AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i292_bsub_mtub_300.orf -o292_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 ycsD 85 similar to hypothetical proteins from B. subtilis #2 ycsE 202 similar to hypothetical proteins from B. subtilis #3 ycsF 204 similar to lactam utilization protein #4 ycsG 203 alternate gene name: ycsH; similar to branched chain amino acids transporter #5 ycsI 23 similar to hypothetical proteins #6 ycsJ 43 similar to allophanate hydrolase #7 Rv0264c 95 hypothetical protein Rv0264c #8 fecB2 21 fecB2 #9 Rv0266c 176 hypothetical protein Rv0266c Motif number 1 AACGGCCTCCTTTTGTGTTTTTTCCA 1 7 1 CTCCTTTTGT 0.964259 -79 TTTATATCTCCTTTTTTTGACCATTAT 1 69 0 CTCCTTTTTT 0.982204 -17 GTTTGTTTTGCTGTTTTTTTTCTGTCATGT 2 53 1 CTGTTTTTTT 0.977206 -150 ATATGTACCTCTCTTTATCTTTTTGTTG 2 185 0 CTCTCTTTAT 0.924538 -18 CATCTTAGGACTCTCTTTTT 3 1 0 CTCTCTTTTT 0.985584 -204 CTAAGATGGACTCTCTTTTTAGTTTGGCAG 3 23 1 CTCTCTTTTT 0.985584 -182 GAGCTGTTTTCTGATTTTTTGCGCAAATGT 4 66 0 CTGATTTTTT 0.913617 -138 TTTTTTCCTGCTGTCTTTTTCTGCTGCTCC 4 163 0 CTGTCTTTTT 0.985584 -41 GACCAGCTGCCCGCTTTTTTCCTGCTGTCT 4 177 0 CCGCTTTTTT 0.920067 -27 TTCGGCCCGTCTGCCGTTGTGAGGACGGGA 9 128 1 CTGCCGTTGT 0.899723 -49 ********** Masking position 7 Map Score: 15.058 Number of sites scoring better than the average of aligned sites = 783 Number in coding regions = 541 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 2 GAATCGGATCGGTTAAGTCGTTGTGCTCGGGG 2 10 1 CGGTAGTCTT 0.951577 -193 GGAAAACAAACGGTGAGGTGATCAAACATGACA 2 75 0 CGGTAGTGTC 0.986096 -128 CATTTAAAAGCGGTTCAGTTTTCATTTATGGAG 4 16 1 CGGTCGTTTC 0.95545 -188 TGATTTTTTGCGCAAATGTCAGCGCATGGGCTC 4 52 0 CGCAAGTCGC 0.919952 -152 AAGATTGCAGCGCTACCGTCGACGCATGAGTGT 7 60 1 CGCTCGTCAC 0.975944 -36 CGGTTAGGTCTCCTGTCGACAAG 9 1 1 CGGTAGTCCC 0.995886 -176 CCGTCATTACCGCTGATGTCGCCCGCTTGTCGA 9 26 0 CGCTAGTCCC 0.994909 -151 GACGGCTCGACGCTAAAGAGACCCTGTTACCGG 9 54 1 CGCTAGAGCC 0.915963 -123 CGCTCGCAGCCGGTCCCGTCCTCACAACGGCAG 9 138 0 CGGTCGTCTC 0.993988 -39 **** * *** ** Masking position 1 Map Score: 11.8564 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 121 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 AGGATATAATGGAAAAAACACAAAAGGAGG 1 16 0 GGAAAAAACA 0.874379 -70 GAGATATAATGGTCAAAAAAAGGAGATATA 1 64 1 GGTCAAAAAA 0.956634 -22 AAAAAAAACAGCAAAACAAACCAAATGAAA 2 44 0 GCAAAACAAA 0.944496 -159 CAAACATGACAGAAAAAAAACAGCAAAACA 2 56 0 AGAAAAAAAA 0.722434 -147 ATGAATAAGAGGAAAACAAACGGTGAGGTG 2 88 0 GGAAAACAAA 0.97459 -115 ATACCCAGCGGGACAAAAAAGCGATTTCCT 2 131 0 GGACAAAAAA 0.985877 -72 ATAGAGAGAAGCACAACAAAAAGATAAAGA 2 172 1 GCACAACAAA 