AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons008_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251893 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0237 67 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase #1 TM0258 300 DNA topoisomerase #2 TM0590 128 penicillin-binding protein 2 #3 TM0826 127 hypothetical protein #4 TM0828 29 sugar kinase, pfkB family #5 TM0839 54 rod shape-determining protein RodA #6 TM0871 112 hypothetical protein #7 TM0872 300 conserved hypothetical protein #8 TM0887 55 methylated-DNA-protein-cysteine methyltransferase #9 TM0916_TM0917 340 TM0916: conserved hypothetical protein, TM0917: phosphate permease, putative #10 TM1279 37 hypothetical protein #11 TM1575 271 hypothetical protein Motif 1 AGTGTTAAAATTCCTTCAGAGGTGGTTCTACT 0 45 1 CAGTTCCTCCACCTCTTAAAAAGATTCTTCTTCCCAAA 1 272 0 CCAATCACCTCCAGGATAGATTTTAACCCTGGAG 3 5 1 CGCTCCTCTCGAAAATATCCTTCATCTTTTC 7 2 1 TCATAATTCTCACCTCCGGTTCATTATATTAGCACTTAA 7 52 1 CAACCAAAAATCCCTTCAATTCGGCATTTTAAGAGGCCT 7 190 1 TCTATCACGCCTTCTGATCCTCGTGTGGAAACATTA 7 274 0 CGCCTCCTGATAGAATTATATCAGGGCCT 8 36 0 TACGACCCCTCCTGTGGTGTGTTTTCTATTGTAT 9 5 1 CACATCGGGCCACATTTGGCGGGGTTTTTATACAAAAAA 9 269 0 GAGTATCCCTCCTTAATATGATATTTGCTGTGTA 9 316 0 TGGAAACGGCTTCCTGTGGTGACGCTTGTTTACGATGGA 11 105 1 * ***** * * * * MAP Score: 11.0336 Motif 2 TGTTAAAATTCCTTCAGAGGTGGTTCTACT 0 47 1 CCCATTCGAGCTCTCCGTGGTGCGAAAGAATT 1 104 0 CGAATGGGGTTCACCCGTGGTTCCAAAGACGA 1 128 1 TTCTCTTCAGTGTTGCTCCCCGCTG 2 3 1 TCAGTGTTGCTCCCCGCTGTTGTCCTTGTGGC 2 16 1 TTGCTTTCCGCCGCCACTGGCATCGTGTTCAT 2 88 1 TAATAAAACGTCTCCAGGGTTAAAATCTATCC 3 23 0 ATTCGTTTGTTCTCGTGTGGTATGGTCCCACC 5 10 0 CTCTGGTTTACCTTCGCTGGCAGA 6 2 0 GCCTTCTGATCCTCGTGTGGAAACATTATAAC 7 270 0 TACGACCCCTCCTGTGGTGTGTTTTCTAT 9 7 1 CCCGCCAAGGCCGTGGGGGGTGTATCTCAAGG 9 220 0 GTACTTTACTTCCTCGGTGATGCGACTCCGAC 11 45 1 ATGGAAACGGCTTCCTGTGGTGACGCTTGTTT 11 104 1 ** ** ****** MAP Score: 10.597 Motif 3 AGTAGAACCACCTCTGAAGGAA 0 55 0 ACATAATTCTTTCGCACCACGGAGAGCTCGA 1 100 1 TCTATCGTCTTTGGAACCACGGGTGAACCCC 1 133 0 CAGTTCCTCCACCTCTTAAAAAG 1 287 0 TCTCTTCAGTGTTGCTCCCCGCTGTTGTCCT 