gi_545778205_gb_U000_305

cmsearch-Rfam

Family :

SSU_rRNA_microsporidia

Id:

RF02542

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea; Viroids;

Ontology:

GO:0003735 structural constituent of ribosomeRF02542

Description:

not description

Score:

729.8

E-value:

4.9e-222

From sequence:

4166664

To sequence:

4168195

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 4166664 GAAGAGUUUGAUCAUGGCUCAGAUUGaACGCUGGCGGCAGGC-CUAACACAUGCAAGUcGAACGGU*[30]*AGUGGCGGA 4166767
                               ***********************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 4166768 CGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGcauaacgucgca 4166847
                               *******************9.9********************************************9969*********** PP

                                                                         v            v                          NC
                               ...............................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>> CS
               RF02542     153 ...............................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUA 202    
                                                              ::::C::AUG: :::::: :::AU AGCUAGU:GGU: GGUAA GGC :A
  gi_545778205_gb_U000 4166848 agaccaaagagggggaccuucgggccucuugCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCA 4166928
                               ********************************************************************************* 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 4166929 CCUAGGCGACGAUCCCU-AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAG 4167008
                               *****************.*************************************************************** 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 4167009 GCAGCAGUGGGGAAUAUUGCACAAUGGGCgCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGaaggcCUUCGGGUUGUAA 4167089
                               *****************************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 4167090 A*[54]*ACCCGCAGAagAAGCAC-CGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGA 4167217
                               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 4167218 AUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGA 4167298
                               ****************************************************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 4167299 UacUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG 4167379
                               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 4167380 GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUA 4167460
                               ********************************************************************************* 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 4167461 GUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUgcccuuGAG-gcGUGGCUUCCGGAGCUAACGCguuAAGUC----GA 4167536
                               **********************************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 4167537 CCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCG-CACAAGCGGUGGAGCAUGUGGUUUA 4167616
                               *******************************************************.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 4167617 AUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGacaUCCACGG*[34]*CGUGAGACAGGUGCUGCAUGGCUGUCGUCA 4167725
                               ********************************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 4167726 GCUCGUGUUGUGAAAUgUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAuccuuuguugccagcgguccggccgggaacU 4167806
                               *************************************************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 4167807 CAAAGGAGACUGCCAGUgAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA-UCAUGGCCCUU-ACGACCAGGGCUACA 4167885
                               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 4167886 CACGUGCUACAAUGGCGCAUACAAAGAGAAGC*[31]*UGCGUCguAGUCCGGAUUGGAGUCUGCAACucGACUCCAUGAA 4167991
                               *******************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 4167992 GUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAU 4168072
                               ********************************************************************************* 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 4168073 GGGAGUGGGUUGCAAAAGAAGUAGGUAGcuuaaccuucgggagggcgCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGU 4168153
                               *************99877666655555569*****************66666677899*********************** PP

                                                                          NC
                               >>-->>,,,,<<<<<<<<<<____>>>>>>>>>>:::::::: CS
               RF02542    1271 CGUAaCAAGGcugCugucGGaGAACCggcaGcagGAUCAuua 1312   
                               CGUAACAAGG:::C:GU:GG GAACC:GC:G:::GAUCA   
  gi_545778205_gb_U000 4168154 CGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCU 4168195
                               ****************************************** PP

>>

RNAfold

>gi_545778205_gb_U000_305
AAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAU
GCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGC
GGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUAC
UGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGAC
CUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGU
GGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGA
CCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCA
GUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUG
UAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGA
GUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGG
CUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUC
GGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUG
AAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAG
UCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGA
UCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGC
UCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCC
ACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUC
CGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUA
AAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUU
UAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAG
UUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAU
GGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAG
CGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAG
ACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUG
GCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGA
AGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGA
UUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGG
AUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGU
CACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGA
GGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGU
AACCGUAGGGGAACCUGCGGUUGGAUCACCU
....((((((((........))))))))((((.((((..((.........))..))))..))))..((((((((((....))))))).)))((((.((((((.((((((..(((.(((((((((.(((((((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))...((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).)).)))))).((((((.....)))))).(((((((.......)))))))........((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..))))...))))....(((((((((((((....))))))))).....)))) (-586.30)

Length sequence

: 1531

Length match:

1530