AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_ctra_reg_100.orf -o00710_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -x5 -e 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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 araD 83 Ribulose-P Epimerase #2 rpiA 94 Ribose-5-P Isomerase A #3 CT214 300 hypothetical protein #4 tpiS 196 Triosephosphate Isomerase #5 CT330 208 hypothetical protein #6 pykF 96 Pyruvate Kinase #7 mdhC 190 Malate Dehyrogenase #8 CT389 181 hypothetical protein #9 aspC 89 Aspartate Aminotransferase #10 tyrB 187 Aromatic AA Aminotransferase #11 pgk 127 Phosphoglycerate Kinase #12 tktB 300 Transketolase Motif number 1 GATGACGCACATACACTTCAATCTTGTGGTCAAAAAT 1 44 0 ACTTTCTTGT 0.828701 -40 GAAAAATCGCAGAGTCTTTCATTTTCTTTACCTCACC 3 191 0 ACTTTTTTCT 0.956121 -110 AAAAACTATTTTCTCTTTTTAATTTTT 3 284 0 ACTATCTCTT 0.819423 -17 GTTGATTCATAAGGTCTATGATCTCTTCCAAACGTTT 5 45 0 ACTATCTCTT 0.81943 -164 CCACGTCTTTAGAAGCTTCTCTTGCCTTGTATGAAGA 5 85 1 ACTTTTGCCT 0.717523 -124 GCTGTTTAATACGTGCTTCGACTTCTTGAATGCGAGA 5 150 0 ACTTCTTCTT 0.519126 -59 TGAAAAATAGATGAGCTTTTTTTTGCCAAAAGCTTTT 7 42 1 ACTTTTTGCC 0.678215 -149 TAAGGAATCTAGGTACTTGATTCTTTTATCATCCAAA 7 81 1 ACTTTCTTTT 0.914817 -110 TCTTCTCCTAAAAATCTTGTTTTTTCTCTACTTCCGA 8 121 1 ACTTTTTTCT 0.956121 -61 ATTACCGTCCACCATTTTGACTCTCCCGTGTTTC 9 66 1 ATTTTCTCCC 0.699167 -24 TGTAAACATGATAACCTAGTTTCTTCCCTCGGGGTAT 10 85 0 ACTATCTTCC 0.916528 -103 GCACTGAGATAAAGGCTTGAGTTTTCCTTTGCTTAGG 11 66 1 ACTTTTTTCC 0.917978 -62 TAACTGCGTTAGCGGCTACCCCCTTCTCCTTTTTAGT 12 59 0 ACTACCTTCT 0.833035 -242 TAACGCAGTTACCCCCTTTTCTTTTCTCTAAAATACC 12 85 1 ACTTTTTTCT 0.956121 -216 TTTTCTCTAAAATACCTTCTCTCTTCTTCTTGCTGTA 12 106 1 ACTTTCTTCT 0.980221 -195 ATTATCTCTAATTCTCTACTATCTTCTTCCTTATCCT 12 154 1 ACTATCTTCT 0.955313 -147 TAGGGACTTAATTTATTTTATTCTCCTTATTATCGAA 12 211 1 ATTTTCTCCT 0.819002 -90 * *** ****** Masking position 7 Map Score: 12.8131 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 418 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 TGTACACTCTCCTTCTTATCGTAGAGG 1 8 1 TCTCCTTCTT 0.978982 -76 TTTCTTTACCTCACCTTCTCAAAGATCTTA 3 176 0 TCACCTTCTC 0.758776 -125 GCAGAGTCTTTCATTTTCTTTACCTCACCT 3 190 0 TCATTTTCTT 0.727995 -111 TGATTTATTTTCTATTGCTTTGATATAAAT 4 89 0 TCTATTGCTT 0.640094 -108 AGCGTAATACTCGATTTCTTGCAAGGAAGG 4 131 0 TCGATTTCTT 0.799273 -66 TTTAGAAGCTTCTCTTGCCTTGTATGAAGA 5 92 1 TCTCTTGCCT 0.716925 -117 AATACGTGCTTCGACTTCTTGAATGCGAGA 5 150 0 TCGACTTCTT 0.931931 -59 AAGCCACCCTCTCTTTACTTTTACAAAAC 7 172 0 TCTCTTTACT 0.627977 -19 CGCTCGAGTGTCGGCTTCTTTCGGATTTGA 8 90 0 TCGGCTTCTT 0.833501 -92 TTGTTTTTTCTCTACTTCCGAGTTATAACG 8 137 1 TCTACTTCCG 0.831148 -45 CAACAAGCTGTCATCTTACTGGAAAAAAAG 10 132 1 TCATCTTACT 0.534154 -56 GCTACCCCCTTCTCCTTTTTAGTCTGTGAC 12 52 0 TCTCCTTTTT 0.754176 -249 ATACCTTCTCTCTTCTTCTTGCTGTAATCC 12 117 1 TCTTCTTCTT 0.952102 -184 TTCTCTACTATCTTCTTCCTTATCCTGAAA 12 165 1 TCTTCTTCCT 0.937038 -136 TTTATTTTATTCTCCTTATTATCGAATTTT 12 222 1 TCTCCTTATT 0.885738 -79 GTATAGGTAATCAACTTCTGCTAAAGGAAA 12 277 1 TCAACTTCTG 0.752695 -24 ********** Masking position 6 Map Score: 8.66599 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 650 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 ACCTCTCAAAGGAAAGAATCTAACAAGGGC 2 73 0 GGAAAGAATC 0.882324 -22 TTTATTTCGTAGGAGAAAACCTCAAGATAA 3 122 1 AGGAGAAAAC 0.883575 -179 TAAAGACTCCAGGAAAGATCGTTTATCTTG 3 144 0 AGGAAAGATC 0.866254 -157 CTTTAGAACGGGGAAAAATCGCAGAGTCTT 3 210 0 GGGAAAAATC 0.976352 -91 AAACGTGGAAAAAATCTCTTTTGAAG 5 7 1 GGAAAAAATC 0.901129 -202 TGAAACGTTTGGAAGAGATCATAGACCTTA 5 43 1 GGAAGAGATC 0.638451 -166 AGTTAATTGTGTGAGGAAACGTAAAAACG 8 10 0 GTGAGGAAAC 0.679995 -172 CTCGGAAGTAGAGAAAAAACAAGATTTTTA 8 129 0 GAGAAAAAAC 0.723774 -53 AATACCCCGAGGGAAGAAACTAGGTTATCA 10 84 1 GGGAAGAAAC 0.961048 -104 TCAGTGCCACATGAAGAATCACTCAGACAA 11 43 0 ATGAAGAATC 0.703135 -85 GCCTAAGCAAAGGAAAACTCAAGCCTTTAT 11 74 0 AGGAAAACTC 0.762369 -54 CTTCTGCTAAAGGAAAAAAC 12 291 1 AGGAAAAAAC 0.93139 -10 ********** Masking position 4 Map Score: 8.45022 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 299 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 CTATAAATCTTTCTTAGCATGCAAACATTTATTTCGT 3 95 1 TTTTAGGCAA 0.99241 -206 CTCTTTTTAATTTTTATTCTGCACACATTGAACACCA 3 262 0 TTTTATGCAA 0.952953 -39 TTGACTAAGAATTTTAGGAGGCAATGAAATCCAGAAT 8 57 0 ATTTAGGCAA 0.969973 -125 TCCAGCGTAATTTTTAGAGAGCACTGAGAAAAG 9 7 0 TTTTAGGCAA 0.992417 -83 ATTAGCTCAGTTGGTAGAGCGCAACAATGGCATTGTT 10 50 0 TTGTAGGCAA 0.979324 -138 AGACAAAACATTTTTAGTCTGCATATAGAGAGTTGCG 11 12 0 TTTTAGGCAA 0.99242 -116 ** **** *** * Masking position 6 Map Score: 3.68347 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 ACGATAAGAAGGAGAGTGTACA 1 3 0 GGAGAGTGTA 0.918087 -81 CCTTCTTATCGTAGAGGGTTAAAATTTTTG 1 21 1 GTAGAGGGTT 0.832705 -63 AAGGAATCTTGAAGAGGTTGTAGGATTACT 2 28 1 GAAGAGGTTG 0.915451 -67 TTCTTTCCTTTGAGAGGTTT 2 85 1 TGAGAGGTTT 0.824412 -10 CCGCTCTGACGGAGAGTGTGTTGCGCTTTT 3 46 0 GGAGAGTGTG 0.971589 -255 TTAAGATCTTTGAGAAGGTGAGGTAAAGAA 3 175 1 TGAGAAGGTG 0.875844 -126 TGCCTTGTATGAAGAGGCTGATCAATTAAT 5 107 1 GAAGAGGCTG 0.863967 -102 AACGTAGTGTTGAGAGTATGTGCGTTTTGT 7 149 1 TGAGAGTATG 0.555872 -42 GTAAAAGTAAAGAGAGGGTGGCTT 7 177 1 AGAGAGGGTG 0.980685 -14 AGTGCGCTATAGAGAGGTTTTATT 10 174 1 AGAGAGGTTT 0.824412 -14 CTAAAAAGGAGAAGGGGGTAGCCGCTAACG 12 60 1 GAAGGGGGTA 0.683446 -241 CAAGAAGAAGAGAGAAGGTATTTTAGAGAA 12 108 0 AGAGAAGGTA 0.698067 -193 ********** Masking position 3 Map Score: 5.11276 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 360 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 TTTTAATATAACTGATCTTTAGAACGGGGA 3 226 0 ACTGATCTTT 0.852315 -75 AGTATTACGCTTTGATCTATCTTACAAAAT 4 150 1 TTTGATCTAT 0.734848 -47 GTATGAAGAGGCTGATCAATTAATGCGTAT 5 113 1 GCTGATCAAT 0.859125 -96 GTTAAAGTCGGCTCATCTATTGAAAAATAG 7 22 1 GCTCATCTAT 0.967737 -169 GCAAAAAAAAGCTCATCTATTTTTCAATAG 7 38 0 GCTCATCTAT 0.967737 -153 AAGATGAGACTCTCATCTGTCCAGCGTAAT 9 33 0 TCTCATCTGT 0.917947 -57 CAGATGAGAGTCTCATCTTTATATTACCGT 9 44 1 TCTCATCTTT 0.950192 -46 GCTTATCTGATCCTTAACCTAAATT 11 113 0 TCTGATCCTT 0.854419 -15 ********** Masking position 5 Map Score: 3.0259 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 42 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 CTACGAAATAAATGTTTGCATGCTAAGAAA 3 104 0 AATGTTTGCA 0.955312 -197 CTTGGTGTTCAATGTGTGCAGAATAAAAAT 3 260 1 AATGTGTGCA 0.946589 -41 TTTGCTGAATAACCTGTGCATGTATTTTGT 4 173 0 AACCTGTGCA 0.92323 -24 GACGCTATGAAACGTTTGGAAGAGATCATA 5 36 1 AACGTTTGGA 0.970646 -173 GGTCCCAACATACGTTTGGATGATAAAAGA 7 102 0 TACGTTTGGA 0.946588 -89 CTCTCAACACTACGTTTGCAACTAACTAAT 7 135 0 TACGTTTGCA 0.971352 -56 ********** Masking position 5 Map Score: 2.88264 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 29 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ACCCAAAAAAGCGCAACACACTCTCCGTCAG 3 40 1 GCGCAACCAC 0.970195 -261 ATAGATCAAAGCGTAATACTCGATTTCTTGC 4 139 0 GCGTAATCTC 0.942878 -58 CGACACTCGAGCGCTCTTCTCCTAAAAATCT 8 107 1 GCGCTCTCTC 0.974406 -75 CGGTTCGATCCCGCTATGCTCCAATTTCTGT 10 11 0 CCGCTATCTC 0.915593 -177 AGTTGGTAGAGCGCAACAATGGCATTGTTGA 10 48 0 GCGCAACATG 0.895869 -140 CCTCTCTATAGCGCACTGCTGCTTACTGTCT 10 160 0 GCGCACTCTG 0.971817 -28 GCGCAACTCTCTATATGCAGA 11 1 1 GCGCAACCTC 0.993661 -127 ******* *** Masking position 3 Map Score: 2.74112 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 35 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 ACAAGGGCTTCTATTCCTCAAACAGTAATCC 2 50 0 CTATCCTCAA 0.739395 -45 CTTTCATTTTCTTTACCTCACCTTCTCAAAG 3 182 0 CTTACCTCAC 0.770161 -119 TGAAAGAAGCCTTCAACTATACAAAATATTT 6 25 0 CTTAACTATA 0.746447 -72 GATGAGCCGACTTTAACTGAATAAGAAC 7 8 0 CTTAACTGAA 