AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ipdhR_ctra_opreg_300.orf -g0.413 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pdhA 221 Pyruvate Dehydrogenase Alpha #2 sucB_2 245 Dihydrolipoamide Succinyltransferase #3 ribC 300 Riboflavin Synthase #4 CT552 300 hypothetical protein #5 fmu 124 RNA Methyltransferase #6 brnQ 149 Amino Acid (Branched) Transport #7 CT555 174 SWI/SNF family helicase #8 CT556 177 hypothetical protein #9 lpdA 208 Lipoamide Dehydrogenase Motif number 1 TTCTGGGTAGTGCCGAAAAGTTTTTTTTTGTAGCATA 1 42 1 TCAAAGTTTT 0.816135 -180 TCAAAAGATTTATTTGAAAGACATTCTAGAATTTTTC 1 170 1 TTAAAGTTCT 0.979281 -52 AGATTCTCTTGGATAAAGGGTTCCTGAAAAATTCT 1 197 0 TGAAAGTCCT 0.974153 -25 TGTTATTAAACCCTCAAAAGGCATTTTTTATCTGTAA 2 143 1 CTAAAGTTTT 0.897856 -103 CTGTGTCTTGTGTTGAAAAGAACCTCTTCTTAGAAAG 3 115 1 TTAAAGCTCT 0.911932 -186 AAGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGCGG 3 132 1 TTAAAGTTCT 0.979281 -169 TTTTCAAGATTGCTAAAAAGTATTGTTGTCACGACCT 3 253 1 TTAAAGTGTT 0.816135 -48 ATACGAAGACTCATTAAAAGAATTCGTTGCTTTAAAG 4 32 0 TTAAAGTCGT 0.942659 -269 GAAAAAAGGGTTAGAAAAAGTTTTTGTCGCACGAGGT 4 135 0 TGAAAGTTGT 0.942659 -166 GGAAAAAAAGTCCGCTAAAGATTTCTTAGATAGAGAG 4 178 0 TGAAAGTCTT 0.953742 -123 TTTTTCCGCTTTTTTCTAAGATTTCCTGGTTGTTAGA 4 208 1 TTTAAGTCCT 0.783146 -93 TTCCTGGTTGTTAGAGAAAGTCTTTTTTCCTGTCCCG 4 230 1 TGAAAGTTTT 0.958487 -71 CTGTCCCGTTCTTTCTCAAGAGCTTTTGTTCGGATTG 4 259 1 CTCAAGTTTT 0.672292 -42 TTGTTCGGATTGCGTAAAAGGACTCCT 4 284 1 TGAAAGTCCT 0.974153 -17 TCTTCCCCAATAGGAGAAAGCAACCGTGTAGCTGCGT 5 58 1 TGAAAGCCGT 0.762811 -67 ATCCTTTATTCTTTCCAAAGAACTTCTGTGACTTGGG 6 78 1 CTAAAGTTCT 0.941412 -72 TAGATAGGTGTCTTCTAAAGGCGTTTTTTGGGTTGCT 7 79 0 TTAAAGTTTT 0.962765 -96 AAGAGGATTCTCCTTCCAAGCCTTTCTAGGAAAGGAA 9 119 0 TTCAAGTTCT 0.916882 -90 * * **** **** Masking position 17 Map Score: 20.289 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 246 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 TGCAAGGCCGGCGCGGAAAAGTAACCGGAAA 1 124 0 GGCGGAAAAG 0.894282 -98 AAAGAAAACGAAGAGAGAAAACCCTCTTCGT 2 21 0 AGAGAGAAAA 0.761217 -225 TTAACTCAATATGAGAAGAAGATTATCAACT 2 185 0 AGAGAAGAAG 0.936018 -61 AAAACTAGATACACGAAAAAGCCCTCTCCGG 3 225 0 AACGAAAAAG 0.72273 -76 CCAAACAAAGAGTAGGATAAGAACGTAAGTT 4 84 0 ATAGGATAAG 0.744369 -217 AGAAAAAAGGGTTAGAAAAAGTTTTTGTCGC 4 142 0 GTAGAAAAAG 0.843928 -159 ATAGAGAGTTAAGAGAAAAAAGGGTTAGAAA 4 155 0 AGAGAAAAAA 0.942316 -146 TCTTAGAAAAAAGCGGAAAAAAAGTCCGCTA 