AlignACE 3.0 10/20/99 AlignACE2 -i PH/PH_operons013_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944255892 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 PH0822 159 121aa long hypothetical protein #1 PH0879 300 367aa long hypothetical hydrogenase expression/formation protein hypD #2 PH0880 112 116aa long hypothetical protein #3 PH0896 300 295aa long hypothetical cation efflux system protein czcD #4 PH0981 62 309aa long hypothetical protein #5 PH0982 61 286aa long hypothetical protein #6 PH1078 293 450aa long hypothetical fmu protein #7 PH1079 24 221aa long hypothetical protein #8 PH1227 117 189aa long hypothetical protein Motif 1 ATATAAATAAACCTTTTCATAACTTAGGTCATTT 0 106 0 TATTGGTAAGCACTTCTTAATGGTGAAGCTAATG 1 51 1 AGTCTAACCTCCCTTTTCACACCTCCAAAATCAA 1 137 0 GTTAGACTTGACCTTCTAACCGATGTAAGAGCTG 1 163 1 GTATTTCCTTAGCTTTTTCCTCGTCGAGTTTTTC 1 232 0 ATGGCAAATAAGCTTTTTCCATTTATCATTCCGA 2 38 0 CAATAGGATAATCTTCTCTCCCTTCTTTACCTTC 3 83 1 TCCCTTCTTTACCTTCTTTGCCTTTGAAAGGAGC 3 101 1 GCTCCTTAACCTCTTCTTCAACTTCCTCTTTCTT 3 133 1 TTTCTTTATCATCTTTTTCTTTTTCTTACAACCG 3 161 1 AATGTTTGAAAACTTTTTTTATATTACTTCACTT 3 256 1 TCATTAGCTCCCCTTCTTCACCCTGAGGAGGAGA 6 20 1 TTCAAACAGGCTCTTCTTAACGATCCTAATTATC 6 52 0 CTATTTCGGGCCCTTTTCCTCTGTTCATAGCTTT 6 149 0 GTACATCATTATCTTATCCCCTATCTCGACTATT 6 178 0 * ******* * * MAP Score: 14.1921 Motif 2 ATTTTTGCCCAGTAAAGTTTAAATGTGTTCGATA 0 52 0 GTGTAACTAAAGACAAGTTTAAATGACCTAAGTT 0 86 1 CCTAAGTTATGAAAAGGTTTATTTATATGAGCAT 0 112 1 GGGATAGGTTGAAAACTTTTGGTTT 1 1 1 ACTTCTTAATGGTGAAGCTAATGTGTCTTGCCGT 1 62 1 TGCCGTCCCAGGAAAGGTTCTTGAAATTAAAGGA 1 90 1 ACTCGACGAGGAAAAAGCTAAGGAAATACTTGAA 1 237 1 ATGATAAATGGAAAAAGCTTATTTGCCATCTAAA 2 43 1 TCTCAATTAAAAACAACCTGAGGTGAGATC 2 92 1 TGTTCCACTTGATGAAGTTGATATCGATAGTGTC 3 14 0 TTTCAAAGGCAAAGAAGGTAAAGAAGGGAGAGAA 3 96 0 GGAAGTTGAAGAAGAGGTTAAGGAGCTCCTTTCA 3 125 0 GTAAGAAAAAGAAAAAGATGATAAAGAAAGAGGA 3 156 0 AAGTAATATAAAAAAAGTTTTCAAACATTAAGTA 3 251 0 