0.865276 -183 TTGCCAAAAGCTTTTACTAAGGAATCTAGGT 7 64 1 CTTTACTAAG 0.773045 -127 CCTCTCTTTACTTTTACAAAACGCACATACT 7 163 0 CTTTACAAAA 0.67691 -28 CTCGAGCGCTCTTCTCCTAAAAATCTTGTTT 8 112 1 CTTTCCTAAA 0.971754 -70 ATGACAGCTTGTTGTCCTAAATCGTGTAAAC 10 115 0 GTTTCCTAAA 0.785345 -73 TTATCTGATCCTTAACCTAAATTTTCTTATA 11 105 0 CTTACCTAAA 0.961511 -23 TATCTTCTTCCTTATCCTGAAATAGAGTTTA 12 173 1 CTTTCCTGAA 0.943872 -128 CCCTAGAGTTCTTAAACTCTATTTCAGGATA 12 185 0 CTTAACTCTA 0.677012 -116 AGGTAATCAACTTCTGCTAAAGGAAAAAAC 12 281 1 CTTTGCTAAA 0.86866 -20 *** ******* Masking position 2 Map Score: 3.67508 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 244 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 CTTGTCTTACTTTTTTCTGTGAATTTGCTTA 4 38 0 TTTTTCTGTG 0.986872 -159 CTTTTCTCAGTGCTCTCTAAAA 9 2 1 TTTTTCAGTG 0.981295 -88 ACTAAAAATGTTTTGTCTGAGTGATTCTTCA 11 31 1 TTTTTCTGAG 0.958067 -97 ACTCAAGCCTTTATCTCAGTGCCACATGAAG 11 57 0 TTATTCAGTG 0.940987 -71 CCTTCTCCTTTTTAGTCTGTGACTAAGATCT 12 44 0 TTTATCTGTG 0.958068 -257 **** ****** Masking position 6 Map Score: 1.03388 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 14 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 CAAGATTGAAGTGTATGTGCGTCATCTCTACA 1 55 1 GTATGTGCGT 0.990672 -29 CAATTAATGCGTATATGTGAGTCTCGCATTCA 5 129 1 GTATGTGAGT 0.979226 -80 CGGGATACCGGTATTAGTGAGTAGAATATCTT 6 71 0 GTTAGTGAGT 0.909078 -26 GTAGTGTTGAGAGTATGTGCGTTTTGTAAAAG 7 152 1 GTATGTGCGT 0.990672 -39 AAAGAAAAGGGGGTAACTGCGTTAGCGGCTAC 12 77 0 GTAACTGCGT 0.954649 -224 * ********* Masking position 8 Map Score: 0.640803 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 13 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 CGACTTTAACTGAATAAGAAC 7 2 0 TGAATAAGAA 0.860981 -189 CCAAAAGCTTTTACTAAGGAATCTAGGTAC 7 67 1 TTACTAAGGA 0.65583 -124 CTTTCGGATTTGACTAAGAATTTTAGGAGG 8 73 0 TGACTAAGAA 0.979482 -109 CTCTATATGCAGACTAAAAATGTTTTGTCT 11 19 1 AGACTAAAAA 0.849991 -109 TTTTAGTCTGTGACTAAGATCTTATATAAT 12 36 0 TGACTAAGAT 0.954066 -265 TCTTAGTCACAGACTAAAAAGGAGAAGGGG 12 47 1 AGACTAAAAA 0.849991 -254 AGAGATAATTTGACTAGGATTACAGCAAGA 12 133 0 TGACTAGGAT 0.864652 -168 ********** Masking position 6 Map Score: 0.743135 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 64 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: -3.6705e-13 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 14 ********** No masking Map Score: -3.6705e-13 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 15 ********** No masking Map Score: -3.6705e-13 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