AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -inarL_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 CT065 300 ADP/ATP Translocase #2 CT134 300 hypothetical protein #3 CT135 58 hypothetical protein #4 CT483 300 hypothetical protein #5 sdhB 236 Succinate Dehydrogenase #6 sdhC 25 Succinate Dehydrogenase #7 CT593.1 221 hypothetical protein-possible frameshift with CT593 #8 ycfH 84 PHP superfamily hydrolase #9 dsbD 152 Thio:disulfide Interchange Protein Motif number 1 CCTTGAGTGGAGGGCATCTCCTCCTCACGTAA 1 143 1 AGGGACTCCT 0.826495 -158 ACGAAGATTTAAAGTATTTCTTTAAAAAGTCG 1 222 0 AAAGATTCTT 0.668118 -79 CTCTACTTAGAGAAAATCTCCTAAGTCGAAGA 2 21 0 AGAAACTCCT 0.901525 -280 ACTAGGAACTTAAAAAAATCCTGATAAAAGCT 2 72 0 TAAAAATCCT 0.795262 -229 GAAAACCAATAAGATAGATCTTGCTTATGCAG 2 151 0 AAGAAATCTT 0.720953 -150 CGATAGAAAGTAAGGAAATCCTGCGGCGGGAG 2 269 1 TAAGAATCCT 0.711922 -32 AGGCCTTTTTAAGAAGGATCTTCTCTGTTTAC 4 30 1 AAGAGATCTT 0.815424 -271 TCTGTTTACAAAGACGATTCCTAAAGCTTGCT 4 53 1 AAGAGTTCCT 0.847073 -248 TTCATTAGTAAAAAAAACTCTTAAATATAAAG 4 168 0 AAAAACTCTT 0.934212 -133 TACAGAGAGAAATGAGTCTCCTATTCCATAAA 4 214 1 AATGGCTCCT 0.716005 -87 ATACCAAGGTAAAATATCTCCTATTTTACTCC 4 251 1 AAAAACTCCT 0.939487 -50 CCTGAAATAAAAGGATCCTCTGTAGATGG 4 282 0 TAAAGATCCT 0.862179 -19 ATATTCAAAATAAATGTCTCTTTCAAATTAGC 5 172 0 TAAAGCTCTT 0.901589 -65 ATGATGTTTGAGGAGGGCTCTTTATGGAAGGG 7 87 1 AGGAGCTCTT 0.663842 -135 CCTCCTCATATGAACGCCTCCTTATTCGCTGT 7 134 0 TGAAGCTCCT 0.876533 -88 TTTTCCGCTAAAAGGGCTTCTTCCTTCATGAT 8 30 1 AAAGGTTCTT 0.762535 -55 ATTACATACCAAAAAGGATCTTGGTTCTATAC 9 62 0 AAAAGATCTT 0.906174 -91 TGCAAAAACAAAAACAACTCTTCTGTTGTTTG 9 98 1 AAAAACTCTT 0.934854 -55 **** * ***** Masking position 9 Map Score: 16.9613 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 577 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 TTTCTGCCATTTTTTATTCCGCCCTCCTGG 1 110 1 TTTTTATTCC 0.976009 -191 CGTGAAAAAATTTTGATTTCACGACTCCCT 1 194 0 TTTTGATTTC 0.920346 -107 ATCTTATTGGTTTTCATTCCAATTAAAGAG 2 168 1 TTTTCATTCC 0.980051 -133 GCTTTACCTCTTTTTATTTCGTTCCCCCAA 3 31 0 TTTTTATTTC 0.962475 -28 CTATACAAACTTTTTATTCCCCTTTCTTTA 4 143 1 TTTTTATTCC 0.976009 -158 ACAGAGGATCCTTTTATTTCAGG 4 288 1 CTTTTATTTC 0.871999 -13 TTCCAGCGAATATTCATTTCCCGATATAGG 5 140 1 TATTCATTTC 0.918955 -97 TTATATGATGTATTCATTCCGTATCGGGAT 7 200 1 TATTCATTCC 0.947327 -22 ********** Masking position 6 Map Score: 10.2881 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 57 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 3 TGCTGAACAAGCAGAAGGGCTCACTGAGAA 1 18 0 GCAGAAGGGC 0.822326 -283 CTCAAGGAGCCCAGGAGGGCGGAATAAAAA 1 120 0 CCAGGAGGGC 0.983261 -181 GGGCTCCTTGAGTGGAGGGCATCTCCTCCT 1 138 1 AGTGGAGGGC 0.921079 -163 CGATTTCTAATTAGGAGAGACCGAAGCTTC 2 240 1 TTAGGAGAGA 0.772009 -61 TCCTGCGGCGGGAGGAGAGCAGTT 2 287 1 GGAGGAGAGC 0.918094 -14 GAAGCCTTTCAGTTGAGGGATATAGCTGCT 7 22 1 AGTTGAGGGA 