AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_ctra_reg_300.orf -o00710_ctra_300.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 ltuA 114 hypothetical protein #9 pgi 112 Glucose-6-P Isomerase #10 phnP 28 predicted metal dependent hydrolase (histidinic triad) #11 artJ 68 Arginine Binding Protein #12 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #13 CT382.1 182 hypothetical protein #14 CT389 181 hypothetical protein #15 aspC 89 Aspartate Aminotransferase #16 greA 113 Transcription Elongation Factor G #17 tyrB 187 Aromatic AA Aminotransferase #18 CT691 160 hypothetical protein #19 pgk 127 Phosphoglycerate Kinase #20 tktB 300 Transketolase Motif number 1 TGTACACTCTCCTTCTTATCGTAGAG 1 7 1 CTCTCCTTCT 0.794672 -77 TTGTTAGATTCTTTCCTTTGAGAGGTTT 2 77 1 CTTTCCTTTG 0.910853 -18 AAGATGCTCCTATTTTAAATATGGTG 3 7 1 CTCCTATTTT 0.535512 -294 ATCGCAGAGTCTTTCATTTTCTTTACCTCA 3 193 0 CTTTCATTTT 0.792347 -108 AAAAACTATTTTCTCTTTTTAATTTTTATT 3 281 0 TTCTCTTTTT 0.704333 -20 TCTTGTCTTACTTTTTTCTGTGAATTTGCT 4 40 0 CTTTTTTCTG 0.634442 -157 AATAGATGAGCTTTTTTTTGCCAAAAGCTT 7 47 1 CTTTTTTTTG 0.667065 -144 GTTTGCAGAGTTTTTATTTTAAATATGTTA 8 48 1 TTTTTATTTT 0.476802 -67 CTGTCTATTACTTCTCTCTTAAAATCGTTT 8 82 1 CTTCTCTCTT 0.660818 -33 GAGAGACCTTCTTTCTTTTTACTTGTACTA 9 66 0 CTTTCTTTTT 0.792347 -47 GATTCTCCTTTTGAGGAAATGT 9 101 0 TTCTCCTTTT 0.897336 -12 ATTCTTATTTTTTTTAAGAAT 11 2 1 TTCTTATTTT 0.631536 -67 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 12 15 1 CTCTTCTCTT 0.942564 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 12 26 0 CTCTTCTCTT 0.942564 -111 CTTTCTATTTCTTTTCTCTTCCCTGTGTGT 12 68 1 CTTTTCTCTT 0.897178 -69 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 12 109 0 TTCTTCTCTT 0.844899 -28 TTAACAAAAGTTTTTCTTTGTCTTCAATGA 13 57 1 TTTTTCTTTG 0.709324 -126 AATTAAATTGTTTTCATTTGAATTTAATTT 13 101 1 TTTTCATTTG 0.48035 -82 CACTCGAGCGCTCTTCTCCTAAAAATCTTG 14 110 1 CTCTTCTCCT 0.706924 -72 AAAGATGAGACTCTCATCTGTCCAGCGTAA 15 34 0 CTCTCATCTG 0.819387 -56 TGTAATATTGCTCTTTTTTGTTATTCGGCG 16 64 1 CTCTTTTTTG 0.79028 -50 GATGGCTCCCCTTTTTAGTCCGGAA 16 99 0 CTCCCCTTTT 0.854637 -15 AAGGCTTGAGTTTTCCTTTGCTTAGGCCTA 19 77 1 TTTTCCTTTG 0.772294 -51 GGCTACCCCCTTCTCCTTTTTAGTCTGTGA 20 53 0 TTCTCCTTTT 0.897336 -248 CAGTTACCCCCTTTTCTTTTCTCTAAAATA 20 90 1 CTTTTCTTTT 0.909692 -211 AAAATACCTTCTCTCTTCTTCTTGCTGTAA 20 114 1 CTCTCTTCTT 0.861426 -187 ********** Masking position 