AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_fusions002_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944250945 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0030 62 oligopeptide ABC transporter, permease protein #1 TM0031 24 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #2 TM0032 300 transcriptional regulator, XylR-related #3 TM0059 28 oligopeptide ABC transporter, permease protein #4 TM0060 300 oligopeptide ABC transporter, permease protein #5 TM0300 237 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative #6 TM0301 64 oligopeptide ABC transporter, permease protein #7 TM0503 300 oligopeptide ABC transporter, permease protein #8 TM0524 209 conserved hypothetical protein #9 TM0526 30 host factor I #10 TM0532 58 oligopeptide ABC transporter, permease protein #11 TM1066 61 oligopeptide ABC transporter, permease protein #12 TM1067 243 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #13 TM1149 43 oligopeptide ABC transporter, permease protein #14 TM1153 25 oligopeptide ABC transporter, permease protein #15 TM1155 82 glucose-6-phosphate 1-dehydrogenase #16 TM1198 69 oligopeptide ABC transporter, permease protein #17 TM1199 154 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #18 TM1222 55 oligopeptide ABC transporter, permease protein #19 TM1223 131 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #20 TM1746 267 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein Motif 1 CCCCGCCCCTCGGGGCGGGGTTTTAAAAAA 18 18 1 ATGGAACTTTCGGGGAGGGGTTCCCCCTCC 16 12 1 CCCCGCCCCGAGGGGCGGGGTCATCATT 18 8 0 CAGAATTTGAAGGGGAGGGGAAGATCCCCT 10 19 0 CCGCCCCGTCTGGGGCGGGGGAATG 6 5 0 CCCGCCCCAGACGGGGCGGGCTCTTCTTTG 6 16 1 TCTATCGGGAGGGGATCTTCCCCT 10 4 1 TTTTCAAGTTAAGGGAGGGGGAACCCCTCC 16 25 0 GGCCCCACTTCGGGGCCGGGTTCCACAAAA 0 19 1 ACATCCATTTAAAGGAGGGGATGTTGT 20 250 1 GGCCCCGAAGTGGGGCCGGGAAAAGA 0 6 0 TGAAATCACATCGAGGGGGGAG 9 18 1 GAAAGCCGCCCCGGGAAGGGGCGGCGGGAG 13 11 0 ACGATAGGGGAGGGCCTCCCTCCC 11 4 1 GATTGATAAACCAGGGGGCGAACGGGTTCG 7 171 0 ATGACACCAGTAGAGGGGGGATTTTC 17 138 1 ACCTTTTTTACGAGGAGGTGGGGACCTCGG 7 113 1 AAACAATTTTCGAGGAGGTGTACTGG 4 284 1 CAATTTACGACCAGGAGGTGTACCAG 7 284 1 CATACTCTTTTAAGGGGGTGTTCTT 19 116 1 AACTTTTTTTTAAGGGGGTGTTTTT 5 222 1 TTCTATAACGCAGGGGGTGGT 12 232 1 GGTGTAAATAAAAGGGAGGGAGGCCCTCCC 11 17 0 AAAATTCCTTAAAAGGGGGG 15 0 0 GGGCTTCGGAAGAGGGCGTGAGAGA 7 5 0 TGCGGGCCCGCCGGGGTGTGGGGAAAGAGG 20 11 0 AACGGGTTCGACGGGGATGGAGTCCCCTGG 7 151 0 ********** MAP Score: 53.2367 