AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_hpyl_reg_300.orf -o071_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01229 50 AE000511 #2 RHP01236 66 AE000511 #3 RHP01237 47 AE000511 #4 RHP00673 300 AE000511 #5 RHP00676 222 AE000511 #6 RHP00677 97 AE000511 #7 RHP00678 69 AE000511 #8 RHP00679 169 AE000511 Motif number 1 TACTCTAAAATTCCGTTATTTTTCAATTCAC 4 5 0 TGTTATTAAT 0.776983 -296 TCTTTAGCGCTCAAGTCATACTCTAAAATTCCGTTAT 4 23 0 TGTCATTAAA 0.878949 -278 GCGTTTTCAATCTGTAATTCTTTCAAATCATAGGGGG 4 71 0 TTAATTTAAA 0.630612 -230 CTCAAGCGTGTTTAGATATTTTAGAAAATAAAGGCAA 4 119 1 TGATATTAAA 0.870315 -182 TTTAAATCTTTAGCTTTATGGCTTAAATACAACAAAC 4 194 0 TTTTATCAAA 0.848244 -107 GGCGCTTTGGTTTTTAAATGCTCTAAAGTCATGCTCA 4 239 0 TTAAATTAAA 0.849813 -62 GGCTTAGCCTTATGATTTTTTGCAAATGCGCATAAG 4 275 0 TGATTTTAAA 0.877105 -26 AATCTAAAGCTGAAGTTATCCTCTAAAAACTTATAAC 5 15 0 TGTTATTAAA 0.97874 -208 TTCCTTTTTATGCTTTTACAATCTAAAGCTGAAGTTA 5 34 0 TTTTACTAAA 0.896625 -189 GAGCAGAATGTCTTGGAATTTTTGAAAACGCTCACTC 5 126 1 TGGAATTAAA 0.909235 -97 ATTGCCCATTTATCTATTTCTTGTAAAATACGAGTTT 5 175 1 TTATTTTAAA 0.798295 -48 CAATTTCTTTACGCTAAAAATAAACTCGTA 5 203 0 TTTTACTAAA 0.896624 -20 TAAACGAATGTGTGATTATAGTAGAAAGTCTCTTATC 6 15 0 TATTATTAAA 0.800875 -83 GGATTTTACATTGTTGAACACTAAAAAATAGGAGCTG 6 68 1 TTGAACTAAA 0.653826 -30 AAATTTTTTGTCATGTTTTAGCAAAAATCGTTCTTAT 7 25 0 TGTTTTCAAA 0.75233 -45 ATACAGCAATTCGGTTAATGGTAAAAACACTCCTAAT 8 48 1 TTTAATTAAA 0.916706 -122 ATCATCTGTTTTAAGGTATAATACAAAAAATCCCCAT 8 83 1 TGGTATTAAA 0.958461 -87 ATTAGGTAGGTGTTGTTATGATAAAAAAGACCTTTGC 8 118 1 TGTTATTAAA 0.978738 -52 * ***** * *** Masking position 1 Map Score: 17.6526 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 418 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 GGCGTAATCATTTTTTAGGAAGT 1 38 1 TTTTTTAGAA 0.604382 -13 GAACGAAGCATTATAGCAAAAAAG 3 4 0 TTATAGCAAA 0.812923 -44 AATAACGGAATTTTAGAGTATGACTTGAGCG 4 22 1 TTTTAGAGAT 0.957392 -279 TGTTTAGATATTTTAGAAAATAAAGGCAAGG 4 127 1 TTTTAGAAAT 0.955337 -174 GTGAGCATGACTTTAGAGCATTTAAAAACCA 4 238 1 CTTTAGAGAT 0.779945 -63 GCCTTATGATTTTTTGCAAATGCGCATAAGG 4 274 0 TTTTTGCAAT 0.912781 -27 CGTTATAAGTTTTTAGAGGATAACTTCAGCT 5 14 1 TTTTAGAGAT 0.957395 -209 TGAAAGCTTCTTTTCGCACAACCACATTTTT 5 91 1 TTTTCGCAAA 0.897294 -132 TGTCTTGGAATTTTTGAAAACGCTCACTCAT 5 134 1 TTTTTGAAAC 0.719489 -89 TAAACTCGTATTTTACAAGAAATAGATAAAT 5 182 0 TTTTACAAAA 0.771233 -41 ACGAGTTTATTTTTAGCGTAAAGAAATTG 5 204 1 TTTTAGCGAA 0.977126 -19 TTTTGTCATGTTTTAGCAAAAATCGTTCTTA 7 26 0 TTTTAGCAAA 0.971873 -44 CAAAGGTCTTTTTTATCATAACAACACCTAC 8 123 0 TTTTATCAAA 0.853464 -47 ******** ** Masking position 10 Map Score: 11.6702 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 1086 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 