AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_bsub_mtub_300.orf -o193_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ytaG 161 similar to hypothetical proteins #2 ytaF 171 ytaF #3 polA 243 DNA polymerase I #4 phoP 211 two-component response regulator #5 citH 43 malate dehydrogenase #6 citC 163 isocitrate dehydrogenase #7 citZ 300 citrate synthase II #8 polA 103 polA #9 rpsA 162 rpsA #10 Rv1631 25 hypothetical protein Rv1631 Motif number 1 GGAAATTGTAAAAAGGAGTGGATCTC 1 146 1 AAAGAGTGTT 0.831949 -16 GAACTTTGTTAAAATAAGAGGAGCTAATGACTATG 3 176 1 AAAAAGAGGT 0.938033 -68 TTTATAGTAAAAAGAGAAAGGCTGTATTAAGCAAG 4 27 0 AAAGAAAGTT 0.962215 -185 TTTTTACTATAAATGAAAGCGCTATCATAAACGTC 4 49 1 AAAAAAGGTT 0.95095 -163 TTTTTAAAAGAAATAAAGACGTTTATGATAGCGCT 4 66 0 AAAAAGAGTA 0.938955 -146 TCTTATATAGAAAATAAAATGATTTTTCCTAACAT 6 90 0 AAAAAAAGTT 0.971665 -74 CTATATAAGAAAAATAAAATGTTTTCTAAATATGA 6 115 1 AAAAAAAGTT 0.971665 -49 AAAAACCCGCAAATAAAGGCGTTTTTTCGGGGAAA 7 12 1 AAAAAGGGTT 0.963958 -289 TGTTCTTTCAAAAGCAAAGGGTTTTAGTTCCAGCA 7 153 1 AAAAAAGGTT 0.950787 -148 CTCTCCCCCAAAAAGAAAATGCTTACATTTTACTG 7 190 0 AAAAAAAGTA 0.917581 -111 GAGTGTTGTAAAAACATGAGGCTTACTTAAAAAGC 7 240 0 AAAATGAGTA 0.620706 -61 AAATTTATTGAAAAGGAGATGTTATAT 7 284 1 AAAGAGAGTT 0.972356 -17 CCCGGGCGTAAAACTGAAACGTGTTGCAGTTCTGC 8 28 1 AAAGAAAGGT 0.889442 -76 *** **** * * * Masking position 3 Map Score: 15.9907 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 330 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 AGCTCATGATTGCCACGGCGATGCTCA 1 8 0 TGCCACGGCG 0.951948 -154 GATTAATAGAAGCCCCGGCAAAAACGCCAT 1 103 0 AGCCCCGGCA 0.955786 -59 TACTGATATATGCACCGACAGCTTGGACAA 2 23 0 TGCACCGACA 0.974687 -149 ATTGTGATGAATCCCGGGCATTTCACATCT 2 111 1 ATCCCGGGCA 0.834325 -61 CTGATACAAGAGCACCAACAGAAAGGAAGA 2 139 1 AGCACCAACA 0.721409 -33 AGTATTATAATTCCCCGACATCCTATTTCT 4 181 0 TTCCCCGACA 0.981558 -31 ATTCTGTGATTTCCCCGAAAAAACGCCTTT 7 26 0 TTCCCCGAAA 0.819824 -275 CAGCCTACCGAGCCCGGGCGTAAAACTGAA 8 16 1 AGCCCGGGCG 0.890013 -88 TGCGCCCGCATTCCACGTCAGCGTCGGTGC 8 70 1 TTCCACGTCA 0.813193 -34 TCACACTTTATGCACCGACGCTGACGTGGA 8 81 0 TGCACCGACG 0.960706 -23 CCCGTCGAGTAGCCTCGTCAGGTACCAATC 9 103 1 AGCCTCGTCA 0.849759 -60 ********** Masking position 3 Map Score: 11.1855 Number of sites scoring better than the average of aligned sites = 857 Number in coding regions = 809 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 CCGTGGCAATCATGAGCTCGCTGTTTGTATC 1 20 1 CAGAGCTCGC 0.843276 -142 GGAACACAAATAGGTTCCCGCCGTCAAAATT 3 95 0 TAGTTCCCGC 0.952466 -149 GGAACCTATTTGTGTTCCCGTCCTTTTTTGT 3 108 1 TGGTTCCCGT 0.854467 -136 ACCTCATTGACGCAAGCCAGCCTCCAATGGT 6 14 0 CGAAGCCAGC 0.817042 -150 CAAAAACCCGCAAATAAAGGC 7 1 1 CAAAACCCGC 0.837393 -300 AATGCGGGCGCAGGTGCCAGCAGAACTGCAA 8 51 0 CAGTGCCAGC 0.94133 -53 ATTCCCGCCCCAGATGCACGCTCGGCAC 9 8 0 CAATGCACGC 0.942292 -155 GAAAAATCGCCGAATTCCCGCCCCAGATGCA 9 21 0 CGATTCCCGC 0.982617 -142 TTTTCCGCCCTGAGTTCACGCTCGGCGCAAT 9 47 1 TGGTTCACGC 0.942076 -116 GGCTACTCGACGGGTACACGCTGGACAAACT 9 86 0 CGGTACACGC 0.966174 -77 TGCAGCTGATCGCGTTCACGTA 10 14 1 CGGTTCACGT 0.910034 -12 ** ******** Masking position 7 Map Score: 8.85387 