AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i340_ecoli_bsub_100.orf -o340_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 glnS 202 glutamine tRNA synthetase #2 yqjA 300 orf, hypothetical protein #3 pssA 195 phosphatidylserine synthase Motif number 1 GCGACGCTCAAGCGTCGCATCAGGCATAAA 1 16 0 AGCGTCGCAT 0.991172 -187 GCGACGCTTGAGCGTCGCATCCAACAATGA 1 28 1 AGCGTCGCAT 0.991172 -175 AACAATGACAAGCGGTGGAGATCTTCTCTG 1 50 1 AGCGGTGGAG 0.961186 -153 TGAAAAAAAAAGCGGCAGAGAAGATCTCCA 1 65 0 AGCGGCAGAG 0.982724 -138 TGATCTTATAAGCGGGACAGGCTGACAACT 1 144 0 AGCGGGACAG 0.986016 -59 TCCCTGTTAAATCGTGAGATAAGAAAGCAT 2 164 0 ATCGTGAGAT 0.889311 -137 TTTTAAAACCAGCGTGGCGTTAACCGATTC 2 267 1 AGCGTGGCGT 0.95232 -34 GTGATCGAATAGCGTTACAGGAAAAATTTT 3 127 0 AGCGTTACAG 0.97432 -69 TTCGATCACTATCGTCAAATAATATAGATG 3 148 1 ATCGTCAAAT 0.726529 -48 ********** Masking position 1 Map Score: 12.4652 Number of sites scoring better than the average of aligned sites = 1331 Number in coding regions = 1133 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 CGACGCTCAAGCGTCGCATCAGGCATAAAG 1 15 0 GCGTCGCATC 0.944731 -188 CGACGCTTGAGCGTCGCATCCAACAATGAC 1 29 1 GCGTCGCATC 0.944731 -174 ACAATGACAAGCGGTGGAGATCTTCTCTGC 1 51 1 GCGGTGGAGA 0.981766 -152 GAAAAAAAAAGCGGCAGAGAAGATCTCCAC 1 64 0 GCGGCAGAGA 0.98161 -139 GATCTTATAAGCGGGACAGGCTGACAACTG 1 143 0 GCGGGACAGG 0.987966 -60 TTTGCTGAATGCAGGGGAGGGTGGCGAGAG 2 49 0 GCAGGGGAGG 0.936344 -252 CAATAACATTGCGGTAGTGCATCTTTTAAA 2 244 1 GCGGTAGTGC 0.920297 -57 TGATCGAATAGCGTTACAGGAAAAATTTTT 3 126 0 GCGTTACAGG 0.967745 -70 ********** Masking position 2 Map Score: 7.0897 Number of sites scoring better than the average of aligned sites = 3325 Number in coding regions = 3193 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 TCTGCTTTATGCCTGATGCGACGCTT 1 7 1 TTATGCCTGA 0.941751 -196 ACTAACAGTTGTCAGCCTGTCCCGCTTATA 1 138 1 GTCAGCCTGT 0.981579 -65 AGTATAAAGTGTCAGCCTGTGTAAATCCTC 2 22 1 GTCAGCCTGT 0.981579 -279 CAGGGAATAGTTCAGGCTGTGTTGATGTAT 2 188 1 TTCAGGCTGT 0.970942 -113 TACCGCAATGTTATTGCTGTTTTGGTATGT 2 230 0 TTATTGCTGT 0.930541 -71 TCATTATTCCTGGTGAATCGGTT 2 288 0 TTATTCCTGG 0.920691 -13 TGGAGAAAAATTTTTCCTGTAACGCTATTC 3 121 1 TTTTTCCTGT 0.926283 -75 ********** Masking position 8 Map Score: 5.23072 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 643 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 GTGGATTCCTCAAAGCGTAAACAACGTATAACGGCGT 1 175 0 CAAGTAAAGT 0.996639 -28 GGTAAGCGAAAAGTATAAAGTGTCAGCCTGTGT 2 7 1 CAAGTAAAGT 0.996639 -294 CAAATTGAATCTAATTGTAACAAAGGTCAACGTTGTT 2 112 0 CAAGTACAGT 0.996881 -189 ATTCATTTTTCAAAAGGTAACAAATGTTGTATAATAA 