comRNA_72bf_250 ../alpha_10seq.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: "../alpha_10seq.fa" Sequences loaded ... 1 E.coli_K12 134 nt 2 S.typhimurium 134 nt 3 S.typhi 134 nt 4 S.paratyphi 134 nt 5 K.pneumonia 134 nt 6 Y.pestis 134 nt 7 V.cholerae 134 nt 8 P.multocida 134 nt 9 A.actinomycetem 134 nt 10 H.influenzae 134 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_K12 6 1 5 1 10 12 14 18 22 7 6 1 S.typhimurium 4 1 4 1 11 18 17 14 25 7 5 1 S.typhi 4 1 4 1 11 18 17 14 25 7 5 1 S.paratyphi 4 1 4 1 11 18 17 14 25 7 5 1 K.pneumonia 4 1 4 2 9 19 15 17 22 7 6 1 Y.pestis 4 0 5 3 12 16 21 26 22 7 4 1 V.cholerae 4 0 1 3 15 14 24 19 16 6 2 2 P.multocida 3 0 1 4 15 12 23 19 23 2 8 2 A.actinomycetem 3 1 2 3 12 12 24 14 18 3 5 0 H.influenzae 3 0 3 2 15 9 17 20 29 3 3 0 Pairwise Sequence Identity (%): 1 2 3 4 5 6 7 8 9 10 1 - 97 97 97 96 86 66 80 79 80 2 97 - 100 100 98 88 68 78 76 77 3 97 100 - 100 98 88 68 78 76 77 4 97 100 100 - 98 88 68 78 76 77 5 96 98 98 98 - 86 67 79 77 76 6 86 88 88 88 86 - 71 77 75 78 7 66 68 68 68 67 71 - 67 64 70 8 80 78 78 78 79 77 67 - 92 91 9 79 76 76 76 77 75 64 92 - 90 10 80 77 77 77 76 78 70 91 90 - 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: 48 61 66 100 112 127 138 179 205 231 409 744 971 1179 1411 1648 1991 2574 3264 3974 4594 5250 5706 6270 6630 6904 7215 Time spent on comparing stems: 1.8 seconds user CPU time; 1.84 seconds real time. =========================== S = 0.56 =========================== Find conserved stems (cliques) ... ==== 49 cliques ==== 30 unique ==== Time spent on finding conserved stems: 0.1 sec CPU time; 0.11 sec clock time. Construct clique topological graph ... ==== 200 edges ==== Assemble conserved stems (cliques) ... ==== 565 structures ==== Time spent on topologically assembling conserved stems: 0.15 sec CPU time; 0.15 sec clock time. Report top 10 structures. ------------------------------------------- Structure #1: Score = 33.4, pattern: 74231, path: 15 4 27 7 0 1 , comseq: 1 2 3 4 5 , incompatible_seq: 15(6) 4() 27() 7() 0() 1() (a) Clique 15: OriginalScore = 3.52, ModifiedScore = 2.93 1, E.coli_K12 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 2, S.typhimurium 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 3, S.typhi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 4, S.paratyphi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 5, K.pneumonia 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] * 6, Y.pestis 13 UAUGUG 18 ... 89 UGCAUA 94 [-6.1 kc/m] (b) Clique 4: OriginalScore = 5.81, ModifiedScore = 5.81 1, E.coli_K12 19 UGUGCGUUUC 28 ... 63 GGAACGUACA 72 [-14.3 kc/m] 2, S.typhimurium 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 3, S.typhi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 4, S.paratyphi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 5, K.pneumonia 19 UGUACGU 25 ... 66 GCGUACA 72 [-11.2 kc/m] 8, P.multocida 16 UUGACACUUUG 26 ... 59 CAAAGUGUCAA 69 [-16.3 kc/m] 9, A.actinomycetem 14 UUGACACUCUG 24 ... 57 CAGAGUGUCAA 67 [-18.5 kc/m] 10, H.influenzae 16 UUGAUAUUCUG 26 ... 59 CAGAAUAUCAA 69 [-14.6 kc/m] (c) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (d) Clique 7: OriginalScore = 5.31, ModifiedScore = 5.31 1, E.coli_K12 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 2, S.typhimurium 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 3, S.typhi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 4, S.paratyphi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 5, K.pneumonia 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 6, Y.pestis 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 8, P.multocida 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] 9, A.actinomycetem 34 CCUG 37 ... 108 CAGG 111 [-6.4 kc/m] 10, H.influenzae 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] (e) Clique 0: OriginalScore = 9.15, ModifiedScore = 9.15 1, E.coli_K12 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 2, S.typhimurium 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 3, S.typhi 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 4, S.paratyphi 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 5, K.pneumonia 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 6, Y.pestis 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] 8, P.multocida 43 ACGGGCU 49 ... 97 GGCCCGU 103 [-15.2 kc/m] 9, A.actinomycetem 41 ACGGGCU 47 ... 97 GGCCCGU 103 [-15.2 kc/m] 10, H.influenzae 43 ACGGGCU 49 ... 97 GGCCCGU 103 [-15.2 kc/m] (f) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli_K12 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 2, S.typhimurium 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 3, S.typhi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 4, S.paratyphi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 5, K.pneumonia 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 6, Y.pestis 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 7, V.cholerae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 8, P.multocida 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 9, A.actinomycetem 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 10, H.influenzae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaaa bbbbbbb bbbbbccccc dddd eeeeeee ccccc bbbbbbbbbbbb fffffffaaaaa eeeeeee dddd fffffff S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbbccccc dddd eeeeeee ccccc bbbb bbbbbbb fffffffaaaaa eeeeeee dddd fffffff S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbbccccc dddd eeeeeee ccccc bbbb bbbbbbb fffffffaaaaa eeeeeee dddd fffffff S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbbccccc dddd eeeeeee ccccc bbbb bbbbbbb fffffffaaaaa eeeeeee dddd fffffff K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaaa bbbbbb b bbbbccccc dddd eeeeeee ccccc bbbb bbbbbbb fffffffaaaaa eeeeeee dddd fffffff Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bb bbbbbbbbbbccccc