comRNA_72bf_250 ../s15_11seq_220.fa -P 0.5 -S 0.56 PARAMETERS: L = 4, Minimum length of a straight stem; E = -5.00 kcal/mol, Maximum stem energy allowed for a stem to be analyzed, in kcal/mol; S = 0.56, Minimum similarity score between two stems; P = 0.50, Minimum percentage of seqs in which common structure should occur; n = 10, Number of common structures to be reported; wa = 0.25, Weight factor for stem_position; wb = 0.25, Weight factor for stem_seq_identity; wc = 0.25, Weight factor for loop_seq_identity; wd = 0.125, Weight factor for stem_length; we = 0.125, Weight factor for stem_energy; m = 4, Maximum number of overlapping nt allowed between two stems; c = 0.30, Maximum percentage of overlap allowed between two stems; j = 0.70, Maximum percentage of overlap allowed between two different cliques; r = 0.40, Minimum percentage of similar stems for two cliques to be considered same when reporting structures; f = 10, Length of flanking nt of a stem to be refolded during structure refinement; v = 5, Maximum relaxation length of a loop from its original structure pattern; a = 1, Use anchor seqs; g = 0, Use topological sort to assemble stem blocks; Sequence file name: "../s15_11seq_220.fa" Sequences loaded ... 1 E.coli 185 nt 2 S.typhi 186 nt 3 S.typhimuriu 186 nt 4 S.paratyphi 187 nt 5 K.pneumonia 188 nt 6 H.influenzae 172 nt 7 Y.pesits 185 nt 8 P.multocida 204 nt 9 A.actin 177 nt 10 V.cholerae 178 nt 11 P.aeruginosa 196 nt Number of stems in each energy bin for each sequence: energy[kc/m] -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 E.coli 2 3 5 4 20 27 41 27 40 5 6 7 S.typhi 7 3 11 16 13 36 33 28 46 2 6 2 S.typhimuriu 7 3 11 16 13 36 33 28 46 2 6 2 S.paratyphi 8 4 9 16 14 35 33 28 46 2 6 2 K.pneumonia 5 4 9 17 20 26 38 55 69 7 3 2 H.influenzae 3 2 3 5 18 23 33 42 45 3 5 0 Y.pesits 8 2 4 9 18 22 30 44 54 6 8 10 P.multocida 7 5 2 14 20 45 43 65 78 13 7 0 A.actin 4 4 9 4 5 22 25 40 33 3 1 1 V.cholerae 6 1 2 11 19 30 32 20 16 5 2 3 P.aeruginosa 10 7 13 22 24 34 33 26 19 8 5 3 Pairwise Sequence Identity (%): 1 2 3 4 5 6 7 8 9 10 11 1 - 88 88 90 75 62 60 64 62 53 49 2 88 - 100 100 75 61 63 63 61 54 50 3 88 100 - 100 75 61 63 63 61 54 50 4 90 100 100 - 77 60 63 64 61 54 49 5 75 75 75 77 - 57 61 62 63 56 54 6 62 61 61 60 57 - 61 72 68 59 54 7 60 63 63 63 61 61 - 57 62 55 48 8 64 63 63 64 62 72 57 - 71 65 46 9 62 61 61 61 63 68 62 71 - 61 48 10 53 54 54 54 56 59 55 65 61 - 55 11 49 50 50 49 54 54 48 46 48 55 - Comparing stems pairwise ... Number of edges that has stem-similarity-score higher than a certain threshold in the stem graph: Score: 0.8 0.78 0.76 0.74 0.72 0.7 0.68 0.66 0.64 0.62 0.6 0.58 0.56 0.54 0.52 0.5 0.48 0.46 0.44 0.42 0.4 0.38 0.36 0.34 0.32 0.3 Num of edges: 30 33 38 50 73 99 127 166 216 316 483 855 1402 2323 3630 5715 8651 12907 18601 26065 35146 45768 57291 69384 81265 92554 123035 Time spent on comparing stems: 14.9 seconds user CPU time; 14.9 seconds real time. =========================== S = 0.56 =========================== Find conserved stems (cliques) ... ==== 74 cliques ==== 29 unique ==== Time spent on finding conserved stems: 0.08 sec CPU time; 0.09 sec clock time. Construct clique topological graph ... ==== 47 edges ==== Assemble conserved stems (cliques) ... ==== 50 structures ==== Time spent on topologically assembling conserved stems: 0.01 sec CPU time; 0.01 sec clock time. Report top 10 structures. ------------------------------------------- Structure #1: Score = 19.8, pattern: 01, path: 4 1 0 , comseq: 2 3 4 5 7 8 , incompatible_seq: 4() 1() 0() (a) Clique 4: OriginalScore = 4.43, ModifiedScore = 4.43 2, S.typhi 43 CGCCGC 48 ... 80 GCGGCG 85 [-13.7 kc/m] 3, S.typhimuriu 43 CGCCGC 48 ... 80 GCGGCG 85 [-13.7 kc/m] 4, S.paratyphi 44 CGCCGC 49 ... 81 GCGGCG 86 [-13.7 kc/m] 5, K.pneumonia 51 UAACGUCCG 59 ... 80 CGGGCGUUG 88 [-14.2 kc/m] 7, Y.pesits 24 GUAGGCC 30 ... 