AlignACE 3.0 10/20/99 AlignACE2 -i CY/CY_fusions004_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944245966 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 ABC 46 ABC transporter #1 hypothetical 229 hypothetical protein #2 ABC 22 ABC transporter #3 hypothetical 231 hypothetical protein #4 nrtD 56 nitrate transport protein NrtD #5 integral 102 integral membrane components of other binding-protein-dependent transport system #6 nrtD 54 nitrate transport protein NrtD #7 nrtC 74 nitrate transport protein NrtC #8 nrtB 85 nitrate transport protein NrtB #9 nrtA 135 nitrate transport 45kD protein #10 sulA 76 cell division inhibitor #11 malK 68 cytoplasmic membrane protein for maltose uptake #12 opcA 163 OpcA #13 ABC 57 ABC transporter #14 ABC 145 ABC transporter #15 ABC 46 ABC transporter #16 modA 21 molybdate-binding periplasmic protein #17 hypothetical 300 hypothetical protein #18 nrtA 252 nitrate transport 45kD protein #19 nrtC 176 nitrate transport protein NrtC #20 nrtD 72 nitrate transport protein NrtD #21 sbpA 228 sulfate binding protein SbpA #22 hypothetical 36 hypothetical protein #23 cysA 161 sulfate transport system permease protein Motif 1 CAAAAACTTCTAACCCCAAGCTCCCAGACA 1 43 1 AAACCGATTTTCACCCCAATCGCCAACCCA 1 116 1 CATTATAGCGGTCCCCCAGGTGGAATTAGG 3 41 1 GAAGGGAAAATTCCCCCAGATATGGTTCTA 3 198 1 TTTTGATTTGTCACCCCCGGACTAACT 7 57 1 TCCCAGTGATTTGCCCCCTGGGGAAAAGTA 8 11 1 CTGGGGAAAAGTACCCCCTTGACTTTTGTA 8 28 1 TGCTGTCAATGTTCCCCAGAGGATCTACCC 10 11 0 TTACTCCTACTCCCCCCAGGGTC 10 63 1 ATCCCCAAAATAGCCCCAATGAAGATGCTA 11 13 1 ACAGTGACCGTCACCCCATTTTAGG 12 5 0 TCAGTAAGTGTCGCCCCCGTAATCCGTCAA 12 34 0 CTGGCGGGGTTTGGCCCCGGATTTTTGGCG 12 110 1 TGCTGCTTTTTTGCCCCTGGTTCCT 14 130 1 CTGTTCGACATTGCCCCACG 15 36 1 CCTAGCCTAGGAGCCCCAGTGCTCTTCCGT 18 159 1 AAGCCCCCCTGCCCCCCCAAATTTGGGGGG 19 21 1 TCACTCGGTTTCCCCCCAAATTTGGGGGGG 19 32 0 CCGAGTGAAAGTTCCCCAGTATTTCTGGAG 19 54 1 ATAACGTCCAGTGCCCCAGTTCACGGTCGG 21 21 1 ********** MAP Score: 20.2709 Motif 2 AGGATAGAATCGATTGTTTGTCCCTATTTCT 1 8 0 TTGGCCACTCCAGGGATTTGTCAGGCTTGTCAC 1 76 1 CCCAGGGAAGGGACTTTTTGGCCAGTCCATTAT 3 14 1 ACCATATCTGGGGGAATTTTCCCTTCCACATCT 3 191 0 GTCAGATTTTTTCCATCATTACAAA 4 2 1 CTAACAGAGTGAGCAAATTGTCACAAAGAAAAA 5 58 0 ATCAGCTTTTTGTCGCCTCTTTTTA 6 