dddd eeeeeee ccccc bbbbbbbbbb bb ffffffffaaaa eeeeeee dddd ffffffff V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbccccc dddd eeeeeee ccccc bbbbbb ffffffffaaaaa eeeeeee dddd ffffffff P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbbbbbbcccccc dddd ddeeeeeee cccccc bbbbbbbbbbb ffffffffaaaaa eeeeeee dd dddd ffffffff A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa bbbbbbbbbbbcccccc dddd ddeeeeeee cccccc bbbbbbbbbbb ffffffff aaaa eeeeeee dd dddd ffffffff H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbbbbbbcccccc dddd ddeeeeeee cccccc bbbbbbbbbbb ffffffffaaaaa eeeeeee dd dddd ffffffff ------------------------------------------- Structure #2: Score = 32.9, pattern: 74210, path: 15 4 27 6 0 3 , comseq: 1 2 3 4 5 , incompatible_seq: 15() 4() 27() 6() 0() 3() (a) Clique 15: OriginalScore = 3.52, ModifiedScore = 3.52 1, E.coli_K12 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 2, S.typhimurium 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 3, S.typhi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 4, S.paratyphi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 5, K.pneumonia 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 6, Y.pestis 13 UAUGUG 18 ... 89 UGCAUA 94 [-6.1 kc/m] (b) Clique 4: OriginalScore = 5.81, ModifiedScore = 5.81 1, E.coli_K12 19 UGUGCGUUUC 28 ... 63 GGAACGUACA 72 [-14.3 kc/m] 2, S.typhimurium 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 3, S.typhi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 4, S.paratyphi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 5, K.pneumonia 19 UGUACGU 25 ... 66 GCGUACA 72 [-11.2 kc/m] 8, P.multocida 16 UUGACACUUUG 26 ... 59 CAAAGUGUCAA 69 [-16.3 kc/m] 9, A.actinomycetem 14 UUGACACUCUG 24 ... 57 CAGAGUGUCAA 67 [-18.5 kc/m] 10, H.influenzae 16 UUGAUAUUCUG 26 ... 59 CAGAAUAUCAA 69 [-14.6 kc/m] (c) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (d) Clique 6: OriginalScore = 5.58, ModifiedScore = 5.58 1, E.coli_K12 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 2, S.typhimurium 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 3, S.typhi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 4, S.paratyphi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 5, K.pneumonia 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 6, Y.pestis 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 7, V.cholerae 40 UCCU 43 ... 84 AGGA 87 [-6.9 kc/m] 8, P.multocida 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] 10, H.influenzae 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] (e) Clique 0: OriginalScore = 9.15, ModifiedScore = 9.15 1, E.coli_K12 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 2, S.typhimurium 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 3, S.typhi 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 4, S.paratyphi 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 5, K.pneumonia 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 6, Y.pestis 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] 8, P.multocida 43 ACGGGCU 49 ... 97 GGCCCGU 103 [-15.2 kc/m] 9, A.actinomycetem 41 ACGGGCU 47 ... 97 GGCCCGU 103 [-15.2 kc/m] 10, H.influenzae 43 ACGGGCU 49 ... 97 GGCCCGU 103 [-15.2 kc/m] (f) Clique 3: OriginalScore = 6.01, ModifiedScore = 6.01 1, E.coli_K12 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 2, S.typhimurium 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 3, S.typhi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 4, S.paratyphi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 5, K.pneumonia 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 6, Y.pestis 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 7, V.cholerae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 8, P.multocida 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 9, A.actinomycetem 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 10, H.influenzae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaaa bbbbbbb bbbbbccccc ddddd eeeeeee ccccc bbbbbbbbbbbb ddddd aaaaa eeeeeee ffff ffff S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbbccccc ddddd eeeeeee ccccc bbbb bbbbbbb ddddd aaaaa eeeeeee ffff ffff S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbbccccc ddddd eeeeeee ccccc bbbb bbbbbbb ddddd aaaaa eeeeeee ffff ffff S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbbccccc ddddd eeeeeee ccccc bbbb bbbbbbb ddddd aaaaa eeeeeee ffff ffff K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaaa bbbbbb b bbbbccccc ddddd eeeeeee ccccc bbbb bbbbbbb ddddd aaaaa eeeeeee ffff ffff Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaaabb bbbbbbbbbbccccc ddddd eeeeeee ccccc bbbbbbbbbb bb ddddd aaaaaa eeeeeee ffff ffff V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaabbbbbb bb cccccccc dddd eeeeeee cccccccc bb bbbbbb dddd aaaaa eeeeeee ffff ffff P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaaa bbbbbbbbbbbcccccc ddddd eeeeeee cccccc bbbbbbbbbbb ddddd aaaaaa eeeeeee ffff ffff A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa a bbbbbbbbbbbcccccc ddddd eeeeeee cccccc bbbbbbbbbbb ddddd a aaaa eeeeeee ffff ffff H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaaa bbbbbbbbbbbcccccc ddddd eeeeeee cccccc bbbbbbbbbbb ddddd aaaaaa eeeeeee ffff ffff ------------------------------------------- Structure #3: Score = 32.4, pattern: 984212, path: 14 16 4 27 6 8 2 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 16() 4() 27() 6(7) 8() 2() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 16: OriginalScore = 3.51, ModifiedScore = 3.51 1, E.coli_K12 10 UUGUAUG 16 ... 101 CGUAUAG 107 [-5.6 kc/m] 2, S.typhimurium 10 UUGUAUG 16 ... 101 CGUAUAG 107 [-5.6 kc/m] 3, S.typhi 10 UUGUAUG 16 ... 101 CGUAUAG 107 [-5.6 kc/m] 4, S.paratyphi 10 UUGUAUG 16 ... 101 CGUAUAG 107 [-5.6 kc/m] 5, K.pneumonia 10 UUGUAUG 16 ... 101 CGUAUAG 107 [-5.6 kc/m] 6, Y.pestis 10 UUGUAUG 16 ... 