JAR3D on RF03046

RF03046 Pseudomonadales-1 RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345
.(((((((..........))))))).............((((((((((((.....))))))))))))((((((((((.....))))))))))............(....(((((((((((((((((((((((....)))....))))))))))))))))))))......).......(((((((..(((.....))).)))))))
>URS0000D6B3CF_12908_1-161
CCUGUUAU---CUGACCAAUAACAGAAUGCACCACAGCGUAAAAU--CAU------------CUGAUUGGGUGAGUUGGUC-GCACCGCCAUUUG----ACGAACGAACGCCAAGCCUAAGCCGUCUU-U-GUGCAUU------AAGUGGGUAAAGG-UUGGU-UAGUAGCGGUU--UCCCC----C---ACGACAA---GGGGU
>URS0000D6942D_12908_1-162
CCUGUUAU---CUGACCAAUAACAGAAUGCACCACAGCGUAAAAU--CAU------------CUGAUUGGGUGAGUUGGUC-GCACCGCCAUUUG----ACGAACGAACGCCAAGCCUAAGCCGUCUU-U-GUGCAUU------AAGUGGGUAAAGG-UUGGUUUAGUAGCGGUU--UCCCC----C---ACGACAA---GGGGU
>URS0000D66CA6_857572_1-161
CCUGUUAU---CUGACCAAUAACAGAAUGCACCACAGCGUAAAAU--CAU------------CUGAUUGGGUGAGUUGGUC-GCACCAAUAUUUG----ACGAACGAACGCCAAGCCUAAGCCGUCUU-U-GUGCAUU------AAGUGGGUAAAGG-UUGGU-UAGUAGCGGUU--UCCCC----C---ACGACAA---GGGGU
>URS0000D66CA6_857573_1-161
CCUGUUAU---CUGACCAAUAACAGAAUGCACCACAGCGUAAAAU--CAU------------CUGAUUGGGUGAGUUGGUC-GCACCAAUAUUUG----ACGAACGAACGCCAAGCCUAAGCCGUCUU-U-GUGCAUU------AAGUGGGUAAAGG-UUGGU-UAGUAGCGGUU--UCCCC----C---ACGACAA---GGGGU
>URS0000D699B3_12908_1-160
CCUGUCG-C--UUGACCAAAGGCAGAAUGCACCAAAGCGUAAAAC--AAU------------CUGAUUGGGUGAGUUGGUC-GCACCACCAAAGA----GAGAACGAAAGCCGACACGCCUGCUGACCC-UGUGCAUU-----GGGU-GGCAGGUAUGGCGGU-UAGUAGCGUUC--GCCCACGACACA-------------GGC
>URS0000D671BD_1221247_1-172
CCCAUGC-AGUUCAUCGC-GCAUGGAUGGGAUAUGCAGGAAAUAC-----------------AUACCAGAUUGGGAGUGAU-GCCCCGCCCUAAAU---CGAGAUGAAAGCUGAAAC-GUAAAAU-ACU-GUGCCCAUC---CAGUGGUUUUAUAAAGUAAGU-GAGUAGCGGUAGGCCACAGU--ACUGUUAUAAA-GCUGUGG
>URS0000D674EE_903898_1-174
CCCAUGC-AGUUCAUCGC-GCAUGGAUGGGAUAUGCAGGAAAUAC-----------------AUACCAGAUUGGGAGUGAU-GCCCCGCCAUUAAAAU-AGAUCUGAAAGCUGAAAC-GUAAAAU-ACU-GUGCCCAUC---CAGUGAUUUUAUAAAGUAAGU-GAGUAGCGGUAGGCCACAGU--ACUGUUAUAAA-GCUGUGG
>URS0000D6B995_886890_1-174
CCCAUGC-AGUUCAUCGC-GCAUGGAUGGGAUAUGCAGGAAAUAC-----------------AUACCAGAUUGGGAGUGAU-GCCCCGCCAUUAAAAU-AGAUCUGAAAGCUGAAAC-GUAAAAU-ACU-GUGCCCAUC---CAGUGGUUUUAUAAAGUAAGU-GAGUAGCGGUAGGCCACAGU--ACUGUUAUAAA-GCUGUGG
>URS0000D6B995_1149135_1-174
CCCAUGC-AGUUCAUCGC-GCAUGGAUGGGAUAUGCAGGAAAUAC-----------------AUACCAGAUUGGGAGUGAU-GCCCCGCCAUUAAAAU-AGAUCUGAAAGCUGAAAC-GUAAAAU-ACU-GUGCCCAUC---CAGUGGUUUUAUAAAGUAAGU-GAGUAGCGGUAGGCCACAGU--ACUGUUAUAAA-GCUGUGG
>URS0000D6A00C_421052_1-175
