AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00100_mtub_reg_100.orf -o00100_mtub_100.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 idsA2 300 idsA2 #2 Rv3137 300 hypothetical protein Rv3137 #3 fadE24 79 fadE24 #4 idsB 300 idsB #5 idsA 22 idsA Motif number 1 TGGCCCCATTGGCGGCCATGGAAGTACTCG 1 20 0 GGCGGCCATG 0.915059 -281 CGGCGCGGCCCACCGGTGGCCCCATTGGCG 1 36 0 CACCGGTGGC 0.885349 -265 ATTTGCGCGACGCGGCGCGGCCCACCGGTG 1 48 0 CGCGGCGCGG 0.971896 -253 GCCATCCTGGGCCGGGCCGGACCAGCCAAC 1 79 1 GCCGGGCCGG 0.889678 -222 TCGATGATTCGGCGGGTGGGCTCGCGGAAA 1 170 0 GGCGGGTGGG 0.981596 -131 CGGCGCGAGTGGCCGCTATCGATGATTCGG 1 188 0 GGCCGCTATC 0.959078 -113 GGCCACTCGCGCCGGCGCGGAATACACTGT 1 204 1 GCCGGCGCGG 0.848784 -97 ATGAGAAAGGGGCGCCGCGCTGAGCCTGAA 1 253 1 GGCGCCGCGC 0.971914 -48 GCACCGGCAGCACCGGCAGCGGTCCAG 1 284 1 CACCGGCAGC 0.906534 -17 ATGTCACCATCGCCGGGATCATCACTGG 2 9 0 CGCCGGGATC 0.940322 -292 ACCGGACGCAGGCGGCCAGCAGTATGTCAC 2 32 0 GGCGGCCAGC 0.981758 -269 GTCAGCCCGCGACCGGACGCAGGCGGCCAG 2 43 0 GACCGGACGC 0.928702 -258 CGCTCCTGGTGACCGGAGTCAGCCCGCGAC 2 60 0 GACCGGAGTC 0.611961 -241 ACCAGGAGCGTGCCGCTGGCCAGATCTCCC 2 80 1 TGCCGCTGGC 0.916995 -221 ATCCCGCGCGGCCCGCGGGGAGATCTGGCC 2 97 0 GCCCGCGGGG 0.501355 -204 CGCGGGATAAGCCGCGGAGCAAGAAATACC 2 119 1 GCCGCGGAGC 0.874128 -182 ATACCGCTAGGACCGCGATCAGTATGAGTA 2 144 1 GACCGCGATC 0.789756 -157 TCCTACCATGGCCGGGTGGGATGGGAGTTT 2 181 0 GCCGGGTGGG 0.880033 -120 GCCATGGTAGGACTGCTGGCATGAGCCGTT 2 199 1 GACTGCTGGC 0.764291 -102 GAGCCGTTATTACGCCGAGCGTGAACTCAG 2 221 1 TACGCCGAGC 0.738694 -80 ACTTAACAAGCACCCCTATCTTACTCCGGA 3 14 1 CACCCCTATC 0.674989 -66 GGTCCGCTATCACCCCGATGACCGAGGCTG 3 56 1 CACCCCGATG 0.693746 -24 TTCCCATCACGGCGGGTAGGTTGCCTTCGA 4 49 0 GGCGGGTAGG 0.977208 -252 AAGTATAGGTCGCCGCAGGGTATGCGTGTC 4 77 1 CGCCGCAGGG 0.915808 -224 TGTAGTGGATGACCCGGGGCGTCTGGACAA 4 111 1 GACCCGGGGC 0.521545 -190 ********** Masking position 3 Map Score: 39.3418 Number of sites scoring better than the average of aligned sites = 63038 Number in coding regions = 58841 Number in noncoding regions = 4197 Number of orfs with sites within 600 bp upstream = 1460 Fraction of orfs with sites within 600 bp upstream = 0.2345 Motif number 2 CCACCGGTGGGCCGCGCCGCGTCGCGCAAA 1 47 1 GCCGCGCCGC 0.835914 -254 GCCATCCTGGGCCGGGCCGGACCAGCCAAC 1 79 1 GCCGGGCCGG 0.990588 -222 GGCCGCTATCGATGATTCGGCGGGTGGGCT 1 178 0 GATGATTCGG 0.62651 -123 GGCCACTCGCGCCGGCGCGGAATACACTGT 1 204 1 GCCGGCGCGG 0.962916 -97 GGGGCGCCGCGCTGAGCCTGAATGCACCGG 1 261 1 GCTGAGCCTG 0.969781 -40 CTGGACCGCTGCCGGTGCTGCCGGTGCATT 1 281 0 GCCGGTGCTG 0.945309 -20 CCAGTGATGATCCCGGCGATGGTGA 2 6 1 GATGATCCCG 0.841464 -295 CATACTGCTGGCCGCCTGCGTCCGGTCGCG 2 36 1 GCCGCCTGCG 0.901556 -265 GCCGCCTGCGTCCGGTCGCGGGCTGACTCC 2 46 1 TCCGGTCGCG 0.73354 -255 CCGGTCGCGGGCTGACTCCGGTCACCAGGA 