77 GGCUUAC 83 [-11.9 kc/m] 8, P.multocida 52 UGACAAAG 59 ... 101 CUUUGUCG 108 [-10.9 kc/m] 11, P.aeruginosa 17 GUGACCGA 24 ... 55 UCGGUCAU 62 [-14.4 kc/m] (b) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 2, S.typhi 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 3, S.typhimuriu 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 4, S.paratyphi 98 CGCUGA 103 AUUAGAGA 112 UCGGCG 117 [-10.8 kc/m] 5, K.pneumonia 100 GCUGA 104 AUUAGAGA 113 UCGGC 117 [-8.8 kc/m] 6, H.influenzae 77 UCGCUGA 83 GUUAGAGA 92 UCGGCGA 98 [-13.1 kc/m] 7, Y.pesits 93 UGCUGA 98 AUUAGAGA 107 UCGGCG 112 [-10 kc/m] 8, P.multocida 109 UAGCUGG 115 AUUAGAGA 124 UCGGCUA 130 [-10.7 kc/m] 9, A.actin 82 UAGCUGA 88 AUUAGAGA 97 UCGGCUA 103 [-11.6 kc/m] 10, V.cholerae 79 GUGUCGGCUGA 89 AUCAGAGA 98 UUGGCUGACAC 108 [-18 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaa aaaaaaa aaa aaa aaaaaaa aaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaaaa aaaaa aa aaa a aaaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaaaa aaaaa aa aaa a aaaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaaaa aaaaa aa aaa a aaaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaaaaaa aaaaaaaaa bbbbbb bbbbb cccccccbbbbbbbbbbb ccccccc H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaaaaa aaa aaa aaaaaaaa bbbbbbbbbbbb cccccccbbbbbbb bbbbb ccccccc Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 aaaaaaa aaa a a aaa aaaaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 aaaaaaaa aaaaaaaabbbbbbb cccccccbbbbbbb ccccccc A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 aaaaaa a aaaa aaaa a a aaaaa bbbbbbbbbbbb cccccccbbbbbb bbbbbb ccccccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 aaaaaaaaaa a a aaaaaaaaaa bbbbbbbbbb ccccccccbbbbbbbbbb cccccccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 aaaaaaaa a aaa aa aa aaa aaaaaaaaa bbbbbbbbbbbb cccccccbbbbbbbb bbbb ccccccc ------------------------------------------- Structure #2: Score = 19, pattern: 41, path: 14 1 0 , comseq: 1 2 3 4 5 6 , incompatible_seq: 14() 1() 0() (a) Clique 14: OriginalScore = 3.66, ModifiedScore = 3.66 1, E.coli 14 GCGAU 18 ... 179 AUCGU 183 [-7.3 kc/m] 2, S.typhi 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 3, S.typhimuriu 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 4, S.paratyphi 15 GCGAU 19 ... 181 AUCGU 185 [-7.3 kc/m] 5, K.pneumonia 15 GCGAU 19 ... 182 AUCGU 186 [-7.3 kc/m] 6, H.influenzae 12 GCGGU 16 ... 166 AUCGU 170 [-6.5 kc/m] (b) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 2, S.typhi 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 3, S.typhimuriu 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 4, S.paratyphi 98 CGCUGA 103 AUUAGAGA 112 UCGGCG 117 [-10.8 kc/m] 5, K.pneumonia 100 GCUGA 104 AUUAGAGA 113 UCGGC 117 [-8.8 kc/m] 6, H.influenzae 77 UCGCUGA 83 GUUAGAGA 92 UCGGCGA 98 [-13.1 kc/m] 7, Y.pesits 93 UGCUGA 98 AUUAGAGA 107 UCGGCG 112 [-10 kc/m] 8, P.multocida 109 UAGCUGG 115 AUUAGAGA 124 UCGGCUA 130 [-10.7 kc/m] 9, A.actin 82 UAGCUGA 88 AUUAGAGA 97 UCGGCUA 103 [-11.6 kc/m] 10, V.cholerae 79 GUGUCGGCUGA 89 AUCAGAGA 98 UUGGCUGACAC 108 [-18 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc aaaaa S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc aaaaa S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc aaaaa S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbb bbbbbb cccccccbbbbbbbbbb ccccccc aaaaa K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaa bbbbbb bbbbb cccccccbbbbbbbbbbb ccccccc aaaaa H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaa bbbbbbbbbbbb cccccccbbbbbbb bbbbb ccccccc aaaaa Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 bbbb bbbbbb cccccccbbbbbbbbbb ccccccc P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 bbbbbbbbbbbb cccccccbbbbbbb bbbbb ccccccc A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 bbbbbbbbbbbb cccccccbbbbbb bbbbbb ccccccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 bbbbbbbbbb ccccccccbbbbbbbbbb cccccccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 ccccccc ccc cccccccccc ------------------------------------------- Structure #3: Score = 17.9, pattern: 620, path: 14 21 1 11 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 21() 1() 11() (a) Clique 14: OriginalScore = 3.66, ModifiedScore = 3.66 1, E.coli 14 GCGAU 18 ... 