AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_bsub_mtub_300.orf -o174_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 yngI 43 similar to long-chain acyl-CoA synthetase #2 yngJ 90 similar to butyryl-CoA dehydrogenase #3 ynzE 270 ynzE #4 yngK 135 alternate gene name: yotA; similar to hypothetical proteins #5 yngL 110 yngL #6 ppsD 24 peptide synthetase #7 ppsB 24 peptide synthetase #8 ppsA 300 peptide synthetase #9 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #10 spoIIIAC 22 spoIIIAC #11 spoIIIAA 75 spoIIIAA #12 yqhV 144 alternate gene name: yqgE #13 efp 24 elongation factor P #14 yqhS 86 similar to 3-dehydroquinate dehydratase #15 yqhR 226 yqhR #16 pca 24 pca #17 Rv2969c 96 hypothetical protein Rv2969c #18 lipN 300 lipN #19 accD5 49 accD5 #20 sseA 40 sseA #21 accA3 107 accA3 Motif number 1 ATCACTTTTTAAAAAAAGACGACTTAGAAA 3 28 0 AAAAAAAGAC 0.965803 -243 CTAAATAAACGAAAAAAGTCCTAAAGCATG 4 24 0 GAAAAAAGTC 0.88856 -112 CATTCTTGATACAAAAAGAAAGACGGACAG 5 38 0 ACAAAAAGAA 0.878035 -73 GATATAAAGTGATAAAAGTATTGTTTTACA 8 65 0 GATAAAAGTA 0.567838 -236 GAAATTTGATAAAAAAAGAAACGAAAAATA 8 97 1 AAAAAAAGAA 0.966478 -204 AAGAAACGAAAAATAAAGAAATAATACTAT 8 112 1 AAATAAAGAA 0.711563 -189 GAAAAATGACAATAAAAGAAATTATATGAC 8 228 0 AATAAAAGAA 0.823138 -73 GAAAAAAGCAGAAAAATGACAATAAAAGAA 8 238 0 GAAAAATGAC 0.851735 -63 AGAAAATGTAGAAAAAAGCAGAAAAATGAC 8 248 0 GAAAAAAGCA 0.960142 -53 GAATGAGGGAAAAAAGCCCGCTAAACAA 9 9 1 GAAAAAAGCC 0.959345 -147 TGACAGCAACGCAAAAAGCCCGCTTGTTTA 9 32 0 GCAAAAAGCC 0.854906 -124 AGTAACCTATAAAAAAAGAAATTTCATACA 9 121 1 AAAAAAAGAA 0.966478 -35 AAAGGAAAAAAGAAGTCTGTTCCC 12 5 1 GAAAAAAGAA 0.973211 -140 TTTTGGGCACAAAAAAAGCCTGCTCCCATT 12 36 0 AAAAAAAGCC 0.949308 -109 TTTTGTGCCCAAAAACAGAATCTTTCTTTT 12 52 1 AAAAACAGAA 0.785239 -93 AAGTGTGCCCAAAAAATGAAATGTCAATAA 15 193 0 AAAAAATGAA 0.823138 -34 ********** Masking position 5 Map Score: 20.2947 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 754 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 2 AGCGGATTAGCGGACAGAGGCCA 5 2 1 GCGGATGCGG 0.996527 -109 TCTTACAGGAGCGGACTTGTGAATTCAACTCT 9 66 0 GCGGACGTGA 0.957924 -90 TGTCAATCTAGAGGTTTAGCGGTGTTTCCTGT 15 67 0 GAGGTTGCGG 0.947857 -160 GACATCCGGATAAGGGAGCCACAC 16 6 1 CCGGATGGGA 0.891427 -19 GGCGCCTCTAGCGTACCGGCGGCAAGCCAGCC 17 16 0 GCGTACGCGG 0.970743 -81 TGTCGCGGCCGCGGTCAGGCGACGGCGCCTCT 17 39 0 GCGGTCGCGA 0.992412 -58 TCGAGCACGTGAGGATCAGCGAAACT 17 81 1 GAGGATGCGA 0.96166 -16 GTTGGGCACGCCGGACTCGCGGCACCTACCGC 18 179 1 CCGGACGCGG 0.99363 -122 CCGGCCGACACCGGGCAAGCGGTAGGTGCCGC 18 197 0 CCGGGCGCGG 0.973319 -104 ACGCGCAGCAACGGACACTCGATCCGCGCCGT 18 254 0 ACGGACTCGA 0.797369 -47 ACCCGCTCACGCGGTTCCTCGAT 21 2 0 