AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_hpyl_reg_300.orf -o00750_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0098 203 threonine synthase (thrC) #2 HP1483 26 gerC2 protein (gerC2) #3 HP1490 103 hemolysin #4 HP1491 138 phosphate permease Motif number 1 CTTTGCGGCAAAATTTTAAACCGCATTATAGTA 1 43 1 AAATTTAAAG 0.977478 -161 AGCATAAATCAAAAATTAAACTGGATTAAAAAG 1 81 1 AAAATTAAAG 0.967014 -123 AGAGCGAATGTAACCTTAAATGGTTTTTTAATG 1 129 0 TAACTTAAAG 0.986605 -75 AGTCGTAGCATACCCTAAAAGAGCGAATGTAAC 1 148 0 TACCTAAAAG 0.959677 -56 GAAATTATCCAAAAATAAAAAGGAATCATTTT 1 182 1 AAAATAAAAG 0.961188 -22 AGATTAAGCCTAACTTTAAAAATCAAGCCTTCA 3 17 0 TAACTTAAAT 0.964353 -87 CTCAGAATTTTAACATAAAAGATTAAGCCTAAC 3 36 0 TAACTAAAAT 0.957946 -68 ACCTAACGATAAATATAAAATATATAAAATCTC 3 66 0 AAATTAAAAT 0.930497 -38 AACTTTAAACCTAAAACCTAACGATAAAT 3 85 0 AAACTAAAAT 0.970881 -19 TCTTAAAGTAAAATTTTAAAGAGAGTTTTAAAA 4 12 0 AAATTTAAAG 0.93353 -127 GCCCTTGAGCCACTCTTAAAAAGCGTTGTTTGA 4 68 0 CACTTTAAAG 0.866095 -71 **** ***** * Masking position 8 Map Score: 15.7503 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 332 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 ACTATGATGAAATTTTTTGCCCTTTGCGGCA 1 22 1 AATTTTTGCC 0.95703 -182 AATGCGGTTTAAAATTTTGCCGCAAAGGGCA 1 39 0 AAATTTTGCC 0.97699 -165 GCATAAATCAAAAATTAAACTGGATTAAAAA 1 82 1 AAATTAAACT 0.884553 -122 ATTTTTGGATAATTTCAAGTCGTAGCATACC 1 167 0 AATTCAAGTC 0.740872 -37 AAAATGATTCCTTTTTATTTT 1 193 0 AAATGATTCC 0.793822 -11 CCTAACTTTAAAAATCAAGCCTTCAAAAACC 3 11 0 AAATCAAGCC 0.982557 -93 TTTAACATAAAAGATTAAGCCTAACTTTAAA 3 30 0 AAATTAAGCC 0.99007 -74 AACTTTAAACCTAAAACCTAA 3 93 0 AATTTAAACC 0.953323 -11 AACTCTCTTTAAAATTTTACTTTAAGATACC 4 18 1 AAATTTTACT 0.765697 -121 ** ******** Masking position 5 Map Score: 6.77787 Number of sites scoring better than the average of aligned sites = 812 Number in coding regions = 717 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 ATAATGCGGTTTAAAATTTTGCCGCAAAGG 1 42 0 TTAAAATTTT 0.916439 -162 TGATTTATGCTTATAATACTATAATGCGGT 1 62 0 TTATAATACT 0.876947 -142 ATCGTTCTCATTAAAAAACCATTTAAGGTT 1 121 1 TTAAAAAACC 0.965061 -83 AAATCAAGCCTTCAAAAACC 3 1 0 TTCAAAAACC 0.865837 -103 AAGCCTAACTTTAAAAATCAAGCCTTCAAA 3 15 0 TTAAAAATCA 0.895453 -89 ATCTTTTATGTTAAAATTCTGAGATTTTAT 3 46 1 TTAAAATTCT 0.982362 -58 TTTTTAAAACTCTCTTTAAAATT 4 4 1 TTAAAACTCT 0.953195 -135 AAAACTCTCTTTAAAATTTTACTTTAAGAT 4 16 1 TTAAAATTTT 0.916439 -123 AAATTTTACTTTAAGATACCATATAATGAG 4 29 1 TTAAGATACC 0.911918 -110 ********** Masking position 6 Map Score: 9.0448 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 732 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 4 TTTTTTAATGAGAACGATTGATCGTCTTTT 1 109 0 AGAACGATTG 0.885742 -95 ATGTAACCTTAAATGGTTTTTTAATGAGAA 1 125 0 AAATGGTTTT 0.735584 -79 TTTTCTTTTTTCATGGCTTGTCT 2 4 0 TCATGGCTTG 0.963093 -23 GGTTTTTGAAGGCTTGATTTTTAAAG 3 7 1 TGAAGGCTTG 0.970951 -97 TTTTTATCAAACAACGCTTTTTAAGAGTGG 4 62 1 ACAACGCTTT 0.956681 -77 CACTATTAGAACAAGGTTTTTATGACGAT 4 120 1 ACAAGGTTTT 0.95762 -19 ********** Masking position 3 Map Score: 1.11544 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 681 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 AACACAGCCTTACTATGATGAAATT 1 6 1 AGCCTTACTA 0.971551 -198 TAAAAGATTAAGCCTAACTTTAAAAATCAA 3 24 0 AGCCTAACTT 0.979971 -80 CCATATAATGAGCCATTTTTATCAAACAAC 4 47 1 AGCCATTTTT 0.955978 -92 TTAGCCCTTGAGCCACTCTTAAAAAGCGTT 4 74 0 AGCCACTCTT 0.986399 -65 ********** Masking position 9 Map Score: 0.340732 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 80 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 6 ********** No masking Map Score: -2.95996e-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 7 ********** No masking Map Score: -2.95996e-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 8 ********** No masking Map Score: -2.95996e-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