GTTTTGGTTTGGTCAAGCTTTAAATTTATTTAGG 4 16 1 ACCACGATTAGGTAAGCCTAAATAAATTTAAAGC 4 32 0 CCTAGAATTAGGTTAGCCTAACGTTTTTAAACGT 5 27 0 TCGAGATAGGGGATAAGATAATGATGTACAGGCA 6 183 1 ATGGTAGGCTAGAAAGCATTATAAAACCAATGTC 6 257 1 GCCTAATTCTAATAAACCTTATATAACTTGTTAG 8 36 0 *** *** * * ** MAP Score: 12.6542 Motif 3 TTGGTAAGCACTTCTTAATGGTGAAGCTAATGT 1 53 1 TCTAACCTCCCTTTTCACACCTCCAAAATCAAC 1 136 0 TAGACTTGACCTTCTAACCGATGTAAGAGCTGG 1 165 1 ATTTCCTTAGCTTTTTCCTCGTCGAGTTTTTCT 1 231 0 GGGAGGAAGTTTTCTCAGCCCTTGGAGGTGAGT 1 275 1 ATGGAAAAAGCTTATTTGCCATCTAAAATTCTG 2 50 1 ATAGGATAATCTTCTCTCCCTTCTTTACCTTCT 3 85 1 CCTTCTTTACCTTCTTTGCCTTTGAAAGGAGCT 3 103 1 TCCTTAACCTCTTCTTCAACTTCCTCTTTCTTT 3 135 1 CAACTTCCTCTTTCTTTATCATCTTTTTCTTTT 3 151 1 ATTAGCTCCCCTTCTTCACCCTGAGGAGGAGAT 6 22 1 CAAACAGGCTCTTCTTAACGATCCTAATTATCT 6 51 0 ATTTCGGGCCCTTTTCCTCTGTTCATAGCTTTT 6 148 0 ACATCATTATCTTATCCCCTATCTCGACTATTT 6 177 0 ****** ** ** MAP Score: 10.8578 Motif 4 CCTTTTCATAACTTAGGTCATTTAAACTTGTCTTTA 0 93 0 CTTTAAATTTATTTAGGCTTACCTAATCGTGGTGAT 4 33 1 CACCTCCTAGAATTAGGTTAGCCTAACGTTTTTAAA 5 30 0 AGGAGGAGATAATTAGGATCGTTAAGAAGAGCCTGT 6 45 1 GAATTAAAGTTAGGATACCCTAAC 7 1 0 CCTCACCCGGAATTAGGTGGCCCTAACAAGTTATAT 8 14 1 GGTTTATTAGAATTAGGCCAGTCGAAAACTTTATAT 8 52 1 * ***** ** ** MAP Score: 10.6548 Motif 5 AGTTGATTTTGGAGGTGTGAAAAGGGAGGT 1 135 1 GTGTGAAAAGGGAGGTTAGACTTGACCTTC 1 149 1 CTCAGCCCTTGGAGGTGAGTGA 1 288 1 AAAAACAACCTGAGGTGAGATC 2 100 1 AAGAAGGTAAAGAAGGGAGAGAAGATTATC 3 89 0 AAGTTGAAGAAGAGGTTAAGGAGCTCCTTT 3 127 0 TAAAGAAAGAGGAAGTTGAAGAAGAGGTTA 3 139 0 CCCACTTTATGGAAGTGAAGTAATATAAAA 3 272 0 CCTAATTCTAGGAGGTGAAGGG 5 49 1 CTCAGGGTGAAGAAGGGGAGCTAATGAAAG 6 17 0 ATGTACAGGCAGAAGTTGGGTCTTGACTAC 6 206 1 CAAAATTTTGAGAGGTGGTGATAA 8 103 1 ********** MAP Score: 9.21831 Motif 6 TCTTAATGGTGAAGCTAATGTGTCTTGCCG 1 65 1 GTGTGAAAAGGGAGGTTAGACTTGACCTTC 1 149 1 AACCGATGTAAGAGCTGGTGATTACGTTAT 1 180 1 CGACGAGGAAAAAGCTAAGGAAATACTTGA 1 240 1 GGAAATACTTGAAGCTTGGGAGGAAGTTTT 1 258 1 