0.761633 -200 TCATGATGTTTGAGGAGGGCTCTTTATGGA 7 85 1 TGAGGAGGGC 0.990836 -137 AGGGCAGGAACCATGAGGGACAGCGAATAA 7 115 1 CCATGAGGGA 0.941457 -107 GGCGTTCATATGAGGAGGGAGATAGTACAA 7 148 1 TGAGGAGGGA 0.987741 -74 CAATCAAAGATCATGAAGGAAGAAGCCCTT 8 41 0 TCATGAAGGA 0.653141 -44 GAAAGATTGATTATGAGGGAAGT 8 72 1 TTATGAGGGA 0.88981 -13 ********** Masking position 6 Map Score: 9.08423 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 207 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 TGCTTGTTCAGCATACAGCCCTTTTCTATTGCCT 1 35 1 GATCGCCTTT 0.97994 -266 CTAAAGGTTGGATTTCTGCCATTTTTTATTCCGC 1 98 1 GTTCGCCTTT 0.991173 -203 AAGAGGATATGCTGGCTGCCCTTTAGAGACCTAT 2 193 1 GTGCGCCTTT 0.994369 -108 TGTTATTTTGGATGTAGGCCTTTTTAAGAAGGAT 4 15 1 GTGAGCCTTT 0.988439 -286 AATTAGGGATGGAAGCCTTTCAGTTGAGGGA 7 8 1 GTGAGCCTTC 0.982898 -214 TGTCCCTCATGGTTCCTGCCCTTCCATAAAGAGC 7 103 0 GTTCGCCTTC 0.986939 -119 AGATCATGAAGGAAGAAGCCCTTTTAGCGGAAAA 8 30 0 GAAAGCCTTT 0.903484 -55 * ** * *** *** Masking position 12 Map Score: 7.17645 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 17 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 5 AGACCGAAGCTTCGATAGAAAGTAAGGAAATCCT 2 257 1 TTATAAAGTA 0.758618 -44 GGAATCGTCTTTGTAAACAGAGAAGATCCTTCTT 4 40 0 TTAAAAAGAA 0.912691 -261 TGCTTTCTCGTTATAAACAAGAAACCACCCTAGA 4 81 1 TTAAAAGAAA 0.912691 -220 AAAAAAACTCTTAAATATAAAGAAAGGGGAATAA 4 156 0 TTATAAAGAA 0.950401 -145 GAGTCTCCTATTCCATAAAAAAAAATACCAAGGT 4 227 1 TTATAAAAAA 0.943394 -74 GAGCCAGAAATTTCATATAAGAAAGTAGATACCC 5 40 1 TTATAAGAAA 0.684483 -197 AGGATCTTGGTTCTATACAAGAAATTTGTTAGGA 9 46 0 TTATAAGAAA 0.932104 -107 TTGCAATTCATTACATACCAAAAAGGATCTTGGT 9 69 0 TTATACAAAA 0.849534 -84 ATGTAATGAATTGCAAAAACAAAAACAACTCTTC 9 87 1 TTAAAAAAAA 0.926866 -66 ** *** * **** Masking position 7 Map Score: 3.79468 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 108 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 6 TACTCTACTTAGAGAAAATCTCCTAAGTCG 2 25 0 AGAGAAAATC 0.922762 -276 TTCCAATTAAAGAGGATATGCTGGCTGCCC 2 184 1 AGAGGATATG 0.88264 -117 CTTTGTAAACAGAGAAGATCCTTCTTAAAA 4 36 0 AGAGAAGATC 0.843307 -265 CTCCGACTACAGAGAGAAATGAGTCTCCTA 4 207 1 AGAGAGAAAT 0.843637 -94 GGATTCACATAGCGGGTATCTACTTTCTTA 5 57 0 AGCGGGTATC 0.905493 -180 ATGTCGTGCTAGAGAATATTCCAGCGAATA 5 122 1 AGAGAATATT 0.954965 -115 AGAATATTCCAGCGAATATTCATTTCCCGA 5 134 1 AGCGAATATT 0.951995 -103 GGGAGAGAGAATTTTTTCTCTTC 6 4 1 AGAGAGAATT 0.93125 -22 CATGAGGGACAGCGAATAAGGAGGCGTTCA 7 126 1 AGCGAATAAG 0.817284 -96 AAGCCCTTTTAGCGGAAAATGTTTCTACTT 8 19 0 AGCGGAAAAT 0.77165 -66 GCTAAACCGGAGAGAGTGTTGTGTTT 9 137 1 AGAGAGTGTT 0.788789 -16 ********** Masking position 1 Map Score: 4.34115 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 199 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 TCCTCACGTAATCGAAGATTCAGCCGGAAT 1 164 1 ATCGAAGATT 0.978395 -137 TGATCAAATCAACGAAGATTTAAAGTATTT 1 235 0 AACGAAGATT 