179 AUCGU 183 [-7.3 kc/m] 2, S.typhi 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 3, S.typhimuriu 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 4, S.paratyphi 15 GCGAU 19 ... 181 AUCGU 185 [-7.3 kc/m] 5, K.pneumonia 15 GCGAU 19 ... 182 AUCGU 186 [-7.3 kc/m] 6, H.influenzae 12 GCGGU 16 ... 166 AUCGU 170 [-6.5 kc/m] (b) Clique 21: OriginalScore = 3.13, ModifiedScore = 3.13 1, E.coli 92 GGGAU 96 ... 116 GUCCU 120 [-8.1 kc/m] 2, S.typhi 92 GGGAU 96 ... 116 GUCCU 120 [-8.1 kc/m] 3, S.typhimuriu 92 GGGAU 96 ... 116 GUCCU 120 [-8.1 kc/m] 4, S.paratyphi 93 GGGAU 97 ... 117 GUCCU 121 [-8.1 kc/m] 5, K.pneumonia 93 AGGGGU 98 ... 118 ACCCUU 123 [-10.3 kc/m] (c) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 2, S.typhi 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 3, S.typhimuriu 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 4, S.paratyphi 98 CGCUGA 103 AUUAGAGA 112 UCGGCG 117 [-10.8 kc/m] 5, K.pneumonia 100 GCUGA 104 AUUAGAGA 113 UCGGC 117 [-8.8 kc/m] 6, H.influenzae 77 UCGCUGA 83 GUUAGAGA 92 UCGGCGA 98 [-13.1 kc/m] 7, Y.pesits 93 UGCUGA 98 AUUAGAGA 107 UCGGCG 112 [-10 kc/m] 8, P.multocida 109 UAGCUGG 115 AUUAGAGA 124 UCGGCUA 130 [-10.7 kc/m] 9, A.actin 82 UAGCUGA 88 AUUAGAGA 97 UCGGCUA 103 [-11.6 kc/m] 10, V.cholerae 79 GUGUCGGCUGA 89 AUCAGAGA 98 UUGGCUGACAC 108 [-18 kc/m] (d) Clique 11: OriginalScore = 3.75, ModifiedScore = 3.75 1, E.coli 135 UUUGGAG 141 ... 153 CUCUAAG 159 [-8.1 kc/m] 2, S.typhi 136 UUUGGAG 142 ... 154 CUCUAAG 160 [-8.1 kc/m] 3, S.typhimuriu 136 UUUGGAG 142 ... 154 CUCUAAG 160 [-8.1 kc/m] 4, S.paratyphi 137 UUUGGAG 143 ... 155 CUCUAAG 161 [-8.1 kc/m] 5, K.pneumonia 138 UUUGGAG 144 ... 156 CUCUAAG 162 [-8.1 kc/m] 7, Y.pesits 132 AUAUUUGGAG 141 ... 153 CUCUAAGUGU 162 [-10.9 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbbb ccccc cccccbbbbb dddd ddddd d d ddddddddd aaaaa S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbbb ccccc cccccbbbbb dddd ddddd d d ddddddddd aaaaa S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbbb ccccc cccccbbbbb dddd ddddd d d ddddddddd aaaaa S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbbb ccccc cccccbbbbb dddd ddddd d d ddddddddd aaaaa K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaa bbbbbb ccccc cccccbbbbbb ddddddd ddddddd ddd ddd ddddddd ddddddd aaaaa H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaa cccccccccccc c c ccccccc ccccc aaaaa Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 cccc cccccc cccccccccc dddddddddd ddd ddd dddddddddd P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 cccccccccccc ccccccc ccccc A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 cccccccccccc cccccc cccccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 ccccccccccc ccccccccccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 aaaaaaa bccc ccc b ddd ddd aaaaaaa ------------------------------------------- Structure #4: Score = 16.7, pattern: 02, path: 2 5 0 , comseq: 2 3 4 7 8 , incompatible_seq: 2() 5() 0() (a) Clique 2: OriginalScore = 4.55, ModifiedScore = 4.55 2, S.typhi 25 GCGCUGCG 32 ... 79 CGCGGCGU 86 [-16 kc/m] 3, S.typhimuriu 25 GCGCUGCG 32 ... 79 CGCGGCGU 86 [-16 kc/m] 4, S.paratyphi 26 GCGCUGCG 33 ... 80 CGCGGCGU 87 [-16 kc/m] 7, Y.pesits 24 GUAGGCC 30 ... 77 GGCUUAC 83 [-11.9 kc/m] 8, P.multocida 52 UGACAAAG 59 ... 101 CUUUGUCG 108 [-10.9 kc/m] 10, V.cholerae 25 GCGAGA 30 ... 75 UCUCGU 80 [-10.4 kc/m] 11, P.aeruginosa 17 GUGACCGA 24 ... 55 UCGGUCAU 62 [-14.4 kc/m] (b) Clique 5: OriginalScore = 4.16, ModifiedScore = 4.16 1, E.coli 98 GCUG 101 ... 