AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_bsub_mtub_300.orf -o063_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 yqhJ 29 similar to glycine dehydrogenase #2 yqhI 300 similar to aminomethyltransferase #3 yusH 66 similar to glycine cleavage system protein H #4 yusI 110 similar to arsenate reductase #5 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #6 yusM 300 similar to proline dehydrogenase #7 ilvG 70 ilvG #8 pgsA2 196 pgsA2 #9 Rv1824 28 hypothetical protein Rv1824 #10 gcvH 37 gcvH #11 Rv1830 300 hypothetical protein Rv1830 #12 Rv1831 52 hypothetical protein Rv1831 #13 gcvB 48 gcvB Motif number 1 TCCAGAGTTGCGTCGAGCAAGAGTTCTTTT 2 120 0 CGTCGAGCAA 0.916544 -181 TAAAAAAGAGCTCCGCGCATGCGGAGCTCA 4 18 0 CTCCGCGCAT 0.912853 -93 GCAGTCAGCGCGGCGAGCGTAAAGGGAGAT 5 119 0 CGGCGAGCGT 0.990562 -149 TTCCCTTCACCTCCGGGCTTAAGTTGCCCG 5 181 1 CTCCGGGCTT 0.938521 -87 AGCCTATAAAAGTCGGGCAACTTAAGCCCG 5 194 0 AGTCGGGCAA 0.722527 -74 TTGAAGATGACGGCGGGAGGGAGTCGG 6 284 1 CGGCGGGAGG 0.904043 -17 AACAGAAATCCTTCGGGCGAAGGTACCCGA 7 29 1 CTTCGGGCGA 0.762045 -42 TCGGCGCTTACGCTGGGCAGC 8 2 0 CGCTGGGCAG 0.864872 -195 CCAGCGTAAGCGCCGAGCGTAACGCCACTG 8 16 1 CGCCGAGCGT 0.98886 -181 GCACCCCTAGCCGCGAGCGTAACGCCACTG 8 68 0 CCGCGAGCGT 0.824987 -129 CGCGCCGAAACGGCGGGCTGTGGGGGCACC 8 93 0 CGGCGGGCTG 0.99373 -104 CCCGCCGTTTCGGCGCGCATCGTCGCCAGG 8 106 1 CGGCGCGCAT 0.96475 -91 CGCGCATCGTCGCCAGGCTAGATCCGATTG 8 119 1 CGCCAGGCTA 0.927761 -78 CGGGCTGAGGAGCCGGGCAATCGGATCTAG 8 136 0 AGCCGGGCAA 0.934908 -61 CGCGCCGAAACGGCGGGCTGAGGAGCCGGG 8 149 0 CGGCGGGCTG 0.99373 -48 CCCGCCGTTTCGGCGCGCATCGTCGCCAGG 8 162 1 CGGCGCGCAT 0.96475 -35 CGCGCATCGTCGCCAGGCTAAGGTCACGGC 8 175 1 CGCCAGGCTA 0.927761 -22 CGCGCATCGTCGCCGCGCTCGGCCTT 11 7 0 CGCCGCGCTC 0.986839 -294 CCCGCCGTCCCGGCGCGCATCGTCGCCGCG 11 20 0 CGGCGCGCAT 0.96475 -281 CGCGCCGGGACGGCGGGCTGAGGAGGCGCG 11 33 1 CGGCGGGCTG 0.99373 -268 CGGGCTGAGGAGGCGCGCGATAAGGCCGAG 11 46 1 AGGCGCGCGA 0.928729 -255 CGCGCATCGTCGCCGCGCTCGGCCTTATCG 11 63 0 CGCCGCGCTC 0.986839 -238 CTCGCCGTCGCGGCGCGCATCGTCGCCGCG 11 76 0 CGGCGCGCAT 0.96475 -225 CGCGCCGCGACGGCGAGCATCCATTATTTG 11 89 1 CGGCGAGCAT 0.988537 -212 CATTATTTGCCGGCCAGCAACGTCACGGCT 11 110 1 CGGCCAGCAA 0.797523 -191 ATTGTCGACACGCCTAGCGGTTAGTGCCTA 11 