0.917846 -66 AATCTCCTAAGTCGAAGACTGTCCACCC 2 9 0 GTCGAAGACT 0.968872 -292 ATGCTTCTGAGTCGCAGCTTTTATCAGGAT 2 57 1 GTCGCAGCTT 0.955725 -244 CTTACTTTCTATCGAAGCTTCGGTCTCTCC 2 253 0 ATCGAAGCTT 0.986151 -48 AATTAGGGATGGAAGCCTTTCAGTTGAG 7 9 1 ATGGAAGCCT 0.931205 -213 ********** Masking position 6 Map Score: 2.5385 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 25 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 ATTTCTTTAAAAAGTCGTGAAAAAATTTTGATTTCACGA 1 200 0 ATTAAATTTT 0.939096 -101 AGAAAACTTAACAATAAACACAAGCTTTTCAGAGGGTGA 1 269 1 ATAAAATTTT 0.844364 -32 TTAAGTTCCTAGTTTCTTCGCAAGTTTTTATATTCTAAG 2 91 1 ATTGAATTTT 0.964657 -210 GTTCCCCCAAATCTTTTTTAGACTGTTTTA 3 2 0 ATTAACTTTT 0.781678 -57 GAACGAAAAGAAACTCTATACAAACTTTTTATTCCCCTT 4 128 1 ATAAAATTTT 0.844336 -173 CGGGAAATGAATATTCGCTGGAATATTCTCTAGCACGAC 5 124 0 ATCGAATTCT 0.757675 -113 TTCCTGGGAAATAATATTGGGAAAGTTTTGAG 5 215 1 ATTGAATTTT 0.96342 -22 ATATAATGAAACGAATGTAGGAAGATTTTTGTACTATCT 7 167 0 AATGAATTTT 0.883657 -55 AACGATTCAAGTAGAAACATTTTCCGCTAAAAG 8 5 1 AATGAATTTT 0.883858 -80 GAGTTCCTAGACGATCCTAACAAATTTCTTGTATAGAAC 9 32 1 ATTAAATTCT 0.880689 -121 * * * * ** **** Masking position 12 Map Score: 1.65502 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 92 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 CAGTGAGCCCTTCTGCTTGTTCAGCATACAG 1 22 1 TTTGCTTGTT 0.846682 -279 TATTGTTAAGTTTTCTTTGTTGATCAAATCA 1 254 0 TTTCTTTGTT 0.903666 -47 GAAAAGCTTGTGTTTATTGTTAAGTTTTCTT 1 268 0 TGTTATTGTT 0.763085 -33 GGGATATAGCTGCTGTTTGTTAACGTCGCGA 7 38 1 TGTGTTTGTT 0.978685 -184 CTGTTCATCATGATGTTTGAGGAGGGCTCTT 7 78 1 TGTGTTTGAG 0.883746 -144 TCTTCCTTCATGATCTTTGATTGAGAAAGAT 8 48 1 TGTCTTTGAT 0.937341 -37 AACAGAAGAGTTGTTTTTGTTTTTGCAATTC 9 94 0 TTTTTTTGTT 0.858446 -59 ACAACTCTTCTGTTGTTTGATGATTTGCTAA 9 111 1 TGTGTTTGAT 0.96624 -42 ** ******** Masking position 7 Map Score: 2.13446 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 87 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 TTTTTAAGTTCCTAGTTTCTTCGCAAGTTTT 2 88 1 CCTAGTTCTT 0.97183 -213 GCAGGATTTCCTTACTTTCTATCGAAGCTTC 2 262 0 CTTACTTCTA 0.696467 -39 CTTAAAAAGGCCTACATCCAAAATAACAACC 4 12 0 CCTACTCCAA 0.871238 -289 AAGAAACCACCCTAGATCCTTTGTACATCGA 4 99 1 CCTAGTCCTT 0.982053 -202 ATAGCGGGTATCTACTTTCTTATATGAAATT 5 48 0 TCTACTTCTT 0.927734 -189 CAAAAATCTTCCTACATTCGTTTCATTATAT 7 175 1 CCTACTTCGT 0.945267 -47 GTTGGTTAGGTCTACGTCCTT 9 1 0 TCTACTCCTT 0.95319 -152 TTGTATAGAACCAAGATCCTTTTTGGTATGT 9 60 1 CCAAGTCCTT 0.90746 -93 ***** ***** Masking position 4 Map Score: 3.33634 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 102 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: 3.28514e-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: 3.28514e-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 13 ********** No masking Map Score: 3.28514e-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