GCGGTTTCGA 0.919076 -106 AACCGCGTGAGCGGGTCAGCGGCGCGACGCTT 21 18 1 GCGGGTGCGG 0.992945 -90 ****** **** Masking position 3 Map Score: 17.5809 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 365 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CTATCATTAAGAAAGGAGGAACAATGA 1 27 1 GAAAGGAGGA 0.887679 -17 ATCATTCCCTGACAAGAAAAGTCTGAAAATT 2 20 0 GACAAGAAAG 0.875489 -71 GAAATGAGAAGGACGGCTTTC 3 1 1 GAAATGAGAG 0.88444 -270 GTGATTTTGGGACAGGAAACGATGGTAAACC 3 53 1 GACAGGAAAG 0.978594 -218 GAGAAACACGTACAGGACGTGTTTTACGTTT 3 196 1 TACAGGACGG 0.826502 -75 CACCTAACCAGACTAGAAATGAAAACGTAAA 3 218 0 GACTAGAAAG 0.650115 -53 AAAATCGTGACAGGAGACATGAAC 6 9 1 GACAGGAGAA 0.961432 -16 AATTTGATAAAAAAAGAAACGAAAAATAAAG 8 99 1 AAAAAGAAAG 0.484085 -202 TTATTATGAGAACTGGAGGGAATCCG 8 285 1 AACTGGAGGA 0.614852 -16 ATGTTCATCTTACAGGAGCGGACTTGTGAAT 9 74 0 TACAGGAGCG 0.809931 -82 CCAATCGGTAGAAAGGAGGAGGCTCTG 11 59 1 GAAAGGAGGG 0.966664 -17 CTTTTATACGGAAATGACAAGACTACTTCAG 12 77 1 GAAATGACAG 0.621909 -68 CATTTTATCATACTGGAAAAGGATTATACA 14 10 0 TACTGGAAAG 0.794169 -77 GAACATTTTTTACATGAGAAACCCTCGCGAA 14 53 1 TACATGAGAA 0.614568 -34 AACCCTCGCGAAAAGGAGAGATTGT 14 72 1 AAAAGGAGAA 0.768866 -15 ACAATAGAGTGAAAGGAAATGGTTAGCAATC 15 36 0 GAAAGGAAAG 0.950251 -191 CACTCTATTGTACAGGAAACACCGCTAAACC 15 56 1 TACAGGAAAA 0.799173 -171 GTGTGCCCAAAAAATGAAATGTCAATAAAAA 15 190 0 AAAATGAAAG 0.54991 -37 GGCACACTTTAACTGGAGGTGCC 15 214 1 AACTGGAGGG 0.854172 -13 GAATCAGCCCGACAGGAGGCGCA 21 95 1 GACAGGAGGG 0.985796 -13 ********* * Masking position 7 Map Score: 16.6793 Number of sites scoring better than the average of aligned sites = 1622 Number in coding regions = 1285 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 317 Fraction of orfs with sites within 600 bp upstream = 0.0509155 Motif number 4 GGAAAAGCAAGGCTATGGCAATTTTTTCAG 15 101 0 GGCTATGGCA 0.799672 -126 CACACTTTTTGGCAGCTGCGAGTAAAATTT 15 156 0 GGCAGCTGCG 0.845533 -71 GCCGCGGTCAGGCGACGGCGCCTCTAGCGT 17 34 0 GGCGACGGCG 0.983152 -63 GTCGCCTGACCGCGGCCGCGACAAGCCGAC 17 48 1 CGCGGCCGCG 0.498038 -49 TCAACACCTGGGCAGGTGCTGAGCCACAGC 18 74 1 GGCAGGTGCT 0.792948 -227 CGTCGCCGAAGGCTGTGGCTCAGCACCTGC 18 85 0 GGCTGTGGCT 0.93389 -216 CACAGCCTTCGGCGACGGCGGCGTAAGCCG 18 98 1 GGCGACGGCG 0.983152 -203 TACTTCCTTAGGCTGGGGCG 19 1 0 GGCTGGGGCG 0.989595 -49 CGATGTTATCGGCTGCCGCACACTACTTCC 19 24 0 GGCTGCCGCA 0.9503 -26 GCGTGAGCGGGTCAGCGGCGCGACGCTTAA 21 22 1 GTCAGCGGCG 0.94746 -86 ********** Masking position 3 Map Score: 11.5455 Number of sites scoring better than the average of aligned sites = 769 Number in coding regions = 724 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 TCAGACTTTTCTTGTCAGGGAATGATTATA 2 25 1 CTTGTCAGGG 0.949174 -66 