2 11 1 CGCTTCGATCCTCCCAGAATGAAC 2 114 0 TACTTGTTCTTTCGCACCAACTTATTTTCAC 6 42 1 CTTAAGGCGGTTACCCCCACGAACAATAACA 6 90 0 TTTCTCATAATTCTCACCTCCGGTTCATTAT 7 48 1 GAGCATGAAAGTTGACCCCCCTATCCCCCTT 9 193 1 GTTTTCCACCCCGAAACGATTAT 10 24 0 TGACGTCGGAGTCGCATCACCGAGGAAGTAA 11 50 0 ** ******** MAP Score: 9.88238 Motif 4 AGTGTTAAAATTCCTTCAGAGGTGGTTCTACT 0 45 1 CCAAGATAGCTCGATTCATCGAGGTTATGGAAAGTT 1 199 1 AAGTTCCGAATCGAATCAGGGTTGGACGGAGTACGA 1 230 1 TTCTCTTCAGTGTTGCTCCCCGCTGTT 2 1 1 TGGCATCGTGTTCATTCTGGGAGGATCGAAGCG 2 105 1 TTGCTGTGTTATTGTTCGTGGGGGTAACCGCCTTAA 6 84 1 ATATCCTTCATCTTTTCGTTCAGGTTTCTCATAATT 7 24 1 CATAGTATAATCGTTTCGGGGTGGAAAAC 10 18 1 ACGGAGTACTTTACTTCCTCGGTGATGCGACTCCGA 11 40 1 GGAAGCCGTTTCCATTCCTCGATGATCTCGATTTCA 11 83 0 ** *** * * ** * MAP Score: 9.74262 Motif 5 GAGCACAAGATCCTCGAGTTAGAGCACATAA 1 75 1 CCATTCGAGCTCTCCGTGGTGCGAAAGAATT 1 104 0 ATAGCTCGATTCATCGAGGTTATGGAAAGTT 1 204 1 CACAAGGACAACAGCGGGGAGCAACACTGAA 2 15 0 TCGTGTTCATTCTGGGAGGATCGAAGCG 2 110 1 TTAAAATCTATCCTGGAGGTGATTGG 3 5 0 TAATAAAACGTCTCCAGGGTTAAAATCTATC 3 24 0 TTTATTACATTCTCCGGGTTTTAATTGTAAT 3 48 1 CTCACTTTTGACTTCGAGGTGATCGT 4 13 1 GTGTTATTGTTCGTGGGGGTAACCGCCTTAA 6 89 1 GGGGTGTATCTCAAGGGGGATAGGGGGGTCA 9 205 0 CGGGCCACATTTGGCGGGGTTTTTATACAAA 9 272 0 TATAATCGTTTCGGGGTGGAAAAC 10 23 1 CGGAGTCGCATCACCGAGGAAGTAAAGTACT 11 44 0 GAAATCGAGATCATCGAGGAATGGAAACGGC 11 84 1 ** ******** MAP Score: 9.71489 Motif 6 TCGAGCTCTCCGTGGTGCGAAAGAATTATGT 1 100 0 CTCGATTCATCGAGGTTATGGAAAGTTCCGA 1 208 1 AATCTATCCTGGAGGTGATTGG 3 1 0 GAATCAAAAACGAGGTGATGCCTC 3 113 1 CTTTTGACTTCGAGGTGATCGT 4 17 1 TGTTATTGTTCGTGGGGGTAACCGCCTTAAG 6 90 1 AGGATATTTTCGAGAGGAGCG 7 0 0 ATAATGAACCGGAGGTGAGAATTATGAGAAA 7 48 0 CCGCCAAGGCCGTGGGGGGTGTATCTCAAGG 9 220 0 AAATGTGGCCCGATGTGATAGAATTTACACA 9 291 1 GAGTACGAAGCGTTGTGAGAGATCTTCTCTC 11 150 1 ********* * MAP Score: 9.04546 Motif 7 AGTAGAACCACCTCTGAAGGAATTTTA 0 50 0 TGAACCCCATTCGAGCTCTCCGTGGTGCGAA 1 110 0 GGTGGGACCATACCACACGAGAACAAA 5 6 1 TACGACCCCTCCTGTGGTGTGT 9 1 1 TACAATAGAAAACACACCACAGGAGGGGTCG 9 12 0 CCCCTTGAGATACACCCCCCACGGCCTTGGC 9 218 1 GCGGGCTCTTTCGAGCCCGCCAAGGCCGTGG 