171 CAGC 174 [-6.9 kc/m] 2, S.typhi 98 GCUG 101 ... 172 CAGC 175 [-6.9 kc/m] 3, S.typhimuriu 98 GCUG 101 ... 172 CAGC 175 [-6.9 kc/m] 4, S.paratyphi 99 GCUG 102 ... 173 CAGC 176 [-6.9 kc/m] 6, H.influenzae 79 GCUG 82 ... 161 CAGC 164 [-6.9 kc/m] 7, Y.pesits 92 UUGCU 96 ... 166 AGCGA 170 [-7.4 kc/m] 8, P.multocida 111 GCUG 114 ... 193 CAGC 196 [-6.9 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaa a aa aa a aaaa bbbb cccccccc cccccccc bbbb S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaaaaa aaaaaaaa bbbb cccccccc cccccccc bbbb S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaaaaa aaaaaaaa bbbb cccccccc cccccccc bbbb S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaaaaa aaaaaaaa bbbb cccccccc cccccccc bbbb K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaaaaaa aaaaaaaaa bbbbb cccccccc cccccccc bbbbb H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaaaaa aaa aaa aaaaaaaa bbbb cccccccc cccccccc bbbb Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 aaaaaaa aaa a a aaa aaaaaaa bbbbb cccccccc cccccccc bbbbb P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 aaaaaaaa aaaaaaaa bbbb cccccccc cccccccc bbbb A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 aaaaaa a aaaa aaaa a a aaaaa bbbbb cccccccc cccccccc bbbbb V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 aaaaaa aaaaaa bbbb cccccccc cccccccc bbbb P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 aaaaaaaa a aaa aa aa aaa aaaaaaaaa bbbbbbb bbccccccc ccc cccccccccc bb bbb bbbb ------------------------------------------- Structure #5: Score = 16.7, pattern: 22, path: 3 5 0 , comseq: 1 2 3 4 7 , incompatible_seq: 3() 5() 0() (a) Clique 3: OriginalScore = 4.49, ModifiedScore = 4.49 1, E.coli 43 UGCCG 47 ... 112 CGGCG 116 [-9.5 kc/m] 2, S.typhi 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 3, S.typhimuriu 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 4, S.paratyphi 44 CGCCG 48 ... 113 CGGCG 117 [-10.3 kc/m] 5, K.pneumonia 45 GCCG 48 ... 114 CGGC 117 [-8.3 kc/m] 7, Y.pesits 39 UGCC 42 ... 109 GGCG 112 [-7.5 kc/m] 11, P.aeruginosa 16 AGUGACCG 23 ... 95 CGGUCAUU 102 [-12.6 kc/m] (b) Clique 5: OriginalScore = 4.16, ModifiedScore = 4.16 1, E.coli 98 GCUG 101 ... 171 CAGC 174 [-6.9 kc/m] 2, S.typhi 98 GCUG 101 ... 172 CAGC 175 [-6.9 kc/m] 3, S.typhimuriu 98 GCUG 101 ... 172 CAGC 175 [-6.9 kc/m] 4, S.paratyphi 99 GCUG 102 ... 173 CAGC 176 [-6.9 kc/m] 6, H.influenzae 79 GCUG 82 ... 161 CAGC 164 [-6.9 kc/m] 7, Y.pesits 92 UUGCU 96 ... 166 AGCGA 170 [-7.4 kc/m] 8, P.multocida 111 GCUG 114 ... 193 CAGC 196 [-6.9 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbb ccccccccaaaaa cccccccc bbbb S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb ccccccccaaaaa cccccccc bbbb S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb ccccccccaaaaa cccccccc bbbb S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbb ccccccccaaaaa cccccccc bbbb K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaa b bbb ccccccccaaaa cccccccc bbb b H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaaa bbbb cccccccc aaaaaa cccccccc bbbb Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 aaaa a aaa bbbbb cccccccc aaaa aaaa cccccccc bbbbb P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 aaaaaa aaaaaaa bbbbb bbb cccccccc aaaaaaa aaaaaa cccccccc bbb bbbbb A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 aaaaaaaa bbbbb cccccccc aaa aaaaa cccccccc bbbbb V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 aaaaaaaa a bbbb cccccccc a aaa aaaaa cccccccc bbbb P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 aa a aaaaaaaa ccccccc aaaaaaaa a aa ccccccc ------------------------------------------- Structure #6: Score = 16.3, pattern: 11, path: 9 3 0 , comseq: 1 2 3 4 5 , incompatible_seq: 9() 3() 0() (a) Clique 9: OriginalScore = 3.82, ModifiedScore = 3.82 1, E.coli 14 GCGAU 18 ... 