AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_ecoli_mtub_100.orf -o057_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 aroL 182 shikimate kinase II #2 serC 198 3-phosphoserine aminotransferase #3 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #4 b1691 220 putative amino acid/amine transport protein #5 aroD 30 3-dehydroquinate dehydratase #6 aroC 34 chorismate synthase #7 yrdD 62 putative DNA topoisomerase #8 smf_2 53 orf, fragment 2 #9 smf_1 129 orf, fragment 1 #10 aroB 56 3-dehydroquinate synthase #11 aroK 199 shikimate kinase I #12 aroA 54 aroA Motif number 1 TCGCTATTCTCATGACACCGGCTTTCGCCGCATTGC 1 135 1 CAGCCCGGCC 0.934923 -48 CGTTGCGTTGCTATTAACCCGCGGTCAATCGATTGC 2 161 0 CTTACCCGCC 0.925563 -38 CGAAATTTTGCTTAATCCCCACAGCCAGCCTGTGGG 3 14 1 CTATCCCACC 0.73712 -57 CTATGACATGCAATATTCCTGGAAACATAAACTTTA 4 97 1 CATTCCTGGC 0.969965 -124 TACTGAAGATGATTTTCCCTGGGTACATGGCATAAA 4 129 0 GATTCCTGGC 0.842393 -92 CAGGCTGACCGCGTGCAGAAAGGGTA 5 1 1 CAGTACCGCC 0.93422 -30 AGTGAGGCCCTTCGCTTCCCGGATTCC 8 2 0 TTGTCCCGGC 0.974627 -52 CCTTATCTCCCTGCCATAAGCAGCCTTA 9 112 0 TTTTCCTGCA 0.645747 -18 CCACCTTAATTACTGTACCCGCAGACGAGTGTATAT 10 21 0 TATTCCCGCC 0.980882 -36 TCCTTGTATGCTAAATACCTGCGCGCGTCAAATAGA 11 54 0 CTATCCTGCC 0.963766 -146 GTTGGTGCTCTTCGCTGCCTGCGTTCCATGATGATG 11 104 1 TTGTCCTGCC 0.981356 -96 GCTTCCTATGGTGCCTGGTACCCACGACACCC 12 7 1 TAGTCCTGGC 0.965281 -48 GCCTGGTACCCACGACACCCGCCGACACGGCAGGAT 12 23 1 CAGCCCCGCC 0.986795 -32 ** * * ***** * Masking position 9 Map Score: 10.3857 Number of sites scoring better than the average of aligned sites = 1848 Number in coding regions = 1737 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 TGTAATTTATTATTTACACTTCATTCTTGA 1 12 1 TATTTACACT 0.86379 -171 TGGAATTTTTTCTTTACAATCGAAATTGTA 1 88 1 TCTTTACAAT 0.73459 -95 GCAAGCCACATTTTTGCCCTCAACGGTTTT 2 63 1 TTTTTGCCCT 0.967225 -136 TAAATAACTCTTTCTGCGCTAACTAAGGAA 4 48 1 TTTCTGCGCT 0.911468 -173 AAACATAAACTTTATGCCATGTACCCAGGG 4 119 1 TTTATGCCAT 0.724614 -102 TTTTTACCCTTTCTGCACGC 5 21 0 TTTTTACCCT 0.964588 -10 GCCTTAGCAATCTTTGCGATTGGTCAGTGA 9 88 0 TCTTTGCGAT 0.86098 -42 TTCTGGCTTTATATACACTCGTCTGCGGG 10 10 1 TATATACACT 0.667108 -47 AGCGGTAATGTTTTTACGCTGAACGTGTTT 11 22 1 TTTTTACGCT 0.972809 -178 TTTGCTGTCTTTTTTACGCTAATCTTACCC 11 160 1 TTTTTACGCT 0.972809 -40 ********** Masking position 5 Map Score: 8.9964 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 526 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 TTCACTTTAAGTGGAATTTTTTCTTTACAATCGA 1 77 1 GGGATTTTCT 0.831813 -106 TTTCTTTACAATCGAAATTGTACTAGTTTGATGG 1 96 1 ACGAATTTCT 0.970878 -87 TGATGGTATGATCGCTATTCTCATGACACCGGCT 1 124 1 ACGCATTTAT 0.844948 -59 CAGTAAAAACATCGGCTTTTTGCTAATAATCCGA 2 11 1 ACGGTTTTCT 0.975945 -188 TCCTGTGGCTATCGGTTTTATCATTCAGTGACAC 2 107 0 ACGGTTTTAT 0.888785 -92 TGCCGAAATTTTGCTTAATCCCCAC 3 2 1 GCGAATTTCT 0.964868 -69 CAGCCAGCCTGTGGGGTTTTTATTTCTGTTGTAG 3 35 1 GGGGTTTTTT 0.765808 -36 TTTGTTTTTGATCGCGATTTTCCTTAGTTAGCGC 4 63 0 ACGCATTTCT 0.965114 -158 TACGTACGGTAACGAAATTATCTTTCAGCAAGGA 4 194 1 ACGAATTTTT 0.90396 -27 TGTCAATCAGAGGGGGATTTGTCTAGAATAGAAG 9 51 0 AGGGATTGCT 0.823404 -79 CAGCCGTAAAAGCGGTAATGTTTTTACGCTGAAC 11 12 1 ACGGAATTTT 0.718887 -188 TTATCATTCAGGCGGCATTTTGCTGTCTTTTTTA 11 142 1 GCGGATTTCT 0.984694 -58 * *** *** * ** Masking position 9 Map Score: 9.80393 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 799 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 4 