9 236 0 GCGGGCTCGAAAGAGCCCGCATTTTTTTGTA 9 247 1 TTTTTGTATAAAAACCCCGCCAAATGTGGCC 9 270 1 GTTTTCCACCCCGAAACGATTATAC 10 22 0 CTTCAGAGAGAAGATCTCTCACAACGCTTCG 11 155 0 CTGGTTCGGGAACACCCCTCATTGTCAAGAT 11 198 1 ******** ** MAP Score: 7.60694 Motif 8 TGAAAGGGCATATAGCAATAGGGGCGGCTATGG 1 8 1 CCCGTGGTTCCAAAGACGATAGAGGCTTTAATAGT 1 141 1 ATCAGGGTTGGACGGAGTACGACAGGAATTTGGGA 1 244 1 CCGACAGCCACAAGGACAACAGCGGGGAGCAACAC 2 19 0 CGTGTTCATTCTGGGAGGATCGAAGCG 2 111 1 AATAACACAGCAACGAGCACAATGGTGAAAATAAG 6 62 0 TGTACTAATTGAGTGGGAAAAGGAGACATTCTGTT 7 133 0 CCTTGAACGAGAAGGAGGAGTAGAAATCC 8 4 0 CTGTCTCAAACAATGAAGACTAGGAAAACCCAACA 9 70 1 ATAAGGTACCCATTTAGGAAAGAAATTAGAATCTT 9 126 1 TAAAATGTACCATGGAGCATGAAAGTTGACCCCCC 9 179 1 GGGTGTATCTCAAGGGGGATAGGGGGGTCAACTTT 9 200 0 TCAATTACAGGATTGAGGAAAACGGAGTACTTTAC 11 19 1 GGAGTCGCATCACCGAGGAAGTAAAGTACTCCGTT 11 39 0 AAATCGAGATCATCGAGGAATGGAAACGGCTTCCT 11 85 1 ** ***** * ** MAP Score: 6.30299 Motif 9 TGTTAAAATTCCTTCAGAGGTGGTTCTACT 0 47 1 CCCATTCGAGCTCTCCGTGGTGCGAAAGAATTATGTG 1 99 0 GCTGTCGGCTGTCTTGTCGGTGAAATTCGGATGCTGA 2 46 1 GCATCGTGTTCATTCTGGGAGGATCGAAGCG 2 107 1 CCTCACTTTTGACTTCGAGGTGATCGT 4 12 1 CTAATATAATGAACCGGAGGTGAGAATTATGAGAAAC 7 47 0 TACGACCCCTCCTGTGGTGTGTTTTCTATTGTAT 9 7 1 AGCCCGCCAAGGCCGTGGGGGGTGTATCTCAAGGGGG 9 217 0 CATCGGGCCACATTTGGCGGGGTTTTTATACAAAAAA 9 269 0 ATAGTATAATCGTTTCGGGGTGGAAAAC 10 19 1 GTACTTTACTTCCTCGGTGATGCGACTCCGACGTCAT 11 45 1 ATGGAAACGGCTTCCTGTGGTGACGCTTGTTTACGAT 11 104 1 * *** * **** * MAP Score: 5.90252 Motif 10 GATTTCTACTCCTCCTTCTCGTTCAAGGCC 8 11 1 GAACAAGTACTCTCGTTCTCTGGTTTACCT 6 21 0 CAACAGAATGTCTCCTTTTCCCACTCAATT 7 132 1 ATAATTCTCACCTCCGGTTCATTATATTAG 7 54 1 TCCTCGATGATCTCGATTTCAGATGACGTC 11 74 0 CAGTTCCTCCACCTCTTAAAAAGAT 1 285 0 CCGCCACTGGCATCGTGTTCATTCTGGGAG 2 98 1 GAGGCATCACCTCGTTTTTGATTCTAACC 3 108 0 GTTGGGTTTTCCTAGTCTTCATTGTTTGAG 9 74 0 AGCACAAGATCCTCGAGTTAGAGCACATAA 1 76 1 AACTCGAGGATCTTGTGCTCTGGAATAGAC 1 65 0 TTATTTTCACCATTGTGCTCGTTGCTGTGT 6 63 1 TCTATCACGCCTTCTGATCCTCGTGTGGA 7 281 0 CGCCTCCTGATAGAATTATATC 8 43 0 ********** MAP Score: 4.65661 Motif 11 TTTTCTTACCTCCTGTCTGGAAAAG 