AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_ecoli_reg_100.orf -o00660_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #2 sdhC 300 succinate dehydrogenase, cytochrome b556 #3 BIME45 63 BIME #4 sucC 85 succinyl-CoA synthetase, beta subunit #5 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #6 ilvG_1 139 acetolactate synthase II, large subunit, cryptic, interrupted #7 ilvM 300 acetolactate synthase II, valine insensitive, small subunit Motif number 1 CGCCAGGTCTCCGGAACACCCTGCAATCCCGAGC 2 85 1 CCGGAACCGC 0.995507 -216 CCCTGCAATCCCGAGCCACCCAGCGTTGTAACGT 2 103 1 CCGAGCCCGC 0.952725 -198 GAAGGAAATCCCGACGTCTCCAGGTAACAGAAAG 2 219 1 CCGACGCCGG 0.991977 -82 ACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAG 2 256 1 CCGTAGCCGG 0.986983 -45 GGGTGACCGACAATGCCCGGAAGCGATACG 4 7 1 CCGACACCGG 0.96699 -79 CAAAACCCCGCCGGCGCAAACCGGGCGGGGTTTT 5 33 1 CCGGCGACGG 0.9606 -73 AGGTGCTTAAACGAAAAACCCCGCCCGGTTTGCG 5 47 0 ACGAAACCGC 0.974998 -59 GCCTTAACGAACTAAGACCCCCGCACCGAAAGGT 6 18 1 ACTAAGCCGC 0.842233 -122 GACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTT 6 33 1 CCGAAACCGG 0.995025 -107 GCCATGGATGCCGAAGGCGCTGGCTAACATGAGG 7 119 0 CCGAAGCTGC 0.974638 -182 AACACATCACCCGGAAAGACCAGGTTGAAGCGGC 7 154 1 CCGGAACCGG 0.991309 -147 TTACTGGCGCCAGGCGGCACCAGCGGCCAGACGT 7 253 0 CAGGCGCCGC 0.971117 -48 ****** ** ** Masking position 13 Map Score: 22.9006 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 1016 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 GAACAGCCTATACTGCCGCCAGGTCTCCGGAAC 2 69 1 TCGCCGCAGG 0.982277 -232 GCTGGGTGGCTCGGGATTGCAGGGTGTTCCGGA 2 94 0 TGGATTCAGG 0.729334 -207 CGTCGGGATTTCCTTCCTCCGGTCTGCTTGCGG 2 202 0 TCTCCTCGGT 0.944795 -99 TTCTGTTACCTGGAGACGTCGGGATTTCCTTCC 2 218 0 TGGACGCGGG 0.979792 -83 TATTATTCCCTGGGGACTACGGGCACAGAGGTT 2 255 0 TGGACTCGGG 0.98508 -46 TAATGCCTTATCCGGTCTACAGTGCAGGTGAAA 3 20 0 TCGTCTCAGT 0.886679 -44 AAGGCATTATCGCCTTCTCCGGCAATTGAA 3 44 1 CCTTCTCGGC 0.558496 -20 GAATATTTCGTATCGCTTCCGGGCATTGTCGGT 4 16 0 TTGCTTCGGG 0.79341 -70 ATACGAAATATTCGGTCTACGGTTTAAAAGATA 4 36 1 TCGTCTCGGT 0.96041 -50 GTGTTCTGTCCATCCTTCAGTAATCGTTATC 4 65 0 TCTCCTCAGT 0.846648 -21 CCCGCCCGGTTTGCGCCGGCGGGGTTTTGGAAT 5 29 0 TGGCCGCGGG 0.994214 -77 TCATGTTAGCCAGCGCCTTCGGCATCCATGGCC 7 121 1 CGGCCTCGGC 0.957481 -180 GTCTGGCCGCTGGTGCCGCCTGGCGCCAGTAAT 7 255 1 TGGCCGCTGG 0.943965 -46 * * **** **** Masking position 10 Map Score: 12.4997 Number of sites scoring better than the average of aligned sites = 2445 Number in coding regions = 2217 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 3 TGAATGTCTGGTTTATTCTGCATTTTTTAT 1 34 1 GTTTATTCTG 0.950221 -194 GAATGTAGAATTTTATTCTGAATGTGTGGG 1 65 1 TTTTATTCTG 0.958579 -163 TTATCGTTTCTTTTCACCTTTCCTCCTGTT 1 193 1 TTTTCACCTT 0.884003 -35 CTTTCCTCCTGTTTATTCTTATTACCCC 1 210 1 GTTTATTCTT 0.862187 -18 GTTTGTCGGGTTTTATCCTGAACAGTGAT 2 10 0 TTTTATCCTG 0.97348 -291 TAGTTTAAGTTTCACCTGCACTGTAGAC 3 9 1 GTTTCACCTG 0.950446 -55 GCTCCAGTCCTTTTCTTCTGGGCCGACTTT 5 86 0 TTTTCTTCTG 0.965454 -20 CGGGGGTTTTTTTTGACCTTAAAAACATAA 6 53 1 TTTTGACCTT 0.839535 -87 AGAAACAGAATTTTGTGCTGTTATTCATTG 6 95 0 TTTTGTGCTG 0.896298 -45 ********** Masking position 4 Map Score: 7.63924 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 630 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 GGTCAGACATGAATGTCTGGTTTATTCTGC 1 25 1 GAATGTCTGG 0.95721 -203 ATTTTATTCTGAATGTGTGGGCTCTCTATT 1 74 1 GAATGTGTGG 0.872019 -154 GTGTTCCGGAGACCTGGCGGCAGTATAGGC 2 74 0 GACCTGGCGG 0.837363 -227 AAAGGACGCTGTCTGACCCGCAAGCAGACC 2 185 1 GTCTGACCCG 0.841503 -116 CTTCTGGGCCGACTTTCCGGGAGGTGCTTA 5 72 0 GACTTTCCGG 