4 198 0 AGCGGAAAAA 0.881413 -103 TTTCCTGGTTGTTAGAGAAAGTCTTTTTTCC 4 229 1 GTAGAGAAAG 0.513435 -72 GAGATGATGGAAGCGAAAAGGAA 5 3 0 AGCGAAAAGG 0.539351 -122 CCTATTGGGGAAGAGAATAAACTATCGAGCA 5 41 0 AGAGAATAAA 0.85118 -84 TCTCTTCCCCAATAGGAGAAAGCAACCGTGT 5 56 1 ATAGGAGAAA 0.741211 -69 TAAAGGATGAATTAGAAGAAACGTCCGTTAG 6 55 0 ATAGAAGAAA 0.725164 -95 AAGTTCTTTGGAAAGAATAAAGGATGAATTA 6 72 0 GAAGAATAAA 0.487948 -78 ATACGTAAAAAGAAGAATAAAAGGTCAATCA 8 20 0 AAAGAATAAA 0.574506 -158 TATAGTTCCTAGGAGGAAAAAATCAAGGTAA 8 50 0 AGAGGAAAAA 0.946618 -128 GTGGTAGCAGGAGAGAAAAAATAGGAACGTA 9 17 0 GGAGAAAAAA 0.920187 -192 TAAAATCTCAATGAGGAGAAGTGGTAGCAGG 9 37 0 AGAGGAGAAG 0.94076 -172 GCCTTTCTAGGAAAGGAAAAGAGAGGTCCTT 9 106 0 GAAGGAAAAG 0.826518 -103 ACACTCATTGAAGAGGAAATGTT 9 196 1 AGAGGAAATG 0.671689 -13 * ********* Masking position 9 Map Score: 15.8078 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 639 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 CAAAAAAAAACTTTTCGGCACTACCCAGAAAAA 1 39 0 CTTTTGACTA 0.799057 -183 TTTCAGGAACCCTTTATCCAAGAGAATCT 1 203 1 CCTTTCAAGA 0.894283 -19 AGATCTTTTAACGAAGAGGGTTTTCTC 2 5 1 CTTTTCAAGA 0.980112 -241 GACAACAATACTTTTTAGCAATCTTGAAAAACT 3 250 0 CTTTTGAATC 0.799057 -51 CACGAGGTTGCTTTTTCCTACGATAGATCCAAA 4 110 0 CTTTTCACGA 0.94469 -191 TTTTTTTCCGCTTTTTTCTAAGATTTCCTGGTT 4 206 1 CTTTTCAAGA 0.980112 -95 CGAACAAAAGCTCTTGAGAAAGAACGGGACAGG 4 258 0 CTCTTGAAGA 0.966946 -43 AGGAGTCCTTTTACGCAATCCGAACAAAAG 4 281 0 CTTTTGAATC 0.799057 -20 ATAGTTTATTCTCTTCCCCAATAGGAGAAAGCA 5 47 1 CTCTTCAATA 0.92896 -78 TCATCCTTTATTCTTTCCAAAGAACTTCTGTGA 6 76 1 TTCTTCAAGA 0.744171 -74 GCAACATCCCCTTGTTTGCAAGACGATACCCCT 8 88 0 CTTGTGAAGA 0.859291 -90 AAGGAGAATCCTCTTCCCTCAGATAATCATCTC 9 141 1 CTCTTCCAGA 0.87437 -68 ***** * **** Masking position 5 Map Score: 8.30586 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 229 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 GAAAAGTAACCGGAAAGGTCCGGCCTTCGC 1 110 0 CGGAAAGGTC 0.904831 -112 AAGGCCGGCGCGGAAAAGTAACCGGAAAGG 1 122 0 CGGAAAAGTA 0.723586 -100 TTAAACCTTAAAGAAAACGAAGAGAGAAAA 2 31 0 AAGAAAACGA 0.485028 -215 TTTGAAACCACAGAAAAGACGCTTAAACCT 2 53 0 CAGAAAAGAC 0.700594 -193 TGATCAGATCCGGAGAGGGCTTTTTCGTGT 3 216 1 CGGAGAGGGC 0.9532 -85 CAGAGAGCGATATCCTCCCT 4 1 1 CAGAGAGCGA 0.890455 -300 GCTCTTGAGAAAGAACGGGACAGGAAAAAA 4 252 0 AAGAACGGGA 0.745821 -49 ATGATGGAAGCGAAAAGGAA 5 1 0 CGAAAAGGAA 0.588101 -124 CCTTCGAGCCAAGAGAGGGATGCTCTTTAA 5 98 0 AAGAGAGGGA 