AlignACE 3.0 10/20/99 AlignACE2 -i CP/CP_operons004_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237264 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 atpE 300 ATP Synthase Subunit E #1 CPn0087 48 CT309 hypothetical protein #2 atpK 94 ATP Synthase Subunit K #3 yscU 300 Yop Translocation Protein U #4 rpsD 114 Sigma-28/WhiG Family #5 flhA 277 Flagellar Secretion Protein #6 polA 23 DNA Polymerase I #7 sohB 123 Protease #8 CPn0708 33 CT668 hypothetical protein #9 CPn0710 21 CT666 hypothetical protein #10 CPn0711 46 CT665 hypothetical protein #11 CPn0713 300 CT663 hypothetical protein #12 yscL 120 Yop Translocation L #13 fliF 291 Flagellar M-Ring Protein #14 xerD 65 Integrase/recombinase Motif 1 TTTTCTACTATTCTTCTTTATCTCTAAGAT 3 161 1 AAAGTAGGCCTTCTTCTAGATCCAAAGATT 0 20 0 CAAAGCAATTTTCTTCTAGAACATCTCTGC 0 152 1 TTTTATAATTTTCATCTTTAAGCTTTTCTG 7 52 1 AGAAAGGCAATTCTTCTTTTTTGAATTCTA 0 61 1 GAGCATGGGATTTATCTTGAAGATATCAAA 0 126 1 TTGTGGCCTCTTGTTCTTTATAATGAAAAA 11 106 1 TTCAGCTCGATTTTTCTTGTGGCCTCTTGT 11 90 1 TGTTTAAAAATTTTTTTTGAATTAATCTAA 4 69 1 TTACCGCTTATTCTTTTAGAAAAGAATTTT 0 274 0 TGCCATCGTATTCTTCTCTATCAAAAAGTA 13 231 0 TGTCGTGTTATTTTTCTATACTTTGTATAA 12 35 0 CTTTTCGTTATTGTTCTTTTTTTCTACTAT 3 142 1 AAATTTTTTTTTATCTAGTTATT 4 101 0 TGAAGCATCTTTGATCTTGTCGACTATTTC 5 173 0 CAAAGCACTCTTGATTTTGAAGGTACTA 3 8 0 TACTTTCGTATTTTTTTTGTTGGTGTAAAT 4 37 1 TCCCCCCAACTTCTTTTAGTAGAAATCCCT 13 13 1 AGAAATCGTTTTTATTTTTAAAGTTCGTAT 11 176 1 ATAGGTTTCGTTTATTTTTATGAAGGACTC 13 269 1 ATCTCTAAGATTCATTTATAATCTTACTAA 3 180 1 TATGCTAACGTTGATCTCTTTTACTCGAAA 5 139 0 ********** MAP Score: 20.4229 Motif 2 GATATATGGAAGAGGGAAGTATGAGAAAAGG 5 230 1 CTTGCCTTTAAGAGAGGAACATGAAAGAAAT 2 19 1 AGGTCCAGAGGAGAGAAATCT 9 6 1 TTAGAGAGTTAGAGGAGAGCATGGGATTTAT 0 110 1 ACGTTAGCATAGAAGGAAATAGTCGACAAGA 5 158 1 ACTTTTTGATAGAGAAGAATACGATGGCAAC 13 232 1 AGAGACCTAGAAGGGAATATGCA 6 8 1 TAAAGGTATTTGAAGGGAGCACATGAGGTAA 2 71 1 