7 Map Score: 26.7005 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 914 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 2 TCTTGTGGTCAAAAATTTTAACCCTCTACG 1 30 0 AAAAATTTTA 0.855097 -54 TCACCTTCTCAAAGATCTTAACTAAAGACT 3 166 0 AAAGATCTTA 0.80375 -135 GCTTTGATATAAATCTCTTGGATATGCTAA 4 73 0 AAATCTCTTG 0.738597 -124 AAACGTGGAAAAAATCTCTTTTGAAGACG 5 10 1 AAAAATCTCT 0.593762 -199 TGCGGTTGCTAAATATTTTGTATAGTTGAA 6 15 1 AAATATTTTG 0.803882 -82 TTCCTTAGTAAAAGCTTTTGGCAAAAAAAA 7 58 0 AAAGCTTTTG 0.729326 -133 CTGCAAACAAAAAAACTTTGCCTAGCCGTC 8 26 0 AAAAACTTTG 0.736103 -89 TTTTTCATTGAAAAATCTTTCTATTTCTTT 12 52 1 AAAAATCTTT 0.579341 -85 GGTATAGCGAAAAAATTTTAACAAAAGTTT 13 40 1 AAAAATTTTA 0.855097 -143 AAGACAAAGAAAAACTTTTGTTAAAATTTT 13 51 0 AAAACTTTTG 0.902188 -132 ATTGCCTCCTAAAATTCTTAGTCAAATCCG 14 69 1 AAAATTCTTA 0.641264 -113 CTCTTCTCCTAAAAATCTTGTTTTTTCTCT 14 120 1 AAAAATCTTG 0.952986 -62 AACAAAAATCTCGATCTTTTATT 16 4 1 AAAAATCTCG 0.898556 -110 AAAAAACAAGAAAAATTTTATTATTAAATA 16 30 0 AAAAATTTTA 0.855097 -84 CTCGAGCGTGAAAAATCTTAGAAAAAAACA 18 42 1 AAAAATCTTA 0.924769 -119 GAAAAAAACAAAAAATTTTGGTTCTTAGTA 18 62 1 AAAAATTTTG 0.896192 -99 ********** Masking position 3 Map Score: 12.6571 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 259 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 TAAAGCTTTGAAGGAATCTTGAAGAGGTTGT 2 18 1 AAGGAATCTG 0.640266 -77 CTCTCAAAGGAAAGAATCTAACAAGGGCTTC 2 70 0 AAAGAATCAA 0.717668 -25 GATCTTAACTAAAGACTCCAGGAAAGATCGT 3 152 0 AAAGACTCAG 0.909185 -149 CCTTCCTTGCAAGAAATCGAGTATTACGCTT 4 131 1 AAGAAATCAG 0.932332 -66 AGCTTTTACTAAGGAATCTAGGTACTTGATT 7 72 1 AAGGAATCAG 0.951088 -119 TTGGATGATAAAAGAATCAAGTACCTAGATT 7 86 0 AAAGAATCAG 0.959483 -105 TGAGTTAAGAGAAGAAACAAGGAAAACAAAT 12 113 1 GAAGAAACAG 0.889957 -24 TTAGGAGGCAATGAAATCCAGAATGAGTATG 14 50 0 ATGAAATCAG 0.557777 -132 CGGAAGTAGAGAAAAAACAAGATTTTTAGGA 14 126 0 GAAAAAACAG 0.851387 -56 ATTATTAAATAAAAGATCGAGATTTTTGTT 16 10 0 AAAAGATCAG 0.694757 -104 TATTACATCACAAAAAACAAGAAAAATTTTA 16 40 0 CAAAAAACAG 0.619347 -74 TACCCCGAGGGAAGAAACTAGGTTATCATGT 17 86 1 GAAGAAACAG 0.889957 -102 AAAATCTTAGAAAAAAACAAAAAATTTTGGT 18 53 1 AAAAAAACAA 0.481167 -108 CTAAGCAAAGGAAAACTCAAGCCTTTATCTC 19 71 0 GAAAACTCAG 0.824654 -57 AATAGAGTTTAAGAACTCTAGGGACTTAATT 20 193 1 AAGAACTCAG 0.85349 -108 ******** ** Masking position 8 Map Score: 8.78443 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 195 