Motif 2 TTAACAAAAAATAACGGCAACCGA 2 1 1 AAATCAGTTGTAACTCAAAGAAAATATTAGAAT 2 139 1 ATTTGAACTATAATTCGAAATAATTCCTGTTAT 2 170 1 TATTCACTCATAATCATAAAAAATGAGTATTAC 2 200 1 AATTTTTTCTTTACAAAAAATAACTTTAGGGTG 4 47 0 TATTTCTTTTTAATTTGAAATAATCGTCTTTTT 5 129 1 TGAGTAAGCTTTACTAAAAACAAAACTTTTTTT 5 199 1 TCCTTATGTCTAATCTCAAAGAAGAGCCCGCCC 6 29 0 TTACAACCCCTTACAACAAAAAAGCGCCCCTTA 12 41 0 AAAACTAATATAATCAATAATAATCAACCATAT 12 82 1 TAAGGAATTTTAACACAAAGGAAATTAGTTATT 15 19 1 AAGAAAAGATTAACCACAAATAAATCTTTCTAT 17 43 0 TTGTTGCAAATAATCAGAAATAAATCTTGATAA 19 17 1 GAAATGACAATAATTCAAAATAAATGGATATAT 20 100 1 TAAATAACACTTACTAATAAAAAGATTATGTTA 20 214 0 **** * *** ** MAP Score: 15.701 Motif 3 GAATTTGAACTATAATTCGAAATAATTCCTGTTAT 2 168 1 AAAAAATTGAGCTTCTTCGATAAGAAATTATACCA 4 72 1 TAATTTGAAAGTTCCTTTCACAATAATGGTATAAT 4 98 0 CAATAATTTCTGCTATTCGAAGTTAATGTGGTGTA 4 152 1 TGGTGCTTGATTTCTTTTGATGTGATAGTGTAGAA 4 198 1 TCCTCGAAAATTGTTTTCGAAATCAGAAGTTACAA 4 265 0 TATCGTTCCATATTTTTTCATATCACATTTACGCA 5 86 0 CATATTTCTTTTTAATTTGAAATAATCGTCTTTTT 5 127 1 GAAATAATCGTCTTTTTTGAGATTTTGAATGAAAA 5 145 1 CGGGGCGGGCTCTTCTTTGAGATTAGACATAAGGA 6 27 1 TTCAATTCCTGGTATTTCGACATCAACCGATTGTG 8 128 0 TTCTATTTTGAAATCACATCGAGGGG 9 1 1 ATTTATCTCTTATAGTTCGATATTAGGATTATTTT 12 113 1 CCTTGTTGTATGTTTGTTGATATTATATTGATAAC 12 165 1 TTCCTCCTTTGTTCTTTTCAAGTTAAGGGAGGGGG 16 34 0 AATAAATCTTTCTATTTCCAGATAATCACCTGTAA 17 23 0 ACTTAACCCTGTCGCTTCGAAATGACAATAATTCA 20 82 1 * * ***** ** * MAP Score: 15.0926 Motif 4 TCAATTCTCACTCCCCACTCTGTTTT 0 46 0 CTTCTTCCTCTTCCACACACCTATCACC 3 7 0 ATTATAACGTTTCCCACGAACTAAGCAAACGT 5 53 1 CATTCCCCCGCCCCAGACGGGGCG 6 2 1 TCTCTCACGCCCTCTTCCGAAGC 7 1 1 CCGTCGAACCCGTTCGCCCCCTGGTTTATCAA 7 167 1 GGGAGGGGATCTTCCCCTCCCCTTCAAATTCT 10 16 1 ACTCCCGCCGCCCCTTCCCGGGG 13 1 1 CGGGGAGGGGTTCCCCCTCCCTTAACTTGAAA 16 22 1 AATGATGACCCCGCCCCTCGGGGCGGG 18 5 1 CCCTCTTTCCCCACACCCCGGCGGGCC 20 5 1 GATTCATCTTCCACCACGCACTTAACCCTGTC 20 63 1 ** **** **** MAP Score: 13.6641 Motif 5 CGGCCCCGAAGTGGGGCCGGGAAAAGA 0 6 0 CGGCCCCACTTCGGGGCCGGGTTCCACAAAA 0 18 1 GAAGATAGATAAGAAGCAGGAGGAATATGGA 2 279 1 TGATAGGTGTGTGGAAGAGGAAGAAG 3 12 1 GAAAACAATTTTCGAGGAGGTGTACTGG 4 282 1 CGCCCCGTCTGGGGCGGGGGAATG 6 3 0 CCCCGCCCCAGACGGGGCGGGCTCTTCTTTG 6 15 1 TGGCTGGGCTTCGGAAGAGGGCGTGAGAGA 7 9 0 CCACCTTTTTTACGAGGAGGTGGGGACCTCG 7 111 1 GAACGGGTTCGACGGGGATGGAGTCCCCTGG 7 151 0 TAAACCAGGGGGCGAACGGGTTCGACGGGGA 7 164 0 CCCAATTTACGACCAGGAGGTGTACCAG 7 282 1 ACTGAGGCCAAGAAGGCGGAAGCATTTCAG 8 9 1 TTGAAATCACATCGAGGGGGGAG 9 17 1 