AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i188_ecoli_mtub_100.orf -o188_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 menD 88 2-oxoglutarate decarboxylase; SHCHC synthase #2 menF 300 isochorismate hydroxymutase 2, menaquinone biosynthesis #3 menB 271 menB #4 Rv0552 77 hypothetical protein Rv0552 #5 menD 42 menD Motif number 1 CAAAAAAAATGCAGTACCCCGGTGTAGGGA 2 12 0 GCAGTACCCC 0.876478 -289 AGTAGATTTTCCAGCGCCGTAGTAAGTGAT 2 91 0 CCAGCGCCGT 0.96558 -210 TAACCCGAATGCCGGGTGTCGCCGGAATCT 2 138 0 GCCGGGTGTC 0.917164 -163 GTAATCGCGCCCAGGACGACAGCTTCTTCA 2 268 0 CCAGGACGAC 0.920939 -33 GTCCAGCGGGGCTTGGAGAAAG 3 3 1 CCAGCGGGGC 0.930496 -269 GCTCAACAGGGCGGCGCGCCCACCTTTCTC 3 26 0 GCGGCGCGCC 0.544151 -246 AGACCGCATTGCCGAGCGACACTGTGCCGG 3 76 1 GCCGAGCGAC 0.893246 -196 TGAACTGCGAGCAGCGCCATGATCGAGTAC 3 114 1 GCAGCGCCAT 0.947941 -158 TGAGTTGGCGCCCGGGCGGCTTTCTGTGGA 3 154 0 CCCGGGCGGC 0.892233 -118 CGGTATGGTGCCCGGGGCCTTGGTCACATG 3 190 0 CCCGGGGCCT 0.944521 -82 CTGGGCGTCAGCCGGACGGTATGGTGCCCG 3 206 0 GCCGGACGGT 0.94952 -66 AATCATGGCCGCTGGGCGTCAGCCGGACGG 3 217 0 GCTGGGCGTC 0.941685 -55 ATTTGGATCTGCCGTGCCCTCGTAATCTCG 4 35 1 GCCGTGCCCT 0.966912 -43 GGACCGTATGGCCGGGCCGCGC 5 3 0 GCCGGGCCGC 0.672857 -40 GAGTGTCACAGCCGGACCGTATGGCCGGGC 5 16 0 GCCGGACCGT 0.979065 -27 ********** Masking position 4 Map Score: 25.523 Number of sites scoring better than the average of aligned sites = 5236 Number in coding regions = 5026 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 CCCGTATAATGTGAGGCTTTTAACAGGGAGAGGTCCGC 2 48 1 GTGTAACGGG 0.968224 -253 TCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTT 2 112 0 CTGGAATGCG 0.990134 -189 GGCCAGCCAGCTCAAGGCATCAAAAGCGTCTTTGAGAG 2 183 0 CTGCAAAGCG 0.920552 -118 CCATTACGTTGTTGCCAGTAGAATTGCGGGTATGTTTG 2 227 0 GTCGAATGCG 0.970472 -74 CGACGTAAAACGGGTAATCGCGCCCAGGACGA 2 279 0 GTAGAATGCG 0.956851 -22 CGTGGGGCATGTTAAGCGCTCAACAGGGCGGCGCGCCC 3 35 0 GTGGAACGGG 0.993579 -237 AACCGGCACAGTGTCGCTCGGCAATGCGGTCTACTCGT 3 70 0 GTGTCAAGCG 0.956771 -202 CACTGTGCCGGTTCGGTGATGAACTGCGAGCAGCGCCA 3 95 1 GTGGAACGCG 0.998275 -177 GGGCGGCTTTCTGTGGAGGGTCACCGCGTACTCGATCA 3 133 0 CTGGCACGCG 0.994559 -139 CAGTACAGAGTGTCACAGCCGGACCGTATG 5 23 0 GTGGCACGCC 0.981601 -20 ** * * *** *** Masking position 13 Map Score: 13.4359 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 750 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 ACTGCGCCATTTGTCGCAAGAGATTCCGGC 2 118 1 TTGTCGCAAG 0.966655 -183 CGAATGCCGGGTGTCGCCGGAATCTCTTGC 2 133 0 GTGTCGCCGG 0.995538 -168 GCCTTGAGCTGGCTGGCCAGTCAGCAAACA 2 203 1 GGCTGGCCAG 0.961269 -98 CACCATTACGTTGTTGCCAGTAGAATTGCG 2 237 0 TTGTTGCCAG 0.961603 -64 CGGTCTACTCGTGGGGCATGTTAAGCGCTC 3 52 0 GTGGGGCATG 0.833251 -220 AACCGGCACAGTGTCGCTCGGCAATGCGGT 3 78 0 GTGTCGCTCG 0.914045 -194 ATCATGGCGCTGCTCGCAGTTCATCACCGA 3 107 0 TGCTCGCAGT 0.506444 -165 TGGTCGTGAGTTGGCGCCCGGGCGGCTTTC 3 160 0 TTGGCGCCCG 0.879383 -112 CCGGACGGTATGGTGCCCGGGGCCTTGGTC 3 195 0 TGGTGCCCGG 0.834403 -77 GCCATGATTACTGTGGCAGGCATGGGTGAA 3 238 1 CTGTGGCAGG 0.944198 -34 ACACGTTCTAGTCTTGCCAG 4 1 0 GTCTTGCCAG 0.950542 -77 AGACTAGAACGTGTTGCAATTTGGATCTGC 4 17 1 GTGTTGCAAT 0.760248 -61 CAGCCGGACCGTATGGCCGGGCCGCGC 5 8 0 GTATGGCCGG 0.951772 -35 ********** Masking position 7 Map Score: 9.94551 Number of sites scoring better than the average of aligned sites = 4322 Number in coding regions = 4113 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 4 TATCAATATTGCGGCTAAGTATAAGGAGCT 1 57 0 GCGGCTAAGT 0.976 -32 AGATTTTCCAGCGCCGTAGTAAGTGATTGC 2 88 0 GCGCCGTAGT 0.925998 -213 GGCATCAAAAGCGTCTTTGAGAGGGAAAGG 2 176 0 GCGTCTTTGA 0.796118 -125 CAGTAGAATTGCGGGTATGTTTGCTGACTG 2 220 0 GCGGGTATGT 0.826062 -81 ACGGGTAATCGCGCCCAGGACGACAGCTTC 2 272 0 GCGCCCAGGA 0.973227 -29 GTCCAGCGGGGCTTGGAGAAAGGTGGG 3 8 1 GGGGCTTGGA 0.886531 -264 ACAGGGCGGCGCGCCCACCTTTCTCCAAGC 3 21 0 GCGCCCACCT 0.946826 -251 GCCCTGTTGAGCGCTTAACATGCCCCACGA 3 44 1 GCGCTTAACA 0.622091 -228 GCTCGGCAATGCGGTCTACTCGTGGGGCAT 3 63 0 GCGGTCTACT 0.775642 -209 TGGCGCCCGGGCGGCTTTCTGTGGAGGGTC 3 149 0 GCGGCTTTCT 0.955516 -123 ATGGTGCCCGGGGCCTTGGTCACATGTGGT 3 186 0 GGGCCTTGGT 0.924398 -86 CTGACGCCCAGCGGCCATGATTACTGTGGC 3 225 1 GCGGCCATGA 0.967848 -47 TGGATCTGCCGTGCCCTCGTAATCTCGAAG 4 38 1 GTGCCCTCGT 0.78094 -40 ********** Masking position 3 Map Score: 10.6859 Number of sites scoring better than the average of aligned sites = 3813 Number in coding regions = 3625 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 5 AATATTGCGGCTAAGTATAAGGAGCTACAAAAAT 1 49 0 CTGTTAGGAG 0.951684 -40 AATGCAGTACCCCGGTGTAGGGAG 2 1 0 CCGTTAGGAG 0.987709 -300 TTTTGTAGTACCCCGTATAATGTGAGGCTTTTAA 2 37 1 CCGTTATGTG 0.9701 -264 TCCAGCGGGGCTTGGAGAAAGGTGGGCGCGCCGC 3 12 1 CTGAAAGGTG 0.967487 -260 TGCCCGGGGCCTTGGTCACATGTGGTCGTGAGTT 3 178 0 CTGTACTGTG 0.928114 -94 CGCCCAGCGGCCATGATTACTGTGGCAGGCATGG 3 229 1 CCGATATGTG 0.982269 -43 ** ** ** **** Masking position 5 Map Score: 1.18387 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 127 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TAATGAGTCGCATCATTACCGATTCATATC 1 10 1 GCATCATACC 0.934944 -79 GATTGCACGCGGACCTCTCCCTGTTAAAAGC 2 63 0 GGACCTTCCC 0.851105 -238 CCAGCTCAAGGCATCAAAAGCGTCTTTGAGA 2 184 0 GCATCAAAGC 0.84328 -117 AGCTTCTTCATCACCATTACGTTGTTGCCAG 2 247 0 TCACCATACG 0.915202 -54 TCGCAGTTCATCACCGAACCGGCACAGTGTC 3 93 0 TCACCGACCG 0.900919 -179 AAGGCCCCGGGCACCATACCGTCCGGCTGAC 3 199 1 GCACCAACCG 0.987885 -73 ATGGGTGAACGGATCAGATCGCC 3 259 1 GGATCAATCG 0.900748 -13 TAATCTCGAAGGATCACTACGCTTGGAGCCC 4 57 1 GGATCATACG 0.957484 -21 TGTCACAGCCGGACCGTATGGCCGGGCCGCG 5 12 0 GGACCGATGG 0.834413 -31 ****** **** Masking position 3 Map Score: 2.53733 Number of sites scoring better than the average of aligned sites = 2295 Number in coding regions = 2198 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 ********** No masking Map Score: -9.70439e-14 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 8 ********** No masking Map Score: -9.70439e-14 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: -9.70439e-14 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