0.987205 -34 AAAACCCCCGGACCTTTCGGTGCGGGGGTC 6 33 0 GACCTTTCGG 0.859839 -107 GAAAATCGTCTTACTCGATAACCAACG 7 8 1 GTCTTACTCG 0.75448 -293 CTTCAACCTGGTCTTTCCGGGTGATGTGTT 7 154 0 GTCTTTCCGG 0.972173 -147 ACGAACTTGAGAACGTCTGGCCGCTGGTGC 7 241 1 GAACGTCTGG 0.940924 -60 CAACATTTCTGAATTACTGGCGCCAGGCGG 7 270 0 GAATTACTGG 0.915476 -31 ********** Masking position 1 Map Score: 5.57056 Number of sites scoring better than the average of aligned sites = 1943 Number in coding regions = 1841 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 GCTGTAAGTTGTGGGATTCAGCCGATTTATT 1 133 1 GTGGGATCAG 0.774416 -95 GGGGTAATAAGAATAAACAGG 1 217 0 GGGGTATAAG 0.885589 -11 TCGGGATTGCAGGGTGTTCCGGAGACCTGGC 2 86 0 AGGGTGTCCG 0.901113 -215 TTACAACGCTGGGTGGCTCGGGATTGCAGGG 2 103 0 GGGTGGTCGG 0.928038 -198 TATTATTCCCTGGGGACTACGGGCACAGAGG 2 257 0 TGGGGATACG 0.739276 -44 TTTGCGCCGGCGGGGTTTTGGAATCGTGTGT 5 22 0 CGGGGTTTGG 0.841474 -84 CAAACCGGGCGGGGTTTTTCGTTTAAGCACC 5 49 1 GGGGTTTTCG 0.978503 -57 CTTTCGGTGCGGGGGTCTTAGTTCGTTAAGG 6 19 0 GGGGGTTTAG 0.977809 -121 CCAACGGTTAGGGATGGTTCGACAATGGCAG 7 32 1 GGGATGTTCG 0.876208 -269 TTATCAGTAAGGGTGGTTTCGCTGTATCGTT 7 79 0 GGGTGGTTCG 0.959578 -222 TGAGGAAATCGGGGTTATCAGTAAGGGTGGT 7 93 0 GGGGTTTCAG 0.967539 -208 ****** **** Masking position 8 Map Score: 5.73553 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 517 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 AAGGTGAAAAGAAACGATAAAATCCTCCAT 1 183 0 GAAACGATAA 0.913902 -45 TCCAGATGCGAAAACGACACGTTACAACGC 2 125 0 AAAACGACAC 0.943495 -176 ACAATGCCCGGAAGCGATACGAAATATTCG 4 20 1 GAAGCGATAC 0.981732 -66 GGACTGGAACAACACACGATTCCAA 5 6 1 GGAACAACAC 0.932628 -100 TGTTTTTTCAGGAACGATACAGCGAAACCA 7 67 1 GGAACGATAC 0.981732 -234 AGACCAGGTTGAAGCGGCACTCGACACCAT 7 170 1 GAAGCGGCAC 0.970295 -131 ********** Masking position 3 Map Score: 2.9186 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 189 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TGTGAACAGCCTATACTGCCGCCAGGTCTC 2 66 1 CTATACTGCC 0.953936 -235 CCGGAGAAGGCGATAATGCCTTATCCGGTC 3 36 0 CGATAATGCC 0.992921 -28 GGGTGACCGACAATGCCCGGAAGCGAT 4 8 1 CGACAATGCC 0.995412 -78 AGGGATGGTTCGACAATGGCAGCAACTGTT 7 41 1 CGACAATGGC 0.987796 -260 ********** Masking position 5 Map Score: 2.53936 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 98 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 TCTGACCTATTCTGCAATCAG 1 1 0 TCGCAATCAG 0.793886 -227 GTTCCGGAGACCTGGCGGCAGTATAGGCTGT 2 71 0 CCGGCGGCAG 0.928554 -230 CGTTTTCGCATCTGGAAGCAGTGTTTTGCAT 2 139 1 TCGGAAGCAG 0.98188 -162 CGCTGTCTGACCCGCAAGCAGACCGGAGGAA 2 191 1 CCGCAAGCAG 0.9698 -110 GAATAACGCCCACATGCTGTTCTTATTAT 2 282 0 CCACATGCTG 0.837384 -19 GGGCCGACTTTCCGGGAGGTGCTTAAACGAA 5 66 0 TCGGGAGGTG 0.896711 -40 AAAAACATAACCGAGGAGCAGACAATGAATA 6 73 1 CCAGGAGCAG 0.919545 -67 ATTCTGTTTCTCAAGATTCAGGACGGGGAAC 6 114 1 TCAGATTCAG 0.624339 -26 ACCTGGTCTTTCCGGGTGATGTGTTGGCCAT 7 148 0 TCGGGTGATG 0.848772 -153 CCCGGAAAGACCAGGTTGAAGCGGCACTCGA 7 163 1 CCGGTTGAAG 0.692567 -138 CCATCACTGTTCAGCATGGTGTCGAGTGCCG 7 184 0 TCGCATGGTG 0.843375 -117 CTTGAGAACGTCTGGCCGCTGGTGCCGCCTG 7 246 1 TCGGCCGCTG 0.890709 -55 ** ******** Masking position 2 Map Score: 3.27083 Number of sites scoring better than the average of aligned sites = 5613 Number in coding regions = 5341 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 9 ********** No masking Map Score: 9.90086e-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 10 ********** No masking Map Score: 9.90086e-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: 9.90086e-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