AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00430_ecoli_reg_100.orf -o00430_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 gadB 300 glutamate decarboxylase isozyme #2 ggt 119 gamma-glutamyltranspeptidase #3 gadA 210 glutamate decarboxylase isozyme Motif number 1 TTATAAATGCGTTCAAAATAATAATCAAGTACTAA 1 16 1 GTTAAAAAAT 0.82717 -285 AAATCAGACCTTAAAATATCACTATTAGTACTTGA 1 40 0 TTAAATAAAT 0.986204 -261 AGAATGCGCATAAAAATAACAGCATAAAACACCTT 1 98 1 TAAAATAAAT 0.892238 -203 TTGTATTGTTTTTCAATGAAAAAATATTATTCGCG 1 155 1 TTTAATGAAT 0.961199 -146 AGGACTCGTGTTTAAATAACAAAATCCTAATGTTA 1 207 0 TTTAATAAAT 0.986203 -94 TTGGATCGCATTAAAAAAGTAGGATTTATCGATAA 1 257 0 TTAAAAAAAT 0.962142 -44 TTTAAACTCCTTAAAATGATTGGATCGCATTAAAA 1 276 0 TTAAATGTAT 0.74154 -25 TTTGGGCGATTTTTATTACGATAATAAAGTCTGTT 3 37 1 TTTATTAAAT 0.892238 -174 TAAAGTCTGTTTTTAATATTATCATGTTAAATGTT 3 61 1 TTTAATAAAT 0.986203 -150 AAACGACTTTTTATAATATAAACATTTAACATGAT 3 81 0 TTAAATAAAT 0.986204 -130 ACAGGCTTAATTTAAATAACAAAATCCTAAGCAGA 3 117 0 TTTAATAAAT 0.986203 -94 TTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAA 3 167 0 ATAAAAAAAT 0.763548 -44 *** **** * ** Masking position 5 Map Score: 16.8014 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 65 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 TAACAGCATAAAACACCTTACCACCACCCA 1 114 1 AAACACCTTA 0.92192 -187 TTTAAATAACAAAATCCTAATGTTATTTAT 1 202 0 AAAATCCTAA 0.983956 -99 ACTTTATCGATAAATCCTACTTTTTTAATG 1 254 1 TAAATCCTAC 0.956742 -47 TTTAAACTCCTTAAAATGATTGG 1 288 0 AAACTCCTTA 0.982718 -13 TTTAAATAACAAAATCCTAAGCAGAAAAAC 3 112 0 AAAATCCTAA 0.983956 -99 CCATTGCGGATAAATCCTACTTTTTTATTG 3 164 1 TAAATCCTAC 0.956742 -47 TTCGAACTCCTTAAATTTATTTG 3 198 0 GAACTCCTTA 0.962396 -13 ********** Masking position 3 Map Score: 10.1844 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 31 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 GTGATATTTTAAGGTCTGATTTTTACGTGA 1 53 1 AAGGTCTGAT 0.924728 -248 TCGCATTAAAAAAGTAGGATTTATCGATAA 1 257 0 AAAGTAGGAT 0.985487 -44 GGATATCTTCAGAGGAGGATACGCG 2 6 0 AGAGGAGGAT 0.933934 -114 CTTCCCGACAAAACGATGATTAATTCAGAG 2 50 1 AAACGATGAT 0.810227 -70 TTACGATAATAAAGTCTGTTTTTAATATTA 3 52 1 AAAGTCTGTT 0.945394 -159 TATATTATAAAAAGTCGTTTTTCTGCTTAG 3 96 1 AAAGTCGTTT 0.805391 -115 AGGCAATAAAAAAGTAGGATTTATCCGCAA 3 167 0 AAAGTAGGAT 0.985487 -44 ********** Masking position 1 Map Score: 4.11813 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 248 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 AGGTCTGATTTTTACGTGATAATTCAGGAG 1 64 1 TTTACGTGAT 0.951337 -237 TGCTGTTATTTTTATGCGCATTCTGTGTCT 1 92 0 TTTATGCGCA 0.954819 -209 ATCGTGAGATATTACGCGAATAATATTTTT 1 174 0 ATTACGCGAA 0.838131 -127 TCCTACTTTTTTAATGCGATCCAATCATTT 1 268 1 TTAATGCGAT 0.943034 -33 ATCCTTTAAGTTTACTCGCTTCCCGACAAA 2 32 1 TTTACTCGCT 0.941965 -88 TTAATTTGATCGCCCGAACA 3 1 1 TTAATTTGAT 0.803164 -210 ATATAAACATTTAACATGATAATATTAAAA 3 71 0 TTAACATGAT 0.673851 -140 AAAAGTAGGATTTATCCGCAATGGAAGCAA 3 158 0 TTTATCCGCA 0.857193 -53 ACTCCTTAAATTTATTTGAAGGCAATAAAA 3 186 0 TTTATTTGAA 0.863157 -25 ********** Masking position 4 Map Score: 4.11333 Number of sites scoring better than the average of aligned sites = 1039 Number in coding regions = 915 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 TATCACGTAAAAATCAGACCTTAAAATATCA 1 54 0 AAACAGACCT 0.969323 -247 CTTTATCGATAAATCCTACTTTTTTAATGCG 1 255 1 AAACCTACTT 0.963388 -46 AACGATGATTAATTCAGAGTTATATACCAGG 2 61 1 AATCAGAGTT 0.871843 -59 TCAGAGTTATATACCAGGCTTAGCTGGGGTT 2 74 1 ATACAGGCTT 0.961369 -46 GATAATATTAAAAACAGACTTTATTATCGTA 3 53 0 AAACAGACTT 0.99134 -158 TCCTAAGCAGAAAAACGACTTTTTATAATAT 3 97 0 AAAACGACTT 0.929556 -114 GAAGCAAGGCATTACAGGCTTAATTTAAATA 3 134 0 ATTCAGGCTT 0.901582 -77 CATTGCGGATAAATCCTACTTTTTTATTGCC 3 165 1 AAACCTACTT 0.963388 -46 *** ******* Masking position 1 Map Score: 7.47244 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 359 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TAAGGTCTGATTTTTACGTGATAATTCAGGAG 1 62 1 TTTTACGGAT 0.887149 -239 CAATATGAAATTCTTGGGTGGTGGTAAGGTGT 1 126 0 TTTTGGGGGT 0.975731 -175 CTAATGTTATTTATCGTGAGATATTACGCGAA 1 184 0 TTTCGTGGAT 0.976647 -117 CGTTATTCTCCAGAGATTAAGGGGCAA 2 103 0 TTTCCAGGAT 0.908313 -17 CAAACATTGCTGTTCGGGCGATCAAATTAA 3 9 0 TGTCGGGGAT 0.993069 -202 CGAACAGCAATGTTTGGGCGATTTTTATTACG 3 25 1 TGTTGGGGAT 0.989151 -186 ** ***** *** Masking position 4 Map Score: 1.06779 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 122 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ********** No masking Map Score: -1.31207e-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 8 ********** No masking Map Score: -1.31207e-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: -1.31207e-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