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 4 TGTGCATGTATTTTGTAAGATAGATCAAAG 4 159 0 TTTTGTAAGA 0.821535 -38 AGTATGTGCGTTTTGTAAAAGTAAAGAGAG 7 163 1 TTTTGTAAAA 0.738258 -28 TCGTATCACATTTCCTCAAAAGGAGAATC 9 94 1 TTTCCTCAAA 0.812651 -19 CCCTTAATCGTTTTCTAAAA 10 1 0 TTTTCTAAAA 0.909587 -28 ATTCTTATTTTTTTTAAGAATCATGTTGG 11 10 1 TTTTTTAAGA 0.74854 -59 TTTAATTTTATTTTTTAAGATCTATTTGTT 13 123 1 TTTTTTAAGA 0.74854 -60 ATTTTCTCACAAAACACAATA 13 172 0 TTTTCTCACA 0.893866 -11 CGTTTTTACGTTTCCTCACACAATTAACTA 14 11 1 TTTCCTCACA 0.74483 -171 CTTTTCTCAGTGCTCTCTAAA 15 2 1 TTTTCTCAGT 0.698058 -88 TTTTTTGTTTTTTTCTAAGATTTTTCACGC 18 47 0 TTTTCTAAGA 0.944997 -114 TTGGGAGCATTTTTCTCAAAGACAATTAAA 18 131 1 TTTTCTCAAA 0.92584 -30 CCCTTTTCTTTTCTCTAAAATACCTTCTCT 20 98 1 TTCTCTAAAA 0.649617 -203 ********** Masking position 8 Map Score: 6.65761 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 164 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 CTACGATAAGAAGGAGAGTGTACA 1 4 0 AAGGAGATGT 0.605858 -80 AAGGAATCTTGAAGAGGTTGTAGGATTACTG 2 28 1 GAAGAGGTGT 0.954163 -67 CCGCTCTGACGGAGAGTGTGTTGCGCTTTTT 3 45 0 GGAGAGTTGT 0.681053 -256 AAAGACTCCAGGAAAGATCGTTTATCTTGAG 3 142 0 GGAAAGACGT 0.904073 -159 GAAACGTTTGGAAGAGATCATAGACCTTATG 5 44 1 GAAGAGACAT 0.709566 -165 TGCCTTGTATGAAGAGGCTGATCAATTAATG 5 107 1 GAAGAGGTGA 0.796177 -102 TTGTAAAAGTAAAGAGAGGGTGGCTT 7 175 1 AAAGAGAGGT 0.912315 -16 TAGATGAAAAGATCGATTGTTCTACA 9 6 1 GAAAAGACGA 0.72731 -107 ACAAGTAAAAAGAAAGAAGGTCTCTCGTATC 9 70 1 AGAAAGAGGT 0.709571 -43 CTCTTGAAGAGAAGAGAACGTTTAATGATG 12 10 0 GAAGAGACGT 0.97569 -127 CTCTTCAAGAGAAGAGGGCGTTTTTTTCATT 12 30 1 GAAGAGGCGT 0.976132 -107 GACTAAAAAGGAGAAGGGGGTAGCCGCTAAC 20 58 1 GAGAAGGGGT 0.807841 -243 TTAGAGAAAAGAAAAGGGGGTAACTGCGTTA 20 85 0 GAAAAGGGGT 0.935415 -216 AGCAAGAAGAAGAGAGAAGGTATTTTAGAGA 20 109 0 AGAGAGAGGT 0.873401 -192 ******* *** Masking position 5 Map Score: 7.87835 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 391 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 TCAATGTGTGCAGAATAAAAATTAAAAAGA 3 268 1 CAGAATAAAA 0.887641 -33 ATAACAAAGGGGCTAAAACCAACTATTT 4 9 1 GGGGCTAAAA 0.891215 -188 AACGTATGTTGGGACCAAAATTAGTTAGTT 7 116 1 GGGACCAAAA 0.891215 -75 CGTATATTTCCGGACTAAAAAGGGGAGCCA 16 92 1 CGGACTAAAA 0.9722 -22 TCTCTATATGCAGACTAAAAATGTTTTGTC 19 18 1 CAGACTAAAA 0.966622 -110 ATCTTAGTCACAGACTAAAAAGGAGAAGGG 20 46 1 CAGACTAAAA 0.966622 -255 CGATAATAAGGAGAATAAAATAAATTAAGT 