160 1 CGCCTAGCGG 0.750707 -141 GTATCGCGGTCGCCGGGCGCATTAGGCACT 11 182 0 CGCCGGGCGC 0.994264 -119 GAATCGCACGCGGCAGGCTCCTCGG 12 38 1 CGGCAGGCTC 0.930545 -15 ********** Masking position 7 Map Score: 68.6013 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 868 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 ATGTTTTTTAGCTGCGCCGTTGATAAAGGGGA 2 271 1 GCTGGCCGTG 0.948251 -30 CTCCGCGCATGCGGAGCTCATGGCCAA 4 6 0 GCGGGCTCTG 0.82172 -105 GTTTTCCGCCGCCGTAATGCTGAGTCGGACCG 5 85 1 GCCGAATGTG 0.916101 -183 TTCTGTTTGTGAGGAGACGTCGACC 7 4 0 GAGGGACGCG 0.977615 -67 GACGATGCGCGCCGAAACGGCGGGCTGTGGGG 8 98 0 GCCGAACGCG 0.991019 -99 CGGATCTAGCCTGGCGACGATGCGCGCCGAAA 8 113 0 CTGGGACGTG 0.948922 -84 GACGATGCGCGCCGAAACGGCGGGCTGAGGAG 8 154 0 GCCGAACGCG 0.991019 -43 TGACCTTAGCCTGGCGACGATGCGCGCCGAAA 8 169 0 CTGGGACGTG 0.948922 -28 GAGCCGTGACCTTAGCCTGGCGAC 8 183 0 GCCGGACCTA 0.900504 -14 AAGGCCGAGCGCGGCGACGATGCGCGCCGGGA 11 11 1 GCGGGACGTG 0.998367 -290 GACGATGCGCGCCGGGACGGCGGGCTGAGGAG 11 26 1 GCCGGACGCG 0.998494 -275 AAGGCCGAGCGCGGCGACGATGCGCGCCGCGA 11 67 1 GCGGGACGTG 0.998367 -234 GACGATGCGCGCCGCGACGGCGAGCATCCATT 11 82 1 GCCGGACGCG 0.998494 -219 ATGAGACGCAGCCGTGACGTTGCTGGCCGGCA 11 117 0 GCCGGACGTG 0.998367 -184 CCTAATGCGCCCGGCGACCGCGATACTTTGAT 11 186 1 CCGGGACCCG 0.978451 -115 **** **** ** Masking position 4 Map Score: 39.0093 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 280 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 CAGTTTGCTCCTTCGGCGCCTGTATCCCGAG 2 70 0 CTTGGCGCCT 0.826053 -231 CGCAAACCACCTTTGGGGACGTCTTTGCGTA 2 167 1 CTTGGGGACG 0.88223 -134 AAGCAGCCGTGGGAAGCAGCTGCATTAT 5 8 1 CGTGGAAGCA 0.582011 -260 CTCAGCATTACGGCGGCGGAAAACGGACAAG 5 78 0 CGGGGCGGAA 0.86245 -190 AAAAATCCGTCTTCAGCGGCAGTCAGCGCGG 5 136 0 CTTAGCGGCA 0.716794 -132 AACTCGACCGCGTCGGACACATGCATCATGA 6 35 0 CGTGGACACA 0.641785 -266 GATCCTGGCACTGCTGCGCCATGAAATGCGC 6 81 1 CTGTGCGCCA 0.674766 -220 ATTTCTGTTTGTGAGGAGACGTCGACC 7 7 0 GTGGGAGACG 0.408325 -64 AACAGAAATCCTTCGGGCGAAGGTACCCGAA 7 29 1 CTTGGGCGAA 0.399587 -42 GCTGCCCAGCGTAAGCGCCGAGCGTAACGC 8 10 1 CGTAGCGCCG 0.806991 -187 AAACGGCGGGCTGTGGGGGCACCCCTAGCCG 8 85 0 CTGGGGGGCA 0.979571 -112 AAACGGCGGGCTGAGGAGCCGGGCAATCGGA 8 141 0 CTGGGAGCCG 0.975227 -56 AAGGCCGAGCGCGGCGACGATGCGCG 