CCCACAC-AGUUCAUCGA-GUGUGAAUAGGAUAUGCAGGAAAGUG---------------AAAAUCUAAAUUGGGAGUGAU-GCCCC-ACACAAAAUUGAAUGAUGAAACUGAAAAGUAAAGAAU-ACUG-UGCCUAUU---CAGUGGUUCUUUAAA-GUAGG-GAGUAGCUAUG--GGCCACAG-CAUAGAUCUU-CUGUGGUA
>URS0000D6C5FB_421052_1-174
CCCACAC-AGUUCAUCGA-GUGUGAAUAGGAUAUGCAGGAAAGUGAUAAUCU---------------GAAUUGGGAGUGAU-GCCCCACCAUAAA-UUGAAUGAUGAAA-CCGAAAGUAAAGAAU-ACUG-UGCCUAUU---CAGUGGUUCUUUAAAGUAGG--GAGUAGCUAUG--GACCACAG-CAUAGAUAUU-CUGUGGUA
>URS0000D6716A_12908_1-173
CCCAUGC-AGUUCAUCGA-GCAUGAAUAGGAUAUGCAGGAAAGUG----------------AAAUCAGAAUUGGGAGUGAU-GCCCCGCCGAAAAAU--CAGAACGAAACCGAAAAAUUGAUUAGUACCG-UGCCUAUU---AGGUGGCAAUCAAA--GUAGG-GAGUAGCUAUG--GACCACAGCAUAGAUCUA--CUGUGGUG
>URS0000D68A46_1217714_1-168
CCCAUGC-AGUUUAUCGC-GCAUGGAUGGGAUAUGCAGGAAAGCAAUAAU----------------CAAGUUGGGAGUGAU-GCCCCGCCAUACAUG--CAGAACGAAAGCUGAAAACUAAAAAUACUG--UGCCCAUC----CAGUGGUUUUUAAAGUAGGU-GAGUAGCGUCU--AGCCC----CGCGAGAGAUU---GGGCA
>URS0000D66378_1120927_1-174
CCCAUGC-AGUUCAUCGA-GCAUGGAUAGGAUAUGCAGGAAAGCAAGAAUCA---------------GAUUUGGGAGUGAU-GCCCCGCCAAAAAAU--GAAUACGAAAGCUGAAAACUAAAAAUACUGU--GCCUAU----CCAGUGGUUUUUAAAGUAAGC-GAGUAGCCGUG--GACCACAG-CACUGAGCUU-CUGUGGUU
>URS0000D6C480_1120927_1-174
CCCAUGC-AGUUCAUCGA-GCAUGGAUAGGAUAUGCAGGAAAGCAAGAAUCA---------------GAUUUGGGAGUGAU-GCCCCGCCAAAAAAU--GAAUACGAAAGCUGAAAACUAAAAAUACUG--UGCCUAUC----CAGUGGUUUUUAAAGUAAGC-GAGUAGCCGUG--GACCACAG-CACUGAGCUU-CUGUGGUA
>URS0000D6B657_903945_1-174
CCCGUGC-AGUUCAUCGA-GCAUGAAUAGGAUAAGCAGGAAAGCGACAAUCA---------------GACUUGGGAGUGAU-GCCCCGCCUUAAAUUA-UGAUUCGAAACCGAAAAUUGAUUAGUACC-A-UGCCUAUA---A-GGUGGCAAUCAAAG-UAGG-GAGUAGCUAUG--GACCACAG-CAUAGAGCUU-CUGUGGUG
>URS0000D6CB3B_12908_1-173
CCCAUGC-AGUUCAUCGA-GCAUGAAUAGGAUAUGCAGGAAAGUAACUAUCA---------------GAUUUGGGAGUGAU-GCCCCGCCUUAAAAU--GACAACGAAACCGAAAAUUGAUUAGUACUG--UGCCUAUU----CAGUGGCAAUCAAA-GUAGG-GAGUAGCUAUG--GACCACAGCAUAGGACUU--CUGUGGUG
>URS0000D66F03_1217656_1-173
CCCAUGC-AGUUCAUCGA-GCAUGAAUAGGAUAUGCAGGAAAGCGACAAUCA---------------GAAUUGGGAGUGAU-GCCCCGCACUAAAUU--GACAUCGAAACUGAAAAUUGAUUAGUACC-A-UGCCUAUA---A-GGUGGCAAUCAAAG-UAGG-GAGUAGCUAUG--GACCACAGCAUAGGACUU--CUGUGGUG
>URS0000D6C8DA_12908_1-175
CCCAUGU-AGUUCAUCGA-GCAUGAAUAGGAUAUGCAGGAAAGCG----------------AAAUCAGAUUUGGGGGUGAU-GCCCCGCCAUUAAAUAAGAUAAUGAAACUGAAAAUUGAUUAGUAGUG--UGCCUAUU----CACUGGCAAUCAAA-GUAGG-GAGUAGCUAUG--GACCACAGCUAUAGAUCUU-CUGUGGUG
>URS0000D6579E_903890_1-161
CCAGUAUGAUUUCGUCA-CAUGCUGAGUUAGCCUCAGAGUGCUAA------------------------UUUGUGGGUUAC-ACCCCAACCUAA-----GAA-UUGAAAGACACCAAAGCAGAUU--GAUAGCUAACU-----UUGAGAAGUGCAU-AGUGUU-GAGUAGCCUUA--GGCCACAG-UGCGGAUAAUGCUGUGGCA