20 216 0 GAGAATAAAA 0.857439 -85 ********** Masking position 7 Map Score: 4.19689 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 7 TAAAGATCAGTTATATTAAAATAACCTTGGTGT 3 235 1 TTATAAAATA 0.570753 -66 CAACATACGTTTGGATGATAAAAGAATCAAGTA 7 94 0 TTATATAAAA 0.931425 -97 AGAAAGATTTTTCAATGAAAAAAACGCCCTCTT 12 41 0 TTATAAAAAA 0.893468 -96 CAAATAGATCTTAAAAAATAAAATTAAATTCAA 13 118 0 TTAAATAAAA 0.753289 -65 ACACAATAGTTTCTATTATAAAACTAAAACAAA 13 147 0 TTATATAAAA 0.686681 -36 ATTTTCTCACAAAACACAATAGTT 13 169 0 TTCTACAAAA 0.72432 -14 CGATCTTTTATTTAATAATAAAATTTTTCTTGT 16 22 1 TTATATAAAA 0.686681 -92 AAGAGCAATATTACATCACAAAAAACAAGAAAA 16 46 0 TTATACAAAA 0.928189 -68 GACTAAGATCTTATATAATAAAATGCTTGGCGA 20 22 0 TTATATAAAA 0.686681 -279 ** ** ****** Masking position 8 Map Score: 3.91143 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 78 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 CTGTTTGAGGAATAGAAGCCCTTGTTAGAT 2 56 1 AATAGAAGCC 0.93369 -39 AAATCATATAAAAATAAGCCTTCCTTGCAA 4 113 1 AAAATAAGCC 0.944663 -84 TATCCGAAATGAAAGAAGCCTTCAACTATA 6 35 0 GAAAGAAGCC 0.956103 -62 GCTTTTGGCAAAAAAAAGCTCATCTATTTT 7 45 0 AAAAAAAGCT 0.732014 -146 TTTTCAATGAAAAAAACGCCCTCTTCTCTT 12 36 0 AAAAAACGCC 0.932667 -101 AGTCAAATCCGAAAGAAGCCGACACTCGAG 14 88 1 GAAAGAAGCC 0.956103 -94 TTAGTCCGGAAATATACGCCGAATAACAAA 16 80 0 AATATACGCC 0.77968 -34 ATCTTACTGGAAAAAAAGACAGTAAGCAGC 17 144 1 AAAAAAAGAC 0.732014 -44 ********** Masking position 6 Map Score: 2.9552 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 122 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 TTTCTTAGCATGCAAACATTTATTTCGTAG 3 104 1 TGCAAACATT 0.95562 -197 ATTTTTATTCTGCACACATTGAACACCAAG 3 260 0 TGCACACATT 0.868863 -41 TATGATCTCTTCCAAACGTTTCATAGCGTC 5 36 0 TCCAAACGTT 0.916474 -173 TCTTTTATCATCCAAACGTATGTTGGGACC 7 102 1 TCCAAACGTA 0.934585 -89 ATTAGTTAGTTGCAAACGTAGTGTTGAGAG 7 135 1 TGCAAACGTA 0.971312 -56 ATAAAAACTCTGCAAACAAAAAAACTTTGC 8 35 0 TGCAAACAAA 0.853392 -80 CATTCTAGATTGCAAATATATATATGAAGG 18 92 1 TGCAAATATA 0.784335 -69 ********** Masking position 6 Map Score: 1.67537 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 23 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 10 CTATAAATCTTTCTTAGCATGCAAACATTTATTT 3 95 1 TTTAGCGCAA 0.883123 -206 CTCTTTTTAATTTTTATTCTGCACACATTGAACA 3 265 0 TTTATTGCAC 0.719548 -36 GATCAGCCTCTTCATACAAGGCAAGAGAAGCTTC 5 96 0 TTTACAGCAA 0.867074 -113 CCTAGCCGTCTCCGTAGAAAGCACT 