gi_545778205_gb_U000_294

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:

683.4

E-value:

4.2e-205

From sequence:

2731152

To sequence:

2729621

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 2731152 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU*[30]*AGUGGCGGA 2731049
                               ***********************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 2731048 CGGGUGAGUAAUGUCUGGGA-AGCUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaaugucgca 2730969
                               *******************9.*********************************************9969*********** PP

                                                                         v            v                          NC
                               ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS
               RF02542     153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202    
                                                              ::::C::AUG  :::::: :::AU AGCU+GU:GGU: GGUAA GGC :A
  gi_545778205_gb_U000 2730968 agaccaaagagggggaccuucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUUGUUGGUGGGGUAACGGCUCA 2730888
                               ********************************************************************************* 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 2730887 CCAAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 2730808
                               *****************.*************************************************************** 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 2730807 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 2730727
                               *****************************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 2730726 A*[54]*ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 2730599
                               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 2730598 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 2730518
                               ****************************************************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 2730517 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 2730437
                               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 2730436 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 2730356
                               ********************************************************************************* 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 2730355 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 2730280
                               **********************************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 2730279 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 2730200
                               *******************************************************.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 2730199 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG*[34]*CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 2730091
                               ********************************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 2730090 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 2730010
                               *************************************************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 2730009 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 2729931
                               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 2729930 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC*[31]*UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 2729825
                               *******************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 2729824 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 2729744
                               ********************************************************************************* 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 2729743 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 2729663
                               *************99877666655555569*****************66666677899*********************** PP

                                                                          NC
                               >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS
               RF02542    1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312   
                               CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA   
  gi_545778205_gb_U000 2729662 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 2729621
                               ****************************************** PP

RNAfold

>gi_545778205_gb_U000_294
CGCGUUGCGUGAUAUUUUCGUGUAGGGUGAGCUUUCAUUAAUAGAAAGCG
AACGGCCUUAUUCUCUUCAGCCUCACUCCCAACGCGUAAACGCCUUGCUA
UUCACUUUUCAUCAGACAAUCUGUGUGAGCACUGCAAAGUACGCUUCUUU
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
UAAUCCCAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAAGGUCCCCCUCU
UUGGUCUUGCGACAUUAUGCGGUAUUAGCUACCGUUUCCAGUAGUUAUCC
CCCUCCAUCAGGCAGCUUCCCAGACAUUACUCACCCGUCCGCCACUCGUC
AGCGAAGCAGCAAGCUGCUUCCUGUUACCGUUCGACUUGCAUGUGUUAGG
CCUGCCGCCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUCAAUUUAAAA
GUUUGAUGCUCAAAGAAUUAAACUUCGUAAUGAAUUACGUGUUCACUCUU
GAGACUUGGUAUUCAUUUUUCGUCUUGCGACGUUAAGAAUCCGUAUCUUC
GAGUGCCCACACAGAUUGUCUGAUAAAUUGUUAAAGAGCAGUGCCGCUUC
G
(((((((.((((.........(((((((..((((((.......)))))).....)))))))...........))))...))))))).....((.(((((.((.((..((.(((((((((((((((((.(((((..((.(((((.(((((....((((.((((((.....((((.(((....))).)))))))))).))))((((.......))))((((((..((((((((...(((.........((((......))))........)))...)))))....(((((.((((((.(((((((((((((((((((((....))).))).)))....(((((...)))))..((((((.(.(((((((((((((.(.((((.((..(((.....))))).)))).)))))))))))))).)(((((....)))))))))))....))))))))))))......(((((.((((((((((((((.....))))).((((((.....)))))).........(((((((.....))))).))..(((((((.....(((((......)))))...)))))))...))))))))).)).)))(((......)))............((((((((((.((((((((((((((.(.((((...((((....((((((.......(((((.((........)).)))))....((((......))))(((((.((((.............((((.((......)).))))(((....)))((((.....))))............(((((((.((....)))))))))......((.((((((((((..(((((((((...(((......)))....((.(((...))).))))))))).))..((((((.....))))))..........((((((........)))))).(((((.(((..(((((((((..........)))......(((((.....((.((........))))...))))).......))))))..))))))))......(((((((((((((((.(((((((.(((...))).)))))))...)))))))...........((..((((.((..((((.....))))...))....))))..)).....((((......)))).))))))))))))))))))))((((((..((.(((((..........(((.((((.......)))).)))........))))).))))))))....)))).))))))))))).....)).)).)))).))))))))..)))((((((.....))))))...(((..(((.((((.....)))).)))..)))...)))))))))))..)))(((((((((.........)))))))))(((((....((.((((((...........))))))...))..))))).((((((.....(((((((...((((((.(((((......)))))))))))((........))((...(((((((........)))))))...))..))))).))......)))))).........))))))))))).....(((.(((((((....)))))))))).....(((((..(((.((((....((....))....)))).)))..)))))....((((((((.((......)).)))))))).(((((.((....(((..(((((....))))).)))...)))))))..)))..))))))....((((....))))..)))))..))))).))..))))).))))))))))))))))).))..)).))..))))).))....... (-600.80)

Length sequence

: 1851

Length match:

1530