95 AUCGC 99 [-8.6 kc/m] 2, S.typhi 14 GCGAU 18 ... 95 AUCGC 99 [-8.6 kc/m] 3, S.typhimuriu 14 GCGAU 18 ... 95 AUCGC 99 [-8.6 kc/m] 4, S.paratyphi 15 GCGAU 19 ... 96 AUCGC 100 [-8.6 kc/m] 5, K.pneumonia 15 GCGAU 19 ... 97 GUCGC 101 [-8.7 kc/m] 6, H.influenzae 12 GCGGU 16 ... 76 AUCGC 80 [-7.8 kc/m] (b) Clique 3: OriginalScore = 4.49, ModifiedScore = 4.49 1, E.coli 43 UGCCG 47 ... 112 CGGCG 116 [-9.5 kc/m] 2, S.typhi 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 3, S.typhimuriu 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 4, S.paratyphi 44 CGCCG 48 ... 113 CGGCG 117 [-10.3 kc/m] 5, K.pneumonia 45 GCCG 48 ... 114 CGGC 117 [-8.3 kc/m] 7, Y.pesits 39 UGCC 42 ... 109 GGCG 112 [-7.5 kc/m] 11, P.aeruginosa 16 AGUGACCG 23 ... 95 CGGUCAUU 102 [-12.6 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbbb aaaaa ccccccccbbbbb cccccccc S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbbb aaaaa ccccccccbbbbb cccccccc S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbbb aaaaa ccccccccbbbbb cccccccc S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbbb aaaaa ccccccccbbbbb cccccccc K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaa bbbb aaaaa ccccccccbbbb cccccccc H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaa aaaaa cccccccc cccccccc Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 aaaaaa bbbb b bbb aaaaaaccc c c ccccccccc bbbb bbbb cccccccc c c c ccc P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 aaaaa bbbbbb bbbbbbb aaaaaccc ccccccccc bbbbbbb bbbbbb cccccccc c ccc A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 aaaa aa aa aaa bbb bb b bbb bb aaaaa aa aaaa ccccccccbbbbb b bb bbb cccccccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 aaaa aa aaaaaa bbbbbbbb b aaaaaaaaaaaa cccccccc b bbb bbbbb cccccccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 bb b bbbbbbbb ccccccc bbbbbbbb b bb ccccccc ------------------------------------------- Structure #7: Score = 16.2, pattern: 41, path: 14 3 0 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 3() 0() (a) Clique 14: OriginalScore = 3.66, ModifiedScore = 3.66 1, E.coli 14 GCGAU 18 ... 179 AUCGU 183 [-7.3 kc/m] 2, S.typhi 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 3, S.typhimuriu 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 4, S.paratyphi 15 GCGAU 19 ... 181 AUCGU 185 [-7.3 kc/m] 5, K.pneumonia 15 GCGAU 19 ... 182 AUCGU 186 [-7.3 kc/m] 6, H.influenzae 12 GCGGU 16 ... 166 AUCGU 170 [-6.5 kc/m] (b) Clique 3: OriginalScore = 4.49, ModifiedScore = 4.49 1, E.coli 43 UGCCG 47 ... 112 CGGCG 116 [-9.5 kc/m] 2, S.typhi 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 3, S.typhimuriu 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 4, S.paratyphi 44 CGCCG 48 ... 113 CGGCG 117 [-10.3 kc/m] 5, K.pneumonia 45 GCCG 48 ... 114 CGGC 117 [-8.3 kc/m] 7, Y.pesits 39 UGCC 42 ... 109 GGCG 112 [-7.5 kc/m] 11, P.aeruginosa 16 AGUGACCG 23 ... 95 CGGUCAUU 102 [-12.6 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbbb ccccccccbbbbb cccccccc aaaaa S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbbb ccccccccbbbbb cccccccc aaaaa S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbbb ccccccccbbbbb cccccccc aaaaa S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbbb ccccccccbbbbb cccccccc aaaaa K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaa bbbb ccccccccbbbb cccccccc aaaaa H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaa cccccccc cccccccc aaaaa Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 bbbb b bbb ccc c c ccccccccc bbbb bbbb cccccccc c c c ccc P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 ccc ccccccccc cccccccc c ccc A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 cccccccc cccccccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 ccc ccccccccc ccccccc cc ccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 bb b bbbbbbbb ccccccc bbbbbbbb b bb ccccccc ------------------------------------------- Structure #8: Score = 15.8, pattern: 42, path: 14 5 0 , comseq: 1 2 3 4 6 , incompatible_seq: 14() 5() 0() (a) Clique 14: OriginalScore = 3.66, ModifiedScore = 3.66 1, E.coli 14 GCGAU 18 ... 