0.975535 -31 CCGAATTTCGGGACAATAAATGACATAAAG 3 155 1 GGACAATAAA 0.945121 -50 GCTGACATTTGCGCAAAAAATCAGAAAACA 4 62 1 GCGCAAAAAA 0.891614 -142 TCAGAACAGAGGTCAACATAAAGGAGGAAC 4 126 1 GGTCAACATA 0.817422 -78 ********** Masking position 5 Map Score: 12.4516 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 354 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 TCGCTTTTTTGTCCCGCTGGGTATAATGTAT 2 137 1 GTCCGCTGGG 0.974413 -66 AGAATCCCTCCTGCCAAAGCAAACG 3 190 0 TCCCCCTGCC 0.981578 -15 GCCCGCTTTTTTCCTGCTGTCTTTTTCTGCT 4 168 0 TTCCGCTGTC 0.903922 -36 CAGCAATGACCAGCTGCCCGCTTTTTTC 4 186 0 GACCGCTGCC 0.994116 -18 ATTTGCTAAGGCACCTCTGGCAGTCTCGAAA 7 13 1 GCACTCTGGC 0.878721 -83 CGCTGATGTCGCCCGCTTGTCGACAGGAGAC 9 18 0 GCCCCTTGTC 0.850971 -159 CCTGTTACCGGCCCGGATGCGCGCTGTTACA 9 76 1 GCCCGATGCG 0.973576 -101 GGTGGCTTCGGCCCGTCTGCCGTTGTGAGGA 9 122 1 GCCCTCTGCC 0.994075 -55 GTGAGGACGGGACCGGCTGCGAGCGTGAAGG 9 146 1 GACCGCTGCG 0.988994 -31 **** ****** Masking position 8 Map Score: 10.9452 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 534 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 AAAACAAACCAAATGAAAACCCCGAGCACA 2 32 0 AAATGAAAAC 0.885171 -171 AGGTGATCAAACATGACAGAAAAAAAACAG 2 63 0 ACATGACAGA 0.916588 -140 TCGGGACAATAAATGACATAAAGCATATCG 3 162 1 AAATGACATA 0.879167 -43 AACCGCTTTTAAATGACACA 4 1 0 AAATGACACA 0.915138 -203 CCATCTCCATAAATGAAAACTGAACCGCTT 4 23 0 AAATGAAAAC 0.885171 -181 TTTTTTGCGCAAATGTCAGCGCATGGGCTC 4 52 0 AAATGTCAGC 0.957667 -152 GCTGGAATTGAAGTGACAGCTATTTCAGAA 4 102 1 AAGTGACAGC 0.971039 -102 GAGCAGCAGAAAAAGACAGCAGGAAAAAAG 4 164 1 AAAAGACAGC 0.957667 -40 ACATCAGCGGTAATGACGGCTCGACGCTAA 9 40 1 TAATGACGGC 0.840904 -137 ********** Masking position 5 Map Score: 5.89715 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 696 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 AACGGCCTCCTTTTGTGTTTTTTC 1 5 1 GCCTCCTTTT 0.826694 -81 ACTAAAAAGAGAGTCCATCTTAGGACTCTC 3 16 0 GAGTCCATCT 0.898989 -189 TCAGCGCATGGGCTCCATCTCCATAAATGA 4 37 0 GGCTCCATCT 0.99137 -167 CTCCATCTATTGTTCCTCCTTTATGTTGAC 4 137 0 TGTTCCTCCT 0.847772 -67 CTTTTTCTGCTGCTCCATCTATTGTTCCTC 4 149 0 TGCTCCATCT 0.982338 -55 TTTGTTTAATTGCTCCACTTATA 5 4 0 TGCTCCACTT 0.948247 -20 CCGGACTCCCCCTTCACGCTCGC 9 164 0 GACTCCCCCT 0.954784 -13 ********** Masking position 4 Map Score: 2.57109 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 400 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 TCGACGCATGAGTGTGATGGACGTCTTT 7 78 1 AGTGTGATGG 0.983591 -18 AGCGTGAGGGTATCGCGCGC 8 12 0 AGCGTGAGGG 0.99589 -10 ACCGGCTGCGAGCGTGAAGGGGGAGTCCGG 9 157 1 AGCGTGAAGG 0.993921 -20 ********** Masking