AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_bsub_reg_100.orf -o00660_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 ydaO 300 similar to hypothetical proteins #2 mutT 58 mutator protein #3 ydaP 66 similar to pyruvate oxidase #4 sucC 172 succinyl-CoA synthetase (beta subunit) #5 sucD 28 succinyl-CoA synthetase (alpha subunit) #6 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #7 alsD 61 alpha-acetolactate decarboxylase #8 alsS 154 alpha-acetolactate synthase (pH6) Motif number 1 GTTGGGGTGAATCCTTTTTAGGTAGGGCTA 1 30 1 ATCCTTTTTA 0.837194 -271 CGATGTCTTCCCCTTTTAATTTCTCAT 1 284 0 TTCCCCTTTT 0.844745 -17 CCCCATACCTCCTTTTCCCGCTAAA 2 44 0 TACCTCCTTT 0.927386 -15 ATCCTCCTTTTTCCTTTTTTCAATACCACA 3 42 0 TTCCTTTTTT 0.948864 -25 AACGTATCCTCCTTTTTCCTTTTTT 3 52 0 ATCCTCCTTT 0.990439 -15 AATATTCCCCATCCTTCTTTGAAATTTATG 4 15 1 ATCCTTCTTT 0.98237 -158 AAATCTTTTAATCCTTCTAAACATTCAAAC 4 62 0 ATCCTTCTAA 0.851708 -111 AGACTGCGCTTTCATTCTATAATAATACTG 4 117 0 TTCATTCTAT 0.856265 -56 TTCCCATCCTCCTAACTTATGTAAC 4 158 0 ATCCTCCTAA 0.914367 -15 TCCCCTGCCTTTCATTCTTTC 5 2 0 TTCATTCTTT 0.948864 -27 TCCTTTAAAGATCATCTTTTCATTAGCTAG 6 256 0 ATCATCTTTT 0.895392 -45 CTTTTGGATTTTCATCCTTTAAAGATCATC 6 270 0 TTCATCCTTT 0.971829 -31 TTTAGTTCCTCCTTTTGGATTTTCA 6 286 0 TTCCTCCTTT 0.991736 -15 ********** Masking position 8 Map Score: 20.1656 Number of sites scoring better than the average of aligned sites = 1232 Number in coding regions = 756 Number in noncoding regions = 476 Number of orfs with sites within 600 bp upstream = 556 Fraction of orfs with sites within 600 bp upstream = 0.0893029 Motif number 2 TTTGCCGTTGGGGTGAATCCTTTTTAGGTA 1 24 1 GGGTGAATCC 0.634091 -277 GAGGTTAGCTGACGGATTCGGGCATATGAG 1 63 0 GACGGATTCG 0.776328 -238 GAGAGGAGATGAATGAAACCTGTGTTCGAT 1 105 1 GAATGAAACC 0.776743 -196 AGCGGGAAAAGGAGGTATGGGG 2 47 1 GGAGGTATGG 0.838563 -12 CAATACCACAGGAGAAAGGCTTTAAAACCC 3 22 0 GGAGAAAGGC 0.878096 -45 AAAGGAAAAAGGAGGATACGTT 3 55 1 GGAGGATACG 0.942947 -12 AAATTTCAAAGAAGGATGGGGAATATTTTA 4 12 0 GAAGGATGGG 0.968842 -161 TATTATTATAGAATGAAAGCGCAGTCTATT 4 120 1 GAATGAAAGC 0.884138 -53 ACATAAGTTAGGAGGATGGGAA 4 161 1 GGAGGATGGG 0.982996 -12 GAAAGAATGAAAGGCAGGGGACCA 5 5 1 GAATGAAAGG 0.943621 -24 AGCTAAAAGGGGCGAAAAGGCTTTTCTTTC 6 164 0 GGCGAAAAGG 0.861212 -137 GCTGATTGTGGGCGGAAGGGCTTTTTTTAT 6 211 1 GGCGGAAGGG 0.987375 -90 TAAATAAAAGGAGTGAAGGGAAAT 7 48 1 GAGTGAAGGG 0.91985 -14 ********** Masking position 1 Map Score: 10.7251 Number of sites scoring better than the average of aligned sites = 2350 Number in coding regions = 1934 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 351 Fraction of orfs with sites within 600 bp upstream = 0.0563765 Motif number 3 CAACGGCAAAAAGCCGTTCTATT 1 4 0 AAGCCGTTCT 0.951851 -297 ATATGAGAGTTAGCCCTACCTAAAAAGGAT 1 40 0 TAGCCCTACC 0.968953 -261 ATGTTGATGATAGTCCTTTCTGCTATGATG 1 209 0 TAGTCCTTTC 0.884016 -92 CCGGGTTTTAAAGCCTTTCTCCTGTGGTAT 3 20 1 AAGCCTTTCT 0.959218 -47 CAAAATCTTTTAATCCTTCTAAACATTCAA 4 64 0 TAATCCTTCT 0.70114 -109 TCACCCGGCCAAGTCCTACTGTCATTTCAG 6 52 0 AAGTCCTACT 0.925027 -249 GCGGAAAGAAAAGCCTTTTCGCCCCTTTTA 6 161 1 AAGCCTTTTC 0.895103 -140 TCAATAAAAAAAGCCCTTCCGCCCACAATC 6 214 0 AAGCCCTTCC 0.992741 -87 ********** Masking position 2 Map Score: 5.83638 Number of sites scoring better than the average of aligned sites = 665 Number in coding regions = 568 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 AGACATCATAGCAGAAAGGACTATCATCAA 1 206 1 GCAGAAAGGA 0.985885 -95 CCTTTTTAGCGGGAAAAGGAGGTATGGGG 2 40 1 