101 CGUAUAG 107 [-5.6 kc/m] (c) Clique 4: OriginalScore = 5.81, ModifiedScore = 5.81 1, E.coli_K12 19 UGUGCGUUUC 28 ... 63 GGAACGUACA 72 [-14.3 kc/m] 2, S.typhimurium 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 3, S.typhi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 4, S.paratyphi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 5, K.pneumonia 19 UGUACGU 25 ... 66 GCGUACA 72 [-11.2 kc/m] 8, P.multocida 16 UUGACACUUUG 26 ... 59 CAAAGUGUCAA 69 [-16.3 kc/m] 9, A.actinomycetem 14 UUGACACUCUG 24 ... 57 CAGAGUGUCAA 67 [-18.5 kc/m] 10, H.influenzae 16 UUGAUAUUCUG 26 ... 59 CAGAAUAUCAA 69 [-14.6 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 6: OriginalScore = 5.58, ModifiedScore = 4.96 1, E.coli_K12 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 2, S.typhimurium 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 3, S.typhi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 4, S.paratyphi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 5, K.pneumonia 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 6, Y.pestis 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] * 7, V.cholerae 40 UCCU 43 ... 84 AGGA 87 [-6.9 kc/m] 8, P.multocida 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] 10, H.influenzae 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] (f) Clique 8: OriginalScore = 5.29, ModifiedScore = 5.29 1, E.coli_K12 48 CGGG 51 ... 122 CCUG 125 [-6 kc/m] 2, S.typhimurium 48 CGGG 51 ... 122 CCUG 125 [-6 kc/m] 3, S.typhi 48 CGGG 51 ... 122 CCUG 125 [-6 kc/m] 4, S.paratyphi 48 CGGG 51 ... 122 CCUG 125 [-6 kc/m] 5, K.pneumonia 48 CGGG 51 ... 122 CCUG 125 [-6 kc/m] 6, Y.pestis 48 CGGG 51 ... 122 CCUG 125 [-6 kc/m] 7, V.cholerae 47 CGGG 50 ... 122 CCUG 125 [-6 kc/m] 8, P.multocida 44 CGGG 47 ... 122 CCUG 125 [-6 kc/m] 10, H.influenzae 44 CGGG 47 ... 122 CCUG 125 [-6 kc/m] (g) Clique 2: OriginalScore = 6.05, ModifiedScore = 6.05 1, E.coli_K12 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 2, S.typhimurium 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 3, S.typhi 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 4, S.paratyphi 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 5, K.pneumonia 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 6, Y.pestis 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 7, V.cholerae 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 8, P.multocida 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 9, A.actinomycetem 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] 10, H.influenzae 87 AGUGC 91 ... 111 GCAUU 115 [-6.7 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa a bbbbbbb ccccccc cccccddddd d eeee ffff d ddddd cccccccccccc eeeeggggg ga aaaa bbbbbbb g ggggg ffff S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbbb cccccc c ccccddddd d eeee ffff d ddddd cccc ccccccc eeeeggggg ga aaaa bbbbbbb g ggggg ffff S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbbb cccccc c ccccddddd d eeee ffff d ddddd cccc ccccccc eeeeggggg ga aaaa bbbbbbb g ggggg ffff S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbbb cccccc c ccccddddd d eeee ffff d ddddd cccc ccccccc eeeeggggg ga aaaa bbbbbbb g ggggg ffff K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa a bbbbbbb cccccc c ccccddddd d eeee ffff d ddddd cccc ccccccc eeeeggggg ga aaaa bbbbbbb g ggggg ffff Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbbb cc ccccccccccddddd d eeee ffff d ddddd cccccccccc cc eeeeggggg ga aaaa bbbbbbb g ggggg ffff V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaa bbbb bb cccccc cc dddddddeeee ffff ddddddd cc cccccc eeee ggggg g aaabb bbbb g ggggg ffff P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 ccccccccccc cc eeee ffff cc ccccccccccc eeeeggggg g gggg ggggg ggggg ffff A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 ccccccccccc cc cc ccccccccccc ggggg ggggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 ccccccccccc cc eeee ffff cc ccccccccccc eeeeggggg g gggg ggggg ggggg ffff ------------------------------------------- Structure #4: Score = 31.7, pattern: 962131, path: 14 17 10 27 7 13 1 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 17() 10() 27() 7() 13() 1() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 17: OriginalScore = 3.5, ModifiedScore = 3.5 1, E.coli_K12 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 2, S.typhimurium 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 3, S.typhi 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 4, S.paratyphi 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 5, K.pneumonia 11 UGUAUGU 17 ... 66 GCGUACA 72 [-9.3 kc/m] (c) Clique 10: OriginalScore = 4.71, ModifiedScore = 4.71 1, E.coli_K12 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 2, S.typhimurium 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 3, S.typhi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 4, S.paratyphi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 5, K.pneumonia 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 8, P.multocida 23 UUUGUUU 29 ... 41 AAACGGG 47 [-5.9 kc/m] 9, A.actinomycetem 21 UCUGUUU 27 ... 39 AAACGGG 45 [-8.4 kc/m] 10, H.influenzae 23 UCUGUUU 29 ... 41 AAACGGG 47 [-8.4 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 7: OriginalScore = 5.31, ModifiedScore = 5.31 1, E.coli_K12 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 2, S.typhimurium 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 3, S.typhi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 4, S.paratyphi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 5, K.pneumonia 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 6, Y.pestis 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 8, P.multocida 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] 9, A.actinomycetem 34 CCUG 37 ... 