GCTTCACTCTTGAGAAAAACAAGAGCATAAG 3 225 1 TGGTTCTATATGAAGAAAGTATTAGGTAGGG 3 75 0 TTCAAGCTACAGAGAGAAAACC 14 1 0 GAAGAATAGTAGAAAAAAAGAACAATAACGA 3 146 0 GATTTACCTCAGAAGAGAAAACACCGCTCCT 12 70 0 CAAAGAATGGTTAGAGAAGGATTTTAAGTTG 13 122 0 GAGGGAAGTATGAGAAAAGGCAGGGATTCTC 5 241 1 GACAATACGTAGAAGGAAAACTCC 5 3 0 AATCTTAGAGATAAAGAAGAATAGTAGAAAA 3 161 0 ATGAAAAAGATGAGCAAAGAAAAGCGCTCAA 11 128 1 TATACAAAGTATAGAAAAATAACACGACAAT 12 36 1 GCTTATTCTTTTAGAAAAGAATTTTCTTTAA 0 268 0 GAGAGGAACATGAAAGAAATCTTGTCAAGTT 2 30 1 AAATAAGGGATGAGCAGAAAAGCTTAAAGAT 7 65 0 AAATAACTAGATAAAAAAAAATTT 4 100 1 ATAACTCGATTTAAAGGAAGAAAAAGCAGGT 11 210 1 ********* * MAP Score: 19.1986 Motif 3 GAAAGGCAATTCTTCTTTTTTGAATTCTATGTTTAT 0 62 1 TTATAGGAATTTTTTCTTAGAGAGTTAGAGGAGAGC 0 94 1 ATCAAAGCAATTTTCTTCTAGAACATCTCTGCAACC 0 150 1 GCAACCCGTTTCTTATTTGTGGATCAGTTGAATTAA 0 180 1 TAGAAAAGAATTTTCTTTAAAAAAGATGTTATTATG 0 252 0 TCGATTGAAGTTTTCCCTACCTAATACTTTCTTCAT 3 61 1 TACTTTCGTATTTTTTTTGTTGGTGTAAATATTGTT 4 37 1 AAATTTTTTTTTATCTAGTTATTTATTAGA 4 94 0 GGAGTTTTCCTTCTACGTATTGTCGGATAG 5 4 1 TACTCGAAAATTTTATTTTACGGAGTATAGCGCAGC 5 112 0 CTCTTTAGAGTTTTACTTGCAGATATATGGAAGAGG 5 209 1 AATTTTATAATTTTCATCTTTAAGCTTTTCTGCTCA 7 50 1 TTGCTCATCTTTTTCATTATAAAGAACAAGAGGCCA 11 109 0 CATTGAGCGCTTTTCTTTGCTCATCTTTTTCATTAT 11 125 0 AAGAAATCGTTTTTATTTTTAAAGTTCGTATTGGCA 11 175 1 AAAACCTGCTTTTTCTTCCTTTAAATCGAGTTATGC 11 208 0 AGGAGCGGTGTTTTCTCTTCTGAGGTAAATCAGCCT 12 70 1 GGCTCTAAAATTTTCATTCAAAATTTTCCAAGTCCT 13 160 1 GCCATCGTATTCTTCTCTATCAAAAAGTAGGAATTA 13 224 0 GGTTTTCTCTCTGTAGCTTGAAAATTGC 14 2 1 ******** * * MAP Score: 14.7859 Motif 4 AGCATGGGATTTATCTTGAAGATATCAAAGCAA 0 127 1 AATACTTTAGGTCACTTCAAGATGGTTCTATAT 3 95 0 CTATTCTTCTTTATCTCTAAGATTCATTTATAA 3 168 1 TTTTCTCTCTGTAGCTTGAAAATTGCTCCGCTC 14 12 1 TAGTACCTTCAAAATCAAGAGTGCT 3 2 1 TAAACTTCCCTTGCCTTTAAGAGAGGAACATGA 2 10 1 GTTGATCTCTTTTACTCGAAAATTTTATTTTAC 5 127 0 TCTTTAGAGTTTTACTTGCAGATATATGGAAGA 5 210 1 TAGAAAAGAATTTTCTTTAAAAAAGATGTTATT 