2 57 1 GCTGACTCCG 0.792223 -244 TGGCCAGCGGCACGCTCCTGGTGACCGGAG 2 72 0 CACGCTCCTG 0.538404 -229 CTCCCCGCGGGCCGCGCGGGATAAGCCGCG 2 105 1 GCCGCGCGGG 0.714142 -196 TGCTACTCATACTGATCGCGGTCCTAGCGG 2 147 0 ACTGATCGCG 0.576207 -154 TCCTACCATGGCCGGGTGGGATGGGAGTTT 2 181 0 GCCGGGTGGG 0.962864 -120 CCGTTATTACGCCGAGCGTGAACTCAGTGC 2 224 1 GCCGAGCGTG 0.90826 -77 CCATCCTTTCGCCGAGCGTGTACCCAGTGC 2 274 0 GCCGAGCGTG 0.90826 -27 CACCCCGATGACCGAGGCTGCCGT 3 66 1 ACCGAGGCTG 0.666689 -14 GAGTTGTCCAGACGCCCCGGGTCATCCACT 4 114 0 GACGCCCCGG 0.956196 -187 TAACAACCCTGATGGTCGTGTTGGTCGACG 4 162 1 GATGGTCGTG 0.788469 -139 GCGACTCACTGTTGCTCCGGTGAGGTTAAG 4 280 1 GTTGCTCCGG 0.715203 -21 ********** Masking position 4 Map Score: 28.8696 Number of sites scoring better than the average of aligned sites = 46576 Number in coding regions = 43588 Number in noncoding regions = 2988 Number of orfs with sites within 600 bp upstream = 1282 Fraction of orfs with sites within 600 bp upstream = 0.205911 Motif number 3 CGGCCCACCGGTGGCCCCATTGGCGGCCATGG 1 29 0 GTGGCCCTTG 0.827399 -272 CGTGTTTATGCTGTCTTCAGCGCCCTTGGGTT 1 106 0 CTGTTTCGCG 0.945398 -195 AGCAACTTGTGTGGTTTCCGCGAGCCCACCCG 1 156 1 GTGGTTCGCG 0.985341 -145 GGCCGCTATCGATGATTCGGCGGGTGGGCTCG 1 176 0 GATGTTCGCG 0.733672 -125 TGGCCCGACAGTGTATTCCGCGCCGGCGCGAG 1 209 0 GTGTTTCGCG 0.982241 -92 GCCGGTGCATTCAGGCTCAGCGCGGCGCCCCT 1 260 0 TCAGCTCGCG 0.835387 -41 CCAGTGATGATCCCGGCGATGGTGACAT 2 7 1 ATGACCCGCG 0.799825 -294 TTGCTCCGCGGCTTATCCCGCGCGGCCCGCGG 2 109 0 GCTTTCCGCG 0.959284 -192 TAGCGGTATTTCTTGCTCCGCGGCTTATCCCG 2 121 0 TCTTCTCGCG 0.806788 -180 CATACTGATCGCGGTCCTAGCGGTATTTCTTG 2 138 0 GCGGCCTGCG 0.905883 -163 TACGCCGAGCGTGAACTCAGTGCAAGAACGCA 2 231 1 GTGACTCGTG 0.87235 -70 TTCGCCGAGCGTGTACCCAGTGCGATTTTTCG 2 265 0 GTGTCCCGTG 0.975328 -36 AGAAAGACACGCATACCCTGCGGCGACCTATA 4 80 0 GCATCCCGCG 0.979727 -221 CAACATGTACCTATGCCCGTCGACCAACACGA 4 177 0 CTATCCCTCG 0.64762 -124 CAGTGAGTCGCTATTTTCAGCGAACGAGCAAT 4 259 0 CTATTTCGCG 0.84813 -42 GCGACTCACTGTTGCTCCGGTGAGGTTAAGA 4 280 1 GTTGTCCGTG 0.883108 -21 **** *** *** Masking position 12 Map Score: 16.4519 Number of sites scoring better than the average of aligned sites = 17957 Number in coding regions = 16819 Number in noncoding regions = 1138 Number of orfs with sites within 600 bp upstream = 768 Fraction of orfs with sites within 600 bp upstream = 0.123354 Motif number 4 TCCTGGGCCGGGCCGGACCAGCCAACCCAAGGGCGCT 1 83 1 GGCGGCCACC 0.991101 -218 CGGAATACACTGTCGGGCCATAGGCACGCCAAATGAG 1 221 1 TGCGGCCAGC 0.994518 -80 CTGCCGGTGCTGCCGGTGCATTCAGGCTCAGCGCGGC 1 266 0 TGCGGGCACC 0.985437 -35 CCCGCGGGGAGATCTGGCCAGCGGCACGCTCCTGGTG 2 79 0 GACTGCCAGC 0.959141 -222 TCAGTATGAGTAGCACGCCAAACTCCCATCCCACCCG 2 162 1 TACACCCACC 0.927725 -139 CTCGGCGTAATAACGGCTCATGCCAGCAGTCCTACCA 2 203 0 