108 CAGG 111 [-6.4 kc/m] 10, H.influenzae 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] (f) Clique 13: OriginalScore = 4, ModifiedScore = 4 1, E.coli_K12 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 2, S.typhimurium 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 3, S.typhi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 4, S.paratyphi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 5, K.pneumonia 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 6, Y.pestis 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] (g) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli_K12 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 2, S.typhimurium 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 3, S.typhi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 4, S.paratyphi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 5, K.pneumonia 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 6, Y.pestis 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 7, V.cholerae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 8, P.multocida 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 9, A.actinomycetem 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 10, H.influenzae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa a bbbbbbb ccccc ddddd d eeee ccccc d ddddd ffff bbbbbbb gggggggg a aaaaffff eeee gggggggg S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb ccccccddddd eeee cccccc ddddd ffff bbbbbb gggggggg a aaaaffff eeee gggggggg V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 fffffff f gggggggg f fffffff gggggggg P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbbcccccccddd d eeee ccccccc d ddd fff bbbbbbb ggggggggaaaaafff eeee gggggggg A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaaa bbbbbbbcccccccddd d eeee ccccccc d ddd fff bbbbbbb gggggggg aaaaa fffeeee gggggggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbbcccccccddd d eeee ccccccc d ddd fff bbbbbbb ggggggggaaaaafff eeee gggggggg ------------------------------------------- Structure #5: Score = 31.2, pattern: 962131, path: 14 21 10 27 7 13 1 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 21() 10() 27() 7() 13() 1() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 21: OriginalScore = 3.09, ModifiedScore = 3.09 1, E.coli_K12 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 2, S.typhimurium 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 3, S.typhi 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 4, S.paratyphi 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 5, K.pneumonia 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] (c) Clique 10: OriginalScore = 4.71, ModifiedScore = 4.71 1, E.coli_K12 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 2, S.typhimurium 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 3, S.typhi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 4, S.paratyphi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 5, K.pneumonia 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 8, P.multocida 23 UUUGUUU 29 ... 41 AAACGGG 47 [-5.9 kc/m] 9, A.actinomycetem 21 UCUGUUU 27 ... 39 AAACGGG 45 [-8.4 kc/m] 10, H.influenzae 23 UCUGUUU 29 ... 41 AAACGGG 47 [-8.4 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 7: OriginalScore = 5.31, ModifiedScore = 5.31 1, E.coli_K12 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 2, S.typhimurium 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 3, S.typhi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 4, S.paratyphi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 5, K.pneumonia 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 6, Y.pestis 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 8, P.multocida 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] 9, A.actinomycetem 34 CCUG 37 ... 108 CAGG 111 [-6.4 kc/m] 10, H.influenzae 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] (f) Clique 13: OriginalScore = 4, ModifiedScore = 4 1, E.coli_K12 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 2, S.typhimurium 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 3, S.typhi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 4, S.paratyphi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 5, K.pneumonia 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 6, Y.pestis 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] (g) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli_K12 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 2, S.typhimurium 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 3, S.typhi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 4, S.paratyphi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 5, K.pneumonia 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 6, Y.pestis 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 7, V.cholerae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 8, P.multocida 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 9, A.actinomycetem 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 10, H.influenzae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa a bbbbbbb ccccc ddddd d eeee ccccc d ddddd ffff bbbbbbb gggggggg a aaaaffff eeee gggggggg S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa a bbbbbb bbbbccccc ddddd d eeee ccccc d ddddd ffffbbbb bbbbbb gggggggg a aaaaffff eeee gggggggg Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb ccccccddddd eeee cccccc ddddd ffff bbbbbb gggggggg a aaaaffff eeee gggggggg V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 fffffff f gggggggg f fffffff gggggggg P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaa bbbbb cccccccddd d eeee ccccccc d ddd fffffff bbbbb gggggggg aaaa fffffffeeee gggggggg A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 ccccccc eeee ccccccc gggggggg eeee gggggggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbb cccccccddd d eeee ccccccc d ddd ffffffbbbbb gggggggg aaaaa ffffffeeee gggggggg ------------------------------------------- Structure #6: Score = 31.1, pattern: 972131, path: 14 15 10 27 7 13 1 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 15(6) 10() 27() 7() 13() 1() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 15: OriginalScore = 3.52, ModifiedScore = 2.93 1, E.coli_K12 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 2, S.typhimurium 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 3, S.typhi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 4, S.paratyphi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 5, K.pneumonia 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] * 6, Y.pestis 13 UAUGUG 18 ... 