>URS0000D68A8B_1217663_1-154
CCAAUGUGAUUUCGUCA-CAUAUUGAGUUAGCCUUAGAGCCAUAA------------------------AUUGUGGGUGAC-ACCCCGACUAAU-----CAAGAUGAAAGACAC--AAAGCGGAUCAA-UAGCUAACU------UUGAGAAGUUUAUUGUGUC-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC
>URS0000D6C042_1257043_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUCAA------------------------AUUGUGGGUGAC-UCCCCAACCAAU-----GGAAUUGAAAGACAC--AGAGCAGAUCAA-UAGCUAACU------UUAAAAUGUUUGUCGUGUU-GAGUAGCGGUA--GAUCAG--AU---GCCGAG---CUGAUC
>URS0000D68ECF_1217655_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCCUAA------------------------GCUGUGGGUGAC-UCCCCGACCAAA-----GAGAUUGAAAGACAC--AGAGCAGAUCAA-UAGCUAACU------UUGAGAUGUUUGUCGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D65A6F_1029823_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUCAA------------------------AUUGUGGGUGAC-ACCCCGACCAAA-----GAGAAUGAAAGACAC--AGAGCGGAUCAA-UAGCUAACU------UUGAGAUGUUUGUCGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D6C8E8_1029823_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUCAA------------------------AUUGUGGGUGAC-ACCCCGACCAAA-----GAGAAUGAAAGGCAC--AAAGCAGAUCAA-UAGCUAACU------UUGAGAUGUUUGUCGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D6D416_1217655_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUUAA------------------------AUUGUGGGUGAC-UCCCCGACCAAU-----GGAAUUGAAAGACACA--GAACAGAUCAA-UAGCUAACU------UUGAGAUGUUUGUCGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D67CCA_12908_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUUAA------------------------AGAGUGGGUGAC-GCCCCGACCAAU-----GGAAUUGAAAGACAC--AGAGCAGAUCAA-UAGCUAACU------UUGAUAUGUUUGUUGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D6636F_1217656_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUUAA------------------------AGCGUCGGUGAC-UCCCCGACCAAU-----GGAAUUGAAAGACAC--AGAGCGGAUCAA-UAGCUAACU------UUGAGAUGUUUGUUGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D6636F_12908_1-154
CCAAUGUGAUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUUAA------------------------AGCGUCGGUGAC-UCCCCGACCAAU-----GGAAUUGAAAGACAC--AGAGCGGAUCAA-UAGCUAACU------UUGAGAUGUUUGUUGUGUU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUC
>URS0000D68C36_1217655_1-159
CCUAUGUGGUUUCGUCA-CACAUUGAGUUAGCCUCAGAGCCUUAA------------------------AUUGUGGGUGAC-UCCCCGACCAAA-----GAGAUUGAAAGACACAGAGCAGAUCAAU---AGCUAACUUUGAGAAGUUUG-UUGUGUUGUGUU-GAGUAGCGGUA--GAUCGGU--A---GCCGA---GCUGAUC
>URS0000D69D41_575588_1-156