0 1 1 CTCTAACCATAGCCGCCCCTATTGCTATATGCCC 1 15 0 GGTTTTGCTTTCCGCCGCCACTGGCATCGTGTTC 2 84 1 GTACTTGTTCTTTCGCACCAACTTATTTTCACCA 6 41 1 GTTTCTCATAATTCTCACCTCCGGTTCATTATAT 7 47 1 TCTATCACGCCTTCTGATCCTCGTGT 7 284 0 GGATTTCTACTCCTCCTTCTCGTTCAAG 8 4 1 TACGACCCCTCCTGTGGTGTGTTT 9 0 1 CCCCTTGAGATACACCCCCCACGGCCTTGGCGGG 9 218 1 TTTGTATAAAAACCCCGCCAAATGTGGCCCGATG 9 272 1 TCCTCGGTGATGCGACTCCGACGTCATCTGAAAT 11 55 1 ATCGTAAACAAGCGTCACCACAGGAAGCCGTTTC 11 107 0 * ** * ** **** MAP Score: 4.43014 Motif 12 TAGAACCACCTCTGAAGGAATTTTAACACTTTA 0 42 0 CTCTCCGTGGTGCGAAAGAATTATGTGCTCTAA 1 93 0 TTGGACGGAGTACGACAGGAATTTGGGAAGAAG 1 251 1 CAATCACCTCCAGGATAGATTTTAACCCTGGAG 3 11 1 AATAAGTTGGTGCGAAAGAACAAGTACTCTCGT 6 35 0 CGCCTCCTGATAGAATTATATCAGGGCC 8 37 0 CTTCATTGTTTGAGACAGATGTATCATGAAAAG 9 55 0 GGTACCCATTTAGGAAAGAAATTAGAATCTTCT 9 130 1 TGTGGCCCGATGTGATAGAATTTACACAGCAAA 9 294 1 TACGAAGCGTTGTGAGAGATCTTCTCTCTGAAG 11 153 1 ** ** **** ** MAP Score: 4.0769 Motif 13 CTTTATTTAAAGCTTTTCCAGACAGGAGGTAAGAAAA 0 10 0 AAAGTGTTAAAATTCCTTCAGAGGTGGTTCTACT 0 43 1 AAAGTTCCGAATCGAATCAGGGTTGGACGGAGTACGA 1 229 1 GGGAAGAAGAATCTTTTTAAGAGGTGGAGGAACTG 1 275 1 CCAATCACCTCCAGGATAGATTTTAACCCT 3 3 1 AATGTAATAAAACGTCTCCAGGGTTAAAATCTATCCT 3 22 0 TCCATACAAGTCCAATTAAAGGTTTGGGGTTAGAATC 3 81 1 AAAATAAGGTACCCATTTAGGAAAGAAATTAGAATCT 9 123 1 TTTTAAATGTAACAGGTTAAGAGAAGATTCTAATTTC 9 147 0 CACAGCAAATATCATATTAAGGAGGGATACTC 9 318 1 ATCATAGTATAATCGTTTCGGGGTGGAAAAC 10 16 1 TTCTTGCTTTCAATTACAGGATTGAGGAAAACGGA 11 8 1 CAGTCAGTACTCCTTCTTCAGAGAGAAGATCTCTCAC 11 164 0 * * * **** *** MAP Score: 3.683 Motif 14 CGGGTGAACCCCATTCGAGCTCTCCGTGGT 1 115 0 CCAATCACCTCCAGGATAGATTTTA 3 5 1 ATAGATTTTAACCCTGGAGACGTTTTATTA 3 25 1 ACGATCACCTCGAAGTCAAAAGTGA 4 14 0 TGGGACCATACCACACGAGAACAAACGAAT 5 12 1 AGGCGGTTACCCCCACGAACAATAACACAG 6 87 0 CGCTCCTCTCGAAAATATCCTTCA 7 4 1 TATAATGTTTCCACACGAGGATCAGAAGGC 7 272 1 AGAAAACACACCACAGGAGGGGTCGTA 9 7 0 CCCCCCTATCCCCCTTGAGATACACCCCCC 9 208 1 GAGATACACCCCCCACGGCCTTGGCGGGCT 9 224 1 TGTATAAAAACCCCGCCAAATGTGGCCCGA 9 274 1 ACAAGCGTCACCACAGGAAGCCGTTTCCAT 11 104 0 ********** MAP Score: 3.25464