AlignACE 3.0 10/20/99 AlignACE2 -i AA/AA_operons013_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944235425 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 rpsP 81 ribosomal protein S16 #1 aq_142 300 putative protein #2 xcpC 253 chromosome assembly protein homolog #3 aq_632 22 hypothetical protein #4 thdF 145 thiophene and furan oxidation protein #5 prfA 260 peptide chain release factor RF-1 #6 ftsY 33 cell division protein FtsY #7 aq_922 26 putative protein #8 aq_1057 52 hypothetical protein #9 htrA 28 periplasmic serine protease #10 rpoD 38 RNA polymerase sigma factor RpoD #11 dnaG 66 DNA primase #12 ffh 40 signal recognition particle receptor protein #13 aq_1723 24 hypothetical protein #14 prfB 255 peptide chain release factor RF-2 Motif 1 GAAAATTTACGGAGGTACGGGAAA 0 67 1 ATTCCCTATGGGAGGTAAGGC 1 289 1 TTTAGAGTTAGGAGGTAAGAGA 10 26 1 TCAGCAAAATGGCGGAAGGGCTAGTTGAGAA 2 34 1 TAGGGGGTGTGGCGGAATTGGCAGACGCGGG 4 76 0 GGAATTTGAAGGAGGTAAGAAAGAAGAGTAA 5 236 1 CTCCTTTTGTGGAGAGAAGCGTAAAGGTGTT 5 117 0 CTTACATAAGGGCGGGAAAAGTTGAAAAAGC 2 139 1 ATTCTTTATGGGCGAAAAGGAGTTAAAAATT 14 18 1 AAAAAGCGAGGGAGGTATACAAACAACTGAG 2 163 1 AAGTTTCCCTGGAAGAAGGGAAGGCGAAAGT 14 125 1 TGGTGGGGGTGGAGGGAGTCGAACCCTCACG 4 17 1 CCCAGGAACTGGAAGAAGAGGTAAAGAAAAA 2 70 1 TATCTTGCGAGGAGGTAGGTAAATGAAGAAG 5 38 1 GGTTGGGTGGTGGGGGTGGAGGGAGT 4 5 1 AAATCCCCTGGGCGAAAAGCCCGTGAGGGTT 4 38 0 AAGGAGTATCGGAGGTGGAAGTTTCCCTGGA 14 107 1 AGATGTTTGGCAAAAAAGGCGTTTTCAGC 2 8 1 CTCCACAAAAGGAGGAACTGTTTACTTAGAA 5 134 1 AAGAAGGGAAGGCGAAAGTAAAACTCGAAAA 14 137 1 ******* *** MAP Score: 17.411 Motif 2 AATTTACGGAGGTACGGGAAA 0 70 1 TTCAAGAATAAGGAGTGGAAGATGGAGCTGT 1 14 1 AAATACCTCTCGAAAAGGAAAAGTATGAGAT 1 51 1 ATTACTCTATAGAAGGGGAAGGTTTAGTAAT 1 144 1 TTTATGATCCGGAAGTGGCAAGAAAAATTAA 1 210 1 GCAAAATGGCGGAAGGGCTAGTTGAGAAGTT 2 37 1 AGTTAGCCCAGGAACTGGAAGAAGAGGTAAA 2 64 1 GGGTGGTGGGGGTGGAGGGAGTCGAACCCTC 4 14 1 GGGGTGTGGCGGAATTGGCAGACGCGGGGGA 4 73 0 TTTTATCTTGCGAGGAGGTAGGTAAATGAAG 5 35 1 TTTCGTATGCGGTTGCGGAAACACCTTTACG 5 98 1 TTTTGTGGAGAGAAGCGTAAAGGTGTTTCCG 5 113 0 AAATGCTTGCGGAATTTGAAGGAGGTAAGAA 5 226 1 GAGGTAAGAAAGAAGAGTAAAAA 5 247 1 GAGCATTGAGTGAAGTTGAAGGAGTATCGGA 14 89 1 AAGGAGTATCGGAGGTGGAAGTTTCCCTGGA 14 107 1 CTGGAAGAAGGGAAGGCGAAAGTAAAACTCG 