TCTATCGGGAGGGGATCTTCCCCT 10 3 1 AATTTGAAGGGGAGGGGAAGATCCCCTCCCG 10 15 0 TCAAATTCTGTTCAAAGAGGTGATCTTGC 10 39 1 ACGATAGGGGAGGGCCTCCCTCCC 11 3 1 TGTAAATAAAAGGGAGGGAGGCCCTCCCCTA 11 14 0 CCTTAGATAGAACGAGGTGGTAAATC 11 45 1 ATCATTCTATAACGCAGGGGGTGGT 12 228 1 GCCCCGGGAAGGGGCGGCGGGAGT 13 3 0 TAAAATTCCTTAAAAGGGGGG 15 0 0 TAAAAATCCAGAAAGGCAGGTGAGATC 15 65 1 TCATGGAACTTTCGGGGAGGGGTTCCCCCTC 16 10 1 TTTCAAGTTAAGGGAGGGGGAACCCCTCCCC 16 23 0 TATGACACCAGTAGAGGGGGGATTTTC 17 137 1 ACCCCGCCCCGAGGGGCGGGGTCATCATT 18 8 0 GGTTTTAAAAAAAGAAGGAGGTAGGAGTC 18 36 1 CCGGGGTGTGGGGAAAGAGGG 20 0 0 AACATCCATTTAAAGGAGGGGATGTTGT 20 249 1 * ********* MAP Score: 12.5669 Motif 6 GGTTGCCGTTATTTTTTGTTAA 2 2 0 ATTTCGATGGATTTTTTGTTACACACATTC 2 60 1 TCAAATTCTAATATTTTCTTTGAGTTACAA 2 146 0 AAGAAGCTCAATTTTTTCTTTACAAAAAAT 4 59 0 GGTGCTTGATTTCTTTTGATGTGATAGTGT 4 199 1 ATCGTTCCATATTTTTTCATATCACATTTA 5 90 0 TAAAAACAAAACTTTTTTTTAAGGGGGTGT 5 213 1 CTTCTGACGCTTCTTTTCTTTATGATCTTT 8 53 1 TTTCTTTATGATCTTTGTTTTTCTCGTGAG 8 67 1 CTGTTCCTCTATCTTTGTCTTCAATTCCTG 8 152 0 ATATTAGTTTTCCTTTTGCTTACAACCCCT 12 63 0 GTTCGATCTTTTCCTCCTTTGTTCT 16 54 0 TTTGTGGTTAATCTTTTCTTTTTCTTTTTT 17 56 1 TCTTTTCTTTTTCTTTTTTTCAACCTTTTC 17 67 1 CTTTTTTTCAACCTTTTCTTATTCTTGATT 17 79 1 TCCTACCTCCTTCTTTTTTTAAAACCCCGC 18 32 0 CCATAACATAATCTTTTTATTAGTAAGTGT 20 211 1 ********** MAP Score: 10.0848 Motif 7 CGGGGTTTTAAAAAAAGAAGGAGGTAGGAG 18 33 1 TCAAAATCTCAAAAAAGACGATTATTTCAA 5 143 0 GAATCTTTGAAAAAAAAACGGGCCCACTGC 20 38 0 ACTTGAAAAGAACAAAGGAGGAAAAGATCG 16 46 1 CGGGTTCCACAAAAACAGAGTGGGGAGTGA 0 35 1 TTCAAATTAGAAAAACGAAGATATTCTGCA 4 124 1 AGCTCACGAGAAAAACAAAGATCATAAAGA 8 69 0 AACCCCTTACAACAAAAAAGCGCCCCTTAT 12 40 0 TCATAATCATAAAAAATGAGTATTACTCGT 2 207 1 GAAAAAAAGAAAAAGAAAAGATTAACCACA 17 58 0 GATCATAAAGAAAAGAAGCGTCAGAAGTCC 8 50 0 ACCTCCTCGTAAAAAAGGTGGGACAAAGAA 7 102 0 AACACCCCCTTAAAAAAAAGTTTTGTTTTT 5 214 0 TTAACAAAAAATAACGGCAACCGATC 2 6 1 TTTATCCATATACAAAGGAGGT 1 12 1 TTTGTAAAGAAAAAATTGAGCTTCTTCGAT 4 63 1 ATGTGATATGAAAAAATATGGAACGATAAG 5 93 1 ********** MAP Score: 8.70049 Motif 8 TTTGAACTATAATTCGAAATAATTCCTGTTATTCAC 2 171 1 TTTTTGAGTCATATCGTTATAATTTCTTTCTGAGGA 2 245 1 AAATAACTTTAGGGTGATATAATTTCCCAAAAGAAG 4 27 0 TCCTTTCACAATAATGGTATAATTTCTTATCGAAGA 4 85 0 AAACGAAGATATTCTGCAATAATTTCTGCTATTCGA 4 136 1 ATTCGAAGTTAATGTGGTGTAATCGCCGTTAATGGT 4 166 1 ATTTCTTTTTAATTTGAAATAATCGTCTTTTTTGAG 5 130 1 AAATCTTTCTATTTCCAGATAATCACCTGTAATTGT 17 19 0 GATTTCTAATATTGCGGAATAATTACTCTTCACTTC 20 141 1 * ** ****** * MAP Score: 7.00106