89 UGCAUA 94 [-6.1 kc/m] (c) Clique 10: OriginalScore = 4.71, ModifiedScore = 4.71 1, E.coli_K12 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 2, S.typhimurium 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 3, S.typhi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 4, S.paratyphi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 5, K.pneumonia 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 8, P.multocida 23 UUUGUUU 29 ... 41 AAACGGG 47 [-5.9 kc/m] 9, A.actinomycetem 21 UCUGUUU 27 ... 39 AAACGGG 45 [-8.4 kc/m] 10, H.influenzae 23 UCUGUUU 29 ... 41 AAACGGG 47 [-8.4 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 7: OriginalScore = 5.31, ModifiedScore = 5.31 1, E.coli_K12 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 2, S.typhimurium 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 3, S.typhi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 4, S.paratyphi 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 5, K.pneumonia 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 6, Y.pestis 40 CCUG 43 ... 108 CAGG 111 [-6.4 kc/m] 8, P.multocida 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] 9, A.actinomycetem 34 CCUG 37 ... 108 CAGG 111 [-6.4 kc/m] 10, H.influenzae 36 CCUG 39 ... 108 CAGG 111 [-6.4 kc/m] (f) Clique 13: OriginalScore = 4, ModifiedScore = 4 1, E.coli_K12 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 2, S.typhimurium 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 3, S.typhi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 4, S.paratyphi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 5, K.pneumonia 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 6, Y.pestis 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] (g) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli_K12 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 2, S.typhimurium 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 3, S.typhi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 4, S.paratyphi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 5, K.pneumonia 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 6, Y.pestis 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 7, V.cholerae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 8, P.multocida 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 9, A.actinomycetem 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 10, H.influenzae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa bbbbb ccccc ddddd d eeee ccccc d ddddd ffff gggggggbbbbb aaaaffff eeee ggggggg S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbb cc ccccc ddddd d eeee ccccc ccd ddddd fffff gggggggbbbbb aaaa fffff eeee ggggggg S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbb cc ccccc ddddd d eeee ccccc ccd ddddd fffff gggggggbbbbb aaaa fffff eeee ggggggg S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbb cc ccccc ddddd d eeee ccccc ccd ddddd fffff gggggggbbbbb aaaa fffff eeee ggggggg K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa bbbbb cc ccccc ddddd d eeee ccccc ccd ddddd fffff gggggggbbbbb aaaa fffff eeee ggggggg Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbb ccccccddddd eeee cccccc ddddd ffff ggggggggbbbb aaaaffff eeee gggggggg V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 fffffff f gggggggg f fffffff gggggggg P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaa bbbbb cccccccddd d eeee ccccccc d ddd fffffff ggggggggbbbbb aaa fffffffeeee gggggggg A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaa bbbb cccccccddd d eeee ccccccc d ddd fffffff gggggggg bbbbaaa fffffffeeee gggggggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaa bbbbbcccccccddd d eeee ccccccc d ddd fffff gggggggg bbbbbaaa fffff eeee gggggggg ------------------------------------------- Structure #7: Score = 30.8, pattern: 6311, path: 15 4 5 0 1 , comseq: 1 2 3 4 5 , incompatible_seq: 15(6) 4() 5() 0() 1() (a) Clique 15: OriginalScore = 3.52, ModifiedScore = 2.93 1, E.coli_K12 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 2, S.typhimurium 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 3, S.typhi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 4, S.paratyphi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 5, K.pneumonia 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] * 6, Y.pestis 13 UAUGUG 18 ... 89 UGCAUA 94 [-6.1 kc/m] (b) Clique 4: OriginalScore = 5.81, ModifiedScore = 5.81 1, E.coli_K12 19 UGUGCGUUUC 28 ... 63 GGAACGUACA 72 [-14.3 kc/m] 2, S.typhimurium 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 3, S.typhi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 4, S.paratyphi 19 UGUACGU 25 ... 66 ACGUACA 72 [-11.2 kc/m] 5, K.pneumonia 19 UGUACGU 25 ... 66 GCGUACA 72 [-11.2 kc/m] 8, P.multocida 16 UUGACACUUUG 26 ... 59 CAAAGUGUCAA 69 [-16.3 kc/m] 9, A.actinomycetem 14 UUGACACUCUG 24 ... 57 CAGAGUGUCAA 67 [-18.5 kc/m] 10, H.influenzae 16 UUGAUAUUCUG 26 ... 