AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_bsub_mtub_300.orf -o078_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 yfnI 300 alternate gene name: yetP; similar to hypothetical proteins #2 yfnH 235 similar to glucose-1-phosphate cytidylyltransferase #3 spsI 24 alternate gene name: ipa-71d #4 spsA 300 alternate gene name: ipa-63d #5 Rv0331 113 hypothetical protein Rv0331 #6 Rv0332 74 hypothetical protein Rv0332 #7 Rv0333 26 hypothetical protein Rv0333 #8 rmlA 29 rmlA #9 rmlD 75 rmlD #10 Rv3463 253 hypothetical protein Rv3463 #11 rmlB 72 rmlB Motif number 1 AACATAAATATTCCGGCTTGCCGCGGTGTATT 1 207 1 TCCGGCTGCC 0.991606 -94 TTCTGAAAAACAGCGGCTGCCCAGAGCGAAAT 4 168 0 CGCGGCTCCC 0.977331 -133 CACGCCGGTGGGCGCGGCCCCCTA 6 3 1 CCCGGTGGCG 0.992725 -72 CCACGGCTCCTACCGGCGCCCCTGAAACACCA 6 35 1 TCCGGCGCCC 0.983235 -40 CAGCGGTTATCCACAGTCTGGT 6 63 0 CGCGGTTTCC 0.875129 -12 GGTCGGCGAACGGCAGTTAGGA 8 1 1 GTCGGCGACG 0.84119 -29 AACGGCGCCCTGTCGGGTAGCCAACCCCGGCG 9 27 1 TTCGGGTGCC 0.816512 -49 GGGTAGCCAACCCCGGCGTGCCCGAGGCGTGC 9 41 1 CCCGGCGGCC 0.995999 -35 TTCTCTTCCTTGTCGGTGCACCCGATTCCGGC 10 27 1 TTCGGTGACC 0.890263 -227 GTGCACCCGATTCCGGCGCAGCACGTGCTCGG 10 42 1 TCCGGCGAGC 0.916091 -212 GAATTTCCACCACCGGCTCACGTTTGTAGTCC 10 72 0 CCCGGCTACG 0.967876 -182 CGGTGTCCCGTGCCGGTTTGGCGTGCCCAGTT 10 130 0 TCCGGTTGGC 0.967241 -124 TGGGTTGGCGGTGCGGTGTCCCGTGCCGGTTT 10 143 0 GGCGGTGCCC 0.961249 -111 GCGTGGCCTACGGCGTTTTGCGCAGAGCACGG 10 189 0 CGCGTTTGCG 0.836273 -65 ACCGGTGCTATTCCGGTGAGCGCGTGGCCTAC 10 210 0 TCCGGTGGCG 0.988897 -44 ACCGGAATAGCACCGGTGAGCCGAGCGGTTAG 10 225 1 CCCGGTGGCC 0.995331 -29 CCGGTGAGCCGAGCGGTTAGAGCAACC 10 237 1 GGCGGTTGAG 0.7701 -17 GTTCGCAACCCTCCGTTTCGGGA 11 2 0 CCCGTTTGGG 0.712875 -71 ACCCAACTGGTCGCGGCTCCACTCGGTTAAGG 11 32 1 TGCGGCTCAC 0.728345 -41 CTCGGTTAAGGCTCGGTTAGGGTTTGATCC 11 53 1 GTCGGTTGGG 0.808815 -20 * ****** *** Masking position 5 Map Score: 29.4288 Number of sites scoring better than the average of aligned sites = 1807 Number in coding regions = 1682 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 GCAATGCGCCCGCTCAAGGCTCTTTTTCATC 2 10 0 CGCAAGGCTC 0.987471 -226 GCATTGCCTTCGCTCAAGGCTCTTTTTTTGGT 2 35 1 CGCAAGGCTC 0.987471 -201 GGTGAGTCATCGCGGAGCGTTCACCTATACAT 4 35 0 CGCAGCGTTC 0.966852 -266 CTGATTCCTTCGCATCGAGTTCCATATATCTT 5 88 0 CGCCGAGTTC 0.912212 -26 TCGATGCGAAGGAATCAGGCTC 5 102 1 GGACAGGCTC 0.920311 -12 GCCGTGGTAGGGGGCCGCGCCCACCGGCGTG 6 10 0 GGGCGCGCCC 0.753678 -65 GGTTGGCTACCCGACAGGGCGCCGTTACACAA 9 21 0 CCGAGGGCGC 0.825268 -55 GAGTCTGGCACGCCTCGGGCACGCCGGGGTTG 9 48 0 CGCCGGGCAC 0.983081 -28 GTGCTGCGCCGGAATCGGGTGCACCGACAAGG 10 34 0 GGACGGGTGC 0.839322 -220 CCGATTCCGGCGCAGCACGTGCTCGGACTACA 10 48 1 CGCCACGTGC 0.931017 -206 GTGGAAATTCCGCGAAGGGCTCCGAGAAATTT 10 94 1 CGCAGGGCTC 0.994984 -160 AAACGCCGTAGGCCACGCGCTCACCGGAATAG 10 203 1 GGCCGCGCTC 0.988394 -51 CGGCTCCACTCGGTTAAGGCTCGGTTAGGGTT 11 45 1 CGGAAGGCTC 0.968454 -28 *** ******* Masking position 12 Map Score: 17.682 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 