2 1 TTCCCAGTGATTTGCCCCCTGGGGAAA 8 4 1 AAAGTCAAGGGGGTACTTTTCCCCAGGGGGCAA 8 21 0 CATTCCTAGACTGGATTTTTTCCTTGTAAATAT 9 66 0 ATCAACACTGGCGGGGTTTGGCCCCGGATTTTT 12 103 1 GGTTTGGCCCCGGATTTTTGGCGATCGCCGGTT 12 117 1 ACTATTGTTGCTGCTTTTTTGCCCCTGGTTCCT 14 122 1 GTGTTTTCCTGTGAGTATTGCCCAGT 17 284 1 CATGATTGAGCTGGGGTTTGCCCGACCGTGAAC 21 39 0 TTTAGTTTCCCGGAAATTTGGCAGGGAAAGTGA 23 14 0 GGGGACAGACCAAAATTTTGTCAACATAGCCTG 23 78 1 * * * ******* MAP Score: 12.5468 Motif 3 CAAAAAGTCCCTTCCCTGGGCTTT 3 4 0 CATTATAGCGGTCCCCCAGGTGGAATTAGG 3 41 1 TTTGATTTGTCACCCCCGGACTAACT 7 58 1 CCCAGTGATTTGCCCCCTGGGGAAAAGTAC 8 12 1 TTACTCCTACTCCCCCCAGGGTC 10 63 1 ATGGTTTACCCATCCCCGGGGATTATCAAC 12 79 1 TGGCGGGGTTTGGCCCCGGATTTTTGGCGA 12 111 1 TGCTGCTTTTTTGCCCCTGGTTCCT 14 130 1 GACTTTGCCTTGCCCTTGGCCATGGTCGA 17 9 1 GATGTTAGACTTGCCTCGGACCCATCGATA 17 72 0 TCTGATTACCGTCCTCCGGGGCGGTTTTTT 17 228 1 GATCATTCAAGTCCCCTTGGATTAGTCATT 18 92 1 CAGTTTAAAGCGTCCCCTGGTTTACCTAGC 18 135 1 CCTAGCCTAGGAGCCCCAGTGCTCTTCCGT 18 159 1 CTGTTTAAAAGCCCCCCTGCCCCCCCAAAT 19 13 1 CCGAGTGAAAGTTCCCCAGTATTTCTGGAG 19 54 1 ATAACGTCCAGTGCCCCAGTTCACGGTCGG 21 21 1 ********** MAP Score: 10.6894 Motif 4 GGGCTTTTGAACGAAAGGAGGT 0 34 0 GGCCACTCCAGGGATTTGTCAGGCTTGTCACG 1 78 1 GTTGGGGTTTTTGTAACGTTTTCGTAA 1 212 0 CCATATCTGGGGGAATTTTCCCTTCCACATCT 3 191 0 TTCCCAGTGATTTGCCCCCTGGGGAAAA 8 6 1 CCCATCCCCGGGGATTATCAACACTGGCGGGG 12 87 1 CAACACTGGCGGGGTTTGGCCCCGGATTTTTG 12 105 1 GGGGGCAGGGGGGCTTTTAAACAGGCT 19 5 0 AGAAATACTGGGGAACTTTCACTCGGTTTCCC 19 48 0 TTACCTAACAGGGTTTTGGAACCAAACCGATA 20 16 1 CCGTGAACTGGGGCACTGGACGTTATCTCTGA 21 15 0 TGATTGAGCTGGGGTTTGCCCGACCGTGAACT 21 38 0 *** **** *** MAP Score: 10.6455 Motif 5 GATTTTCACCCCAATCGCCAACCCAGAGAA 1 121 1 CCAATCCCCAAAATAGCCCC 11 0 1 CCATGGTTTACCCATCCCCGGGGATTATCA 12 77 1 AAATCCGGGGCCAAACCCCGCCAGTGTTGA 12 104 0 ATTACAACCGGCGATCGCCAAAAATCCGGG 12 125 0 TCAGCCATTGCCGTAAACTGCCT 15 3 1 TAACATCTAGGCGATCGCCGCGATTCACTC 17 95 1 TCACGGTCGGGCAAACCCCAGCTCAATCAT 21 41 1 ATGACACAGACCGAATCCCGACAGAACGGA 21 69 1 ********** MAP Score: 10.3295 Motif 6 CGCCAAAAATCCGGGGCCAAACCCCGCCAG 12 110 0 AACTGCCTGCCCGAGGACAATGACTAATCC 18 110 0 AGGAACCAGGGGCAAAAAAGCAGCAA 14 129 0 GGGCAATACTCACAGGAAAACACCTTTCCC 17 277 0 CAAATCCCTGGAGTGGCCAATGATGTCTGG 1 66 0 CGCTATAATGGACTGGCCAAAAAGTCCCTT 