ATCAAATGAGAGAGTTTTTGGCTACTATCT 2 24 1 AGAGTTTTTG 0.983658 -43 TGCTTCGTTCAAATTTTATGGTTAGGTTTT 3 25 1 AAATTTTATG 0.637942 -23 CTTGAGCGCTAAAGATTTTGATTTGCCCCC 4 45 1 AAAGATTTTG 0.845823 -256 AAGCGTGTTTAGATATTTTAGAAAATAAAG 4 122 1 AGATATTTTA 0.774809 -179 CTTAGCCTTATGATTTTTTGCAAATGCGCA 4 279 0 TGATTTTTTG 0.922645 -22 TTGCGTTATAAGTTTTTAGAGGATAACT 5 9 1 TAAGTTTTTA 0.719637 -214 AGAATGTCTTGGAATTTTTGAAAACGCTCA 5 130 1 GGAATTTTTG 0.819871 -93 CTAAGAGATCAAATTTTTTGTCATGTTTTA 7 42 0 AAATTTTTTG 0.932737 -28 CTGTATAGTTAGCGTTTTTAATTCAAAATG 8 24 0 AGCGTTTTTA 0.821806 -146 GATGATTAGGAGTGTTTTTACCATTAACCG 8 59 0 AGTGTTTTTA 0.75679 -111 TACCTAATGGGGATTTTTTGTATTATACCT 8 96 0 GGATTTTTTG 0.948585 -74 ********** Masking position 6 Map Score: 5.73809 Number of sites scoring better than the average of aligned sites = 1370 Number in coding regions = 1214 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 CATTTGATTAAATCAAAGGGA 2 2 0 AATCAAAGGG 0.973535 -65 GATTTAATCAAATGAGAGAGTTTTTGGCTA 2 18 1 AATGAGAGAG 0.980153 -49 CTATCTAGGAAATGAGAGGGTAGCATTTA 2 48 1 AATGAGAGGG 0.993204 -19 AATTCTTTCAAATCATAGGGGGGCAAATCA 4 63 0 AATCATAGGG 0.984818 -238 ATTTGCAAAAAATCATAAGGCTAAGCC 4 284 1 AATCATAAGG 0.90938 -17 TAAATACGCTAATGAGTGAGCGTTTTCAAA 5 146 0 AATGAGTGAG 0.924149 -77 ********** Masking position 5 Map Score: 6.0997 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 110 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 ACTTCCTAAAAAATGATTACGCCAT 1 36 0 CTAAAAAATG 0.986104 -15 TGGCTACTATCTAGGAAATGAGAGGGTAGC 2 42 1 CTAGGAAATG 0.904647 -25 CCTTTATTTTCTAAAATATCTAAACACGCT 4 123 0 CTAAAATATC 0.859662 -178 ATTCTGCTCTCTTAAAAATGTGGTTGTGCG 5 105 0 CTTAAAAATG 0.945963 -118 TTGTTGAACACTAAAAAATAGGAGCTGTTT 6 78 1 CTAAAAAATA 0.931497 -20 ACGATTTTTGCTAAAACATGACAAAAAATT 7 31 1 CTAAAACATG 0.969666 -39 ********** Masking position 6 Map Score: 2.90338 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 109 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TAACCATAAAATTTGAACGAAGCATTATAG 3 19 0 ATTTGAACGA 0.95425 -29 CCCCCCTATGATTTGAAAGAATTACAGATT 4 70 1 ATTTGAAAGA 0.950791 -231 AAAGCTAAAGATTTAAAAGAGGGTGTGAGC 4 214 1 ATTTAAAAGA 0.924743 -87 TTGTAAAAGCATAAAAAGGAATTTTCTAAC 5 50 1 ATAAAAAGGA 0.878164 -173 TATCCATCGCATAAGAACGATTTTTGCTAA 7 15 1 ATAAGAACGA 0.95425 -55 TGTTGTTATGATAAAAAAGACCTTTGCATC 8 128 1 ATAAAAAAGA 0.924743 -42 ********** Masking position 6 Map Score: 2.73837 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 95 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ********** No masking Map Score: -1.70287e-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: -1.70287e-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: -1.70287e-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