TGTCATGAGAATAGCGATCATACCATCAAA 1 122 0 ATAGCGATCA 0.972626 -61 CTTTCGCCGCATTGCGACCTATTGGGGAAA 1 156 1 ATTGCGACCT 0.985432 -27 GGTTTTACTCATTGCGATGTGTGTCACTGA 2 87 1 ATTGCGATGT 0.946796 -112 CGGTCAATCGATTGCGACCACAGGTAATAC 2 146 0 ATTGCGACCA 0.98979 -53 ACTAAGGAAAATCGCGATCAAAAACAAACT 4 69 1 ATCGCGATCA 0.98137 -152 ********** Masking position 7 Map Score: 4.09297 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 95 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 5 CAGTAAAAACATCGGCTTTTTGC 2 3 1 GAAAAACATC 0.94236 -196 CCGAAATTTTGCTTAATCCCCACAGCCAGCC 3 13 1 GTTAATCCCC 0.845141 -58 ATGTACCCAGGGAAAATCATCTTCAGTATAG 4 137 1 GAAAATCATC 0.978003 -84 AGTTGTTATGGCGAAATCAGCACTGTTCACG 7 32 1 GGAAATCAGC 0.921495 -31 TTCTATTCTAGACAAATCCCCCTCTGATTGA 9 52 1 GCAAATCCCC 0.947083 -78 CACGTTCAGCGTAAAAACATTACCGCTTTTA 11 18 0 GAAAAACATT 0.646104 -182 CCGCCTGAATGATAAATCATCATCATGGAAC 11 126 0 GTAAATCATC 0.976501 -74 CGCTCTGGCGATAAATCACCGGGTAAGATT 11 180 0 GTAAATCACC 0.980191 -20 * ********* Masking position 6 Map Score: 2.92307 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 551 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 CCCAATAGGTCGCAATGCGGCGAAAGCCGG 1 152 0 CGCAATGCGG 0.973919 -31 TGACACACATCGCAATGAGTAAAACCGTTG 2 83 0 CGCAATGAGT 0.942164 -116 TTAATAGCAACGCAACGTGGTGAGGGGAA 2 180 1 CGCAACGTGG 0.993077 -19 TATTACGCACCGTGAACAGTGCTGA 7 48 0 CGCACCGTGA 0.982692 -15 AAGAATCGCACCTTGTTTTATTAACC 8 38 0 CGCACCTTGT 0.950457 -16 ********** Masking position 4 Map Score: 1.49225 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 301 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TACATTATTCCTGTGGCTATCGGTTTTATC 2 119 0 CTGTGGCTAT 0.982592 -80 CACAGGCTGGCTGTGGGGATTAAGCAAAAT 3 18 0 CTGTGGGGAT 0.991355 -53 CACAGCCAGCCTGTGGGGTTTTTATTTCTG 3 33 1 CTGTGGGGTT 0.983991 -38 CTGAACACATCTCTGGAGATTT 9 3 0 CTCTGGAGAT 0.976698 -127 TTCTGGCTTTATATACACTC 10 1 1 TTCTGGCTTT 0.823946 -56 CGCTCTGGCGATAAATCACCGG 11 188 0 CTCTGGCGAT 0.994046 -12 ********** Masking position 4 Map Score: 6.19328 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 199 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TCAATACACCCCTTACTATACCAATAAATAT 1 42 0 CTTACTATAC 0.973834 -141 CGGTTTACATAATTACTATACTGAAGATGAT 4 152 0 ATTACTATAC 0.971813 -69 AAGATAATTTCGTTACCGTACGTATTGTTCT 4 187 0 CTTACCGTAC 0.977468 -34 CATCCACCTTAATTACTGTACCCGCAGACGA 10 29 0 ATTACTGTAC 0.97384 -28 GCGCGCAGGTATTTAGCATACAAGGAGTACC 11 64 1 ATTAGCATAC 0.91357 -136 * ********* Masking position 5 Map Score: 0.688214 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 34 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 9 TCGGATTATTAGCAAAAAGCCGATGTTTTT 2 15 0 AGCAAAAAGC 0.977733 -184 ATTATCTTTCAGCAAGGAGCT 4 210 1 AGCAAGGAGC 0.990803 -11 GAATCCGGGAAGCGAAGGGCCTCACTGGTT 8 12 1 AGCGAAGGGC 0.984422 -42 TGGTTAATAAAACAAGGTGCGATTCTT 8 37 1 AACAAGGTGC 0.920831 -17 GAACGCAGGCAGCGAAGAGCACCAACTCTC 11 100 0 AGCGAAGAGC 0.990803 -100 TAAAAAAGACAGCAAAATGCCGCCTGAATG 11 146 0 AGCAAAATGC 0.968398 -54 ********** Masking position 5 Map Score: 6.66772 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 151 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 ********** No masking Map Score: -7.50743e-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 11 ********** No masking Map Score: -7.50743e-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 12 ********** No masking Map Score: -7.50743e-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