14 133 1 AAGTAAAACTCGAAAAGGAAGTGCCCTTTGA 14 152 1 AAACCCTAAAGGAAGCTGTAGAAACTTGGGG 14 182 1 GGGGATACAAGGTAGTGGAATAATTGAAAAT 14 209 1 ***** ***** MAP Score: 14.2424 Motif 3 CGAAAATTTACGGAGGTACGGGAAA 0 66 1 TTCAAGAATAAGGAGTGGAAGATGGAGCTG 1 14 1 ATTACTCTATAGAAGGGGAAGGTTTAGTAA 1 144 1 TTTATGATCCGGAAGTGGCAAGAAAAATTA 1 210 1 AATTCCCTATGGGAGGTAAGGC 1 288 1 AGTTAGCCCAGGAACTGGAAGAAGAGGTAA 2 64 1 TGCTTACATAAGGGCGGGAAAAGTTGAAAA 2 137 1 GAAAAAGCGAGGGAGGTATACAAACAACTG 2 162 1 GTTGGGTGGTGGGGGTGGAGGGAGTCGAAC 4 11 1 GCAGACGCGGGGGACTTAAAATCCCCTGGG 4 57 0 TTCTTTAGTTAGGGGGTGTGGCGGAATTGG 4 86 0 CTTGCGAGGAGGTAGGTAAATGAAGAAGGG 5 41 1 CGGAATTTGAAGGAGGTAAGAAAGAAGAGT 5 235 1 TTTTAGAGTTAGGAGGTAAGAGA 10 25 1 CTTTCTCTTTAGAAGTGATATTTTATTTCT 12 19 1 ATGGGCGAAAAGGAGTTAAAAATTCAGGGC 14 25 1 GAGCATTGAGTGAAGTTGAAGGAGTATCGG 14 89 1 AAGGAGTATCGGAGGTGGAAGTTTCCCTGG 14 107 1 TTTCCCTGGAAGAAGGGAAGGCGAAAGTAA 14 128 1 GGGGATACAAGGTAGTGGAATAATTGAAAA 14 209 1 ********** MAP Score: 13.7071 Motif 4 TACATTCAAGAATAAGGAGTGGAAGATGGAGCTG 1 3 1 AGACGTTTATGATCCGGAAGTGGCAAGAAAAATTAAGCAGG 1 205 1 TTTCAGCAAAATGGCGGAAGGGCTAGTTGAGAAGTTAGCCC 2 32 1 TGAGAAGTTAGCCCAGGAACTGGAAGAAGAGGTAAAGAAAA 2 59 1 AAATCCCAAAGATCCTGAACTACTTTTTAAGCTCGGAATTG 2 98 1 AAGGGCGGGAAAAGTTGAAAAAGCGAGGGAGGTATACAAAC 2 146 1 GAGAAACTTAGACAAAGAAAAGGCTAACGAACTACTTGACA 2 191 1 GGTTGGGTGGTGGGGGTGGAGGGAGTCGAAC 4 0 1 GTTAGGGGGTGTGGCGGAATTGGCAGACGCGGGGGACTTAA 4 68 0 AACTTTTTTATCTTGCGAGGAGGTAGGTAAATGAAGAAGGG 5 30 1 AAAGCCCGCTTACTACGAAATGCTTGCGGAATTTGAAGGAG 5 209 1 AATGCTTGCGGAATTTGAAGGAGGTAAGAAAGAAGAGTAAA 5 227 1 CTTTAATAAATTTTTAGAGTTAGGAGGTAAGAGA 10 14 1 TCTGTGTCAAGCTGAAGAAATACCTGTAAAATCAAATT 11 7 0 ATTATTCTTTATGGGCGAAAAGGAGTTAAAAATTCAGGGCA 14 15 1 AGCATTGAGTGAAGTTGAAGGAGTATCGGAGGTGGAAGTTT 14 90 1 AGAAGGGAAGGCGAAAGTAAAACTCGAAAAGGAAGTGCCCT 14 138 1 AGTAAAACTCGAAAAGGAAGTGCCCTTTGAAACCCTAAAGG 14 153 1 * *** ** * *** MAP Score: 11.6119 Motif 5 CTTGTTCTAGTACTTTAAACTTTCCTTTATAC 1 248 1 CTTTAAACTTTCCTTTATACTTAATAAAAATT 1 260 1 CAGATACGGATAAATTATACTTCGTAAATTCT 2 231 0 GATTTTATTAATTTAATTCTGT 3 2 0 ACTAAAGAAATATATTATACTTATAGAAAGAA 4 107 1 AGGAACTTTATTTTATACTTGTAGGT 7 8 1 TTTGTAATTTTATCCCTTAAATAACAT 8 35 0 CAAAAGAATTTATTTTATTTCTGATCTGTGTC 11 40 0 TTAGAAGTGATATTTTATTTCTT 12 