3 21 0 ATGGCCAAGGGCAAGGCAAAGTC 17 3 0 CTGCGGAGGGGACAGACCAAAATTTTGTCA 23 71 1 TTAAGATGTGGAAGGGAAAATTCCCCCAGA 3 188 1 AATTAATCGACCATGGCCAAGGGCAAGGCA 17 15 0 ATCGCCAACCCAGAGAACAACAATAGTTTA 1 134 1 TTGCCCTCTTCCCAGAAAAAAACCGCCCCG 17 244 0 CATTAACGATGCGAGCAAAATATTTTTATG 21 120 1 AAAAAAGGCAGACAGAAAAATTAAATAAGC 18 209 0 GTGGAATTAGGCATGGAAAAGAACGAATTA 3 60 1 GGGGAACATTGACAGCACAATGCAGGTTTT 10 24 1 TTTCTGGGAAGAGGGCAAAATGGGAAAGGT 17 256 1 TCCGTGACAAGCCTGACAAATCCCTGGAGT 1 82 0 CTTTCACTTTCCCTGCCAAATTTCCGGGAA 23 11 1 TACTTTTCCCCAGGGGGCAAATCACTGGGA 8 11 0 AGGTTAAAAAGAGGCGACAAAAAGCTGAT 6 9 0 CAAATTGTCACAAAGAAAAATCAAAATCCC 5 48 0 CAAATATTTACAAGGAAAAAATCCAGTCTA 9 63 1 TTCCTCCTCACACACGAAAATCTGATTACC 17 208 1 ACTAAGGCCAGAAAGGGCAACTGCTGACGA 9 102 0 ATTTTCACCCCAATCGCCAACCCAGAGAAC 1 122 1 TTGGCTAACAGAGTGAGCAAATTGTCACAA 5 65 0 ********** MAP Score: 9.74457 Motif 7 ACAAATCCCTGGAGTGGCCAATGATGTCTGGGA 1 64 0 GTTGTTCTCTGGGTTGGCGATTGGGGTGAAAAT 1 122 0 AGTATTAGGGAAATTGATTGGCTAACAGAG 5 82 0 TTTCCCCAGGGGGCAAATCACTGGGAA 8 4 0 CCCCGGGGATGGGTAAACCATGGCCTAGAATAA 12 67 0 CCATGGCCAAGGGCAAGGCAAAGTC 17 2 0 ACTAATCCAAGGGGACTTGAATGATCTGATTAT 18 85 0 AAGTCCCCTTGGATTAGTCATTGTCCTCGGGCA 18 100 1 CTCCTAGGCTAGGTAAACCAGGGGACGCTTTAA 18 139 0 CCGTAAACCGGGGATATCCATGGCGCTTATTTA 18 185 1 CAAATTTGGGGGGAAACCGAGTGAAAGTTCCCC 19 38 1 GTTCACGGTCGGGCAAACCCCAGCTCAATCATG 21 39 1 AAATTTGGCAGGGAAAGTGAAAGG 23 1 0 *** ** *** ** MAP Score: 9.3304 Motif 8 AAAATCTGATTACCGTCCTCCGGGGCGGTTTTTT 17 224 1 GGCCATGGTTTACCCATCCCCGGGGATTATCAAC 12 75 1 CCCAGTGCTCTTCCGTAAACCGGGGATATCCATG 18 173 1 TGGCCAAAAAGTCCCTTCCCTGGGCTTT 3 4 0 CAGTCCATTATAGCGGTCCCCCAGGTGGAATTAG 3 36 1 CCCGGATTTTTGGCGATCGCCGGTTGTAATTTAG 12 125 1 TCATGACACAGACCGAATCCCGACAGAACGGAGA 21 67 1 GGGTTTGCCCGACCGTGAACTGGGGCACTGGACG 21 25 0 CGAAACTATTTCCCGCTCACCGAT 20 58 1 TTTCCCATTTTGCCCTCTTCCCAGAAAAAAACCG 17 249 0 CAAAAATCCGGGGCCAAACCCCGCCAGTGTTGAT 12 103 0 CAAAATTTAGGGCCCTCCACTCACCCGATTGAGT 17 121 0 CTGTTTAAAAGCCCCCCTGCCCCCCCAAATTTGG 19 13 1 TCGTCAGCAGTTGCCCTTTCTGGCCTTAGTTATT 9 102 1 TTCACCCCAATCGCCAACCCAGAGAACAACAATA 1 125 1 TCTAACATCTAGGCGATCGCCGCGATTCACTCAA 17 93 1 CAGACATCATTGGCCACTCCAGGGATTTGTCAGG 1 67 1 TCAGCCATTGCCGTAAACTGCCTTAACTGTTC 15 8 1 CGTCAACAGTGACCGTCACCCCATTTTAGG 12 6 0 