AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ecoli_mtub_100.orf -o150_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #2 atpD 26 membrane-bound ATP synthase, F1 sector, beta-subunit #3 atpG 50 membrane-bound ATP synthase, F1 sector, gamma-subunit #4 atpF 61 membrane-bound ATP synthase, F0 sector, subunit b #5 atpE 46 membrane-bound ATP synthase, F0 sector, subunit c #6 atpI 300 membrane-bound ATP synthase, dispensable protein, affects expression of atpB #7 Rv1303 256 hypothetical protein Rv1303 #8 atpE 48 atpE #9 atpF 30 atpF #10 atpA 44 atpA #11 atpD 39 atpD Motif number 1 TTTCGAGTTTGCTGACCCGGGAGTGAGTCTTGT 1 146 1 GCTCCCGGGG 0.897627 -69 CCTGCCCTAAGGCAAGCCGCCAGACG 3 4 0 GGCGCCGCCG 0.998829 -47 CTTGCCTTAGGGCAGGCCGCAAGGCATTGAGGA 3 21 1 GGCGCCGCAG 0.996542 -30 CAAATTATACGGTGCGCCCCCGTGATTTCAAAC 6 202 0 GGTGCCCCCT 0.974278 -99 CTCCCTTCGAGGTATGCCGCGTGTCGTATAAAA 6 273 0 GGTGCCGCGG 0.998732 -28 GGTACGGTGCGGCTAGAACCCCGAAGGAGACCT 7 59 1 GGCGAACCCG 0.873626 -198 GCCGGGGGCCGGCAACCCGCGAGGTCTCCTTCG 7 80 0 GGCCCCGCGG 0.996322 -177 ATACGCATCCGATGGGCCGGGGGCCGGCAACCC 7 95 0 GATGCCGGGG 0.964846 -162 GTCGTGAATCGGCGCGACCGGATACGCATCCGA 7 116 0 GGCGACCGGT 0.897562 -141 GGGTGATTCCGGTGCGACGACTGCGATACGCTC 7 170 1 GGTGACGACG 0.958621 -87 ACTGATCGGTGGCCCGCCGAGCGTATCGCAGTC 7 188 0 GGCGCCGAGG 0.992663 -69 GCCCAAGCTAGGTTAGCCCCACGAGGAAGCGAA 11 11 1 GGTGCCCCAG 0.989259 -29 *** ****** * Masking position 1 Map Score: 20.6327 Number of sites scoring better than the average of aligned sites = 1679 Number in coding regions = 1610 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 CAGAAATTATCCGGGAGACGAGA 1 3 0 CCGGGAGCGA 0.942368 -212 AAGACTCACTCCCGGGTCAGCAAACTCGAAA 1 146 0 CCCGGGTAGC 0.915952 -69 GGCCGCAAGGCATTGAGGAGAAGCTC 3 35 1 CATTGAGAGA 0.664309 -16 TGATTTCAAACAATAAGTAGCCAAAAGGTGA 6 182 0 CAATAAGAGC 0.819712 -119 TGTTTGAAATCACGGGGGCGCACCGTATAAT 6 201 1 CACGGGGCGC 0.992396 -100 CCCGGAGCCGAGAACTACGAC 7 1 1 CCCGGAGCGA 0.978821 -256 AGAACTACGACAAGGAGTAGTAGTGGTGTCT 7 21 1 CAAGGAGAGT 0.893216 -236 CGCACCGTACCACAAGGTAGACACCACTACT 7 39 0 CACAAGGAGA 0.774346 -218 CGGCTAGAACCCCGAAGGAGACCTCGCGGGT 7 68 1 CCCGAAGAGA 0.961065 -189 ATCCGATGGGCCGGGGGCCGGCAACCCGCGA 7 91 0 CCGGGGGCGG 0.889741 -166 CGGAATCACCCAAGGGGTAGCTCCCTATGTC 7 150 0 CAAGGGGAGC 0.99043 -107 CCAGAGCCATCAAGGAGGATAAGGAA 8 33 1 CAAGGAGATA 0.710363 -16 CAAATGGTTGCAATAGGTAGCA 9 19 1 CAATAGGAGC 0.879467 -12 AGGTTAGCCCCACGAGGAAGCGAAGAAGAT 11 20 1 CACGAGGAGC 0.985857 -20 ******* *** Masking position 1 Map Score: 12.7155 Number of sites scoring better than the average of aligned sites = 1706 Number in coding regions = 1546 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 GAAATTATCCGGGAGACGAGA 1 1 0 GGGAGACGAA 0.972803 -214 CACAAATAATGGGAGCGTCAATTTTTCGAGT 1 123 1 GGGAGCGTCA 0.93489 -92 CTGCCCTAAGGCAAGCCGCCAGACG 3 5 0 GCAAGCCGCA 0.985699 -46 TTGCCTTAGGGCAGGCCGCAAGGCATTGAGG 3 22 1 GCAGGCCGCA 0.922085 -29 CCCGGAGCCGAGAACTACGACAA 7 3 1 CGGAGCCGAA 0.974755 -254 CGTACCACAAGGTAGACACCACTACTACTCC 7 34 0 GGTAGACACA 0.64529 -223 CCTTGTGGTACGGTGCGGCTAGAACCCCGAA 7 53 1 CGGTGCGGCA 0.819381 -204 CCGGGGGCCGGCAACCCGCGAGGTCTCCTTC 7 81 0 GCAACCCGCA 0.930995 -176 GTGAATCGGCGCGACCGGATACGCATCCGAT 7 115 0 GCGACCGGAA 0.910393 -142 TCCGGGCTGATGGAGCGGAAACCACCCGATC 7 222 0 TGGAGCGGAA 0.899713 -35 TGATGGCTCTGGTAGCCGTTACCAGCATCCG 8 14 0 GGTAGCCGTA 0.895089 -35 AACCGAAGTAGGAAGACGAAAAGCT 10 30 1 GGAAGACGAA 0.949514 -15 AGCCCCACGAGGAAGCGAAGAAGAT 11 25 1 GGAAGCGAAA 0.892677 -15 ********* * Masking position 11 Map Score: 10.0164 Number