AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_bsub_reg_100.orf -o00720_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yjmC 104 similar to malate dehydrogenase #2 sucC 172 succinyl-CoA synthetase (beta subunit) #3 sucD 28 succinyl-CoA synthetase (alpha subunit) #4 citB 227 aconitate hydratase #5 pps 300 phosphoenolpyruvate synthase #6 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #7 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #8 citH 43 malate dehydrogenase #9 citC 163 isocitrate dehydrogenase #10 ytcI 172 similar to acetate-CoA ligase #11 acsA 160 acetyl-CoA synthetase #12 yukF 300 similar to hypothetical proteins from B. subtilis #13 ald 67 L-alanine dehydrogenase #14 citG 300 fumarate hydratase Motif number 1 AAAAACTGAAAAGGAAGGAGGCACTTGC 1 87 1 AAGGAAGGAG 0.957706 -18 AATTTCAAAGAAGGATGGGGAATATTTTAG 2 11 0 AAGGATGGGG 0.955194 -162 GAAAGAATGAAAGGCAGGGGACCAAATA 3 11 1 AAGGCAGGGG 0.949101 -18 TTTATGAATGGGGACTCTACGAA 5 4 1 ATGAATGGGG 0.73673 -297 GATTACTAGAGGGAGAGGGGCTATC 6 19 1 GGGAGAGGGG 0.9844 -15 ATATACGCAGGAGAGAGGGGAGACAGAT 7 9 0 GAGAGAGGGG 0.984109 -284 GCTCAAACAGGGGGGAGGATTACAGAATGA 7 43 1 GGGGGAGGAT 0.805312 -250 ACGCCCTTTTGAGGGAGGAGTAAAATGAAA 7 181 1 GAGGGAGGAG 0.986253 -112 TGAAAGAAGTGGGGGAAGAGATTTAGCACA 7 243 1 GGGGGAAGAG 0.886967 -50 CTAGCCATAAAGGAGAAGAGAGAC 8 30 1 AGGAGAAGAG 0.818562 -14 ATAATGGCTTAGGAGTGGGGGTATCCCCAC 10 24 1 AGGAGTGGGG 0.975352 -149 AAAAATGAAAAAGAGTGGGGATACCCCCAC 10 38 0 AAGAGTGGGG 0.974895 -135 TTTATGTATAATGGGTGGAGAAAGTGAGGA 10 152 1 ATGGGTGGAG 0.925956 -21 TGGGTGGAGAAAGTGAGGAG 10 163 1 AAGTGAGGAG 0.895432 -10 ATCATAATAAAAGGAAGGGGATGAG 12 286 1 AAGGAAGGGG 0.976411 -15 ********** Masking position 3 Map Score: 20.6084 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 261 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 TTACAAATTATTTTAAATATTCTTTATATTATATTG 1 7 0 TTTTTATATT 0.943828 -98 CTTATTGTATTTAATAAAAACATTGATATTTACTTATGTA 4 107 1 TAATTATATT 0.626326 -121 TCCATCACAATTTTCTCACAATTTCATATTAAAACAAAAT 4 149 0 TTTTTATATT 0.943828 -79 GCTAGGAAGCTCTTGTCAATATTTTTTTTTGAAGGGGAGA 5 265 1 TTTTTTTTTT 0.829397 -36 TTTATCAATATATATTTCTTGCTTAATTTTTCATAAGAAT 7 80 0 TTATTATTTT 0.928525 -213 ATTGATTAGTTGATTGAAAAATTTTATTTTATCAATATAT 7 107 0 TATTTATTTT 0.874466 -186 TTTATTAAGATTTATTGACAATTTCATTTTACTCCTCCCT 7 192 0 TTATTATTTT 0.928525 -101 AATAAAATGATTTTTCCTAACATTCAATTTAAAGTGTAAC 9 73 0 TTTTTAATTT 0.819625 -91 GTAATTCATATTTAGAAAACATTTTATTTTTCTTATATAG 9 115 0 TTATTATTTT 0.928524 -49 ATAAAATCTATGTTTACAGAGGTTGCTTTTAGGCATATCC 10 94 1 TTTTTCTTTT 0.803389 -79 TTATAAAGCGTTTTCAACATGGTTTATATTTTAAAAATTG 11 69 1 TTTTTATATT 0.943828 -92 GTCACAATTATTATAGTATATATTCATATTCTTCTCAATT 11 104 0 TATTTATATT 0.795354 -57 TAGCATCAAATTTTCTGAAAGGTTTTTTTTGGGAGTTGGA 12 29 0 TTTTTTTTTT 0.829397 -272 TTTTTGCTTCTGTTCTTTGTTGTTGATTTTCACAAACAAC 12 242 1 