8 2 0 TCTAGAGCAC 0.96796 -113 TAAAATTTTTTCGCTATACCGCAAAATGATTGCG 13 26 0 TCTATAGCAA 0.901326 -157 TCCAGCGTAATTTTTAGAGAGCACTGAGAAAAG 15 10 0 TTTAGAGCAC 0.973421 -80 ATTAGCTCAGTTGGTAGAGCGCAACAATGGCATT 17 53 0 TTTAGAGCAA 0.965978 -135 AATAAAACCTCTCTATAGCGCACTGCTGCTTAC 17 165 0 TCTATAGCAC 0.92193 -23 TTCTTAGTACATTCTAGATTGCAAATATATATAT 18 83 1 ATTAGAGCAA 0.817579 -78 ** **** **** Masking position 6 Map Score: 1.79606 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 TTAAAAAGAGAAAATAGTTTTT 3 289 1 AAAATGTTTT 0.907255 -12 CTTCTCTCTTAAAATCGTTTTTTTAGGGGCT 8 92 1 AAAATGTTTT 0.907255 -23 ATAAGGCCCCTTAATCGTTTTCTAAAA 10 7 0 TTAATGTTTT 0.920686 -22 TTCAATGAATTTAATGGTTTTAAATTAAATT 13 79 1 TTAATGTTTT 0.920686 -104 GGTTTTAAATTAAATTGTTTTCATTTGAATT 13 94 1 TAAATGTTTT 0.937368 -89 TAAGCCTTTTTTAATTGTCTTTGAGAAAAAT 18 139 0 TTAATGTCTT 0.781326 -22 TATGCAGACTAAAAATGTTTTGTCTGAGTGA 19 24 1 AAAAAGTTTT 0.696529 -104 ***** ***** Masking position 4 Map Score: 1.77792 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 48 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 CAAGATTGAAGTGTATGTGCGTCATCTCTACA 1 55 1 GTTTGTGCGT 0.975348 -29 CAATTAATGCGTATATGTGAGTCTCGCATTCA 5 129 1 GTTTGTGAGT 0.979476 -80 CGGGATACCGGTATTAGTGAGTAGAATATCTT 6 71 0 GTTAGTGAGT 0.979476 -26 GTAGTGTTGAGAGTATGTGCGTTTTGTAAAAG 7 152 1 GATTGTGCGT 0.907068 -39 AGACCATTGAGTCGGAGTGAGT 11 57 1 GTGAGTGAGT 0.945798 -12 AAAATGTTTTGTCTGAGTGATTCTTCATGTGG 19 35 1 GTTAGTGATT 0.880708 -93 ** * ******* Masking position 8 Map Score: 0.481651 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 TGACGGAGAGTGTGTTGCGCTTTTTTGGGT 3 40 0 TGTGTTGCGC 0.842499 -261 ATACGCATTAATTGATCAGCCTCTTCATAC 5 113 0 ATTGATCAGC 0.762204 -96 CTATTTTTCAATAGATGAGCCGACTTTAAC 7 22 0 ATAGATGAGC 0.923503 -169 CTATTGAAAAATAGATGAGCTTTTTTTTGC 7 38 1 ATAGATGAGC 0.923503 -153 TTGCAAACGTAGTGTTGAGAGTATGTGCGT 7 144 1 AGTGTTGAGA 0.797981 -47 CAACAATGGCATTGTTGAGGTCAGCGGTTC 17 36 0 ATTGTTGAGG 0.856586 -152 CAACAATGCCATTGTTGCGCTCTACCAACT 17 49 1 ATTGTTGCGC 0.968206 -139 CTGCATATAGAGAGTTGCGC 19 1 0 AGAGTTGCGC 0.948997 -127 ********** Masking position 6 Map Score: 0.569487 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 86 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: -5.17032e-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 15 ********** No masking Map Score: -5.17032e-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