CCAGUGCGAUUUCGUCA-CGUACUGAGUGGGCCUAAGAGAAAUAC---------------------UAGAUCUGGGAUGAC-AACCCGACCCAUAC---AGG-ACGAAAGUUAAGAAGUCAGAUUGA--UAGCCCAUU-------UCGAGAUGAUGGAUUAAU-GAGUAGCGUUU--GGCCC----U---GCGAAAA---GGGCU
>URS0000D6C3DD_1173062_1-156
CCAGUGCGAUUUCGUCA-CGUACUGAGUGGGCCUAAGAGAAAUAC---------------------UAGAUCUGGGAUGAC-AACCCGACCCAUA----CAGAACGAAAGUUAAGAAGUCAGAUCGG--UAGCCCAUU-------UCGAGAUGAUGGAUUAAU-GAGUAGCGCCU--GGCCC----C---GCGGAGA---GGGCU
>URS0000D6CC49_1217693_1-156
CCAGCAUGAUUUAGUCA-CGUGCUGAGUGGGCCUAAGAGAAAUAC---------------------UAGAUCUGGGAUGAC-AACCCGACCCAUA----CAGAACGAAAGUUAAGAAGUCAGAUUGA--UAGCCCAUU-------UCGAGAUGAUGGAUUAAU-GAGUAGCGUCU--AGCCC----C---GCGGAGA---GGGCU
>URS0000D6A57D_1217693_1-163
CCAGUGCGAUUUCGUCA-CGUACUGAGUGAGCCUCAGAGUAAAUCAUAA------------------AAUUGGGGAGUGACUCUCCCGACCUUAAA---AGAAUUGAAAGCCAAGAAGUUAGAUUGA--UAGCUCAUU-------UCGAGAUGAUGGGUUGGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC
>URS0000D67B67_1217662_1-172
CCUGUGAG--UGUGCCGGCUUACAGAACAUGCCUU-GAGUAAACGCCUAGUUAUUUUAGGCAAUUCCAGCUAGGGCUUGGC-AACCCGACCUUAAU---GAGAAUGAAAGCAAGUGAAGUUGACC----GUGCAUGUA--------AGGUUGAUGU-GAUUGU-GAGUAGCGUUU--GGCCC----C---GCGGAGA---GGGCU
>URS0000D6594D_1217663_1-174
CCUGUGAG--UGUGCCAGCUUACAGAACAUGCCUU-GAGUAAACGCCUAGAUGGUUUAGGCAAUUCCAGCUAGGGCUUGGC-AACCCGACCUUAAA---GAGAAUGAAAGCAAGUAAAGUUAACC----GUGCAUGUA--------AGGUUGAUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGAUU
>URS0000D6A044_12908_1-174
CCUGUGAG--UGUGCCAGCUUACAGAACAUGCCUU-GAGUAAACGCCUAGAUGGUUUAGGCAAUUCCAGCUAGGGCUUGGC-AACCCGACCUUAAA---GAGAAUGAAAGCAAGUAAAGUUAACC----GUGCAUGUA--------AGGUUGAUGU-GAUUGU-GAGUAGCGGUA--GUUCAGU--U---GCCGA---GCUGAUU
>URS0000D68F9D_12908_1-174
CCUGUGAG--UGUGCCAGCUUGCAGUACAUGCCUU-GAGUAAAUGCCUAGAUCAUUUAGGCAAUUCCAGCUAGGGCUUGGC-AACCCGACCUUAAA---GAGAACGAAAGCAAGUGAAAUUGACC----GUGCAUGUA--------AGGUUGAUGU-GAUUGU-GAGUAGCGGUA--GUUCAGU--U---GCCGA---GCUGAUU
>URS0000D6A8B0_1071390_1-177
CCUGCAAG--UGUGCCAGCUUGCAGAACAUGCCUU-GAGUAAACGCCUAGAUGUUGUAGGCA-UUCUGGCUAGGGCUUGGC-AACCCGACCUUUAAA--GAGAGUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUUUGUGU-GAUUGU-GAGUAGU---GCGGGCCACAG-CGUAGACCA--CUGUGGC-
>URS0000D6B8AC_280145_1-157
CCUACUGG--AGUGCCGACCAGUAGAGCAUGCCUUCGAGUAAAACCACAA------------------AGCAGGGUUUGGC-AACCCGACUAAAAG---AGGAUUGAAAGCAAGUGAAGCAGACC----GCGCAUGUU--------AGGUUUGUGU-GAUUGU-GAGUAGCGGUG--GACUAGU--U---GCCGA---GCUGGUU
>URS0000D6B8AC_1217658_1-157
CCUACUGG--AGUGCCGACCAGUAGAGCAUGCCUUCGAGUAAAACCACAA------------------AGCAGGGUUUGGC-AACCCGACUAAAAG---AGGAUUGAAAGCAAGUGAAGCAGACC----GCGCAUGUU--------AGGUUUGUGU-GAUUGU-GAGUAGCGGUG--GACUAGU--U---GCCGA---GCUGGUU