0 255 0 AAAATCAAGAGTGCTTTGAAAATGATAAAAAAC 3 20 1 ATCAAAGCAATTTTCTTCTAGAACATCTCTGCA 0 150 1 TGCATATTCCCTTCTAGGTCTCT 6 4 0 AAGCTAAATCTTTACTTATAAAGCTT 12 3 0 CCTTTCTATGTTTGTTTGAAAGTAGGCCTTCTT 0 35 0 GAAATCGTTTTTATTTTTAAAGTTCGTATTGGC 11 177 1 AGAGCATAAGGTAATTTGCAGATAATTCCGAAT 3 246 1 GCTCTAAAATTTTCATTCAAAATTTTCCAAGTC 13 161 1 ** *** ***** MAP Score: 7.51856 Motif 5 ACTCTCTAAGAAAAAATTCCTATAAACATAGAATTCA 0 82 0 TCTTTTAGAAAAGAATTTTCTTTAAAAAAGATGTTAT 0 256 0 TCTTTTCTAAAAGAATAAGCGGTAAAATATT 0 279 1 TGAAAATGATAAAAAACCACTATAATCGATTGAAGTT 3 36 1 AGGTCACTTCAAGATGGTTCTATATGAAGAAAGTATT 3 83 0 CTTTATCTCTAAGATTCATTTATAATCTTACTAAGAA 3 176 1 AGATTAATTCAAAAAAAATTTTTAAACAATATTTACA 4 60 0 ATTGCTCCCAAAGCAACCGCGCTAACCAAGCTGCGCT 5 83 1 GTTGATAGAAAAACTCTGTGTTATTCTCGGTGAGCA 7 9 1 GGCCACAAGAAAAATCGAGCTGAATCCATAACAAGAA 11 77 0 TTTATAAGTAAAGATTTAGCTTTATACAAAGTATAGA 12 14 1 CTAGCAACTTAAAATCCTTCTCTAACCATTCTTTGGA 13 118 1 **** ** *** * MAP Score: 5.04927 Motif 6 AGATTAGTGGAATCATAATAACATCTTTTTTAAAG 0 239 1 GACAACTTTAAATATTGAGAAGATCTTTTCATGAC 1 20 0 ACATGAAAGAAATCTTGTCAAGTTCGTAATTATTT 2 37 1 AGTGACCTAAAGTATTGCTAAATTCAACAACTTTT 3 112 1 ATTCATTTATAATCTTACTAAGAACAAAACGTTTG 3 189 1 TTTGGGCTTCACTCTTGAGAAAAACAAGAGCATAA 3 220 1 CTCTTAATCGAACCTTGGCAACAGC 3 285 1 TTTTTGAATTAATCTAATAAATAACTAGATAAAAA 4 82 1 AAAAGTAGGAATTATTGACAATTGCATCTCCTCTT 13 203 0 * ***** ** * * MAP Score: 3.93909 Motif 7 TTTGGATCTAGAAGAAGGCCTACTTTCAAAC 0 24 1 CATAGAATTCAAAAAAGAAGAATTGCCTTTC 0 62 0 TTCTTTTCTAAAAGAATAAGCGGTAAAATAT 0 278 1 GCCTTTAAGAGAGGAACATGAAAGAAATCTT 2 22 1 GAATAGTAGAAAAAAAGAACAATAACGAAAA 3 143 0 GAATCTTAGAGATAAAGAAGAATAGTAGAAA 3 162 0 TCACTCTTGAGAAAAACAAGAGCATAAGGTA 3 228 1 ACACCAACAAAAAAAATACGAAAGTAATAGT 4 32 0 ATGGAAGAGGGAAGTATGAGAAAAGGCAGGG 5 235 1 TTTTCATTATAAAGAACAAGAGGCCACAAGA 11 104 0 TGTTCTTTATAATGAAAAAGATGAGCAAAGA 11 117 1 CGATTTAAAGGAAGAAAAAGCAGGTTTTAGA 11 216 1 ATTCCTCAGGGAACAAAGACAACCATTGCTG 11 262 