11 6 1 CGACGCGGCG 0.805159 -295 GGACGGCGGGCTGAGGAGGCGCGCGATAAGG 11 40 1 CTGGGAGGCG 0.982419 -261 GCGATAAGGCCGAGCGCGGCGACGATGCGCG 11 62 1 CGACGCGGCG 0.805159 -239 GTATCGCGGTCGCCGGGCGCATTAGGCACTA 11 181 0 CGCGGGCGCA 0.767424 -120 ATACGCTGTTCGATGGGCGCGATGCTCCCGG 11 235 0 CGAGGGCGCG 0.90066 -66 ACAGCCATTACTGAGGGCCCGAGTGTTAGAG 11 269 0 CTGGGGCCCG 0.9521 -32 TAATGGCTGTCGGGGGAGCCA 11 290 1 CGGGGAGCCA 0.972529 -11 CCGAGGAGCCTGCCGCGTGCG 12 42 0 CCGGGAGCCT 0.533651 -11 *** ******* Masking position 6 Map Score: 12.0628 Number of sites scoring better than the average of aligned sites = 2234 Number in coding regions = 2027 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 TGTATCCCGAGGTTTTCGGTCAGGTCTCTCC 2 50 0 GTTTTCGGTC 0.93312 -251 TCGAGCAAGAGTTCTTTTGCCTGAGAGATTC 2 107 0 GTCTTTTGCC 0.933199 -194 GTAAAATGAAGGTTCTCTGTCCTGGCACCTG 2 213 0 GTTCTCTGTC 0.990403 -88 TACATGAGGTGTTTCTCTGTCCTTTTTTGTA 2 241 1 GTTCTCTGTC 0.990404 -60 GCTGAAGACGGATTTTTTTTCTCTCGTACCA 5 150 1 GTTTTTTTTC 0.6681 -118 AGATACAAATGATCCTTTGTCGAAATAACGG 6 152 1 GTCCTTTGTC 0.970824 -149 ACGCCACTGCGATTTTCTGCCCGAAATTTCG 8 46 0 GTTTTCTGCC 0.977441 -151 CGATTGCCCGGCTCCTCAGCCCGCCGTTTCG 8 143 1 GTCCTCAGCC 0.92638 -54 TGCCGCGTGCGATTCTGTGTCTGTTCGCGGG 12 22 0 GTTCTGTGTC 0.959449 -31 * ********* Masking position 6 Map Score: 8.57484 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 332 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 GCGCCTGTATCCCGAGGTTTTCGGTCAGGT 2 56 0 CCCGAGGTTT 0.971349 -245 AGTTCTTTTGCCTGAGAGATTCACTCCGCA 2 99 0 CCTGAGAGAT 0.8987 -202 TGTCCTGGCACCTGAAAGTTTACTTTGCAT 2 197 0 CCTGAAAGTT 0.95876 -104 GCTTAAGTTGCCCGACTTTTATAGGCTTCA 5 197 1 CCCGACTTTT 0.848785 -71 GGTACCTTCGCCCGAAGGATTTCTGTTTGT 7 26 0 CCCGAAGGAT 0.964374 -45 GGCGAAGGTACCCGAAGGTTGTCGATAGGC 7 44 1 CCCGAAGGTT 0.988461 -27 CGATTTTCTGCCCGAAATTTCGCAGTGGCG 8 38 0 CCCGAAATTT 0.95876 -159 TTGATCACGACCTGATAGTTAACCGGGAGC 11 213 1 CCTGATAGTT 0.876026 -88 TTACTGAGGGCCCGAGTGTTAGAGAGCATA 11 263 0 CCCGAGTGTT 0.978683 -38 ********** Masking position 5 Map Score: 10.6491 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 102 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ATTTTTTCTTGGAGAGAGGAGACAACAC 1 12 1 GGAGAGAGCA 0.880761 -18 GACAGCAAGGGGAGAGACCTGACCGAAAACCTCG 