>URS0000D6801E_1311804_1-168
CCUACUGG--AGUGCUGACCAGCGGAACAUGCCUUCGAGUAAACUUCCUUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGGUA--GAUCGGU--U---GCCGA---GCCGAUU
>URS0000D6AFBF_1217710_1-168
CCUACUGG--AGUGCUGACCAGUGGAACAUGCCUUUGAGUAAACUUCCUUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC
>URS0000D67783_1217663_1-168
CCUACUGG--AGUGCUGACCAGUGGAACAUGCCAUCGAGUAAACUUCCCUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---UCUGGUC
>URS0000D6BBC6_1221296_1-168
CCUGCUGG--AGUGCUGACCAGUGGAACAUGCCUUCGAGUAAACCUCCUUCGGGAAUUCAGA-------CUAGGGAGUAGC-GCCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC
>URS0000D6A3D8_1311804_1-168
CCUACUGG--AGUGCUGACCAGUGGAACAUGCCAUCGAGUAAACUUCCUUCGGGAAUCUAGA-------CCAGGGAGUAGC-GCCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCAA---GCUGGUC
>URS0000D69C77_1144673_1-168
CCUGCUGG--AGUGCUGACCAGUGGAACAUGCCAUCGAGUAAACCUCCUUCGGGAAUCUAGA-------CCAGGGAGUAGC-GCCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC
>URS0000D68C8B_1311804_1-168
CCUUCUGG--AGUGCCGAGCAGUGGAACAUGCCAUCGAGUAAACUUCCUUCGGGAAUUUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCGGACC----GUGCAUGUU--------AGGUGUGUGG-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC
>URS0000D65C61_1144662_1-166
CCUACUGG--AGUGCUGACCAGCGGAACAUGCCUUCGAGUAAACUUCCUUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGU-GUGAUUGU-GAGUAGCGUCU--GGCCC----U---GCGAAAA---GGGCU
>URS0000D68A97_1144674_1-166
CCUACUGG--AGUGCUGACCAGUGGAACAUGCCUUCGAGUAAACUUCCUUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGU-GUGAUUGU-GAGUAGCGUUU--GGCCC----U---GCGAAAA---GGGCU
>URS0000D6AEC8_12908_1-166
CCUACUGG--AGUGCAGACCAGUGGAACAUGCCUUCGAGUAAACUUCCUUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGUCU--GGCCC----C---GCGAAGA---GGGCU
>URS0000D6675C_981327_1-166
CCUGCUGG--AGUGCUGACCAGUGGAACAUGCCUUUGAGUAAACUUCCUUCGGGAAUCUAGA-------CUAGGGAGUAGC-GUCCCGACCUAAAG---AGGAUUGAAAGCAAGUAAAGCAGACC----GUGCAUGUU--------AGGUGUGUGU-GAUUGU-GAGUAGCGUCU--GGCCC----U---GCGAAAA---GGGCU
>URS0000D6C9F2_1392540_1-160
CCUGUAG--AUUUACCAC-CUACAGAACAUGCCAUCGAGUAAAACCCCGAACU----------------AGGGUUAUUGGU-AUGCCCACCUUAAU---GAA-UCGAAAGCAAGUAAAGUUAGCC----AUGCAUGUA--------GGGCGGAUGU-GAUUGU-GAGUAGCGGUG--UAUUAGC--AGUGGCCGA---GCUAAUA
>URS0000D6B762_1222033_1-161
CCUAUAGG--CUGACCA-CCUGUAGAACAUGCCAUCGAGUAAAAACCAUCCCAGU--------------AGGGUUAUUGGU-ACGCCCGCCAUUAAA--GAGAUUGAAAGCAAGUGAAAUUGACC----GUGCAUGUU--------AGGUAUGUGU-GAUUGU-GAGUAGCGGUA--GAUCAGU--U---GCCGA---GCUGGUC