TTTTTATTTT 0.967863 -59 TATGTGATATTTTTAGTGTAGCTTGATATTTTGGAAAATT 13 21 0 TTTTTATATT 0.943828 -47 GTTCAAATGATCTAATGAGCTGTTCAATTTCTTCTTGTTT 14 83 0 TTATTAATTT 0.662172 -218 TATTTTTCGATCTTGGCAGATTTTAATTTTAATTCAAGAT 14 204 0 TTTTTATTTT 0.967863 -97 * ** ** ***** Masking position 13 Map Score: 19.576 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 233 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 TGAAATTTATGTTTTTAATAAAGTAAAAGTTT 2 34 1 GTTTTTAAAA 0.657708 -139 TTACCGGTACATTTTTCTCATAAGTCGAACTT 4 78 1 ATTTTTCTAA 0.935389 -150 AAATATCAATGTTTTTATTAAATACAATAAGT 4 106 0 GTTTTTATAA 0.80588 -122 ATTCCATCACAATTTTCTCACAATTTCATATT 4 159 0 AATTTTCTAA 0.935389 -69 TCCATCTTATAATTTTATTATATCCTGCTAGG 5 239 1 AATTTTATAA 0.900211 -62 TGATCCTGTAATTCTTATGAAAAATTAAGCAA 7 70 1 ATTCTTATAA 0.85674 -223 ATTGTCAATAAATCTTAATAAAGTGCTTACAA 7 210 1 AATCTTAAAA 0.734639 -83 AAAACATTTTATTTTTCTTATATAGAAAATAA 9 108 0 ATTTTTCTAA 0.935389 -56 CGTCCCATCAATTCTTATCAAAAATACATGCC 11 19 1 ATTCTTATAA 0.856769 -142 ATTCTTCTCAATTTTTAAAATATAAACCATGT 11 85 0 ATTTTTAAAA 0.804823 -76 TGTAGCATCAAATTTTCTGAAAGGTTTTTTTT 12 39 0 AATTTTCTAA 0.935388 -262 TTATCCTATTAATCTTCTAAGAAAGTCATCGG 12 121 0 AATCTTCTAA 0.905656 -180 CTTTGTTGTTGATTTTCACAAACAACAACAAT 12 256 1 GATTTTCAAA 0.755156 -45 TCAAACAAAGAATTTTCCAAAATATCAAGCTA 13 11 1 AATTTTCCAA 0.751194 -57 ******** * * Masking position 10 Map Score: 10.868 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 311 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 AATCATAATATGGCTTCTTTTATTGTGTTAT 4 23 1 TGCTTCTTTT 0.965354 -205 ATCCTAAAGTTGGGTTCTTTTTGAACTTACT 5 41 0 TGGTTCTTTT 0.985082 -260 GAAATTTCACCAGGTTCTTTTCTTAATTTCC 5 125 0 CGGTTCTTTT 0.987614 -176 TGAAATTTCCCAGGTTCTTTTTATATTGCAC 5 147 1 CGGTTCTTTT 0.987614 -154 TTATAGGCCGCTGGTCCTTTTTTATATGTAA 10 67 0 CGGTCCTTTT 0.960839 -106 GGAGAGTTATTTGGGTCTTTT 12 1 0 TGGGTCTTTT 0.953091 -300 AATTGTTTTTTTGCTTCTGTTCTTTGTTGTT 12 235 1 TGCTTCTGTT 0.895544 -66 * ********* Masking position 8 Map Score: 6.57221 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 47 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TTATTATAGAATGAAAGCGCAGTCTATTTT 2 122 1 ATGAAAGCGC 0.98068 -51 ATTGTGTTATATGAGAGAGCGTAAACAGTA 4 44 1 ATGAGAGAGC 0.926625 -184 ACTTTTTAACTAGAAAGCGCACGTAGTGTG 5 201 0 TAGAAAGCGC 0.908754 -100 TAATATACGCAGGAGAGAGGGGAGACAGAT 7 11 0 AGGAGAGAGG 0.822854 -282 AAAGGGCGTCAAGAAAACGCGTACATAAAT 7 160 0 AAGAAAACGC 0.899155 -133 GCAAGGAAAAAGCCTAAAACTAG 8 4 1 AGGAAAAAGC 0.910914 -40 CATATCCTTACGGAAAGAGCCTGTATTTAT 10 127 1 CGGAAAGAGC 0.905659 -46 ATAAACCATGTTGAAAACGCTTTATAATTT 11 66 0 TTGAAAACGC 0.858959 -95 AAGTTTTTTTATGAAAGCGGAGGATACGAA 14 29 1 ATGAAAGCGG 0.93925 -272 ********** Masking position 6 Map Score: 4.62685 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 600 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 