AGGCAGTTTAAAGCGTCCCCTGGTTTACCTAGCC 18 132 1 * *** * ***** MAP Score: 9.15284 Motif 9 CCAGACATCATTGGCCACTCCAGGGATTTGTCA 1 66 1 AAGGGACTTTTTGGCCAGTCCATTATAGCGGTC 3 21 1 AGGCCATGGTTTACCCATCCCCGGGGATTATCA 12 74 1 CCAAAAATCCGGGGCCAAACCCCGCCAGTGTTG 12 105 0 CCCCGGATTTTTGGCGATCGCCGGTTGTAATTT 12 124 1 TCAGCCATTGCCGTAAACTGCCT 15 0 1 CGTGGGGCAATGTCGAACAGTTAAG 15 31 0 TGCCTTGCCCTTGGCCATGGTCGATTAATTTGG 17 15 1 GTCTAACATCTAGGCGATCGCCGCGATTCACTC 17 92 1 CAGTTCACGGTCGGGCAAACCCCAGCTCAATCA 21 37 1 * ***** **** MAP Score: 6.87829 Motif 10 CCCAGACATCATTGGCCACTCCAGGGATTTG 1 65 1 GAAGGGACTTTTTGGCCAGTCCATTATAGCG 3 20 1 ATAAAACACTTTTTGCTTTTCTGAGTTAAAT 3 131 0 TCTGGGGGAATTTTCCCTTCCACATCTTAAC 3 187 0 TTTGTGACAATTTGCTCACTCTGTTAGCCAA 5 64 1 TGCTCACTCTGTTAGCCAATCAATTTCCCTA 5 76 1 ATCGTCAGCAGTTGCCCTTTCTGGCCTTAGT 9 101 1 TAGGCCATGGTTTACCCATCCCCGGGGATTA 12 73 1 ACAAGCGCCCTTTGCTTAATCTGTTCTTAAC 13 25 1 GACTTTGCCTTGCCCTTGGCCATG 17 3 1 TTTATCTATTTTTAGCTTTCCTTAATAATCA 18 61 1 CGTCCCCTGGTTTACCTAGCCTAGGAGCCCC 18 145 1 TGAGCTGGGGTTTGCCCGACCGTGAACTGGG 21 35 0 ATCGTTAATGTTTTGTTATTCGTGTGAATTC 21 99 0 CCTTTCACTTTCCCTGCCAAATTTCCGG 23 7 1 GGTACTTTTATTTAGTTTCCCGGAAATTTGG 23 26 0 TTGACAAAATTTTGGTCTGTCCCCTCCGCAG 23 71 0 ******** ** MAP Score: 6.47009 Motif 11 AAAGCCCAGGGAAGGGACTTTTTGGCCAGTCC 3 10 1 TAGCGGTCCCCCAGGTGGAATTAGGCATGGAA 3 46 1 ACATCCATAGGAAGGCCGTTTTTCCTAGCTAC 7 14 1 ATTGACAGCACAATGCAGGTTTTCATTTTAAC 10 31 1 ACAGATTAAGCAAAGGGCGCTTGTTGCTCCAT 13 17 0 TTGCCCTTGGCCATGGTCGATTAATTTGGAAA 17 19 1 TTACCGTCCTCCGGGGCGGTTTTTTTCTGGGA 17 233 1 GGCAAAATGGGAAAGGTGTTTTCCTGTGAGTA 17 269 1 AATGACTAATCCAAGGGGACTTGAATGATCTG 18 90 0 TTGTCCTCGGGCAGGCAGTTTAAAGCGTCCCC 18 120 1 CTAGGTAAACCAGGGGACGCTTTAAACTGCCT 18 132 0 CCGGGGATATCCATGGCGCTTATTTAATTTTT 18 192 1 ATTTGGGGGGGCAGGGGGGCTTTTAAACAGGC 19 11 0 TGGAGCTTTAGCAGGTCGATTTAGAGGGCGGA 19 79 1 CAATTCCAAGCAGTTTTGATTGAAGCT 22 5 1 ****** * *** MAP Score: 2.73859 Motif 12 TAATCGGAGGGATTTTGATTTTTCTTTGTGA 5 40 1 CTAGTTCTCAATTTTTGATTTGTCACCCCCG 7 45 1 GATGTAAATTGATTTCGGTTTCCGCT 11 52 1 GAGGGCCCTAAATTTTGGTTTAGAATCGTAG 17 138 1 AGCGGGAAATAGTTTCGGTTTGAGTTTTATC 20 44 0 AATTCCAAGCAGTTTTGATTGAAGCTAATTA 22 11 1 ATGTTGACAAAATTTTGGTCTGTCCCCTCCG 23 74 0 AACTAACACCATTTTTGAGTTTGACAATCTA 23 112 1 * ********* MAP Score: 1.28075