27 1 AAAAAAGGTATTTTAATCTTAGTG 13 8 1 GTTAAATTATTCTTTATGGGCGAA 14 2 1 ** ***** *** MAP Score: 11.4981 Motif 6 TTAATAACAGCTCCATCTTCCACTCCTTATTCTTG 1 16 0 ATAGAGTAATCTGGCTCTCCTCTCAAGTCTTTATG 1 119 0 AACTTCTCAACTAGCCCTTCCGCCATTTTGCTGAA 2 33 0 GGATTTTTCTTTACCTCTTCTTCCAGTTCCTGGGC 2 69 0 CTCCCTCCACCCCCACCACCCAACC 4 0 0 GATTTTAAGTCCCCCGCGTCTGCCAATTCCGCCAC 4 64 1 TCTGCCAATTCCGCCACACCCCCTAACTAAAGAAA 4 82 1 TTACACAATGCTGGCACGTCATGCCCTGAATTTTT 14 42 0 TCCGATACTCCTTCAACTTCACTCAATGCTCTTTT 14 85 0 TCCAGGGAAACTTCCACCTCCGATACTCCTTCAAC 14 103 0 TTTACTTTCGCCTTCCCTTCTTCCAGGGAAACTTC 14 124 0 CCCCAAGTTTCTACAGCTTCCTTTAGGGTTTCAAA 14 178 0 ** ** * *** ** MAP Score: 10.5077 Motif 7 TTAAAAATACCTCTCGAAAAGGAAAAGTATGAGATAA 1 47 1 ATAAAGGAATATCCTGAAACGGGAACGATGTTAATAG 1 80 1 GACGTTTATGATCCGGAAGTGGCAAGAAAAATTAAGC 1 206 1 TTAGCCCAGGAACTGGAAGAAGAGGTAAAGAAAAATC 2 66 1 AGGGCGGGAAAAGTTGAAAAAGCGAGGGAGGTATACA 2 147 1 CAACTGAGAAACTTAGACAAAGAAAAGGCTAACGAAC 2 186 1 ATGCTTGCGGAATTTGAAGGAGGTAAGAAAGAAGAGT 5 228 1 GTATTTCTTCAGCTTGACACAGATCAGAAATAAAATA 11 25 1 GCATTGAGTGAAGTTGAAGGAGTATCGGAGGTGGAAG 14 91 1 GTGGAAGTTTCCCTGGAAGAAGGGAAGGCGAAAGTAA 14 121 1 GCGAAAGTAAAACTCGAAAAGGAAGTGCCCTTTGAAA 14 148 1 * ** **** ** * MAP Score: 9.75079 Motif 8 TTCGAGAGGTATTTTTAATAACAGCTCCATCTTCCAC 1 28 0 TTCAGGATATTCCTTTATCTCATACTTTTCCTTTTCG 1 61 0 GCTCCTGCTTAATTTTTCTTGCCACTTCCGGATCATA 1 212 0 TAGTACTTTAAACTTTCCTTTATACTTAATAAAAATT 1 255 1 GATCTTTGGGATTTTTCTTTACCTCTTCTTCCAGTTC 2 75 0 AAGCGAAGAACTTTTATAATAACTTTTTTATCTTG 5 8 1 TAAAACCCACAACTTTCGTATGCGGTTGCGGAAACAC 5 85 1 TTGCGGAAACACCTTTACGCTTCTCTCCACAAAAGGA 5 110 1 TTTTTACTCTTCTTTCTTACCTCCTTCAAATTCCGC 5 234 0 AGGAACTTTATTTTATACTTGTAGGT 7 3 1 TTAACTTTAATAAATTTTTAGAGTTAGGA 10 2 1 ATACTCCTTCAACTTCACTCAATGCTCTTTTTACGGT 14 79 0 TCGCCTTCCCTTCTTCCAGGGAAACTTCCACCTCCGA 14 115 0 TTCCTTTTCGAGTTTTACTTTCGCCTTCCCTTCTTCC 14 135 0 AAGTTTCTACAGCTTCCTTTAGGGTTTCAAAGGGCAC 14 172 0 * ***** * *** MAP Score: 8.93389 Motif 9 AAGGTTTTTTGTGGTAAACTTATTGTGTTAAAAT 0 24 1 TAAACTTATTGTGTTAAAATTATTCGTCCGAAAA 0 38 1 GGAAAAGTATGAGATAAAGGAATATCCTGAAACG 1 67 1 ACTGGAAGAAGAGGTAAAGAAAAATCCCAAAGAT 2 77 1 AAAAGCGAGGGAGGTATACAAACAACTGAGAAAC 2 164 1 ACAGAATTAAATTAATAAAATC 3 3 1 CCACACCCCCTAACTAAAGAAATATATTATACTT 4 95 1 