AGAGTGCCCAAAAAACTGAAAAGGAAGGAG 1 77 1 AAAAACTGAA 0.91902 -28 TTACTTTATTAAAAACATAAATTTCAAAGA 2 30 0 AAAAACATAA 0.768059 -143 GAAAGAATGAAAGGCAGGGGA 3 2 1 AAAGAATGAA 0.539744 -27 CATATAACACAATAAAAGAAGCCATATTAT 4 27 0 AATAAAAGAA 0.599993 -201 ATATTAAAACAAAATCATACATAAGTAAAT 4 134 0 AAAATCATAC 0.16458 -94 TATGGAAATTAAGAAAAGAACCTGGTGAAA 5 122 1 AAGAAAAGAA 0.803586 -179 TTTGTGCAATATAAAAAGAACCTGGGAAAT 5 151 0 ATAAAAAGAA 0.56338 -150 TATATTGCACAAAAACAGACACGGTGATAT 5 168 1 AAAAACAGAC 0.923237 -133 TTTTATATGTAAAAAATGAAAAAGAGTGGG 10 49 0 AAAAAATGAA 0.88937 -124 TTTTACATATAAAAAAGGACCAGCGGCCTA 10 65 1 AAAAAAGGAC 0.639869 -108 TAAGGAAAGAAAAAACTGAACCTTTCAGAA 12 78 0 AAAAACTGAA 0.91902 -223 ATCAACAACAAAGAACAGAAGCAAAAAAAC 12 239 0 AAGAACAGAA 0.852411 -62 TCAAACAAAGAATTTTCCAAAA 13 3 1 AAACAAAGAA 0.672785 -65 GCTTTCATAAAAAAACTTACTCCATGAAAT 14 17 0 AAAAACTTAC 0.533064 -284 GGCTAGCTGGAAAACAAGAAGAAATTGAAC 14 72 1 AAAACAAGAA 0.672785 -229 ********** Masking position 9 Map Score: 3.84346 Number of sites scoring better than the average of aligned sites = 2065 Number in coding regions = 1629 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 409 Fraction of orfs with sites within 600 bp upstream = 0.0656923 Motif number 7 ATTATCACCTCAATCATAATATGGCTTCTT 4 12 1 CAATCATAAT 0.935383 -216 ACATTACATTCCATCACAATTTTCTCACAA 4 168 0 CCATCACAAT 0.813639 -60 TCAATTCGGAAAATTATAATTTATGTACGC 7 142 1 AAATTATAAT 0.775574 -151 AATTGTCAATAAATCTTAATAAAGTGCTTA 7 209 1 AAATCTTAAT 0.734509 -84 TCTTGTTCAGACATCAAAATTGGGTTACAC 9 50 1 ACATCAAAAT 0.862965 -114 CAAACAACAACAATCATAATAAAAGGAAGG 12 274 1 CAATCATAAT 0.935383 -27 TGTATAAGAGACATCATAATGCTGTTCAAA 14 116 0 ACATCATAAT 0.945061 -185 TCTTGAATTAAAATTAAAATCTGCCAAGAT 14 205 1 AAATTAAAAT 0.558522 -96 TTGCTTCAATAGATCATAATTCGCCAATGA 14 260 0 AGATCATAAT 0.865176 -41 ********** Masking position 4 Map Score: 2.8539 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 251 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 GATCTGATCTGAAGGGGGATTTTGGAGA 4 210 1 GAAGGGGGAT 0.981297 -18 TTTATGAATGGGGACTCTACGAACA 5 6 1 GAATGGGGAC 0.809258 -295 TTTTTTTTTGAAGGGGAGATGTAGA 5 286 1 AAGGGGAGAT 0.929608 -15 ACTAGAGGGAGAGGGGCTATC 6 23 1 GAGGGGCTAT 0.82314 -11 ACGCAGGAGAGAGGGGAGACAGAT 7 5 0 GAGGGGAGAC 0.970791 -288 CCATAAAGGAGAAGAGAGAC 8 34 1 GAAGAGAGAC 0.769113 -10 TGGCTTAGGAGTGGGGGTATCCCCACTCTT 10 28 1 GTGGGGGTAT 0.865128 -145 CAACTTCAGCAAAGGGGGATGTTTGGGC 11 143 1 AAAGGGGGAT 0.945042 -18 AGCAACCGTTATGGAGGGATACATAA 14 285 1 ATGGAGGGAT 0.677656 -16 ********** Masking position 9 Map Score: 2.69199 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 242 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 9 AATGTTTAGAAGGATTAAAAGATTTTGCATCGA 2 67 1 AGATAAAGAT 0.498324 -106 CTCATATAACACAATAAAAGAAGCCATATTATG 4 26 0 AAATAAGAAG 0.752789 -202 CTAGCTATGGAAATTAAGAAAAGAACCTGGTGA 5 117 1 AATTAAAAAG 0.773164 -184 