JAR3D on RF03046

RF03046 Pseudomonadales-1 RNA

Input Summary

      0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222222
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000
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.(((((((..........)))))))..........................................((.(((((((.....))))))).))...........(((...(((((((((((((((((((..(......)......))))))))))))))))))).......)))....(((((((..............)))))))
>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 2IL Column numbers: 69-71, 89-91
Loop 3HL Column numbers: 77-83
Loop 4IL Column numbers: 106-110, 163-171
Loop 5IL Column numbers: 128-131, 138-145
Loop 6HL Column numbers: 131-138
Loop 7HL Column numbers: 184-199

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 Internal loop

Column numbers: 69-71, 89-91

    Scored sequences and counts

    
    -CU*ACC    9

    
    GCU*ACC    5

    
    -AU*ACC    5

    
    -AG*ACC    4

    
    AUU*CCA    3

    
    GAU*ACC    3

    
    GAU*CCA    3

    
    GGG*CCA    3

    
    AGC*ACU    2

    
    GGG*AUA    2

    
    -CC*ACC    2

    
    AAU*ACA    1

    
    AAU*CAC    1

    
    AAU*CCA    1

    
    AAU*CCG    1

    
    ACU*CCU    1

    
    AGU*CCA    1

    
    AUU*ACC    1

    
    AUU*CCU    1

    
    GAU*CCC    1

    
    -AG*GCC    1

    
    -AU*ACU    1

    
    -GC*ACC    1

    
    -UU*ACC    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_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	83.33	-28.26	2	0	Isolated non-canonical cWW pair
2	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	70.37	-18.46	3	0	Isolated cWS basepair
3	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	68.52	-23.50	2	1	Isolated non-canonical cWW pair
4	Motif group IL_67095.2 View motif instance in 3D Basepair signature: cWW-tWW-cWW	62.96	-30.91	3	1	Isolated tWW turn
5	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	61.11	12.36	3	1	Stack and bulge
6	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	55.56	13.91	3	1
7	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	51.85	-26.69	4	1	Isolated non-canonical cWW pair
8	Motif group IL_28037.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	51.85	-59.27	3	1	Isolated non-canonical cWW pair
9	Motif group IL_10796.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	46.30	-8.03	4	1
10	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	42.59	-16.04	4	1	Major groove platform

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

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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 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: 106-110, 163-171

    Scored sequences and counts

    
    GAAAG*U-GAGUAGC   38

    
    GAAAC*G-GAGUAGC    6

    
    GAAAG*C-GAGUAGC    3

    
    GAACG*U-UAGUAGC    3

    
    GAACG*UUUAGUAGC    1

    
    GAAAG*U-GAGUAGU    1

    
    GAAAG*U-UAGUAGC    1

    
    GAAA-*--GAGUAGC    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_54041.2 View motif instance in 3D Basepair signature: cWW-L-R-L-R-tWH-L-cWW	98.15	41.53	2	1	tHW-tHW cross-strand stack
2	Motif group IL_77045.1 View motif instance in 3D Basepair signature: cWW-L-tSW-L-tHW-cWW-L	96.30	19.05	7	3	Kink-turn

Loop 5 Internal loop

Column numbers: 128-131, 138-145

    Scored sequences and counts

    
    A-UA*U------U    9

    
    CU-G*UC---CAG    4

    
    U-U-*U------A    4

    
    CUG-*UU---CAG    2

    
    C-A-*UA---A-G    2

    
    UG--*UC----CA    2

    
    UG--*UU----CA    2

    
    CCG-*UU---AGG    1

    
    GAUA*U-----UU    1

    
    UGU-*U----CCA    1

    
    CC-U*U-----GG    1

    
    Omitted sequenced and counts

    
    --GU*U-------   13

    
    --GU*A-------    4

    
    --UA*U-------    4

    
    --GC*U-------    2

    
    ---A*UUUGAGAA    1

    
    --AU*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_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	44.83	-42.39	3	2	Multiple bulged bases
2	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	44.83	-103.10	3	2	Single stack bend
3	Motif group IL_89505.4 View motif instance in 3D Basepair signature: cWW-L-cWW	44.83	-115.18	3	2	Single bulged U
4	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	44.83	-170.44	3	2	Major groove platform
5	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	37.93	-16.91	3	1	Stack and bulge
6	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	37.93	-18.23	4	1
7	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	31.03	-51.06	3	2	Multiple bulged bases
8	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	31.03	-123.91	5	2
9	Motif group IL_10569.1 View motif instance in 3D Basepair signature: cWW-L-cWW	31.03	-181.00	4	2
10	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	20.69	-49.17	3	1	Isolated non-canonical cWW pair