497 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AAATATTCCGGCTTGCCGCGGTGTATTTATT 1 212 1 GCTGCCGCGG 0.971841 -89 CCTTGCGCAAGACTGCGGCGGAATCTAATAT 5 53 1 GATGCGGCGG 0.955163 -61 AGCCGTGGTAGGGGGCCGCGCCCACCGGCGT 6 12 0 GGGGCCGCGC 0.989242 -63 GAAAGTTACCGTGTGCGGCGG 7 1 0 GTTGCGGCGG 0.987112 -26 GTGTTTGAGTCTGGCACGCCTCGGGCACG 9 57 0 GTTGGCACGC 0.922695 -19 CGGTGCACCCGATTCCGGCGCAGCACGTGCT 10 40 1 GATCCGGCGC 0.935955 -214 GCTCACGTTTGTAGTCCGAGCACGTGCTGCG 10 58 0 GTGTCCGAGC 0.874103 -196 TCCCGTGCCGGTTTGGCGTGCCCAGTTTTGA 10 126 0 GTTGGCGTGC 0.961444 -128 TGGCGGTGCGGTGTCCCGTGCCGGTTTGGCG 10 139 0 GTTCCCGTGC 0.965703 -115 GGTAATGTGGGTTGGCGGTGCGGTGTCCCGT 10 151 0 GTGGCGGTGC 0.983112 -103 GCAAAACGCCGTAGGCCACGCGCTCACCGGA 10 200 1 GTGGCCACGC 0.980739 -54 AATAGCACCGGTGAGCCGAGCGGTTAGAGCA 10 230 1 GTAGCCGAGC 0.938129 -24 ** ******** Masking position 10 Map Score: 14.8369 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 696 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 ATGAAAAAGAGCCTTGAGCGGGCGCATTGCC 2 12 1 GCCTTGGCGG 0.99418 -224 CAAAAAAAGAGCCTTGAGCGAAGGCAATGCG 2 34 0 GCCTTGGCGA 0.989547 -202 TCGGGGAAATGCCTTGATAGATTGTGAAGAT 2 171 1 GCCTTGTAGA 0.807153 -65 TATCTCTTTCACCTTATGAGGCTGATGCTTG 4 104 1 ACCTTAGAGG 0.626941 -197 AACAGCGGCTGCCCAGAGCGAAATCTGATCG 4 161 0 GCCCAGGCGA 0.897709 -140 TCACCCCAAGACCTTGCGCAAGACTGCGGCG 5 42 1 ACCTTGGCAA 0.535777 -72 GCCGGTAGGAGCCGTGGTAGGGGGCCGCGCC 6 21 0 GCCGTGTAGG 0.933511 -54 TCTGAAAGTTACCGTGTGCGGCGG 7 4 0 ACCGTGGCGG 0.98452 -23 GCTCCTAACTGCCGTTCGCCGACC 8 4 0 GCCGTTGCCG 0.879896 -26 GTGTAACGGCGCCCTGTCGGGTAGCCAACCC 9 23 1 GCCCTGCGGG 0.883878 -53 AGCCAACCCCGGCGTGCCCGAGGCGTGCCAG 9 45 1 GGCGTGCCGA 0.855035 -31 CACGTGCTGCGCCGGAATCGGGTGCACCGAC 10 38 0 GCCGGATCGG 0.787114 -216 ATTTCTCGGAGCCCTTCGCGGAATTTCCACC 10 93 0 GCCCTTGCGG 0.962563 -161 TACCCGCATCGCCGTGCTCTGCGCAAAACGC 10 178 1 GCCGTGTCTG 0.847484 -76 TGCGCAAAACGCCGTAGGCCACGCGCTCACC 10 197 1 GCCGTAGCCA 0.903225 -57 CCCTAACCGAGCCTTAACCGAGTGGAGCCGC 11 44 0 GCCTTACCGA 0.932366 -29 GGATCAAACCCTAACCGAGCCTTAACCG 11 55 0 ACCCTACCGA 0.749437 -18 ****** **** Masking position 3 Map Score: 17.209 Number of sites scoring better than the average of aligned sites = 1509 Number in coding regions = 1406 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 ACGAAAAATAGGTTTTGCAGACAG 1 3 0 GGTTTGAGAC 0.701051 -298 TTATTACAACCATTTGGAAACCAATCACTGGA 1 159 0 CATTTGAACC 0.967984 -142 AAATAGATTCCATTTGGTCACCAAGGCTGGCT 2 85 1 CATTTGCACC 0.945605 -151 CATTACAGTAGATTTTGAAACCGGATTGAAAT 2 128 1 GATTTGAACC 0.952536 -108 TATGAATATTGAGTTCGAAACCTGGTACATCT 2 198 0 GAGTTGAACC 0.943465 -38 TTGACTGACTCGGTCAGTCACCCCAAGACCTT 5 25 1 CGGTCGCACC 0.911299 -89 CGGCGAACGGCAGTTAGGAGCCAGTT 8 14 1 CAGTTGAGCC 0.967194 -16 GGGCACGCCGGGGTTGGCTACCCGACAGGGCG 9 32 0 GGGTTGTACC 0.95226 -44 GCGACCAGTTGGGTTCGCAACCCTCCGTTTCG 11 14 0 GGGTTGAACC 0.923385 -59 ***** * **** Masking position 4 Map Score: 8.44038 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 