There are no chains in PDB that we map to Rfam family RF03046.

Jump to results for:

Loop 1HL Column numbers: 8-19
Loop 2HL Column numbers: 50-56
Loop 3HL Column numbers: 77-83
Loop 4IL Column numbers: 105-110, 163-170
Loop 5IL Column numbers: 129-130, 139-144
Loop 6HL Column numbers: 132-137
Loop 7IL Column numbers: 184-187, 197-199
Loop 8HL Column numbers: 189-195

Loop 1 Hairpin loop

Column numbers: 8-19

    Scored sequences and counts

    
    GAUUUCGUCA-C   13

    
    -AGUUCAUCGA-    9

    
    G--AGUGCUGAC    9

    
    -AGUUCAUCGC-    4

    
    G--UGUGCCAGC    4

    
    U---CUGACCAA    4

    
    G--AGUGCCGAC    2

    
    GAUUUAGUCA-C    1

    
    GGUUUCGUCA-C    1

    
    -AGUUUAUCGC-    1

    
    G--AGUGCAGAC    1

    
    G--AGUGCCGAG    1

    
    G--UGUGCCGGC    1

    
    --AUUUACCAC-    1

    
    -C--UUGACCAA    1

    
    G--CUGACCA-C    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_18978.1 View motif instance in 3D Basepair signature: cWW-F-F-tHW-F-F-F	44.44	-16.53	5.5	4
2	Motif group HL_49941.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	42.59	-27.40	6	4	tRNA D-loop
3	Motif group HL_41543.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	37.04	-24.98	4	4
4	Motif group HL_04642.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	22.22	-22.56	6	4.5	tRNA D-loop
5	Motif group HL_45175.1 View motif instance in 3D Basepair signature: cWW-cWS-F-F	22.22	-30.86	5	3.5	tRNA D-loop
6	Motif group HL_66853.7 View motif instance in 3D Basepair signature: cWW-cWS-F-cSH	22.22	-37.77	5	3.5
7	Motif group HL_07951.3 View motif instance in 3D Basepair signature: cWW-F-F	22.22	-51.92	6	4	tRNA D-loop
8	Motif group HL_99867.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	22.22	-914.73	5	5
9	Motif group HL_23115.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	16.67	-49.92	7.5	5.5	tRNA D-loop
10	Motif group HL_20811.4 View motif instance in 3D Basepair signature: cWW-cWS-F	16.67	-92.50	5	3	tRNA D-loop