2 40 1 GGAGAGACCC 0.765894 -261 CAAACACTCTCCAGAGTTGCGTCGAGCAAGAGTT 2 125 0 CCAGAGTGCG 0.965761 -176 CTTTGCATACGCAAAGACGTCCCCAAAGGTGGTT 2 171 0 GCAAAGAGCC 0.826793 -130 AGGTGCCAGGACAGAGAACCTTCATTTTACATGA 2 214 1 ACAGAGACCA 0.4074 -87 CCGCCGTAATGCTGAGTCGGACCGGCATCTCCCT 5 93 1 GCTGAGTGCG 0.969012 -175 TGAACAGAAACCAAAGGAGGATCACAATGGATAA 6 209 0 CCAAAGGGCA 0.628155 -92 CCGAAATTTCGCAGTGGCGTTACGCTCGGCGCTT 8 23 0 GCAGTGGGCG 0.987316 -174 GCAGAAAATCGCAGTGGCGTTACGCTCGCGGCTA 8 57 1 GCAGTGGGCG 0.987316 -140 GAAACGGCGGGCTGTGGGGGCACCCCTAGCCGCG 8 83 0 GCTGTGGGCC 0.894678 -114 GAAACGGCGGGCTGAGGAGCCGGGCAATCGGATC 8 139 0 GCTGAGGGGG 0.890668 -58 AAGGCCGAGCGCGGCGACGATGCGCGCCGGGACG 11 11 1 GCGGCGAGCG 0.943244 -290 GGGACGGCGGGCTGAGGAGGCGCGCGATAAGGCC 11 39 1 GCTGAGGGCG 0.991055 -262 AAGGCCGAGCGCGGCGACGATGCGCGCCGCGACG 11 67 1 GCGGCGAGCG 0.943244 -234 ACAATTGCAGCCAGAGATGAGACGCAGCCGTGAC 11 131 0 CCAGAGAGCG 0.984196 -170 CCGAGAGTTCCCCCGCGAACAGACA 12 2 1 CGAGAGTCCG 0.646524 -51 TCCTGACAAAGCAGAGGACTAGCGGCCCTCTCCC 13 18 0 GCAGAGGCCG 0.989278 -31 ******* * ** Masking position 6 Map Score: 19.7375 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 703 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 TTGGCCATGAGCTCCGCATGCGC 4 4 1 GCCATGAGCT 0.894692 -107 ACAAGTCAAAATCAGCAGTATAAAAAACAT 5 53 0 ATCAGCAGTA 0.353762 -215 GCTGAGTCGGACCGGCATCTCCCTTTACGC 5 103 1 ACCGGCATCT 0.833692 -165 GGACACATGCATCATGATCACTATCAAAGA 6 22 0 ATCATGATCA 0.584906 -279 GCGCAGCAGTGCCAGGATCAAACGTTAAAG 6 70 0 GCCAGGATCA 0.922174 -231 CGCTTTTTTCATCGCGAGCAAATTCCAGTT 6 109 1 ATCGCGAGCA 0.864174 -192 ACAATGGATAATCAGCAGCAATCTCAAATG 6 190 0 ATCAGCAGCA 0.836062 -111 ACTCCCTCCCGCCGTCATCTTCAAAACACC 6 278 0 GCCGTCATCT 0.784548 -23 ATCGGCAGCCTATCGACAAC 7 61 0 ATCGGCAGCC 0.738983 -10 GGCACCCCTAGCCGCGAGCGTAACGCCACT 8 69 0 GCCGCGAGCG 0.832421 -128 GAGCCGTGACCTTAGCCTGGCG 8 185 0 GCCGTGACCT 0.723313 -12 TATCGCGGTCGCCGGGCGCATTAGGCACTA 11 181 0 GCCGGGCGCA 0.915163 -120 TAACTATCAGGTCGTGATCAAAGTATCGCG 11 204 0 GTCGTGATCA 0.859566 -97 CTGATAGTTAACCGGGAGCATCGCGCCCAT 11 224 1 ACCGGGAGCA 0.977525 -77 CCTCTGCTTTGTCAGGAGTTCACC 13 35 1 GTCAGGAGTT 0.556626 -14 ********** Masking position 3 Map Score: 6.45907 Number of sites scoring better than the average