59 CAGAAUAUCAA 69 [-14.6 kc/m] (c) Clique 5: OriginalScore = 5.58, ModifiedScore = 5.58 1, E.coli_K12 41 CUGAAAA 47 CGGGC 53 UUUUCAG 59 [-8.5 kc/m] 2, S.typhimurium 41 CUGAAAA 47 CGGGC 53 UUUUCAG 59 [-8.5 kc/m] 3, S.typhi 41 CUGAAAA 47 CGGGC 53 UUUUCAG 59 [-8.5 kc/m] 4, S.paratyphi 41 CUGAAAA 47 CGGGC 53 UUUUCAG 59 [-8.5 kc/m] 5, K.pneumonia 41 CUGAAAA 47 CGGGC 53 UUUUCAG 59 [-8.5 kc/m] 6, Y.pestis 41 CUGAAAA 47 CGGGC 53 UUUUCAG 59 [-8.5 kc/m] 8, P.multocida 38 UGAAAA 43 CGGGC 49 UUUUCA 54 [-6.8 kc/m] 9, A.actinomycetem 36 UGAAAA 41 CGGGC 47 UUUUCA 52 [-6.8 kc/m] 10, H.influenzae 38 UGAAAA 43 CGGGC 49 UUUUCA 54 [-6.8 kc/m] (d) Clique 0: OriginalScore = 9.15, ModifiedScore = 9.15 1, E.coli_K12 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 2, S.typhimurium 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 3, S.typhi 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 4, S.paratyphi 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 5, K.pneumonia 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 6, Y.pestis 47 ACGGGCU 53 ... 97 GGCCCGU 103 [-15.2 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] 8, P.multocida 43 ACGGGCU 49 ... 97 GGCCCGU 103 [-15.2 kc/m] 9, A.actinomycetem 41 ACGGGCU 47 ... 97 GGCCCGU 103 [-15.2 kc/m] 10, H.influenzae 43 ACGGGCU 49 ... 97 GGCCCGU 103 [-15.2 kc/m] (e) Clique 1: OriginalScore = 7.35, ModifiedScore = 7.35 1, E.coli_K12 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 2, S.typhimurium 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 3, S.typhi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 4, S.paratyphi 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 5, K.pneumonia 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 6, Y.pestis 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 7, V.cholerae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 8, P.multocida 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 9, A.actinomycetem 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] 10, H.influenzae 83 UAGGAGUG 90 ... 118 CAUUCCUG 125 [-11 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaaa bbbbbbb bbbbb cccccccdddddccccccc bbbbbbbbbbbb eeeeeeeaaaaa ddddd eeeeeee S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbb cccccccdddddccccccc bbbb bbbbbbb eeeeeeeaaaaa ddddd eeeeeee S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbb cccccccdddddccccccc bbbb bbbbbbb eeeeeeeaaaaa ddddd eeeeeee S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaaa bbbbbb b bbbb cccccccdddddccccccc bbbb bbbbbbb eeeeeeeaaaaa ddddd eeeeeee K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaaa bbbbbb b bbbb cccccccdddddccccccc bbbb bbbbbbb eeeeeeeaaaaa ddddd eeeeeee Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bb bbbbbbbbbbb cccccccdddddcccccccbbbbbbbbbbb bb eeeeeeeeaaaa ddddd eeeeeeee V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbb bb ccc ccddddddd cc cccbb bbbbbb eeeeeeeeaaaaa ddddddd eeeeeeee P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbbbbbb bb ccccccdddddcccccc bb bbbbbbbbbbb eeeeeeeeaaaaa ddddd eeeeeeee A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa bbbbbbbbbbb bb ccccccdddddcccccc bb bbbbbbbbbbb eeeeeeee aaaaddddd eeeeeeee H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaa bbbbbbbbbbb bb ccccccdddddcccccc bb bbbbbbbbbbb eeeeeeeeaaaaa ddddd eeeeeeee ------------------------------------------- Structure #8: Score = 30.6, pattern: 972110, path: 14 15 10 27 6 13 3 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 15() 10() 27() 6() 13() 3() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 15: OriginalScore = 3.52, ModifiedScore = 3.52 1, E.coli_K12 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 2, S.typhimurium 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 3, S.typhi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 4, S.paratyphi 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 5, K.pneumonia 13 UAUGU 17 ... 90 GCAUA 94 [-5.9 kc/m] 6, Y.pestis 13 UAUGUG 18 ... 89 UGCAUA 94 [-6.1 kc/m] (c) Clique 10: OriginalScore = 4.71, ModifiedScore = 4.71 1, E.coli_K12 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 2, S.typhimurium 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 3, S.typhi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 4, S.paratyphi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 5, K.pneumonia 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 8, P.multocida 23 UUUGUUU 29 ... 41 AAACGGG 47 [-5.9 kc/m] 9, A.actinomycetem 21 UCUGUUU 27 ... 39 AAACGGG 45 [-8.4 kc/m] 10, H.influenzae 23 UCUGUUU 29 ... 41 AAACGGG 47 [-8.4 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 6: OriginalScore = 5.58, ModifiedScore = 5.58 1, E.coli_K12 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 2, S.typhimurium 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 3, S.typhi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 4, S.paratyphi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 5, K.pneumonia 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 6, Y.pestis 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 7, V.cholerae 40 UCCU 43 ... 84 AGGA 87 [-6.9 kc/m] 8, P.multocida 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] 10, H.influenzae 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] (f) Clique 13: OriginalScore = 4, ModifiedScore = 4 1, E.coli_K12 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 2, S.typhimurium 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 3, S.typhi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 4, S.paratyphi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 5, K.pneumonia 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 6, Y.pestis 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] (g) Clique 3: OriginalScore = 6.01, ModifiedScore = 6.01 1, E.coli_K12 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 2, S.typhimurium 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 3, S.typhi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 4, S.paratyphi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 5, K.pneumonia 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 6, Y.pestis 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 