CTCAGCCCTTGGAGGTGAGTGA 1 288 1 CAAAGATTGGGAAACTAAAGGAGGATGTTC 3 43 0 CAAAGGCAAAGAAGGTAAAGAAGGGAGAGA 3 97 0 AAGTTGAAGAAGAGGTTAAGGAGCTCCTTT 3 127 0 AAAGAAAGAGGAAGTTGAAGAAGAGGTTAA 3 138 0 CCCACTTTATGGAAGTGAAGTAATATAAAA 3 272 0 TAACGTTTTTAAACGTTGTGCATATGCACA 5 13 0 CAACGTTTAAAAACGTTAGGCTAACCTAAT 5 25 1 CCTAATTCTAGGAGGTGAAGGG 5 49 1 GTGAAGAAGGGGAGCTAATGAAAGGGACTG 6 11 0 CCTTCTTGAAAAACCTGGGGAAATTTTTCA 6 91 1 ATGTACAGGCAGAAGTTGGGTCTTGACTAC 6 206 1 CAAAATTTTGAGAGGTGGTGATAA 8 103 1 ********** MAP Score: 7.87595 Motif 7 AACTATAACGTAATCACCAGCTCTTACATCGGT 1 181 0 ACGATCCTAATTATCTCCTCCTCAGGGTGAAGA 6 34 0 TTATCACCACCTCTCAAAATTTT 8 104 0 GTCCCTTTCATTAGCTCCCCTTCTTCACCCTGA 6 13 1 GTAATCGCCCAATCTATGAAAAAA 0 145 0 CATCATTATCTTATCCCCTATCTCGACTATTTC 6 176 0 TTTGATCCCCCACTTTATGGAAGTG 3 285 0 TACAATAGGATAATCTTCTCTCCCTTCTTTACC 3 81 1 AGGTCAAGTCTAACCTCCCTTTTCACACCTCCA 1 144 0 AAAGGCATTTCAATCGCCAGCCCACATTATTTT 3 195 1 TCCTCTTTCTTTATCATCTTTTTCTTTTTCTTA 3 156 1 AGGAGCTCCTTAACCTCTTCTTCAACTTCCTCT 3 129 1 TTTCGGGCCCTTTTCCTCTGTTCATAGCTTTTA 6 147 0 TCTTGACTACTATCCCTCAACCCAGGATATAAT 6 226 1 ***** ** *** MAP Score: 7.73662 Motif 8 GGCTGAGAAAACTTCCTCCCAAGCTTCAAGT 1 264 0 TCACTCACCTCCAAGGGCTGAG 1 288 0 GATCTCACCTCAGGTTGTTTTT 2 100 0 CAATAGGATAATCTTCTCTCCCTTCTTTACC 3 83 1 GAGGTTAAGGAGCTCCTTTCAAAGGCAAAGA 3 115 0 GAGCTCCTTAACCTCTTCTTCAACTTCCTCT 3 131 1 TTTTTATATTACTTCACTTCCATAAAGTGGG 3 271 1 CCCTTCACCTCCTAGAATTAGG 5 49 0 CCCTTTCATTAGCTCCCCTTCTTCACCCTGA 6 15 1 GATCCTAATTATCTCCTCCTCAGGGTGAAGA 6 34 0 GTACATCATTATCTTATCCCCTATCTCGACT 6 181 0 AACTCCTCACCCGGAATTAGG 8 0 1 TTATCACCACCTCTCAAAATTTTGTG 8 101 0 * ********* MAP Score: 7.45632 Motif 9 AGATATATCGAACACATTTAAACTTTACTGGGCAAAAAT 0 47 1 CATATAAATAAACCTTTTCATAACTTAGGTCATTTAAAC 0 102 0 TTTATATGAGCATTTTTTCATAGATTGGGCGATTAC 0 133 1 AGTGCTTACCAATATTTTTAGACATTTTTAAAACCAAAA 1 26 0 AACTTCCTCCCAAGCTTCAAGTATTTCCTTAGCTTTTTC 1 247 0 TAATATAAAAAAAGTTTTCAAACATTAAGTAGTCAGAGC 3 243 0 