179 AUCGU 183 [-7.3 kc/m] 2, S.typhi 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 3, S.typhimuriu 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 4, S.paratyphi 15 GCGAU 19 ... 181 AUCGU 185 [-7.3 kc/m] 5, K.pneumonia 15 GCGAU 19 ... 182 AUCGU 186 [-7.3 kc/m] 6, H.influenzae 12 GCGGU 16 ... 166 AUCGU 170 [-6.5 kc/m] (b) Clique 5: OriginalScore = 4.16, ModifiedScore = 4.16 1, E.coli 98 GCUG 101 ... 171 CAGC 174 [-6.9 kc/m] 2, S.typhi 98 GCUG 101 ... 172 CAGC 175 [-6.9 kc/m] 3, S.typhimuriu 98 GCUG 101 ... 172 CAGC 175 [-6.9 kc/m] 4, S.paratyphi 99 GCUG 102 ... 173 CAGC 176 [-6.9 kc/m] 6, H.influenzae 79 GCUG 82 ... 161 CAGC 164 [-6.9 kc/m] 7, Y.pesits 92 UUGCU 96 ... 166 AGCGA 170 [-7.4 kc/m] 8, P.multocida 111 GCUG 114 ... 193 CAGC 196 [-6.9 kc/m] (c) Clique 0: OriginalScore = 8.03, ModifiedScore = 8.03 1, E.coli 104 UUAGAGAU 111 ... 151 GUCUCUAA 158 [-11 kc/m] 2, S.typhi 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 3, S.typhimuriu 104 UUAGAGAU 111 ... 152 GUCUCUAA 159 [-11 kc/m] 4, S.paratyphi 105 UUAGAGAU 112 ... 153 GUCUCUAA 160 [-11 kc/m] 5, K.pneumonia 106 UUAGAGAU 113 ... 154 GUCUCUAA 161 [-11 kc/m] 6, H.influenzae 85 UUAGAGAU 92 ... 138 GUCUCUAA 145 [-11 kc/m] 7, Y.pesits 100 UUAGAGAU 107 ... 151 GUCUCUAA 158 [-11 kc/m] 8, P.multocida 117 UUAGAGAU 124 ... 170 GUCUCUAA 177 [-11 kc/m] 9, A.actin 90 UUAGAGAU 97 ... 143 GUCUCUAA 150 [-11 kc/m] 10, V.cholerae 91 UCAGAGAU 98 ... 144 GUCUCUGA 151 [-13.1 kc/m] 11, P.aeruginosa 87 AGCAGGC 93 ... 134 GCCUGUU 140 [-12.4 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbb cccccccc cccccccc bbbb aaaaa S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb cccccccc cccccccc bbbb aaaaa S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb cccccccc cccccccc bbbb aaaaa S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbb cccccccc cccccccc bbbb aaaaa K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaa cccccccc cccccccc aaaaa H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaa bbbb cccccccc cccccccc bbbb aaaaa Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 bbbbb cccccccc cccccccc bbbbb P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 bbbbb bbb cccccccc cccccccc bbb bbbbb A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 cccccccc cccccccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 ccc ccccccccc ccccccc cc ccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 ccccccc ccc cccccccccc ------------------------------------------- Structure #9: Score = 15.5, pattern: 00, path: 4 1 11 , comseq: 2 3 4 5 7 , incompatible_seq: 4() 1() 11() (a) Clique 4: OriginalScore = 4.43, ModifiedScore = 4.43 2, S.typhi 43 CGCCGC 48 ... 80 GCGGCG 85 [-13.7 kc/m] 3, S.typhimuriu 43 CGCCGC 48 ... 80 GCGGCG 85 [-13.7 kc/m] 4, S.paratyphi 44 CGCCGC 49 ... 81 GCGGCG 86 [-13.7 kc/m] 5, K.pneumonia 51 UAACGUCCG 59 ... 80 CGGGCGUUG 88 [-14.2 kc/m] 7, Y.pesits 24 GUAGGCC 30 ... 77 GGCUUAC 83 [-11.9 kc/m] 8, P.multocida 52 UGACAAAG 59 ... 101 CUUUGUCG 108 [-10.9 kc/m] 11, P.aeruginosa 17 GUGACCGA 24 ... 55 UCGGUCAU 62 [-14.4 kc/m] (b) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 2, S.typhi 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 3, S.typhimuriu 97 CGCUGA 102 AUUAGAGA 111 UCGGCG 116 [-10.8 kc/m] 4, S.paratyphi 98 CGCUGA 103 AUUAGAGA 112 UCGGCG 117 [-10.8 kc/m] 5, K.pneumonia 100 GCUGA 104 AUUAGAGA 113 UCGGC 117 [-8.8 kc/m] 6, H.influenzae 77 UCGCUGA 83 GUUAGAGA 92 UCGGCGA 98 [-13.1 kc/m] 7, Y.pesits 93 UGCUGA 98 AUUAGAGA 107 UCGGCG 112 [-10 kc/m] 8, P.multocida 109 UAGCUGG 115 AUUAGAGA 124 UCGGCUA 130 [-10.7 kc/m] 9, A.actin 82 UAGCUGA 88 AUUAGAGA 97 UCGGCUA 103 [-11.6 kc/m] 10, V.cholerae 79 GUGUCGGCUGA 89 AUCAGAGA 98 UUGGCUGACAC 108 [-18 kc/m] (c) Clique 11: OriginalScore = 3.75, ModifiedScore = 3.75 1, E.coli 135 UUUGGAG 141 ... 