GTTCATGTCTCCTGTCACGATTTT 6 5 0 CCTGTCACGA 0.827184 -20 ACAATCTCTCCTTTTCGCGAGGGTTTCTCA 14 67 0 CTTTTCGCGA 0.619149 -20 TCGAGGCTGGCTTGCCGCCGGTACGCTAGA 17 12 1 CTTGCCGCCG 0.962688 -85 GGCGCCGTCGCCTGACCGCGGCCGCGACAA 17 42 1 CCTGACCGCG 0.848049 -55 GATTTGTCGGCTTGTCGCGGCCGCGGTCAG 17 53 0 CTTGTCGCGG 0.984364 -44 GCGAATAGTGCTGGTCGGCATTCAACACTT 18 127 1 CTGGTCGGCA 0.848263 -174 TCTTTCGGGTCCTGCCGGCCGACACCGGGC 18 213 0 CCTGCCGGCC 0.954588 -88 AGACATCCAGCCTGACGGCGCGGATCGAGT 18 240 1 CCTGACGGCG 0.974626 -61 TCTTACAAGTCTTGTCGGGGGAAGTTTAAG 21 47 0 CTTGTCGGGG 0.990828 -61 TGCGCCTCCTGTCGGGCTGATTCTTCG 21 91 0 CCTGTCGGGC 0.980876 -17 ********** Masking position 6 Map Score: 9.32419 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 583 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 AACTCGCCTAATAGGATGTTACAAAGATGT 2 56 1 ATAGGATGTT 0.771506 -35 GTCTTTTTTTAAAAAGTGATTTTGGGACAG 3 38 1 AAAAAGTGAT 0.868743 -233 AAAAAGTCCTAAAGCATGTTGTGAACCGCT 4 12 0 AAAGCATGTT 0.706527 -124 CCGGGCTATAAAAGGGTGATTAACAGAATG 4 63 0 AAAGGGTGAT 0.870251 -73 CCTCCAAGAAAAAGGATGATGTTATCATTC 5 84 0 AAAGGATGAT 0.833278 -27 CTTTTGAAAAGGTGTGTGGAATTG 7 7 1 AAAAGGTGTG 0.823587 -18 ATTTCCGGATATAAAGTGATAAAAGTATTG 8 72 0 ATAAAGTGAT 0.725021 -229 CTATATTCAAAAAAAATGTTATAAAAATTT 8 138 1 AAAAAATGTT 0.893227 -163 TTCCAGTATGATAAAATGTTCACGAGAAGT 14 23 1 ATAAAATGTT 0.769181 -64 TTTCTCATGTAAAAAATGTTCACTTCTCGT 14 44 0 AAAAAATGTT 0.893227 -43 CGCAGCTGCCAAAAAGTGTGAGCTTTTTTA 15 166 1 AAAAAGTGTG 0.811644 -61 ********** Masking position 3 Map Score: 4.85924 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 385 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 7 CCTAAAGCATGTTGTGAACCGCTT 4 5 0 GTTGTGAACC 0.843404 -131 CTAATTTTCTTTTGTGCATCATTC 8 5 0 TTTGTGCATC 0.791863 -296 CCTGCTCCCATTTGGGAACAGACTTCTTTT 12 18 0 TTTGGGAACA 0.949131 -127 AGATTCTGTTTTTGGGCACAAAAAAAGCCT 12 45 0 TTTGGGCACA 0.985492 -100 CATTTCATTTTTTGGGCACACTTTAACTGG 15 200 1 TTTGGGCACA 0.985492 -27 CATTCAACACTTTGGTCACCACGTAGAGTT 18 145 1 TTTGGTCACC 0.933052 -156 AGAGTTGGCCGTTGGGCACGCCGGACTCGC 18 169 1 GTTGGGCACG 0.964276 -132 ********** Masking position 8 Map Score: 4.28444 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 65 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ACGACTTAGAAAGCCGTCCTTCTCATTTC 3 10 0 AAGCCGTCCT 0.895732 -261 ACGGCTTTCTAAGTCGTCTTTTTTTAAAAA 3 23 1 AAGTCGTCTT 0.822331 -248 TGAGGGAAAAAAGCCCGCTAAACAAGCGGG 9 14 1 AAGCCCGCTA 0.911263 -142 GCAACGCAAAAAGCCCGCTTGTTTAGCGGG 9 27 0 AAGCCCGCTT 0.695826 -129 TTGAATTCACAAGTCCGCTCCTGTAAGATG 9 70 1 AAGTCCGCTC 0.949785 -86 GCTTGTCATAAAGTCTGCCTCACATCATAC 11 17 1 AAGTCTGCCT 0.935723 -59 GGCACAAAAAAAGCCTGCTCCCATTTGGGA 12 31 0 AAGCCTGCTC 