TACGGTCACC 0.986716 -98 TGGTGCACCATCCTTTCGCCGAGCGTG 2 284 0 TGTGCCCACC 0.955599 -17 ATCGGGGTGATAGCGGACCACCCTATCTTACTCCGGA 3 38 0 TACGGCCACC 0.997344 -42 CTCGGAATTCGAGTTGTCCAGACGCCCCGGGTCATCC 4 117 0 GATTGCCACC 0.901424 -184 TCGCTGAAAATAGCGACTCACTGTTGCTCCGGTGAGG 4 268 1 TACGATCAGC 0.786404 -33 ** *** *** * * Masking position 10 Map Score: 10.5153 Number of sites scoring better than the average of aligned sites = 2284 Number in coding regions = 2099 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 5 GCGCGGCGCCCCTTTCTCATTTGGCGTGCC 1 243 0 CCTTTCTCAT 0.870642 -58 TGCTCCGCGGCTTATCCCGCGCGGCCCGCG 2 110 0 CTTATCCCGC 0.912926 -191 ACGCCAAACTCCCATCCCACCCGGCCATGG 2 176 1 CCCATCCCAC 0.97828 -125 AACAAGCACCCCTATCTTACTCCGGAGTAA 3 18 1 CCTATCTTAC 0.956569 -62 AGCGGACCACCCTATCTTACTCCGGAGTAA 3 34 0 CCTATCTTAC 0.956569 -46 AATTGCCTGGCCTTTCTCGGAG 4 3 0 CCTTTCTCGG 0.956804 -298 ACCTATACTTCCCATCACGGCGGGTAGGTT 4 57 0 CCCATCACGG 0.912407 -244 ********** Masking position 5 Map Score: 2.09747 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 608 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 TTTCGTGTTTATGCTGTCTTCAGCGCCCTT 1 111 0 ATGCTGTCTT 0.864338 -190 CCGATGACCGAGGCTGCCGT 3 70 1 AGGCTGCCGT 0.990263 -10 AGGCAATTGAATGTTGCAGTATTGTCGAAG 4 25 1 ATGTTGCAGT 0.937382 -276 CACGGCGGGTAGGTTGCCTTCGACAATACT 4 42 0 AGGTTGCCTT 0.987348 -259 TGGGAAGTATAGGTCGCCGCAGGGTATGCG 4 73 1 AGGTCGCCGC 0.942586 -228 GCATAGGTACATGTTGCGTTGATATTTGAA 4 193 1 ATGTTGCGTT 0.933819 -108 ********** Masking position 1 Map Score: 1.51767 Number of sites scoring better than the average of aligned sites = 1177 Number in coding regions = 1100 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 GGTGGGCTCGCGGAAACCACACAAGTTGCTTC 1 154 0 CGGAACACAC 0.906573 -147 CACTGTCGGGCCATAGGCACGCCAAATGAGAA 1 228 1 CCATACACGC 0.957084 -73 CAGCCCGCGACCGGACGCAGGCGGCCAGCAGT 2 39 0 CCGGACAGGC 0.970784 -262 GGAGATCTGGCCAGCGGCACGCTCCTGGTGAC 2 77 0 CCAGCCACGC 0.972837 -224 CGTTCTTGCACTGAGTTCACGCTCGGCGTAAT 2 229 0 CTGAGCACGC 0.981061 -72 AACTCAGTGCAAGAACGCACGCGAAAAATCGC 2 244 1 AAGAACACGC 0.877237 -57 AAAAATCGCACTGGGTACACGCTCGGCGAAAG 2 267 1 CTGGGCACGC 0.98796 -34 CATCCACTACAGAAAGACACGCATACCCTGCG 4 90 0 AGAAACACGC 0.908429 -211 GAGCGAATGCTAGATTCACGCA 5 10 1 CTAGACACGC 0.986671 -13 ***** ***** Masking position 9 Map Score: 6.94465 Number of sites scoring better than the average of aligned sites = 1650 Number in coding regions = 1484 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 8 ********** No masking Map Score: -1.07759e-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 9 ********** No masking Map Score: -1.07759e-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 10 ********** No masking Map Score: -1.07759e-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