TGGTTTGGTCAAGCTTTAAATTTATTTAGGCTTACCTAA 4 20 1 AGGTTAGCCTAACGTTTTTAAACGTTGTGCATATGCACA 5 13 0 CACAGCTTGAAAAATTTCCCCAGGTTTTTCAAGAAGGCC 6 89 0 TAATTCTAATAAACCTTATATAACTTGTTAGGGCCACCT 8 28 0 TGCATATGCACAGATATATAAAGTTTTCGACTGGCCTAA 8 64 0 GCATATGCACAAAATTTTGAGAGGTGGTGATAA 8 94 1 ** *** * * ** * MAP Score: 6.63993 Motif 10 AAGTCTAACCTCCCTTTTCACACCTCCAAAATC 1 139 0 CATTCCGATTTCCTTTTTTATGCATTTTCTGGA 2 13 0 TAATCTTCTCTCCCTTCTTTACCTTCTTTGCCT 3 91 1 GTTAAGGAGCTCCTTTCAAAGGCAAAGAAGGTA 3 110 0 AGCTCCTTAACCTCTTCTTCAACTTCCTCTTTC 3 132 1 CTTCAACTTCCTCTTTCTTTATCATCTTTTTCT 3 148 1 TCTTTATCATCTTTTTCTTTTTCTTACAACCGA 3 163 1 GCAGTCCCTTTCATTAGCTCCCCTTCTT 6 5 1 TTCATTAGCTCCCCTTCTTCACCCTGAGGAGGA 6 19 1 ********* * MAP Score: 4.60185 Motif 11 TTTCATTTTACATTTCCTTTATATGTCAGATATA 0 20 1 TATAAATAAACCTTTTCATAACTTAGGTCATTTA 0 105 0 ACTATCCCGATGTTTCCTTTAATTTCAAGAACCT 1 104 0 TCCCTTTTCACACCTCCAAAATCAACTATCCCGA 1 128 0 AAGCTTCAAGTATTTCCTTAGCTTTTTCCTCGTC 1 241 0 TCACTCACCTCCAAGGGCTGAGAAAACTT 1 281 0 CAAGTGGAACATCCTCCTTTAGTTTCCCAATCTT 3 37 1 CTCCCTTCTTTACCTTCTTTGCCTTTGAAAGGAG 3 100 1 AGCTCCTTAACCTCTTCTTCAACTTCCTCTTTCT 3 132 1 CTTCAACTTCCTCTTTCTTTATCATCTTTTTCTT 3 148 1 TATATTACTTCACTTCCATAAAGTGGGGGATCAA 3 275 1 CCCTTCACCTCCTAGAATTAGGTTAGCCT 5 42 0 GCAGTCCCTTTCATTAGCTCCCCTTCTTC 6 5 1 TTCATTAGCTCCCCTTCTTCACCCTGAGGAGGAG 6 19 1 TTATCACCACCTCTCAAAATTTTGTGCATAT 8 96 0 * ******* * * MAP Score: 1.94252 Motif 12 CTGACATAATTTTCATTTTACATTTC 0 4 1 TTAAACTTGTCTTTAGTTACACATTTTTGCCC 0 76 0 CGGCAAGACACATTAGCTTCACCATTAAGAAG 1 63 0 CCGATGTTTCCTTTAATTTCAAGAACCTTTCC 1 100 0 GGAGGTTAGACTTGACCTTCTAACCGATGTAA 1 159 1 GAACATCCTCCTTTAGTTTCCCAATCTTTGTT 3 43 1 TCTCTCCCTTCTTTACCTTCTTTGCCTTTGAA 3 97 1 AGCTCCTTAACCTCTTCTTCAACTTCCTCTTT 3 132 1 CTTCCTCTTTCTTTATCATCTTTTTCTTTTTC 3 154 1 TTTTATATTACTTCACTTCCATAAAGTGGGGG 3 272 1 CAGTCCCTTTCATTAGCTCCCCTTCTTCACCC 6 11 1 TCTTAACGATCCTAATTATCTCCTCCTCAGGG 6 40 0 TCTGCCTGTACATCATTATCTTATCCCCTATC 6 187 0 *** * ****** MAP Score: 0.250799