0.906072 -114 GTTTAATGTCCTCCTATATTCCAA 13 10 0 ATGTCCTCCT 0.692755 -15 TACCGGCGGCAAGCCAGCCTCGAC 17 5 0 AAGCCAGCCT 0.918649 -92 ********** Masking position 1 Map Score: 5.87242 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 409 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 TACCGTAATAGCGAATAGTGAAAGTGATGT 4 96 1 GCGAATAGTG 0.965475 -40 AGCGGATTAGCGGACAGAGGCCATTCTCT 5 10 1 GCGGACAGAG 0.989844 -101 AAAAAGAAAGACGGACAGAGAATGGCCTCT 5 26 0 ACGGACAGAG 0.949177 -85 GGCGTAAGCCGCGAATAGTGCTGGTCGGCA 18 117 1 GCGAATAGTG 0.965475 -184 GCCTGACGGCGCGGATCGAGTGTCCGTTGC 18 249 1 GCGGATCGAG 0.976003 -52 ********** Masking position 5 Map Score: 2.44311 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 73 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TCTGTTTCTTCTCCCCCATTACATC 4 121 0 TTCTTCTCCC 0.921477 -15 TTTATTTTTGCTCCCCTCACGT 10 8 0 TTTTGCTCCC 0.962451 -15 GAAAAAAGAAGTCTGTTCCCAAATGGGAGC 12 15 1 GTCTGTTCCC 0.948593 -130 CACAAAAAAAGCCTGCTCCCATTTGGGAAC 12 29 0 GCCTGCTCCC 0.985893 -116 GTGTGGCTCCCTTATCCGGAT 16 14 0 TGTGGCTCCC 0.910036 -11 GGGCTGCTCCCTACAAAACTC 18 290 0 GGCTGCTCCC 0.991784 -11 ********** Masking position 7 Map Score: 3.19905 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 153 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 TTAAAGAAGCCAATCGGTAGAAAGGAGGAG 11 50 1 CAATCGGTAG 0.972279 -26 CGACACCGGGCAAGCGGTAGGTGCCGCGAG 18 194 0 CAAGCGGTAG 0.984014 -107 GGCCAGGTCGCCAGCGGTAGGCTCGATGAT 20 21 1 CCAGCGGTAG 0.982711 -20 ********** Masking position 3 Map Score: 0.400694 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 5 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 CTGAGAAACTAGTACTAAATAAAAATAAAATCGA 3 161 1 AGCAAATAAA 0.753011 -110 ATCTCCGAACAGCACAAAAAATAATGTGGCACCT 3 244 0 AGCAAAAAAA 0.950835 -27 CAGAATGTCTATCTCACTAAATAAACGAAAAAAG 4 36 0 ATCCTAAAAA 0.857964 -100 AAAGAAAATTAGTCCGATTAAAAAGTAGTGTATA 8 23 1 AGCATTAAAA 0.88276 -278 TATTTTTTAAAGTACAATAAAAAACATTAAATTT 8 162 0 AGCATAAAAA 0.959721 -139 GATTCCCTCCAGTTCTCATAATAAGAGGATAAGA 8 275 0 AGCCATAAAA 0.887238 -26 GAGGGAAAAAAGCCCGCTAAACAAGCGGGCTTTT 9 15 1 AGCCTAAAAA 0.96843 -141 ATTCTGTTTTTGGGCACAAAAAAAGCCTGCTCCC 12 39 0 TGCCAAAAAA 0.796959 -106 AAAAAATGAAATGTCAATAAAAAAGCTCACACTT 15 179 0 ATCATAAAAA 0.824306 -48 ** * ***** ** Masking position 11 Map Score: 2.20986 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 123 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 ********** No masking Map Score: 5.57309e-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: 5.57309e-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 15 ********** No masking Map Score: 5.57309e-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