))))((........))((...(((((((........)))))))...))..))))).))..))..)))))).........))))))))))).....(((.(((((((....)))))))))).....(((((..(((.((((....((....))....)))).)))..)))))....((((((((.((......)).)))))))).(((((.((....(((..(((((....))))).)))...)))))))..)))..))))))....((((....))))..)))))..))))).))..))))).)))))))))))))))).....))..)).)))))))))).))... (-608.70)

Length sequence

: 1851

Length match:

1530