0.928936 -27 CTTACTTATTCAGTAAGGGATGGCTTCAAA 7 29 0 CAGTAAGGGA 0.899182 -146 CTTACTGAATAAGTAAGGGATGTTCTTTTG 7 42 1 AAGTAAGGGA 0.78962 -133 TTCTTTTGCCCGGAAAGCAACCCAAAAAAC 7 64 1 CGGAAAGCAA 0.86848 -111 ATGACCTAGGCAGAAAGGAACGAGTGTTTA 7 120 0 CAGAAAGGAA 0.958782 -55 AGGAAAGGAAAAGAGAGGTCCTTCAGACAA 9 99 0 AAGAGAGGTC 0.690346 -110 AAGCCTTTCTAGGAAAGGAAAAGAGAGGTC 9 109 0 AGGAAAGGAA 0.913934 -100 ********** Masking position 6 Map Score: 10.5522 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 389 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 AAAAATTCTAGAATGTCTTTCAAATAAATC 1 176 0 GAATGTCTTT 0.928954 -46 AGATTCTCTTGGATAAAGGGT 1 211 0 GATTCTCTTG 0.752086 -11 GAATCTCCTTATTTCTGAAC 2 236 0 GAATCTCCTT 0.924403 -10 TTTCTAAGAAGAGGTTCTTTTCAACACAAG 3 121 0 GAGGTTCTTT 0.819707 -180 GGTTGTTAGAGAAAGTCTTTTTTCCTGTCC 4 235 1 GAAAGTCTTT 0.763355 -66 CCAAGAGAGGGATGCTCTTTAAAGTACGCA 5 90 0 GATGCTCTTT 0.962531 -35 TGACGGTCCTTCGAGCCAAGA 5 114 0 GACGGTCCTT 0.897797 -11 CCAAGTCACAGAAGTTCTTTGGAAAGAATA 6 84 0 GAAGTTCTTT 0.90982 -66 ATAAGTAAGGGATGTTCTTTTGCCCGGAAA 7 50 1 GATGTTCTTT 0.925583 -125 AAAAAGAAATGATTGACCTTTTATTCTTCT 8 11 1 GATTGACCTT 0.656853 -167 GAGGGAAGAGGATTCTCCTTCCAAGCCTTT 9 131 0 GATTCTCCTT 0.937754 -78 ********** Masking position 2 Map Score: 6.70075 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 205 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 TCAAAAGATTTATTTGAAAGACATTCTAGAATTTT 1 170 1 TATTAAGCTT 0.727036 -52 TGTTATTAAACCCTCAAAAGGCATTTTTTATCTGT 2 143 1 CCCTAAGCTT 0.923709 -103 AAGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGC 3 132 1 TCTTAAGTTT 0.838911 -169 CTTGATCAGATCCGGAGAGGGCTTTTTCGTGTATC 3 214 1 TCCGAGGCTT 0.838868 -87 ATCTAAGAAATCTTTAGCGGACTTTTTTTCCGCTT 4 184 1 TCTTCGGCTT 0.951233 -117 AAGTCTTTTTTCCTGTCCCGTTCTTTCTCAAGAGC 4 247 1 TCCTCCGTTT 0.756434 -54 TAGATAGGTGTCTTCTAAAGGCGTTTTTTGGGTTG 7 81 0 TCTTAAGCTT 0.971267 -94 ACCTATCTACTCCTAAACACTCGTTCCTTTCTGCC 7 107 1 TCCTCACCTT 0.95362 -68 GAGATCACCTCTTTAACAGTCTTTGGGCCTTTTT 8 154 0 TCTTCAGCTT 0.978431 -24 AAGAGGATTCTCCTTCCAAGCCTTTCTAGGAAAGG 9 121 0 TCCTAAGCTT 0.984684 -88 ATCGTTGCAATCCTAAACACTCATTGAAGAGGAAA 9 180 1 TCCTCACCTT 0.95362 -29 **** *** * ** Masking position 14 Map Score: 6.40167 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 112 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 TTTTAACGAAGAGGGTTTTCTCTCTTCGTT 2 16 1 GAGGGTTTTC 0.775099 -230 GTAACATAGGGAGTGCTTAACCGCCTTCAG 2 94 