AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i309_ecoli_bsub_100.orf -o309_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 prpB 238 putative phosphonomutase 2 #2 prpC 41 putative citrate synthase; propionate metabolism? #3 mmgD 33 citrate synthase III #4 mmgC 27 acyl-CoA dehydrogenase #5 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #6 citZ 300 citrate synthase II Motif number 1 CGGTTTCTTAACTTTGCGGTGCGCT 1 6 0 ACTTTGCGGT 0.923432 -233 CTGAAACGCATATTTGCGGATTAGTTCATG 1 105 1 TATTTGCGGA 0.9905 -134 ATCAACTTGTTATTTGCGTTGATAAAGACA 1 204 0 TATTTGCGTT 0.971566 -35 TCAACCTCCGTTTTTGCGTTTTTTGTCTA 3 10 0 TTTTTGCGTT 0.963292 -24 ACGCGGCTTTTATGTGCGGATGTATGATGT 5 105 1 TATGTGCGGA 0.965144 -45 AAAACGCCTTTATTTGCGGGTTTTTG 6 7 0 TATTTGCGGG 0.995761 -294 AATAAAGGCGTTTTTTCGGGGAAATCACAG 6 23 1 TTTTTTCGGG 0.952709 -278 AAGCATTTTCTTTTTGGGGGAGAGAAATAC 6 201 1 TTTTTGGGGG 0.967594 -100 ********** Masking position 5 Map Score: 10.0628 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 337 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 GAATATTGGGTTTAGTCTTGTTTCATAATTGT 1 35 1 TTTAGCTGTT 0.942786 -204 TCAGGCAATGTTTCACCGCGTTTCATTGCAAC 1 65 0 TTTCACCGTT 0.939064 -174 AAATGTTTAATTTCAATTTGTTAGAGATAAAG 1 136 0 TTTCATTGTT 0.958488 -103 AAATTAAACATTTAATTTTATTAAGGCAATTG 1 155 1 TTTAATTATT 0.889983 -84 CATCCTTTGTTATCAACTTGTTATTTGCGTTG 1 213 0 TATCACTGTT 0.973719 -26 AAATCCCCTTTTTCATCATGTT 5 1 0 TTTCACTGTT 0.987927 -149 AATGTTTACCTATAATTTTTTTTTTCCATTCT 6 51 0 TATAATTTTT 0.718844 -250 CTTATTTAAGTTTAAGCCTATTCTCATTATAA 6 104 0 TTTAACTATT 0.966256 -197 AACAAATTTTTATAAGCTTATTTAAGTTTAAG 6 120 0 TATAACTATT 0.919619 -181 GCCAGTAAAATGTAAGCATTTTCTTTTTGGGG 6 188 1 TGTAACTTTT 0.841667 -113 AAATTTCCCCTTTAAGAGTGTTGTAAAAACAT 6 258 0 TTTAAATGTT 0.90716 -43 ***** * **** Masking position 3 Map Score: 9.98417 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 319 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 ATAATTGTTGCAATGAAACGCGGTGAAACAT 1 59 1 CAATGAACGC 0.951887 -180 CTGAAACGTTAACTGAAACGCATATTTGCGG 1 93 1 AACTGAACGC 0.850798 -146 TAAAGTCATGAACTAATCCGCAAATATGCGT 1 110 0 AACTAACCGC 0.94334 -129 TAGACAAAAAACGCAAAAACGGAG 3 4 1 ACAAAAACGC 0.89773 -30 CGGAATTGCTCAAACAGCCGCCGACGCGGCT 5 82 1 CAAACACCGC 0.986685 -68 ACATCCGCACATAAAAGCCGCGTCGGCGGCT 5 97 0 ATAAAACCGC 0.920862 -53 GGATTCACATCATACATCCGCACATAAAAGC 5 110 0 CATACACCGC 0.938965 -40 CAAAAACCCGCAAATAAAGGC 6 1 1 CAAAAACCGC 0.991001 -300 GTGATTTCCCCGAAAAAACGCCTTTATTTGC 6 20 0 CGAAAAACGC 0.945194 -281 ****** **** Masking position 6 Map Score: 7.33726 Number of sites scoring better than the average of aligned sites = 1055 Number in coding regions = 908 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 4 TTGCCTTAATAAAATTAAATGTTTAATTTCAAT 1 151 0 AAAATAATGT 0.917597 -88 TTGATAAAGACAAAGCAAGGGGTGTGCCACAAT 1 183 0 CAAAGAGGGT 0.966923 -56 TTTATCAACGCAAATAACAAGTTGATAACAAAG 1 208 1 CAAATAAAGT 0.735976 -31 AAGTTGATAACAAAGGATGGGCT 1 226 1 CAAAGAGGGT 