of sites scoring better than the average of aligned sites = 2812 Number in coding regions = 2655 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 CATAATCAGCCACGAGGTGCGCG 1 202 1 CACGAGGTGC 0.926254 -13 CGTCTGGCGGCTTGCCTTAGGGCAG 3 6 1 GGCGGCTTGC 0.962206 -45 CTCAATGCCTTGCGGCCTGCCCTAAGGCAA 3 22 0 TGCGGCCTGC 0.954536 -29 TTATACGACACGCGGCATACCTCGAAGGGA 6 275 1 CGCGGCATAC 0.891297 -26 AAGGAGACCTCGCGGGTTGCCGGCCCCCGG 7 82 1 CGCGGGTTGC 0.982644 -175 GCATCCGATGGGCCGGGGGCCGGCAACCCG 7 94 0 GGCCGGGGGC 0.913023 -163 CGTGAATCGGCGCGACCGGATACGCATCCG 7 117 0 CGCGACCGGA 0.895876 -140 CGCGCCGATTCACGACCGACATAGGGAGCT 7 133 1 CACGACCGAC 0.795442 -124 CTGCGATACGCTCGGCGGGCCACCGATCAG 7 190 1 CTCGGCGGGC 0.987763 -67 TCTTCGCTTCCTCGTGGGGCTAACCTAGCT 11 16 0 CTCGTGGGGC 0.887981 -24 ********** Masking position 3 Map Score: 4.96065 Number of sites scoring better than the average of aligned sites = 4527 Number in coding regions = 4345 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 5 TAGCGCCTTTGTCTTATTGACTTACTGGTAG 1 44 0 GTTTATTGAC 0.951184 -171 CAAAAAAACGGGTTTATTGGCGGATAGAAAA 1 83 1 GGTTATTGGC 0.984869 -132 ATTATGGACGGCGTTATTGGCAAAGTGGAAC 1 177 0 GCTTATTGGC 0.994293 -38 AAGGCATCATTTGCCAAGTAAATA 6 4 1 GCTCATTTGC 0.972071 -297 CAGTGTTTACGCGTTATTTACAGTTTTTCAT 6 88 1 GCTTATTTAC 0.971726 -213 ** ******** Masking position 6 Map Score: 1.77517 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 169 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CCCGGATAATTTCTGGTAGCAAAGCCTACC 1 19 1 TTCTGGTAGC 0.969545 -196 CTTATTGACTTACTGGTAGGCTTTGCTACC 1 33 0 TACTGGTAGG 0.90767 -182 AAAGCACAAATAATGGGAGCGTCAATTTTT 1 119 1 TAATGGGAGC 0.951627 -96 CGGCATACCTCGAAGGGAGCAGGA 6 287 1 CGAAGGGAGC 0.924682 -14 TCACGACCGACATAGGGAGCTACCCCTTGG 7 142 1 CATAGGGAGC 0.936744 -115 TACCGGATGCTGGTAACGGCTACCAGA 8 8 1 TGCTGGTAAC 0.846128 -41 TCCTTGATGGCTCTGGTAGCCGTTACCAGC 8 19 0 CTCTGGTAGC 0.974647 -30 AAATGGTTGCAATAGGTAGCA 9 20 1 AATAGGTAGC 0.791781 -11 ********** Masking position 8 Map Score: 2.41051 Number of sites scoring better than the average of aligned sites = 1309 Number in coding regions = 1247 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 CCCGTTTTTTTGTTGCTATTTAGCGCCTTTG 1 64 0 TTTGCTATTT 0.910101 -151 GAGTGAGTCTTGTTCCACTTTGCCAATAACG 1 166 1 TTTCCACTTT 0.779422 -49 AACGTTCTGATATTGCTCTTTAAATAAAAGC 4 19 0 TTTGCTCTTT 0.962824 -43 TTATTCACCTTTTGGCTACTTATTGTTTGAA 6 178 1 TTGGCTACTT 0.873079 -123 TCCTGCTCCCTTCGAGGTATG 6 290 0 TCTGCTCCCT 0.92213 -11 TAGACACCACTACTACTCCTTGTCGTAGTTC 7 22 0 TCTACTCCTT 0.895216 -235 TTCCTTATCCTCCTTGATGGCTCTG 8 34 0 TATCCTCCTT 0.925621 -15 AGCTTTTCGTCTTCCTACTTCGGTTTGTGC 10 25 0 TTTCCTACTT 0.951732 -20 * ********* Masking position 1 Map Score: 1.23855 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 269 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 8 AGCGTCAATTTTTCGAGTTTGCTGACCCGG 1 136 1 TTTCGAGTTT 0.934758 -79 GACAGTCTCCAGTTTGTTTCAGTTA 5 32 0 TCTCCAGTTT 0.981967 -15 GCACGCTTTATCACCAGTGTTTACGCGTTA 6 74 1 TCACCAGTGT 0.946813 -227 TTACGCGTTATTTACAGTTTTTCATGATCG 6 94 1 TTTACAGTTT 0.906252 -207 TTTAAATATTTTTCCAGTGCATACAATTGC 6 145 0 TTTCCAGTGC 0.960833 -156 ********** Masking position 6 Map Score: 0.140242 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 264 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 ********** No masking Map Score: -1.83077e-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: -1.83077e-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: -1.83077e-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