TGCGAGGAGGTAGGTAAATGAAGAAGGGTATTCA 5 43 1 TACCGACCGGTCGGTATAATAATAGT 8 2 0 TGTTATTTAAGGGATAAAATTACAAA 8 36 1 TTAACTTTAATAAATTTTTAGAGTTAGGAG 10 6 1 ACACAGATCAGAAATAAAATAAATTCTTTTGAGT 11 41 1 AAGAAATAAAATATCACTTCTAAAGA 12 24 0 GGGCGAAAAGGAGTTAAAAATTCAGGGCATGACG 14 27 1 AATTTCAATTGCAATAAATTATAA 14 241 1 * * **** *** * MAP Score: 6.38642 Motif 10 TTTTTAATAACAGCTCCATCTTCCACTCCTTATTCTTGAATGTA 1 9 0 ATTGTGTAAATCTCCCCGTTTTTAAATTCTATTACTAAACCTTCC 1 160 0 GGATTTTTCTTTACCTCTTCTTCCAGTTCCTGGGCTAACTTCTCA 2 59 0 GAGGGTTCGACTCCCTCCACCCCCACCACCCAACC 4 0 0 GATTTTAAGTCCCCCGCGTCTGCCAATTCCGCCACACCCCCTAAC 4 64 1 ACTTAGAAGTTTGCAACCAGTGTCACCCCTTTTACGCGGGCAAAC 5 157 1 TCCGATACTCCTTCAACTTCACTCAATGCTCTTTTTACGGTGTTT 14 75 0 TTCGCCTTCCCTTCTTCCAGGGAAACTTCCACCTCCGATACTCCT 14 108 0 GCTTCCTTTAGGGTTTCAAAGGGCACTTCCTTTTCGAGTTTTACT 14 153 0 * * * * ** * ** * MAP Score: 3.46846 Motif 11 TCAAGAATAAGGAGTGGAAGATGGAGCTGTTATTAAAA 1 15 1 TTACTCTATAGAAGGGGAAGGTTTAGTAATAGAATTTA 1 145 1 AGACGTTTATGATCCGGAAGTGGCAAGAAAAATTAAGC 1 205 1 GTTAGCCCAGGAACTGGAAGAAGAGGTAAAGAAAAATC 2 65 1 GCTTACATAAGGGCGGGAAAAGTTGAAAAAGCGAGGGA 2 138 1 GGTTGGGTGGTGGGGGTGGAGGGAGTCGAACCCT 4 6 1 TTAGTTAGGGGGTGTGGCGGAATTGGCAGACGCGGGGG 4 74 0 CTACGAAATGCTTGCGGAATTTGAAGGAGGTAAGAAAG 5 221 1 ATTCTTTATGGGCGAAAAGGAGTTAAAAATTCAGGGCA 14 18 1 AGTTTCCCTGGAAGAAGGGAAGGCGAAAGTAAAACTCG 14 126 1 CCTAAAGGAAGCTGTAGAAACTTGGGGATACAAGGTAG 14 186 1 GGGATACAAGGTAGTGGAATAATTGAAAATAAATTTCA 14 210 1 * * **** * ** * MAP Score: 2.00863 Motif 12 GAGCTGTTATTAAAAATACCTCTCGAAAAGGA 1 38 1 ATTCTATTACTAAACCTTCCCCTTCTATAGAG 1 148 0 ACGTCTATTGTGTAAATCTCCCCGTTTTTAAA 1 179 0 TTCTAGTACTTTAAACTTTCCTTTATACTTAA 1 252 1 TTATACTTAATAAAAATTCCCTATGGGAGGTA 1 274 1 ACTTCTCAACTAGCCCTTCCGCCATTTTGCTG 2 35 0 CAGTTGTTTGTATACCTCCCTCGCTTTTTCAA 2 160 0 CTTTTCTTTGTCTAAGTTTCTCAGTTGTTTGT 2 181 0 CCCGTGAGGGTTCGACTCCCTCCACCCCCACC 4 18 0 CGCGGGGGACTTAAAATCCCCTGGGCGAAAAG 4 50 0 CCCCCGCGTCTGCCAATTCCGCCACACCCCCT 4 74 1 CCCTTCTTCATTTACCTACCTCCTCGCAAGAT 5 39 0 GCTTGAAAACTTTCTCTTTAGAAGTG 12 4 1 CACTAAGATTAAAATACCTTTTTT 13 4 0 GCCCTGAATTTTTAACTCCTTTTCGCCCATAA 14 23 0 CCGATACTCCTTCAACTTCACTCAATGCTCTT 14 87 0 CTTCTTCCAGGGAAACTTCCACCTCCGATACT 14 111 0 GAGTTTTACTTTCGCCTTCCCTTCTTCCAGGG 14 131 0 * ********* MAP Score: 0.321638