1 TTGCTGCGTTGGAAAACACGAGT 11 287 1 ACAAAGTATAGAAAAATAACACGACAATAAA 12 39 1 TTTTGATAGAGAAGAATACGATGGCAACAAT 13 235 1 ****** **** MAP Score: 1.96247 Motif 8 CATAGAATTCAAAAAAGAAGAATTGCCTTTC 0 62 0 ACTGATCCACAAATAAGAAACGGGTTGCAGA 0 177 0 GAATAGTAGAAAAAAAGAACAATAACGAAAA 3 143 0 TCTTAGAGATAAAGAAGAATAGTAGAAAAAA 3 159 0 CTCTTGAGAAAAACAAGAGCATAAGGTAATT 3 231 1 AAATAACTAGATAAAAAAAAATTT 4 100 1 TGGAAGAGGGAAGTATGAGAAAAGGCAGGGA 5 236 1 TATTCTCGGTGAGCATGAGAATTTTATAATT 7 31 1 AGAAAAGCTTAAAGATGAAAATTATAAAATT 7 50 0 AAAGCAAAAAAACCGTTTTACT 8 21 0 TTATAATGAAAAAGATGAGCAAAGAAAAGCG 11 123 1 TACGAACTTTAAAAATAAAAACGATTTCTTA 11 174 0 ACTCGATTTAAAGGAAGAAAAAGCAGGTTTT 11 213 1 *** ******* MAP Score: 1.02455 Motif 9 ACTTTCAAACAAACATAGAAAGGCAATTCTTCTTT 0 45 1 GTTGCAGAGATGTTCTAGAAGAAAATTGCTTTGAT 0 150 0 AGTTGAATTAAATGCTAGAATGACATAAACTGTTA 0 205 1 TACCGCTTATTCTTTTAGAAAAGAATTTTCTTTAA 0 268 0 GATAAAGAAGAATAGTAGAAAAAAAGAACAATAAC 3 148 0 ATTTATAATCTTACTAAGAACAAAACGTTTGGGCT 3 193 1 AATCTAATAAATAACTAGATAAAAAAAAATTT 4 92 1 CTATCCGACAATACGTAGAAGGAAAACTCC 5 5 0 AAAAGAGATCAACGTTAGCATAGAAGGAAATAGTC 5 147 1 AGAGACCTAGAAGGGAATATGCA 6 2 1 TATAATGAAAAAGATGAGCAAAGAAAAGCGCTCAA 11 124 1 GAGGCTGATTTACCTCAGAAGAGAAAACACCGCTC 12 72 0 AGGACTTGGAAAATTTTGAATGAAAATTTTAGAGC 13 161 0 * ***** **** MAP Score: 0.846933 Motif 10 CTCCTCTAACTCTCTAAGAAAAAATTCCTATAA 0 94 0 TGCTTTGATATCTTCAAGATAAATCCCATGCTC 0 126 0 GCAGAGATGTTCTAGAAGAAAATTGCTTTGATA 0 149 0 ATAACATCTTTTTTAAAGAAAATTCTTTTCTAA 0 256 1 AAAATTCTTTTCTAAAAGAATAAGCGGTAAAAT 0 274 1 TCAAGATGGTTCTATATGAAGAAAGTATTAGGT 3 79 0 TTCTTCTTTATCTCTAAGATTCATTTATAATCT 3 171 1 CGTTTTGTTCTTAGTAAGATTATAAATGAATCT 3 187 0 CTACGTATTGTCGGATAGATTAAAATGAAGTTC 5 22 1 AAGGAAATAGTCGACAAGATCAAAGATGCTTCA 5 170 1 CTTCCATATATCTGCAAGTAAAACTCTAAAGAG 5 209 0 CATAACTCGATTTAAAGGAAGAAAAAGCAGGTT 11 209 1 CCCCCCAACTTCTTTTAGTAGAAATCCCTACAT 13 14 1 GGTTTTCTCTCTGTAGCTTGAAAATTGCTCCG 14 9 1 *** ***** ** MAP Score: 0.447974