Your Settings: Query File: 1-firstRNA.struct Subject File: 1-secondRNA.struct Dissimilarity Threshold: 0.1 #====================== Query RNA ======================# >gnl|11825421 1 GAAUUCGUUUCAGUGACUUCAUUGUGAAUAAGCAGAGAACGCAGGACGUA 50 ..........(((((....)))))..(((((..(((((((((.......( 51 UUUAAAAUAUGCUGGAUAACUUCUCGCAGUGCACUUAAAGAUGCAUACGU 100 ((((........)))))........))....(((((....(((((((... 101 GUGUGCGUGGUUGUAAGUAACCUACUUUAAGUUCUUUUGGCUGCCACCAU 150 .)))))))...(((((((..(((((..............((((((..... 151 CAGCGGCAGCAACAACAAUAAUCACAGGCAGCGGCGUUGCCAGCCGCGAU 200 ....))))))................(((.(((((.......)))))((( 201 UUGUAUGCAGCAAAUUGCCAACGUCCAAGCGUUGAGUUUUUGAGUAGGAU 250 (((.......)))))))))((((......))))..........))))))) 251 UUGCAGGGGGUGUGUAAAGGGGGUUUUUUUUUUUUAUUUUUUCGGAGGAA 300 )))))..)))))..........)))))))....)))))............ #===================== Subject RNA =====================# >gi|118130856 1 GCUCGAGCUGGCGGGCGGCACAGGCAGGCAGCAGCCGCGGCAGGCGCACG 50 (((((......)))))(((....((.(((....))))).((..(((.((. 51 GGCCGCGUCAAGGGAGCCUGGGGCAGCAGGAUUCUAAGAAGAGGGGCGAG 100 ((((..(((..((((.((((......)))).))))...........(((( 101 AGGGGGCCGGGCUGGGUGGGCUAGGGGUACCGCGCUCUCCCAACAGCACG 150 ((((..(((.((((((.((((..((....))..)))).)))...))).)) 151 GGUCCUUUUUGGAAAUUAAUAUUAAAAGAAAAAAAAAAGACAGAGGGGAA 200 )..))))))))...........................)))...(((((. 201 GGUGGGAGCAAGAGAGAAGGCAAGACACACACAGAGAGAGCGAGAGACAC 250 .(((...((..............................))......))) 251 AGAUCCCCACAGUGAGAGGAAGAAAGGCCACAGUCGCAGGCAGCCGAUGU 300 ...))))).................))))...)))))..)).)))..... #################### Common Patterns (1) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 1 12 23 G A A U U C G U U U C A U G U . . . . . . . . . . ( ( ) ) . 35 278 G A A U A A G C A G U U U U U . ( ( ( ( ( . . ( ( ) ) . . . U U U A U U U U U U C G G A G . ) ) ) ) ) . . . . . . . . . 300 G A A . . . #============== Pattern Found in Subject RNA ==============# >gi|118130856 54 58 190 C G C G U A C A G A G G G G A ( . . ( ( ) ) . . . ( ( ( ( ( 203 249 A G G U A C A G A U C C C C A . . ( ( ) ) . . . ) ) ) ) ) . C A G U G A G A G G A A G A A . . . . . . . . . . . . . . . 276 A G . ) #################### Common Patterns (2) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 123 U A C U U U A A G U U C U U U ( ( ( . . . . . . . . . . . . 142 158 U G G C U A G C A A C A A C A . . ( ( ( ) ) ) . . . . . . . 176 220 222 231 A U A A U C A C A A A C G U U . . . . . . . . . ( ( ( ) ) ) 246 G A G U U U U U G A G U A . . . . . . . . . . ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 57 64 83 G U C A A G G G U C U A A G A ( ( ( . . ( ( ( ) ) ) . . . . 99 159 A G A G G G G C G A U U G G A . . . . . . . ( ( ( ) ) ) . . A A U U A A U A U U A A A A G . . . . . . . . . . . . . . . 191 A A A A A A A A A A G A C . . . . . . . . . . ) ) ) #################### Common Patterns (3) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 91 A U G C A U A C G U G U G U G ( ( ( ( ( ( ( . . . . ) ) ) ) 108 C G U ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 98 106 152 G A G A G G G G G G U C C U U ( ( ( ( ( ( ( . . . . ) ) ) ) 160 U U U ) ) ) #################### Common Patterns (4) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 115 123 246 A A G U A A C C U A G G A U U ( ( ( ( . . ( ( ( ) ) ) ) ) ) 252 U ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 62 69 78 G G G A G C C U A G G A U U C ( ( ( ( . ( ( ( ) ) ) . ) ) ) 85 U ) #################### Common Patterns (5) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 91 96 103 108 A U G C A U G U G C G U ( ( ( ( ( ( ) ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 97 102 156 161 C G A G A G U U U U U G ( ( ( ( ( ( ) ) ) ) ) ) #################### Common Patterns (6) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 116 123 246 251 A G U A A C C U A G G A U U ( ( ( . . ( ( ( ) ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 114 120 135 141 G G G U G G G C U C U C C C ( ( ( . ( ( ( ) ) ) . ) ) ) #################### Common Patterns (7) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 112 117 250 255 U G U A A G U U U G C A ( ( ( ( ( ( ) ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 98 103 155 160 G A G A G G C U U U U U ( ( ( ( ( ( ) ) ) ) ) ) #################### Common Patterns (8) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 112 117 250 255 U G U A A G U U U G C A ( ( ( ( ( ( ) ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 97 102 156 161 C G A G A G U U U U U G ( ( ( ( ( ( ) ) ) ) ) ) #################### Common Patterns (9) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 34 39 274 279 A G A G A A U U U U U U ( ( ( ( ( ( ) ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 98 103 155 160 G A G A G G C U U U U U ( ( ( ( ( ( ) ) ) ) ) ) ################### Common Patterns (10) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 34 39 274 279 A G A G A A U U U U U U ( ( ( ( ( ( ) ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 97 102 156 161 C G A G A G U U U U U G ( ( ( ( ( ( ) ) ) ) ) ) ################### Common Patterns (11) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 93 106 G C A U A C G U G U G U G C ( ( ( ( ( . . . . ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 195 201 251 258 G G G G A A G A G A U C C C C ( ( ( ( ( . . . . . ) ) ) ) ) ################### Common Patterns (12) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 140 144 156 160 G C U G C G C A G C ( ( ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 99 103 155 159 A G A G G C U U U U ( ( ( ( ( ) ) ) ) ) ################### Common Patterns (13) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 140 144 156 160 G C U G C G C A G C ( ( ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 98 102 156 160 G A G A G U U U U U ( ( ( ( ( ) ) ) ) ) ################### Common Patterns (14) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 140 144 156 160 G C U G C G C A G C ( ( ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 97 101 157 161 C G A G A U U U U G ( ( ( ( ( ) ) ) ) ) ################### Common Patterns (15) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 198 202 212 216 G A U U U A A A U U ( ( ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 99 103 155 159 A G A G G C U U U U ( ( ( ( ( ) ) ) ) ) ################### Common Patterns (16) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 198 202 212 216 G A U U U A A A U U ( ( ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 98 102 156 160 G A G A G U U U U U ( ( ( ( ( ) ) ) ) ) ################### Common Patterns (17) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 198 202 212 216 G A U U U A A A U U ( ( ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 97 101 157 161 C G A G A U U U U G ( ( ( ( ( ) ) ) ) ) ################### Common Patterns (18) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 178 180 198 200 214 218 G C A G A U A U U G C ( ( . ( ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 48 53 277 284 A C G G G C G C C A C A G U ( ( . ( ( ( ) ) ) . . . ) ) ################### Common Patterns (19) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 177 180 198 199 215 219 G G C A G A U U G C C ( ( ( . ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 102 108 150 156 G G G G G C C G G G U C C U ( ( ( . . ( ( ) ) . . ) ) ) ################### Common Patterns (20) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 177 180 198 199 215 219 G G C A G A U U G C C ( ( ( . ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 197 203 249 256 G G A A G G U A C A G A U C C ( ( ( . . ( ( ) ) . . . ) ) ) ################### Common Patterns (21) ################### #=============== Pattern Found in Query RNA ===============# >gnl|11825421 116 122 247 251 A G U A A C C G G A U U ( ( ( . . ( ( ) ) ) ) ) #============== Pattern Found in Subject RNA ==============# >gi|118130856 107 112 146 151 C C G G G C G C A C G G ( ( ( . ( ( ) ) . ) ) )