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 781 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 TCGATAAAATGGCGTTTTTGCCGGGGCTTCTAT 1 95 1 GGCGTTTGCG 0.994874 -67 CGTCAAAATTGGCTCCTTGGATGAAGGGGTTCT 3 72 0 GGCTTTGGAG 0.948374 -172 TGATGTAAAAGGCGAATTGTCGGAATGTCCTGC 4 101 1 GGCGTTGTCG 0.994874 -111 TCTCCTTTATGGCTAGTTTTAGGCTTTTTCCTT 5 13 0 GGCTTTTTAG 0.963935 -31 CGCAAATAAAGGCGTTTTTTCGGGGAAATCACA 7 19 1 GGCGTTTTCG 0.995746 -282 GCGGGAATTCGGCGATTTTTCCGCCCTGAGTTC 9 31 1 GGCGTTTTCG 0.995746 -132 **** ***** * Masking position 7 Map Score: 7.22021 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 67 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 TCAATGCCGGCCATTTTCTGTCTAAGTGGA 1 59 1 CCATTTTCTG 0.929895 -103 GGCAAAAACGCCATTTTATCGATCCATTTC 1 87 0 CCATTTTATC 0.758943 -75 GCTTCATTGTCCAAGCTGTCGGTGCATATA 2 17 1 CCAAGCTGTC 0.836761 -155 TCCGTTTCTTCCTTTCTGTTGGTGCTCTTG 2 145 0 CCTTTCTGTT 0.937365 -27 ACGGCGGGAACCTATTTGTGTTCCCGTCCT 3 102 1 CCTATTTGTG 0.93211 -142 TGTTCCCGTCCTTTTTTGTGTCTTCTCTTA 3 120 1 CTTTTTTGTG 0.647241 -124 ATTAAGCAAGCCTTTCTCTCTTTTTA 4 7 0 CCTTTCTCTC 0.973777 -205 CTTAATACAGCCTTTCTCTTTTTACTATAA 4 31 1 CCTTTCTCTT 0.910154 -181 TCCCCGACATCCTATTTCTCTATTTTATGT 4 170 0 CCTATTTCTC 0.920074 -42 TTTTTTTTTTCCATTCTGTGATTTCCCCGA 7 38 0 CCATTCTGTG 0.97387 -263 TCGTCAGGTACCAATCTGTCCCTACGACCC 9 117 1 CCAATCTGTC 0.964564 -46 ********** Masking position 7 Map Score: 9.92735 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 440 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 AACACGGATTTTTCACTTTCCCATATATAT 2 80 1 TTTCACTTTC 0.856211 -92 CATATCCGTTTCTTCCTTTCTGTTGGTGCT 2 149 0 TCTTCCTTTC 0.980928 -23 AGTTCACGTATTTTCCTTTCAAATTGAACT 3 151 1 TTTTCCTTTC 0.982142 -93 GAAGCCTCAGGCTTCCATTCATCTCTTACA 3 209 0 GCTTCCATTC 0.706164 -35 TGTCGGAATGTCCTGCTTTCGCTAAAATAA 4 118 1 TCCTGCTTTC 0.823962 -94 GTTTTAGGCTTTTTCCTTGC 5 1 0 TTTTCCTTGC 0.911948 -43 GTCTCTCTTCTCCTTTATGGCTAGTTT 5 27 0 TTCTCCTTTA 0.841438 -17 GGAAAAATCATTTTATTTTCTATATAAGAA 6 96 1 TTTTATTTTC 0.594269 -68 ATAATTTTTTTTTTCCATTCTGTGATTTCC 7 42 0 TTTTCCATTC 0.931721 -259 TTCAATAAATTTCCCCTTTAAGAGTGTTGT 7 266 0 TTCCCCTTTA 0.768716 -35 ATATAACATCTCCTTTTCAATAAATTTC 7 283 0 TCTCCTTTTC 0.832294 -18 ********** Masking position 8 Map Score: 5.56169 Number of sites scoring better than the average of aligned sites = 1491 Number in coding regions = 1169 Number in noncoding regions = 322 Number of orfs with sites within 600 bp upstream = 355 Fraction of orfs with sites within 600 bp upstream = 0.057019 Motif number 7 TGTTTACAAAGGTTTAACAATATCTTC 3 8 1 AAAGGTTTAA 0.89881 -236 TCCTACCAGCATAGGTTTAACAGTGCATGA 3 36 0 ATAGGTTTAA 0.826404 -208 AAAAAGAGAGAAAGGCTTGCTTAATACAGC 4 12 1 AAAGGCTTGC 0.939175 -200 TGTCTGAACAAGAGGCTAACCTCATTGACG 6 33 0 AGAGGCTAAC 0.896231 -131 GACATTTGTTAAATGTTTACCTATAATTTT 7 64 0 AAATGTTTAC 0.838644 -237 TATAATGAGAATAGGCTTAAACTTAAATAA 7 105 1 ATAGGCTTAA 0.923906 -196 CCCAAAAAGAAAATGCTTACATTTTACTGG 7 189 0 AAATGCTTAC 0.930051 -112 TGTAAAAACATGAGGCTTACTTAAAAAGCA 7 239 0 TGAGGCTTAC 0.896209 -62 ********** Masking position 3 Map Score: 2.61528 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 306 