3 33 1 CAAGTACAGT 0.996881 -163 TCACTATCGTCAAATAATATAGATGGTTTTACAATTG 3 153 1 CAAATAAAGT 0.982708 -43 * ** *** * * ** Masking position 9 Map Score: 5.15419 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 GAGATAAGAAAGCATTCAAAAACATAAATT 2 149 0 AGCATTCAAA 0.988539 -152 TAAGGAACATGAAAAGATTGGCATT 3 6 1 AACATGAAAA 0.887881 -190 CAAAAAAAGCAGCATTCAAATTCTATTATT 3 65 0 AGCATTCAAA 0.988539 -131 TTTTTTTGGGAGCATTCTATGTTATCATGC 3 87 1 AGCATTCTAT 0.948177 -109 TTCTCCAATAAGCATGATAACATAGAATGC 3 98 0 AGCATGATAA 0.966489 -98 ********** Masking position 5 Map Score: 3.09823 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 71 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ATGACAAGCGGTGGAGATCTTCTCTGCCGCTTTTTTT 1 54 1 GTGGAGATTC 0.956749 -149 GCAGGGGAGGGTGGCGAGAGGATTTACACAGGCTGAC 2 32 0 GTGGCGATTC 0.997345 -269 TTACATGTCCGTGGAGTCTGATTTTGCTGAATGCAGG 2 64 0 GTGGAGTTTC 0.995924 -237 TAAAACCAGCGTGGCGTTAACCGATTCACCAGGAATA 2 270 1 GTGGCGTGTC 0.991665 -31 ATCATGCTTATTGGAGAAAAATTTTTCCTGTAACGCT 3 110 1 TTGGAGATTC 0.985458 -86 ******* * * * Masking position 15 Map Score: 2.45024 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 48 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GGATTATGGGGATGATTGATGAAAAAAAAAGCGG 1 80 0 GATATTTAAA 0.904126 -123 GCTGACAACTGTTAGTTTTTTAAAATTGATAATC 1 120 0 GTTGTTTAAA 0.970636 -83 CGTGGATTCCTCAAAGCGTAAACAA 1 188 0 GTGATTTAAA 0.982754 -15 GGTCAACGTTGTTCGTTATCAAAATTACATGTCC 2 91 0 GTTGTTCAAA 0.896422 -210 TTCAGGCTGTGTTGATGTATCAAACCCGCAGAAC 2 198 1 GTTATGTAAA 0.933633 -103 CATTGCGGTAGTGCATCTTTTAAAACCAGCGTGG 2 250 1 GTGATCTAAA 0.974853 -51 ATTATTCCTGGTGAATCGGTTAACGCCACGCTGG 2 275 0 GTGATCTAAC 0.898637 -26 AAAGATTGGCATTCATTTTTCAAAAGGTAACAAA 3 23 1 ATTATTTAAA 0.86781 -173 *** *** * *** Masking position 12 Map Score: 1.66915 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 124 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 TTGATAATCTAACAAGGATTATGGGGATGA 1 99 0 AACAAGGATT 0.937645 -104 AACAACGTATAACGGCGTATGATCTTATAA 1 163 0 AACGGCGTAT 0.956258 -40 TCAAAGCGTAAACAACGTATAACGGCGTAT 1 173 0 AACAACGTAT 0.978247 -30 TTTGATAACGAACAACGTTGACCTTTGTTA 2 102 1 AACAACGTTG 0.933944 -199 CTCACGATTTAACAGGGAATAGTTCAGGCT 2 176 1 AACAGGGAAT 0.958779 -125 ********** Masking position 2 Map Score: 0.39397 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 182 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 ********** No masking Map Score: 8.83505e-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: 8.83505e-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: 8.83505e-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