AGGATATAATAAAATTATAAGATGGATATCTAT 5 232 0 AAATAAAGAT 0.892982 -69 TCAAAAAAAAATATTGACAAGAGCTTCCTAGCA 5 264 0 AATTAAAGAG 0.92736 -37 ATTTTTCATAAGAATTACAGGATCATTCTGTAA 7 62 0 AAATAAGGAT 0.91315 -231 CAAGAAATATATATTGATAAAATAAAATTTTTC 7 99 1 AATTAAAAAT 0.758525 -194 TCTTATATAGAAAATAAAATGATTTTTCCTAAC 9 92 0 AAATAATGAT 0.540042 -72 TTTCTATATAAGAAAAATAAAATGTTTTCTAAA 9 112 1 AAAAAAAAAT 0.438199 -52 TATATGTAAAAAATGAAAAAGAGTGGGGATACC 10 43 0 AATGAAAGAG 0.668172 -130 TTCATTTTTTACATATAAAAAAGGACCAGCGGC 10 59 1 AATAAAAAAG 0.544083 -114 TATATTTTAAAAATTGAGAAGAATATGAATATA 11 93 1 AATTAAAGAA 0.744901 -68 CTTTCTTAGAAGATTAATAGGATAAGCTGTCGT 12 128 1 AATTAAGGAT 0.936825 -173 AACAACAATCATAATAAAAGGAAGGGGATGAG 12 279 1 AAATAAGGAA 0.722898 -22 TAAAAATATCACATATACAGGAGGAGACAGAT 13 46 1 AATAAAGGAG 0.849222 -22 CAAAATACAAATATTCAAAGGATTCCCGCGTAT 14 171 1 AATTAAGGAT 0.936824 -130 CAAGATCGAAAAATAAAAAGGATTTTTTGTGTC 14 229 1 AATAAAGGAT 0.838501 -72 * *** * ***** Masking position 7 Map Score: 9.23338 Number of sites scoring better than the average of aligned sites = 729 Number in coding regions = 530 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 10 AAATAAAATGTGTTTGTAGGGGTTTCGCTT 1 45 1 TGTTTGTAGG 0.724239 -60 CTTCCTTTTCAGTTTTTTGGGCACTCTCCA 1 74 0 AGTTTTTTGG 0.772777 -31 TAAATATCAATGTTTTTATTAAATACAATA 4 109 0 TGTTTTTATT 0.518376 -119 TCACCGTGTCTGTTTTTGTGCAATATAAAA 5 165 0 TGTTTTTGTG 0.941235 -136 CTTGTCAATATTTTTTTTTGAAGGGGAGAT 5 276 1 TTTTTTTTTG 0.824472 -25 TTACAGAGGTTGCTTTTAGGCATATCCTTA 10 107 1 TGCTTTTAGG 0.724239 -66 GGAAAGAGCCTGTATTTATGTATAATGGGT 10 138 1 TGTATTTATG 0.839903 -35 AAAGAAGGCATGTATTTTTGATAAGAATTG 11 27 0 TGTATTTTTG 0.839903 -134 TCTGAAAGGTTTTTTTTGGGAGTTGGAGAG 12 26 0 TTTTTTTGGG 0.824299 -275 CTCATGAAATTGTTTTTTTGCTTCTGTTCT 12 228 1 TGTTTTTTTG 0.942333 -73 ATGGAGTAAGTTTTTTTATGAAAGCGGAGG 14 22 1 TTTTTTTATG 0.824472 -279 TTTGAATATTTGTATTTTGGATTTGTCCTG 14 160 0 TGTATTTTGG 0.842418 -141 AATAAAAAGGATTTTTTGTGTCATTGGCGA 14 240 1 ATTTTTTGTG 0.484626 -61 ********** Masking position 5 Map Score: 7.53348 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 613 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 11 TATTCCCCATCCTTCTTTGAAATTTATGTT 2 17 1 CCTTCTTTGA 0.944698 -156 CATTAAAAAACTTGGTTTGAGCTGATTCAA 5 84 0 CTTGGTTTGA 0.923229 -217 TAATCCTCCCCCCTGTTTGAGCTATAATAT 7 35 0 CCCTGTTTGA 0.984832 -258 TACTTTACCCCCTGTTTGATAAGTGCGAA 7 274 0 CCCTGTTTGA 0.984832 -19 TTGGAAAATTCTTTGTTTGA 13 1 0 CTTTGTTTGA 0.963893 -67 ********** Masking position 6 Map Score: 2.33196 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 42 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 ********** No masking Map Score: 2.03458e-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: 2.03458e-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: 2.03458e-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