position 7 Map Score: 1.36549 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 23 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 AAAAAGAGAGTCCTAAGATGGACTCTC 3 6 1 GGATCCTAAG 0.805006 -199 ATTCGGAATAGTCGTTCCGAATTTCGGGACAA 3 139 1 GCGTCCGAAT 0.966616 -66 GAGACTGCCAGAGGTGCCTTAGCAAATGC 7 8 0 GGGGCCTTAG 0.97692 -88 AAAATCCCTGGCCGAGCCGAAGATTGCAGCGC 7 41 1 GCGGCCGAAG 0.997769 -55 TCTCTTTAGCGTCGAGCCGTCATTACCGCTGA 9 43 0 GCGGCCGTCA 0.943797 -134 CACAACGGCAGACGGGCCGAAGCCACCTAAAG 9 117 0 GCGGCCGAAG 0.997769 -60 * ** ******* Masking position 7 Map Score: 1.65637 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 195 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 AAACGATAGGATATAATGGAAAAAACACAA 1 23 0 ATATAATGGA 0.94136 -63 TTAGGCTGAGATATAATGGTCAAAAAAAGG 1 57 1 ATATAATGGT 0.91805 -29 ACAATAAATGACATAAAGCATATCGTTTGC 3 167 1 ACATAAAGCA 0.936379 -38 ACAGAGGTCAACATAAAGGAGGAACAATAG 4 131 1 ACATAAAGGA 0.980954 -73 GGCCGAAGCCACCTAAAGGTATCTCCGCTG 9 105 0 ACCTAAAGGT 0.895228 -72 ********** Masking position 5 Map Score: 0.829395 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 114 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 GGTCAAAAAAAGGAGATATAAA 1 74 1 AGGAGAATAA 0.9622 -12 ACAAACGGTGAGGTGATCAAACATGACAGAA 2 72 0 AGGTGACAAA 0.94569 -131 AATGAATAAGAGGAAAACAAACGGTGAGGTG 2 88 0 AGGAAACAAA 0.916101 -115 CCTATGTTTGAGGAGAATGAATAAGAGGAAA 2 103 0 AGGAGATGAA 0.96341 -100 ATCCTGATGAACGAGAATTAAAGAGGTGAGA 6 20 1 ACGAGATTAA 0.911441 -24 GCTTGTCGACAGGAGACCTAACCG 9 4 0 AGGAGACTAA 0.990209 -173 ****** **** Masking position 6 Map Score: 1.79814 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 139 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 TCGTTGTGCTCGGGGTTTTCATTTGGTTTG 2 28 1 CGGGGTTTTC 0.858747 -175 GGGACAAAAAAGCGATTTCCTATGTTTGAG 2 122 0 AGCGATTTCC 0.978796 -81 TTTCTGACAAAAGTATTTCACAAACTGATA 3 78 1 AAGTATTTCA 0.639887 -127 AGCCGCTTTGAGCTGTTTTCTGATTTTTTG 4 75 0 AGCTGTTTTC 0.925686 -129 TTGAAGTGACAGCTATTTCAGAACAGAGGT 4 109 1 AGCTATTTCA 0.912507 -95 CGGCTCGGCCAGGGATTTTCGAGACTGCCA 7 30 0 AGGGATTTTC 0.967063 -66 AGCCACCTAAAGGTATCTCCGCTGTAACAG 9 99 0 AGGTATCTCC 0.939207 -78 ********** Masking position 6 Map Score: 0.354328 Number of sites scoring better than the average of aligned sites = 709 Number in coding regions = 625 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 12 ********** No masking Map Score: 6.13499e-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 13 ********** No masking Map Score: 6.13499e-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: 6.13499e-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