GGGAAAAGGA 0.967184 -19 CAATACCACAGGAGAAAGGCTTTAAAACCC 3 22 0 GGAGAAAGGC 0.960491 -45 CTGTGGTATTGAAAAAAGGAAAAAGGAGGA 3 41 1 GAAAAAAGGA 0.86197 -26 CATAAGTTAGGAGGATGGGAA 4 162 1 GAGGATGGGA 0.899802 -11 CGTTACTAAAGCGGATAGAAATATCCATGA 6 94 1 GCGGATAGAA 0.929881 -207 GGGTGGTACCGCGGAAAGAAAAGCCTTTTC 6 151 1 GCGGAAAGAA 0.976726 -150 GCTAAAAGGGGCGAAAAGGCTTTTCTTTCC 6 163 0 GCGAAAAGGC 0.982937 -138 CTGATTGTGGGCGGAAGGGCTTTTTTTATT 6 212 1 GCGGAAGGGC 0.988495 -89 ********** Masking position 5 Map Score: 11.6285 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 518 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 TTGCCGTTGGGGTGAATCCTTTTTAGGTAGG 1 25 1 GGTGAATCCT 0.987532 -276 TTATGGCACAGGGGCATCCGTTTGCCTCTGT 1 136 1 GGGGCATCCT 0.981458 -165 GAAATTAAAAGGGGAAGACATCG 1 288 1 GGGGAAGACT 0.970485 -13 AAAGGACCAAGGTGATTCCCTTGGTCCTAGA 2 14 0 GGTGATTCCT 0.934462 -45 AAAGAAGGATGGGGAATATTTTAG 4 4 0 GGGGAATATT 0.942909 -169 CGGCGAAGCTTTACAAGGTGAA 6 2 1 GGCGAAGCTT 0.965476 -299 TTAATCATAAGGCGAATCGATATTGGAGGTC 8 55 1 GGCGAATCGT 0.971964 -100 ********* * Masking position 11 Map Score: 4.76376 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 202 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 GATGTTATGGCACAGGGGCATCCGTTTGCC 1 132 1 CACAGGGGCA 0.992532 -169 CAACAAAAAACACAGAGGCAAACGGATGCC 1 148 0 CACAGAGGCA 0.970984 -153 ACTGTCATTTCAGACTGGCACTCTGAGGCG 6 35 0 CAGACTGGCA 0.970984 -266 GAATCAAGTTCACCCGGCCAAGTCCTACTG 6 61 0 CACCCGGCCA 0.982793 -240 CGCCCACAATCAGCCGCGCAGTAACTGCGA 6 195 0 CAGCCGCGCA 0.976032 -106 ********** Masking position 2 Map Score: 1.21941 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 121 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TGCATTCAAAAATGAACAACAAAAAACACA 1 164 0 AATGAACAAC 0.831689 -137 TTCATTTTTGAATGCAAATCGCATACAGAG 1 178 1 AATGCAAATC 0.901905 -123 TATTGTTTTAATTGAAAAATGAGAAATTAA 1 266 1 ATTGAAAAAT 0.879275 -35 CTCCTGTGGTATTGAAAAAAGGAAAAAGGA 3 38 1 ATTGAAAAAA 0.642653 -29 TCTACAGTTCGATGCAAAATCTTTTAATCC 4 78 0 GATGCAAAAT 0.897338 -95 GGCTTTTTTTATTGAATAATCAGCTATCTA 6 229 1 ATTGAATAAT 0.81954 -72 ATCTTTAAAGGATGAAAATCCAAAAGGAGG 6 274 1 GATGAAAATC 0.777374 -27 TATGGAAAGGAATGCATATTGA 8 3 0 AATGCATATT 0.853929 -152 TTACGTTTAAAATGCATAATAAGGAGTGAG 8 134 1 AATGCATAAT 0.917662 -21 ********** Masking position 6 Map Score: 1.30059 Number of sites scoring better than the average of aligned sites = 827 Number in coding regions = 682 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 8 ********** No masking Map Score: -2.07235e-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 9 ********** No masking Map Score: -2.07235e-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 CCTCTCACGAACGCTTACGAGGTTAGCTGACG 1 79 0 ACGTTACAGG 0.985217 -222 CCTCCTTTTCCCGCTAAAAAGGACCAAGGTGA 2 30 0 CCGTAAAAGG 0.972577 -29 AAAAGTTTGAATGTTTAGAAGGATTAAAAGAT 4 58 1 ATGTTAGAGG 0.908879 -115 CATGAGACGGCCGATTAACAGGCCGTAAACAA 6 119 1 CCGTTAAAGG 0.900831 -182 GATTAACAGGCCGTAAACAAGGGTGGTACCGC 6 131 1 CCGAAACAGG 0.880071 -170 GATTCGCCTTATGATTAATATGTAATACGAAT 8 41 0 ATGTTAAATG 0.857961 -114 TTAAAATTTTACGTTTAAAATGCATAATAAGG 8 126 1 ACGTTAAATG 0.956688 -29 *** **** *** Masking position 7 Map Score: 2.13083 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 149 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ********** No masking Map Score: -2.07235e-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: -2.07235e-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: -2.07235e-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