7, V.cholerae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 8, P.multocida 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 9, A.actinomycetem 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 10, H.influenzae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa bbbbb ccccc ddddd deeeee ccccc d ddddd ffff eeeee bbbbb aaaaffff gggg gggg S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbb cc ccccc ddddd deeeee ccccc ccd ddddd fffff eeeee bbbbb aaaa fffff gggg gggg S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbb cc ccccc ddddd deeeee ccccc ccd ddddd fffff eeeee bbbbb aaaa fffff gggg gggg S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbb cc ccccc ddddd deeeee ccccc ccd ddddd fffff eeeee bbbbb aaaa fffff gggg gggg K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa bbbbb cc ccccc ddddd deeeee ccccc ccd ddddd fffff eeeee bbbbb aaaa fffff gggg gggg Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa bbbbbb ccccccddd deeeee cccccc d ddd ffff eeeee bbbbbb aaaaffff gggg gggg V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 eeee ffffffffff ffff eeee fffffff fffffff gggg gggg P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaa bbbbbb cccccccddd deeeee ccccccc d ddd fffffff eeeee bbbbbb aaa fffffffgggg gggg A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaa bbbbbb cccccccddd deeeee ccccccc d ddd fffffff eeeee bbbbbbaaa fffffffgggg gggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaa bbbbbcccccccddd deeeee ccccccc d ddd fffff eeeee bbbbbaaa fffff gggg gggg ------------------------------------------- Structure #9: Score = 30.6, pattern: 962110, path: 14 17 10 27 6 13 3 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 17() 10() 27() 6() 13() 3() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 17: OriginalScore = 3.5, ModifiedScore = 3.5 1, E.coli_K12 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 2, S.typhimurium 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 3, S.typhi 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 4, S.paratyphi 11 UGUAUGU 17 ... 66 ACGUACA 72 [-9.3 kc/m] 5, K.pneumonia 11 UGUAUGU 17 ... 66 GCGUACA 72 [-9.3 kc/m] (c) Clique 10: OriginalScore = 4.71, ModifiedScore = 4.71 1, E.coli_K12 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 2, S.typhimurium 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 3, S.typhi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 4, S.paratyphi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 5, K.pneumonia 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 8, P.multocida 23 UUUGUUU 29 ... 41 AAACGGG 47 [-5.9 kc/m] 9, A.actinomycetem 21 UCUGUUU 27 ... 39 AAACGGG 45 [-8.4 kc/m] 10, H.influenzae 23 UCUGUUU 29 ... 41 AAACGGG 47 [-8.4 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 6: OriginalScore = 5.58, ModifiedScore = 5.58 1, E.coli_K12 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 2, S.typhimurium 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 3, S.typhi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 4, S.paratyphi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 5, K.pneumonia 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 6, Y.pestis 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 7, V.cholerae 40 UCCU 43 ... 84 AGGA 87 [-6.9 kc/m] 8, P.multocida 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] 10, H.influenzae 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] (f) Clique 13: OriginalScore = 4, ModifiedScore = 4 1, E.coli_K12 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 2, S.typhimurium 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 3, S.typhi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 4, S.paratyphi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 5, K.pneumonia 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 6, Y.pestis 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] (g) Clique 3: OriginalScore = 6.01, ModifiedScore = 6.01 1, E.coli_K12 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 2, S.typhimurium 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 3, S.typhi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 4, S.paratyphi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 5, K.pneumonia 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 6, Y.pestis 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 7, V.cholerae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 8, P.multocida 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 9, A.actinomycetem 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 10, H.influenzae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa a bbbbbbb ccccc ddddd deeeee ccccc d ddddd ffff bbbbbbb eeeee a aaaaffff gggg gggg S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb ccccccddd deeeee cccccc d ddd ffff bbbbbb eeeee a aaaaffff gggg gggg V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 eeee ffffffffff ffff eeee fffffff fffffff gggg gggg P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaaaa bbbbbbbcccccccddd deeeee ccccccc d ddd fff bbbbbbb eeeee aaaaaafff gggg gggg A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaaa bbbbbbbcccccccddd deeeee ccccccc d ddd fff bbbbbbb eeeee aaaaa fffgggg gggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaa aaaaa bbbbbbbcccccccddd deeeee ccccccc d ddd fff bbbbbbb eeeee aaaaaaaaa fffgggg gggg ------------------------------------------- Structure #10: Score = 30.2, pattern: 962110, path: 14 21 10 27 6 13 3 , comseq: 1 2 3 4 5 , incompatible_seq: 14() 21() 10() 27() 6() 13() 3() (a) Clique 14: OriginalScore = 3.9, ModifiedScore = 3.9 1, E.coli_K12 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 2, S.typhimurium 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 3, S.typhi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 4, S.paratyphi 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 5, K.pneumonia 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] 6, Y.pestis 1 GCCA 4 ... 