153 CUCUAAG 159 [-8.1 kc/m] 2, S.typhi 136 UUUGGAG 142 ... 154 CUCUAAG 160 [-8.1 kc/m] 3, S.typhimuriu 136 UUUGGAG 142 ... 154 CUCUAAG 160 [-8.1 kc/m] 4, S.paratyphi 137 UUUGGAG 143 ... 155 CUCUAAG 161 [-8.1 kc/m] 5, K.pneumonia 138 UUUGGAG 144 ... 156 CUCUAAG 162 [-8.1 kc/m] 7, Y.pesits 132 AUAUUUGGAG 141 ... 153 CUCUAAGUGU 162 [-10.9 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaa aaaaaaa aaa aaa aaaaaaa aaaa bbbb bbbbbb bbbbbbbbbb cccc ccccc c c ccccccccc S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaaaa aaaaa aa aaa a aaaaaa bbbb bbbbbb bbbbbbbbbb cccc ccccc c c ccccccccc S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaaaa aaaaa aa aaa a aaaaaa bbbb bbbbbb bbbbbbbbbb cccc ccccc c c ccccccccc S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaaaa aaaaa aa aaa a aaaaaa bbbb bbbbbb bbbbbbbbbb cccc ccccc c c ccccccccc K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaaaaaa aaaaaaaaa bbbbbb bbbbb bbbbbbbbbbb ccccccc ccccccc ccc ccc ccccccc ccccccc H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaaaaa aaa aaa aaaaaaaa bbbbbbbbbbbb b b bbbbbbb bbbbb cccccc cc cc cccccc Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 aaaaaaa aaa a a aaa aaaaaaa bbbb bbbbbb bbbbbbbbbb cccccccccc ccc ccc cccccccccc P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 aaaaaaaa aaaaaaaabbbbbbb bbbbbbb cccccc cccccc A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 aaaaaa a aaaa aaaa a a aaaaa bbbbbbbbbbbb bbbbbb bbbbbb cccc cc cc cccc V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 aaaaaaaaaa a a aaaaaaaaaa bbbbbbbbbbb bbbbbbbbbbb cccccccc cccccccc P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 aaaaaaaa a aaa aa aa aaa aaaaaaaaa bbbbbbbbbbbb bbbbbbbb bbbb cccccc cccccc ------------------------------------------- Structure #10: Score = 15, pattern: 610, path: 14 3 21 11 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 3() 21() 11() (a) Clique 14: OriginalScore = 3.66, ModifiedScore = 3.66 1, E.coli 14 GCGAU 18 ... 179 AUCGU 183 [-7.3 kc/m] 2, S.typhi 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 3, S.typhimuriu 14 GCGAU 18 ... 180 AUCGU 184 [-7.3 kc/m] 4, S.paratyphi 15 GCGAU 19 ... 181 AUCGU 185 [-7.3 kc/m] 5, K.pneumonia 15 GCGAU 19 ... 182 AUCGU 186 [-7.3 kc/m] 6, H.influenzae 12 GCGGU 16 ... 166 AUCGU 170 [-6.5 kc/m] (b) Clique 3: OriginalScore = 4.49, ModifiedScore = 4.49 1, E.coli 43 UGCCG 47 ... 112 CGGCG 116 [-9.5 kc/m] 2, S.typhi 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 3, S.typhimuriu 43 CGCCG 47 ... 112 CGGCG 116 [-10.3 kc/m] 4, S.paratyphi 44 CGCCG 48 ... 113 CGGCG 117 [-10.3 kc/m] 5, K.pneumonia 45 GCCG 48 ... 114 CGGC 117 [-8.3 kc/m] 7, Y.pesits 39 UGCC 42 ... 109 GGCG 112 [-7.5 kc/m] 11, P.aeruginosa 16 AGUGACCG 23 ... 95 CGGUCAUU 102 [-12.6 kc/m] (c) Clique 21: OriginalScore = 3.13, ModifiedScore = 3.13 1, E.coli 92 GGGAU 96 ... 116 GUCCU 120 [-8.1 kc/m] 2, S.typhi 92 GGGAU 96 ... 116 GUCCU 120 [-8.1 kc/m] 3, S.typhimuriu 92 GGGAU 96 ... 116 GUCCU 120 [-8.1 kc/m] 4, S.paratyphi 93 GGGAU 97 ... 117 GUCCU 121 [-8.1 kc/m] 5, K.pneumonia 93 AGGGGU 98 ... 118 ACCCUU 123 [-10.3 kc/m] (d) Clique 11: OriginalScore = 3.75, ModifiedScore = 3.75 1, E.coli 135 UUUGGAG 141 ... 153 CUCUAAG 159 [-8.1 kc/m] 2, S.typhi 136 UUUGGAG 142 ... 154 CUCUAAG 160 [-8.1 kc/m] 3, S.typhimuriu 136 UUUGGAG 142 ... 154 CUCUAAG 160 [-8.1 kc/m] 4, S.paratyphi 137 UUUGGAG 143 ... 155 CUCUAAG 161 [-8.1 kc/m] 5, K.pneumonia 138 UUUGGAG 144 ... 156 CUCUAAG 162 [-8.1 kc/m] 7, Y.pesits 132 AUAUUUGGAG 141 ... 