1 GAGTGCTTAA 0.952674 -152 AATGCCTTTTGAGGGTTTAATAACATGAAA 2 138 0 GAGGGTTTAA 0.973261 -108 AGTTTTTCAAGATTGCTAAAAAGTATTGTT 3 250 1 GATTGCTAAA 0.730274 -51 TTCTTAGATAGAGAGTTAAGAGAAAAAAGG 4 163 0 GAGAGTTAAG 0.823624 -138 TACCTGCACTGATGGTTTAAGATCAAGATT 6 11 0 GATGGTTTAA 0.877562 -139 ACTATAGGACGAGGGCTAACGGACGTTTCT 6 40 1 GAGGGCTAAC 0.922547 -110 AGAAAGGAACGAGTGTTTAGGAGTAGATAG 7 109 0 GAGTGTTTAG 0.965171 -66 AAGGCCCAAAGACTGTTAAAGAGGTGATCT 8 157 1 GACTGTTAAA 0.761686 -21 CCTCTTCAATGAGTGTTTAGGATTGCAACG 9 182 0 GAGTGTTTAG 0.965171 -27 ********** Masking position 7 Map Score: 5.61251 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 68 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ATTTCACTCTGGCTATGCAAGGCCGGCGCGGA 1 138 0 GGCTATAAGG 0.879729 -84 GATAAAAAATGCCTTTTGAGGGTTTAATAACA 2 143 0 GCCTTTAGGG 0.979911 -103 ATTATCAACTGGCTTTTACAGATAAAAAATGC 2 163 0 GGCTTTCAGA 0.787487 -83 CGTAGAGAAAACCTTTCTAAGAAGAGGTTCTT 3 132 0 ACCTTTAAGA 0.847457 -169 ACCGCTGTTTGCCTTGATCAGATCCGGAGAGG 3 202 1 GCCTTGCAGA 0.928361 -99 TGTTGTCACGACCTAGCAAAGGTATTTAATTG 3 276 1 ACCTAGAAGG 0.797224 -25 GGTCCTTCGAGCCAAGAGAGGGATGCTCTTTA 5 99 0 GCCAAGAGGG 0.698253 -26 GAACTTCTGTGACTTGGGAAGGATGATATGCC 6 97 1 GACTTGAAGG 0.862944 -53 CCCAAAAAACGCCTTTAGAAGACACCTATCTA 7 84 1 GCCTTTAAGA 0.973032 -91 CAGTCTTTGGGCCTTTTTATGGCTTCCATACT 8 140 0 GCCTTTATGG 0.924844 -38 CTCCTTCCAAGCCTTTCTAGGAAAGGAAAAGA 9 115 0 GCCTTTAGGA 0.951689 -94 ****** **** Masking position 3 Map Score: 5.28036 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 155 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 AACTTCAAACCAACTTCATCTCT 1 4 1 TTCAAACCAA 0.901371 -218 AAGTCTATGCTACAAAAAAAAACTTTTCGG 1 54 0 TACAAAAAAA 0.698406 -168 TAGAATGTCTTTCAAATAAATCTTTTGAAT 1 168 0 TTCAAATAAA 0.841843 -54 TTTCTGTGGTTTCAAAAAATGTTTAGTGTA 2 67 1 TTCAAAAAAT 0.774587 -179 CTACGATAGATCCAAACAAAGAGTAGGATA 4 96 0 TCCAAACAAA 0.958599 -205 TTTTACGCAATCCGAACAAAAGCTCTTGAG 4 273 0 TCCGAACAAA 0.860137 -28 AAGGGATGGCTTCAAACAATTGCGACTAAG 7 15 0 TTCAAACAAT 0.926452 -160 AGAGAGGTCCTTCAGACAAATACATTTCCC 9 88 0 TTCAGACAAA 0.901371 -121 ********** Masking position 6 Map Score: 1.82359 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 90 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 3.31356e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 3.31356e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: 3.31356e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0