82 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AGTAGATTTTGAAACCGGATTGAAATCGGA 2 134 1 GAAACCGGAT 0.959028 -102 AAACCGGATTGAAATCGGACAAATTATCGG 2 145 1 GAAATCGGAC 0.959028 -91 TATTGAGTTCGAAACCTGGTACATCTTCAC 2 194 0 GAAACCTGGT 0.947301 -42 TGCCCAGAGCGAAATCTGATCGGTCCGCTG 4 153 0 GAAATCTGAT 0.95675 -148 AGACTGCGGCGGAATCTAATATTCCAAAGA 5 62 1 GGAATCTAAT 0.776036 -52 TCGATGCGAAGGAATCAGGCTC 5 102 1 GGAATCAGGC 0.895738 -12 GTGCTGCGCCGGAATCGGGTGCACCGACAA 10 36 0 GGAATCGGGT 0.980667 -218 ********** Masking position 4 Map Score: 3.69812 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 216 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TGTCTGCAAAACCTATTTTTCGTTTTTGCTAGT 1 12 1 ACCTTTTTCT 0.871301 -289 GACGAAAGAAACCTTCATTTCGTTTCACATTTT 1 128 0 ACCTCTTTCT 0.971736 -173 GCCTTCCAATTCCTTCTTTCCAAACAAAATCAA 1 256 0 TCCTCTTCCA 0.943838 -45 GCTCTTTATATCCTGCCTTCCAATTCCTTCTTT 1 270 0 TCCTCTTCCA 0.943838 -31 ATTTACCTGCTCTTTATATCCTGCCTT 1 284 0 ACCTCCTTTT 0.868802 -17 CGGAGCGTTCACCTATACATCCAGAACATGTTT 4 22 0 ACCTTCATCA 0.798076 -279 ATCCTACACCTCCTTCTTGGAACT 4 287 0 TCCTCCCTCT 0.962416 -14 GAGCCTGATTCCTTCGCATCGAGTTCCATATA 5 92 0 TCCTCCATCA 0.961133 -22 TTTCTGGCGATCCTTCTCTTCCTTGTCGGTGCA 10 14 1 TCCTCCTTCT 0.988126 -240 **** * **** * Masking position 4 Map Score: 3.47335 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 441 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 8 TCGGTATCTATTTCTTTTTTCAAAGGCACAC 1 62 1 TTTCTTTTTC 0.952192 -239 AAAAAAAGGATTTCTTTTGTCATGTGTGCCT 1 85 0 TTTCTTTTTC 0.952192 -216 AAGAAATCCTTTTTTTATTTCCGAGAAAAAA 1 100 1 TTTTTTATTC 0.926828 -201 TTCGTTTCACATTTTTTTCTCGGAAATAAAA 1 112 0 ATTTTTTTTC 0.926828 -189 GAAATGAAGGTTTCTTTCGTCCAGTGATTGG 1 140 1 TTTCTTTCTC 0.918557 -161 GCACCATATCATTTTTATTACAACCATTTGG 1 174 0 ATTTTTATAC 0.585914 -127 CGCTCAAGGCTCTTTTTCATC 2 1 0 TCTTTTTCTC 0.753465 -235 CGCTGGTGCGATTTTTATCTCTTTCACCTTA 4 89 1 ATTTTTATTC 0.887586 -212 ******** ** Masking position 6 Map Score: 2.47422 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 458 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 9 AAGGCAATGCGCCCGCTCAAGGCTCTTTTT 2 15 0 GCCCGCTCAA 0.871118 -221 GGCGCATTGCCTTCGCTCAAGGCTCTTTTT 2 32 1 CTTCGCTCAA 0.96195 -204 GGTTTGTATCCCTAGCGCAACTTGAGCATA 4 224 1 CCTAGCGCAA 0.973489 -77 CACCCCAAGACCTTGCGCAAGACTGCGGCG 5 43 1 CCTTGCGCAA 0.984792 -71 GTCTGGCACGCCTCGGGCACGCCGGGGTTG 9 48 0 CCTCGGGCAC 0.91894 -28 TCTCGGAGCCCTTCGCGGAATTTCCACCAC 10 91 0 CTTCGCGGAA 0.944198 -163 CATCGCCGTGCTCTGCGCAAAACGCCGTAG 10 184 1 CTCTGCGCAA 0.954694 -70 ********** Masking position 9 Map Score: 3.22009 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 196 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ********** No masking Map Score: -1.4755e-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 11 ********** No masking Map Score: -1.4755e-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 12 ********** No masking Map Score: -1.4755e-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