0.966923 -13 CAAAAAACGCAAAAACGGAGGTTGAGGAT 3 15 1 AAAAAGAGGT 0.766876 -19 ATGGAAAAAAAAAATTATAGGTAAACATTTAAC 6 54 1 AAAATAAGGA 0.835094 -247 ATTGTTTATAATGAGAATAGGCTTAAACTTAAA 6 99 1 ATGAGAAGGT 0.744235 -202 ATGTTCTTTCAAAAGCAAAGGGTTTTAGTTCCA 6 152 1 AAAAGAAGGT 0.991844 -149 CTCTCCCCCAAAAAGAAAATGCTTACATTTTAC 6 192 0 AAAAGAATGT 0.971681 -109 GAGTGTTGTAAAAACATGAGGCTTACTTAAAAA 6 242 0 AAAACTAGGT 0.766874 -59 AAATTTATTGAAAAGGAGATGTTATAT 6 284 1 AAAAGAATGT 0.971655 -17 ***** * *** * Masking position 4 Map Score: 6.68264 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 289 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 CGCAAAAACGGAGGTTGAGGAT 3 22 1 GAGGTGAGGA 0.987183 -12 ATTCCATCCGGGGGTGGCCGAG 4 16 1 GGGGTGCCGA 0.990973 -12 GCAGGTCAGATGGGGAGCGGAATTGCTCAAA 5 65 1 TGGGGGCGGA 0.991382 -85 TGTGAATCCAGAGGCCGCGGAGGCAGGA 5 132 1 GAGGCGCGGA 0.993089 -18 TTTTCTTTTTGGGGGAGAGAAATACTTGCAT 6 206 1 GGGGGGAGAA 0.98093 -95 ***** ***** Masking position 11 Map Score: 2.72165 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 145 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ACTTTATCTCTAACAAATTGAAATTAAACA 1 135 1 TAACAAATTG 0.984786 -104 TCAACGCAAATAACAAGTTGATAACAAAGG 1 212 1 TAACAAGTTG 0.973234 -27 GGTAAACATTTAACAAATGTCTGATTATTG 6 73 1 TAACAAATGT 0.960988 -228 TGAAAGAACATAACAAATTTTTATAAGCTT 6 133 0 TAACAAATTT 0.976689 -168 ********** Masking position 5 Map Score: 2.51746 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 12 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TCTAACAAATTGAAATTAAACATTTAATTT 1 143 1 TGAAATTAAA 0.664762 -96 CTTTATCAACGCAAATAACAAGTTGATAAC 1 207 1 GCAAATAACA 0.961622 -32 GGATTTGAATGGAAATCAAACAAATCATGG 5 27 1 GGAAATCAAA 0.979775 -123 TCATACATCCGCACATAAAAGCCGCGTCGG 5 102 0 GCACATAAAA 0.921585 -48 CAAAAACCCGCAAATAAAGGCGTTTTTTC 6 10 1 GCAAATAAAG 0.921585 -291 GTTTTTTCGGGGAAATCACAGAATGGAAAA 6 32 1 GGAAATCACA 0.964826 -269 ATCACAGAATGGAAAAAAAAAATTATAGGT 6 46 1 GGAAAAAAAA 0.928064 -255 ACTGGCTGCTGGAACTAAAACCCTTTGCTT 6 164 0 GGAACTAAAA 0.950301 -137 ********** Masking position 3 Map Score: 5.5711 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 190 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 ********** No masking Map Score: 1.37378e-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 AACGCAAAAACGGAGGTTGAGGAT 3 20 1 CGGGGTGAGG 0.992587 -14 CTATTCCATCCGGGGGTGGCCGAG 4 14 1 CGGGGTGCCG 0.955436 -14 CACATAAAAGCCGCGTCGGCGGCTGTTTGAGC 5 89 0 CCGGTCGCGG 0.59438 -61 GATGTGAATCCAGAGGCCGCGGAGGCAGGA 5 130 1 CAGGGCGCGG 0.629217 -20 *** *** **** Masking position 5 Map Score: 0.0445171 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 263 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 ********** No masking Map Score: 1.37378e-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 11 ********** No masking Map Score: 1.37378e-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: 1.37378e-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