153 CUCUAAGUGU 162 [-10.9 kc/m] E.coli 1 UGUUAACCGUCUUGCGAUAACAGGUCGCUACGAGUAGAAUACUGCCGCUUAACGUCGCGUAAAUUGUUUAACACUUUGCGUAACGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUU 185 aaaaa bbbb ccccc bbbbccccc dddd ddddd d d ddddddddd aaaaa S.typhi 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb ccccc bbbbccccc dddd ddddd d d ddddddddd aaaaa S.typhimuriu 1 GUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 186 aaaaa bbbb ccccc bbbbccccc dddd ddddd d d ddddddddd aaaaa S.paratyphi 1 UGUCGCUUCGUCUUGCGAUAAGAGAGCGCUGCGAGUAGAAUACCGCCGCUUAACGUCGCGUAAAUUAUUUAACAGUUUACGCGGCGUACACUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUCUCAUUCUUAAAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUU 187 aaaaa bbbb ccccc bbbbccccc dddd ddddd d d ddddddddd aaaaa K.pneumonia 1 UAAGCGCUUUUCUUGCGAUAAAAGCCUGCUACGAGUAGAAUAUCGCCGCUUAACGUCCGCUAACGUGUUUUAACAUUUUCGGGCGUUGCAUCAGGGGUCGCUGAAUUAGAGAUCGGCACCCUUUCUUUCUUUUAAUUUUUGGAGUUAUAAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUU 188 aaaaa bbbb cccccc bbbbcccccc ddddddd ddddddd ddd ddd ddddddd ddddddd aaaaa H.influenzae 1 UAAUGAAAAGUGCGGUAACUUUAAUCUUUAUCUUGCAUUUGAACUUAUUCAUCGUUAGAAUGCGAUUUCCUUGUCAUCGCUGAGUUAGAGAUCGGCGAAUGAUGUAUUAACAACACUACCUUUUAGGAGUAAAAAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUG 172 aaaaa bbbbb cc cc bbbbb cc cc dddddd dd dd dddddd aaaaa Y.pesits 1 AAUCUGCCAGUAGAAAAUAAAAAGUAGGCCACACGGCCUGCCUUGCGAUCCCGCGAUUCAAAGAGUAGAAUAGUGCGGCUUACAUAUUGGGUUGCUGAAUUAGAGAUCGGCGCCUGUCUUAAUUCAUUUAUAUAUUUGGAGUUGUAUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUG 185 aaaaa bbbb b bbb ccccc bbbb bbbbccccc dddddddddd ddd ddd dddddddddd aaaaa P.multocida 1 UCCUAAGCCUGCGUAUGCAGGCUUUCUUUUUGCGUGAAAGUGCGGUGGAUUUGACAAAGAUUUAUUGCUUUUCUGUAAAUCAAUGCUAAAAUUCACACUCCUUUGUCGUAGCUGGAUUAGAGAUCGGCUAGCGAUGUAUUUUUAACUUAACUUUUAGGAGUUAUCAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUG 204 aaaaa aaaaa bbbbbbb cccccccc bbbbbbb cccccccc dddddd dddddd aaaaa aaaaa A.actin 1 GCGCAAUUAAAUGCGUUGUUAGAGGAUAAAUUCGUUGCUUUUUGAGCGCGCAAUAGCUAGAAUCUGCAUUCCUUAUUAUCGUAGCUGAAUUAGAGAUCGGCUAACGAUGUAUCAUUAACCACCUCAUAUCAGGAGUUAUUAUGUCUCUAAGUACUGAACAAAAAGCAAAAAUCGUUG 177 aaaaaaaaaaa bbbbbbb ccccc bbbbbbbcccccddd dd dd ddd aaaa aaaaaaa V.cholerae 1 AUUCGUGGAAGGGCUCGCUGUAUGGCGAGACAUUCCGCUUGUGCGGAUUAGGAAUAUUCCCUAUAAUCCGCGCUUCUCGUGUCGGCUGAAUCAGAGAUUGGCUGACACAAACUUAAACCUCAAACUCUUUAGGAGAGAAUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUG 178 aaa aaa aa bbbb cccccccccbbbb ccccccccc dddddddd dddddddd aa aaaaaa P.aeruginosa 1 CAUCGGUAUCGGUGAAGUGACCGACGACGGGCGUAUCGCCCCGCGUCGACUGAUUCGGUCAUAAGACCGAUACGAGGGUGGCUGUCAGCAGGCACGGUCAUUCCUCCUUUUAAAACACGGGAAGCGAUUCCCGGCCUGUUCACUCAGAGGAAGCCCAUCAUGGCACUGAGCGUUGAAGAAAAAGCGCAGAUCGUUA 196 aaaa bbbbbbbb ccccc cc bbbbbbbbcc ccccc ddddddddd ddddddddd aaaa Total time spent with S = 0.56: 15.3 seconds CPU time; 35.9 seconds real time. ************************************** Total Time spent: 15.3 seconds CPU time; 35.9 seconds real time. ../pubstruc1_s15_ecoli.bp s15_11seq_220.72out_P0.5_S0.56 Structure 1: TP= 21, FP= 10, FN= 9, CC= 0.69 Structure 2: TP= 10, FP= 12, FN= 20, CC= 0.39 Structure 3: TP= 17, FP= 8, FN= 13, CC= 0.62 Structure 4: TP= 0, FP= 19, FN= 30, CC= 0.00 Structure 5: TP= 0, FP= 17, FN= 30, CC= 0.00 Structure 6: TP= 0, FP= 18, FN= 30, CC= 0.00 Structure 7: TP= 0, FP= 18, FN= 30, CC= 0.00 Structure 8: TP= 0, FP= 17, FN= 30, CC= 0.00 Structure 9: TP= 29, FP= 5, FN= 1, CC= 0.91 Structure 10: TP= 12, FP= 12, FN= 18, CC= 0.45 10 structures, First #1: CC= 0.69, Best #9: CC= 0.91, Average: CC= 0.34 ../pubstruc2_s15_ecoli.bp s15_11seq_220.72out_P0.5_S0.56 Structure 1: TP= 28, FP= 3, FN= 0, CC= 0.95 Structure 2: TP= 17, FP= 5, FN= 11, CC= 0.68 Structure 3: TP= 9, FP= 16, FN= 19, CC= 0.34 Structure 4: TP= 7, FP= 12, FN= 21, CC= 0.30 Structure 5: TP= 7, FP= 10, FN= 21, CC= 0.32 Structure 6: TP= 7, FP= 11, FN= 21, CC= 0.31 Structure 7: TP= 7, FP= 11, FN= 21, CC= 0.31 Structure 8: TP= 7, FP= 10, FN= 21, CC= 0.32 Structure 9: TP= 21, FP= 13, FN= 7, CC= 0.68 Structure 10: TP= 4, FP= 20, FN= 24, CC= 0.15 10 structures, First #1: CC= 0.95, Best #1: CC= 0.95, Average: CC= 0.45