of aligned sites = 2953 Number in coding regions = 2746 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 8 AAAAACATACAAAAAAGGACAGAGAAACACC 2 248 0 AAAAAAGACA 0.956479 -53 ACTTTTCAAAAAAAATTTACA 3 1 0 AAAAATTACA 0.712894 -66 AGTGCTTCTTAAAAAAGAGCTCCGCGCATGC 4 26 0 AAAAAAGGCT 0.927334 -85 TTAAAAACCTAAAACAGTGCTTCTTAAAAAA 4 41 0 AAAACAGGCT 0.87843 -70 AGCAGTATAAAAAACATAACATGGGACAATC 5 39 0 AAAACATACA 0.886956 -229 GCTTCATACAAAAAAATAACAAATTAGCTAT 5 221 1 AAAAAATACA 0.932686 -47 GCTCGCGATGAAAAAAGCGCATTTCATGGCG 6 97 0 AAAAAAGGCA 0.972113 -204 AATTTCGGGCAGAAAATCGCAGTGGCGTTAC 8 49 1 AGAAAATGCA 0.853744 -148 ******* *** Masking position 4 Map Score: 3.02806 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 331 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 CGCCGTTGATAAAGGGGAGGAATTAG 2 285 1 AAAGGGGAGG 0.981695 -16 TTATTTTATTGAGGGGGAAGAAG 4 98 1 GAGGGGGAAG 0.970909 -13 GGCGAGCGTAAAGGGAGATGCCGGTCCGAC 5 108 0 AAGGGAGATG 0.959681 -160 GCCCGGAGGTGAAGGGAATGGTACGAGAGA 5 169 0 GAAGGGAATG 0.852726 -99 AGACAGAGGGAGAGGGCCGCTAGTC 13 6 1 GAGGGAGAGG 0.988281 -43 AACTCCTGACAAAGCAGAGGACTAGCGGCC 13 25 0 AAAGCAGAGG 0.886622 -24 ********** Masking position 8 Map Score: 1.37106 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 181 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 10 CTCTGGAGAGTGTTTGTGCGGATGCGCAAA 2 143 1 TGTTTGTGCG 0.971192 -158 CCTTTGGGGACGTCTTTGCGTATGCAAAGT 2 176 1 CGTCTTTGCG 0.84694 -125 CTTTTTTGTATGTTTTTTAGCTGCGCCGTT 2 262 1 TGTTTTTTAG 0.832207 -39 ACCTCGATTATTTTATTGAGGGGGAAGAAG 4 91 1 TTTTATTGAG 0.601503 -20 CAGTTCAGCATGTCATTGAGATACAAATGA 6 134 1 TGTCATTGAG 0.92982 -167 GAAGGATTTCTGTTTGTGAGGAGACGTCGA 7 13 0 TGTTTGTGAG 0.971747 -58 AGGGCCCGAGTGTTAGAGAGCATACGCTGT 11 257 0 TGTTAGAGAG 0.793481 -44 TGCGATTCTGTGTCTGTTCGCGGGGGAACT 12 16 0 TGTCTGTTCG 0.883151 -37 ********** Masking position 3 Map Score: 0.743902 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 357 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 ********** No masking Map Score: 6.80943e-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: 6.80943e-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 13 ********** No masking Map Score: 6.80943e-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