Loop 6 Hairpin loop

Column numbers: 131-138

    Scored sequences and counts

    
    UGCAUGUU   13

    
    AGCUAACU   11

    
    -UGCCUAU    8

    
    UGCAUGUA    5

    
    GUGCCCAU    4

    
    -GUGCAUU    4

    
    AGCCCAUU    3

    
    CGCAUGUU    2

    
    AGCUCAUU    1

    
    UGUGCAUU    1

    
    -UGCCCAU    1

    
    --GCCUAU    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 HL_85993.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	29.63	-174.42	4	3
2	Motif group HL_26934.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	22.22	-42.84	5	4
3	Motif group HL_50318.1 View motif instance in 3D Basepair signature: cWW-cSH-F-F	22.22	-67.08	5	4
4	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	20.37	-59.87	4	3
5	Motif group HL_10540.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	20.37	-61.67	5	4
6	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	20.37	-113.86	2	2	GNRA
7	Motif group HL_66103.1 View motif instance in 3D Basepair signature: cWW-F-F	16.67	-43.81	4	2
8	Motif group HL_93324.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	9.26	-69.08	4	2	Pseudoknot geometry
9	Motif group HL_38808.1 View motif instance in 3D Basepair signature: cWW-cWW	5.56	-49.84	4	4
10	Motif group HL_30680.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	5.56	-239.59	4	3	Pseudoknot geometry

Loop 7 Hairpin loop

Column numbers: 184-199

    Scored sequences and counts

    
    U--U---GCCGA---G   20

    
    U--ACUGUUAUAAA-G    4

    
    ---C---ACGACAA--    4

    
    ---U---GCGAAAA--    4

    
    ---C---GCGGAGA--    3

    
    AG-CACUGAGCUU-CU    2

    
    AGCAUAGGACUU--CU    2

    
    AG-UGCGGAUAAUGCU    1

    
    AGCUAUAGAUCUU-CU    1

    
    AG-CAUAGAGCUU-CU    1

    
    AG-CAUAGAUAUU-CU    1

    
    AG-CAUAGAUCUU-CU    1

    
    AGCAUAGAUCUA--CU    1

    
    AG-CGUAGACCA--CU    1

    
    ---CGCGAGAGAUU--    1

    
    C--AGUGGCCGA---G    1

    
    ---C---GCGAAGA--    1

    
    --AU---GCCGAG---    1

    
    U--A---GCCGA---G    1

    
    U--U---GCCAA---G    1

    
    U--U---GCCGA---U    1

    
    GACACA----------    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 HL_26934.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	40.74	-101.81	6	5
2	Motif group HL_04259.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	9.26	-188.78	4	3	GNRA with extra cWW
3	Motif group HL_93438.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	7.41	-102.41	5	5
4	Motif group HL_41464.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	7.41	-118.04	5	3.5
5	Motif group HL_81538.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F	7.41	-163.61	5	3	GNRA with tandem sheared
6	Motif group HL_78284.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F-F-F	3.70	-3929.42	6	6
7	Motif group HL_04642.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	1.85	-86.94	5	5	tRNA D-loop
8	Motif group HL_64690.6 View motif instance in 3D Basepair signature: cWW-cSW-F-F-F-F	1.85	-105.85	5	3
9	Motif group HL_40252.4 View motif instance in 3D Basepair signature: cWW-tSH-cWS-F	1.85	-107.40	6	5
10	Motif group HL_83632.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	1.85	-109.58	4	3	tRNA anticodon loop