96 UGGC 99 [-8.1 kc/m] (b) Clique 21: OriginalScore = 3.09, ModifiedScore = 3.09 1, E.coli_K12 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 2, S.typhimurium 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 3, S.typhi 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 4, S.paratyphi 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] 5, K.pneumonia 12 GUAUGU 17 ... 70 ACAUAU 75 [-6.9 kc/m] (c) Clique 10: OriginalScore = 4.71, ModifiedScore = 4.71 1, E.coli_K12 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 2, S.typhimurium 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 3, S.typhi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 4, S.paratyphi 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 5, K.pneumonia 23 CGUUU 27 ... 45 AAACG 49 [-5.9 kc/m] 8, P.multocida 23 UUUGUUU 29 ... 41 AAACGGG 47 [-5.9 kc/m] 9, A.actinomycetem 21 UCUGUUU 27 ... 39 AAACGGG 45 [-8.4 kc/m] 10, H.influenzae 23 UCUGUUU 29 ... 41 AAACGGG 47 [-8.4 kc/m] (d) Clique 27: OriginalScore = 2.87, ModifiedScore = 2.87 1, E.coli_K12 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 2, S.typhimurium 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 3, S.typhi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 4, S.paratyphi 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] 5, K.pneumonia 32 UUGAG 36 ... 55 UUCAG 59 [-5.1 kc/m] (e) Clique 6: OriginalScore = 5.58, ModifiedScore = 5.58 1, E.coli_K12 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 2, S.typhimurium 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 3, S.typhi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 4, S.paratyphi 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 5, K.pneumonia 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 6, Y.pestis 39 UCCUG 43 ... 83 UAGGA 87 [-7.7 kc/m] 7, V.cholerae 40 UCCU 43 ... 84 AGGA 87 [-6.9 kc/m] 8, P.multocida 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] 10, H.influenzae 35 UCCUG 39 ... 83 UAGGA 87 [-7.7 kc/m] (f) Clique 13: OriginalScore = 4, ModifiedScore = 4 1, E.coli_K12 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 2, S.typhimurium 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 3, S.typhi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 4, S.paratyphi 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 5, K.pneumonia 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 6, Y.pestis 61 AUGG 64 ... 100 CCGU 103 [-5.1 kc/m] 7, V.cholerae 46 ACGGGCU 52 ... 97 GGCCCGU 103 [-15.2 kc/m] (g) Clique 3: OriginalScore = 6.01, ModifiedScore = 6.01 1, E.coli_K12 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 2, S.typhimurium 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 3, S.typhi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 4, S.paratyphi 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 5, K.pneumonia 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 6, Y.pestis 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 7, V.cholerae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 8, P.multocida 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 9, A.actinomycetem 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] 10, H.influenzae 108 CAGG 111 CAUUAACAUU 122 CCUG 125 [-6.4 kc/m] E.coli_K12 1 GCCAAUCUUUUGUAUGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa a bbbbbbb ccccc ddddd deeeee ccccc d ddddd ffff bbbbbbb eeeee a aaaaffff gggg gggg S.typhimurium 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg S.typhi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg S.paratyphi 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg K.pneumonia 1 GCCAAUCUUUUGUAUGUCUGUACGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGUGCGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCACAAAC 134 aaaa a bbbbbb bbbbccccc ddddd deeeee ccccc d ddddd ffffbbbb bbbbbb eeeee a aaaaffff gggg gggg Y.pestis 1 GCCAAUCUUUUGUAUGUGACUGCAAUGCUAUUUGAGUAUCCUGAAAACGGGCUUUUCAGAAUGGUAUUGCUGUAUAAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAGAAAC 134 aaaa a bbbbbb ccccccddd deeeee cccccc d ddd ffff bbbbbb eeeee a aaaaffff gggg gggg V.cholerae 1 UACCUUUUGCGUGCAAAAGAAGUAGUAUACCGCAACGUAUCCUCGACGGGCUUUGUUGCGGGUAAUUCUUUGAUGAAAGUACUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 eeee ffffffffff ffff eeee fffffff fffffff gggg gggg P.multocida 1 AGCUCAUUUAUGUCCUUGACACUUUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAAAGUGUCAACUUAGUUAAAUAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaa aaaaa bbbbb cccccccddd deeeee ccccccc d ddd fffffff bbbbb eeeee aaaaaaaaa fffffffgggg gggg A.actinomycetem 1 CUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACUAAUCAAUAAACAAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAGC 134 aaaa bbbbb cccccccddd d eeeccccccc d ddd f ffbbbbb eee aaaa ff f gggg gggg H.influenzae 1 AACUCAUUUAUGUCCUUGAUAUUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAAUAUCAAAUUAAUUAAAAUAUAGGAGUGCAUAGUGGCCCGUAUUGCAGGCAUUAACAUUCCUGAUCAUAAAC 134 aaaa aaaaa bbbbb cccccccddd deeeee ccccccc d ddd ffffffbbbbb eeeee aaaaaaaaa ffffffgggg gggg Total time spent with S = 0.56: 2.54 seconds CPU time; 4.97 seconds real time. ************************************** Total Time spent: 2.54 seconds CPU time; 4.97 seconds real time. ../pubstruc_alpha_ecoli.bp alpha_10seq.72out_P0.5_S0.56 Structure 1: TP= 20, FP= 20, FN= 4, CC= 0.65 Structure 2: TP= 16, FP= 22, FN= 8, CC= 0.53 Structure 3: TP= 12, FP= 32, FN= 12, CC= 0.37 Structure 4: TP= 4, FP= 35, FN= 20, CC= 0.13 Structure 5: TP= 4, FP= 35, FN= 20, CC= 0.13 Structure 6: TP= 4, FP= 31, FN= 20, CC= 0.14 Structure 7: TP= 16, FP= 20, FN= 8, CC= 0.54 Structure 8: TP= 0, FP= 33, FN= 24, CC= 0.00 Structure 9: TP= 0, FP= 36, FN= 24, CC= 0.00 Structure 10: TP= 0, FP= 36, FN= 24, CC= 0.00 10 structures, First #1: CC= 0.65, Best #1: CC= 0.65, Average: CC= 0.25