Loop 2 Hairpin loop

Column numbers: 50-56

    Scored sequences and counts

    
    UCGGGAA   11

    
    UCA----    5

    
    GAUGGUU    2

    
    GAUCAUU    1

    
    GAUGUUG    1

    
    GUUAUUU    1

    
    CCCAGU-    1

    
    AACU---    1

    
    UCU----    1

    
    Omitted sequenced and counts

    
    -------   22

    
    U------    6

    
    A------    2

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	45.83	-48.58	4	2
2	Motif group HL_37369.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F	45.83	-371.99	3.5	2.5
3	Motif group HL_50537.6 View motif instance in 3D Basepair signature: cWW-F-F-F	45.83	-2220.49	5	3	tRNA anticodon loop with synthetase
4	Motif group HL_37344.1 View motif instance in 3D Basepair signature: cWW-F-F	45.83	-2387.13	4.5	3
5	Motif group HL_97917.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	45.83	-2642.89	4	3
6	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	45.83	-3081.12	3	2	Purine riboswitch
7	Motif group HL_30680.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	45.83	-3491.90	3	2	Pseudoknot geometry
8	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	20.83	-43.56	4	3
9	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	8.33	-67.78	2	2
10	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	8.33	-101.50	5	5

Loop 3 Hairpin loop

Column numbers: 77-83

    Scored sequences and counts

    
    GUGAU-G   14

    
    GUAGC-G   11

    
    UUGGC-A    7

    
    GUGAC-U    6

    
    UGGUC-G    5

    
    AUGAC-A    3

    
    GUGAC-A    3

    
    UUGGU-A    2

    
    GUGACUC    1

    
    GUGAC-G    1

    
    GUUAC-A    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_46501.1 View motif instance in 3D Basepair signature: cWW-cWS	68.52	-12.53	3	1
2	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	53.70	-0.94	3	2
3	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	53.70	-1.12	3	2	Mini UNCG
4	Motif group HL_89199.2 View motif instance in 3D Basepair signature: cWW-F-F-F	53.70	-5.55	3	1	Mini UNCG
5	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	53.70	-9.30	2	2	tRNA D-loop
6	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	44.44	-19.75	3	2
7	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	42.59	-9.98	2	1
8	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	40.74	-3.42	3	1
9	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	31.48	-20.64	3	2
10	Motif group HL_86870.2 View motif instance in 3D Basepair signature: cWW-F-F-F	29.63	-25.53	3	2

Loop 4 Internal loop

Column numbers: 105-110, 163-170

    Scored sequences and counts

    
    UGAAAG*U-GAGUAG   33

    
    CGAAAG*U-GAGUAG    6

    
    CGAAAC*G-GAGUAG    4

    
    CGAACG*U-UAGUAG    3

    
    CGAAAG*C-GAGUAG    2

    
    UGAAAC*G-GAGUAG    2

    
    CGAACG*UUUAGUAG    1

    
    CGAAAG*U-UAGUAG    1

    
    UGAAAG*C-GAGUAG    1

    
    UGAAA-*--GAGUAG    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	100.00	92.42	1	0	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	98.15	29.36	5	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
3	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	98.15	6.38	3	2	8x7 Sarcin-Ricin; G-bulge
4	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	96.30	10.26	5	2	tSH-tSH-tHH-tHS
5	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	92.59	37.30	3	1	8x6 Sarcin-Ricin with inserted Y; G-bulge
6	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	88.89	16.68	5	2	8x6 Sarcin-Ricin with bulged A; G-bulge
7	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	88.89	9.72	5	2	7x7 Sarcin-Ricin with intercalated A; G-bulge
8	Motif group IL_87284.1 View motif instance in 3D Basepair signature: cWW-tSH-tHW-tWH-tHS-cWW	77.78	1.03	4	2	tSH-tHW-tWH-tHS
9	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	37.04	5.50	6	3	8x6 Sarcin-Ricin with inserted A; G-bulge
10	Motif group IL_16458.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-cSH-tWH-tHS-cWW	31.48	-1.74	5	3	Sarcin-Ricin target in LSU H95; G-bulge

Loop 5 Internal loop

Column numbers: 129-130, 139-144

    Scored sequences and counts

    
    UG*U---CA    2

    
    CG*U---AG    1

    
    GU*----CC    1

    
    Omitted sequenced and counts

    
    -G*------   19

    
    -U*------   17

    
    U-*C---CA    4

    
    -A*A---A-    2

    
    G-*C----C    2

    
    G-*U----C    2

    
    --*UUGAGA    1

    
    AU*-----U    1

    
    C-*-----G    1

    
    -A*------    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	73.90	1	0	Major groove platform
2	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	56.83	3	0	Single stack bend
3	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	49.46	1.5	0	Single stack bend
4	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	26.13	1	0	Major groove platform
5	Motif group IL_51454.3 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	13.11	1	0	Minor groove platform
6	Motif group IL_63775.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	13.00	3	0
7	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	75.00	39.48	2	1	Major groove intercalation
8	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	75.00	38.56	3	1
9	Motif group IL_61258.15 View motif instance in 3D Basepair signature: cWW-L-cWW	75.00	37.64	1.5	0	Single bulged C
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	75.00	33.20	2	1	Multiple bulged bases