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 ATTGTCGGAATGTCCTGCTTTCGCTAAAAT 4 116 1 TGTCCTGCTT 0.895905 -96 CATTGGAGGCTGGCTTGCGTCAATGAGGTT 6 16 1 TGGCTTGCGT 0.921677 -148 GTGCCGAGCGTGCATCTGGGG 9 2 1 TGCCGAGCGT 0.988513 -161 GCGATTTTTCCGCCCTGAGTTCACGCTCGG 9 42 1 CGCCCTGAGT 0.94144 -121 GTCCCGATTGCGCCGAGCGTGAACTCAGGG 9 54 0 CGCCGAGCGT 0.986177 -109 GGACCGAGTTTGTCCAGCGTGTACCCGTCG 9 80 1 TGTCCAGCGT 0.982342 -83 ********** Masking position 10 Map Score: 1.79772 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 185 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 TAACTCTGGATTAAGGATGCCATTTTCGAAA 2 51 1 TTAAGATGCC 0.973248 -121 AAAGGCTGTATTAAGCAAGCCTTTCTCTCTT 4 15 0 TTAAGAAGCC 0.991715 -197 CTAACCTCATTGACGCAAGCCAGCCTCCAAT 6 17 0 TGACGAAGCC 0.960459 -147 AGGCTTAAACTTAAATAAGCTTATAAAAATT 7 117 1 TTAAAAAGCT 0.814648 -184 ATCGTGCTTTTTAAGTAAGCCTCATGTTTTT 7 235 1 TTAAGAAGCC 0.991715 -66 ***** ***** Masking position 7 Map Score: 1.47967 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 47 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ATAGAAGCCCCGGCAAAAACGCCATTTTAT 1 98 0 CGGCAAAAAC 0.932836 -64 ACCAACAGAAAGGAAGAAACGGATATGCAA 2 152 1 AGGAAGAAAC 0.93408 -20 TCAATTTGAAAGGAAAATACGTGAACTATA 3 148 0 AGGAAAATAC 0.951292 -96 GCAAGGAAAAAGCCTAAAACTAG 5 4 1 AGGAAAAAGC 0.97789 -40 ATTGAATGTTAGGAAAAATCATTTTATTTT 6 85 1 AGGAAAAATC 0.966208 -79 TGTGATTTCCCCGAAAAAACGCCTTTATTT 7 22 0 CCGAAAAAAC 0.909526 -279 CTCCCCCAAAAAGAAAATGCTTACATTTTA 7 193 0 AAGAAAATGC 0.677439 -108 GAACTCAGGGCGGAAAAATCGCCGAATTCC 9 34 0 CGGAAAAATC 0.965549 -129 ********** Masking position 5 Map Score: 5.66294 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 448 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 CTTAGACAGAAAATGGCCGGCATTGATTCC 1 55 0 AAATGGCCGG 0.980447 -107 CGTGATTAATAGAAGCCCCGGCAAAAACGC 1 106 0 AGAAGCCCCG 0.931608 -56 AGTTACTGATATATGCACCGACAGCTTGGA 2 26 0 ATATGCACCG 0.757962 -146 ATCAGATGTGAAATGCCCGGGATTCATCAC 2 114 0 AAATGCCCGG 0.989827 -58 GAAGACACAAAAAAGGACGGGAACACAAAT 3 115 0 AAAAGGACGG 0.95395 -129 CAAAAACCCGCAAATAAAGGC 7 2 1 AAAAACCCGC 0.788196 -299 GGCTTACTTAAAAAGCACGATGCAAGTATT 7 226 0 AAAAGCACGA 0.916426 -75 TTCCCGCCCCAGATGCACGCTCGGCAC 9 8 0 AGATGCACGC 0.922078 -155 CAGGGCGGAAAAATCGCCGAATTCCCGCCC 9 29 0 AAATCGCCGA 0.69362 -134 ********** Masking position 3 Map Score: 2.16828 Number of sites scoring better than the average of aligned sites = 1106 Number in coding regions = 967 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 12 TTTCCAGAGCCCAATCGTGATTAATAGAAG 1 121 0 CCAATCGTGA 0.951088 -41 ATTAAGGATGCCATTTTCGAAACACGGATT 2 60 1 CCATTTTCGA 0.929326 -112 ATCCAAGGAGCCAATTTTGACGGCGGGAAC 3 83 1 CCAATTTTGA 0.981434 -161 AAAGTGTAACCCAATTTTGATGTCTGAACA 6 53 0 CCAATTTTGA 0.981434 -111 ********** Masking position 5 Map Score: 0.0264796 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 29 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 ********** No masking Map Score: 3.32777e-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 14 ********** No masking Map Score: 3.32777e-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: 3.32777e-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