Loop 6 Hairpin loop

Column numbers: 132-137

    Scored sequences and counts

    
    GCAUGU   20

    
    GCUAAC   11

    
    UGCCUA    8

    
    GUGCAU    5

    
    UGCCCA    5

    
    GCCCAU    3

    
    GCUCAU    1

    
    -GCCUA    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance
1	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	75.93	-0.74	3	1
2	Motif group HL_81100.2 View motif instance in 3D Basepair signature: cWW	61.11	9.12	2	1
3	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	46.30	-10.03	4	3
4	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	44.44	0.70	3	2
5	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	38.89	-1.65	3	2
6	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	37.04	-2.33	4	3
7	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	37.04	-12.72	4	3
8	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	37.04	-213.09	3	2
9	Motif group HL_71391.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	31.48	-51.65	5	3
10	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	29.63	-5.47	4	2

Loop 7 Internal loop

Column numbers: 184-187, 197-199

    Scored sequences and counts

    
    AG-C*-CU    6

    
    U--A*A-G    4

    
    AGCA*-CU    3

    
    AG-U*GCU    1

    
    AGCU*-CU    1

    
    Omitted sequenced and counts

    
    U--U*--G   21

    
    ---C*A--    8

    
    ---U*A--    4

    
    GACA*---    1

    
    C--A*--G    1

    
    U--A*--G    1

    
    U--U*--U    1

    
    ---C*U--    1

    
    --AU*---    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	66.67	0.62	3	1	Major groove platform
2	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	46.67	-27.01	3	1	Stack and bulge
3	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	40.00	-1.05	3	1	Major groove intercalation
4	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	40.00	-18.00	4	1
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	40.00	-18.69	2	1	Single bulged G
6	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	40.00	-31.97	2	1	Single stack bend
7	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	40.00	-67.99	3	1	Major groove platform
8	Motif group IL_10796.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	6.67	-59.83	5	1
9	Motif group IL_44465.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	6.67	-60.41	4	2	Isolated non-canonical cWW contact
10	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	6.67	-85.47	3	1	Isolated non-canonical cWW pair

Loop 8 Hairpin loop

Column numbers: 189-195

    Scored sequences and counts

    
    --GCCGA   23

    
    --GCGAA    5

    
    UGUUAUA    4

    
    --ACGAC    4

    
    --GCGGA    3

    
    AGGACUU    2

    
    CUGAGCU    2

    
    UAGAUCU    2

    
    AGAUCUA    1

    
    CGAGAGA    1

    
    CGGAUAA    1

    
    UAGACCA    1

    
    UAGAGCU    1

    
    UAGAUAU    1

    
    UGGCCGA    1

    
    --GCCAA    1

    
    Omitted sequenced and counts

    
    A------    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	22.64	-16.55	3	2
2	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	16.98	-35.02	2	2
3	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	15.09	-37.86	4	3
4	Motif group HL_89893.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	13.21	-78.03	5	4
5	Motif group HL_78347.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F	13.21	-92.98	4	2
6	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	11.32	-17.81	4	2
7	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	11.32	-171.98	6	5
8	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	9.43	-45.25	4	3
9	Motif group HL_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	9.43	-90.74	5	4
10	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	9.43	-109.18	2	1	GNRA

Nucleotide numbers Coloring options:

JAR3D Query RF03046-CCF-3.98 completed Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF03046 Pseudomonadales-1 RNA

Input Summary

Jump to results for:

Loop 1 Hairpin loop

Loop 2 Hairpin loop

Loop 3 Hairpin loop

Loop 4 Internal loop

Loop 5 Internal loop

Loop 6 Hairpin loop

Loop 7 Internal loop

Loop 8 Hairpin loop

JAR3D Query RF03046-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.