AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_hpyl_reg_100.orf -o00750_hpyl_100.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 Motif number 1 TATAATGCGGTTTAAAATTTTGCCGCAAAG 1 43 0 TTTAAAATTT 0.875736 -161 TTTAATCCAGTTTAATTTTTGATTTATGCT 1 81 0 TTTAATTTTT 0.958699 -123 TAAAAAACCATTTAAGGTTACATTCGCTCT 1 132 1 TTTAAGGTTA 0.975465 -72 ACATTCGCTCTTTTAGGGTATGCTACGACT 1 151 1 TTTTAGGGTA 0.923891 -53 AATGATTCCTTTTTATTTTTGGATAATTTC 1 182 0 TTTTATTTTT 0.971415 -22 GACTTTTCTTTTTTCATGGCTTG 2 14 0 TTTTCTTTTT 0.87635 -13 AGGCTTGATTTTTAAAGTTAGGCTTAATCT 3 20 1 TTTAAAGTTA 0.946368 -84 AGGCTTAATCTTTTATGTTAAAATTCTGAG 3 39 1 TTTTATGTTA 0.983439 -65 ATTTTATATATTTTATATTTATCGTTAGGT 3 69 1 TTTTATATTT 0.959542 -35 TATCGTTAGGTTTTAGGTTTAAAGTT 3 88 1 TTTTAGGTTT 0.988401 -16 ********** Masking position 3 Map Score: 15.4944 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 589 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 2 ACTATGATGAAATTTTTTGCCCTTTGCGGCA 1 22 1 AATTTTTGCC 0.964184 -182 AATGCGGTTTAAAATTTTGCCGCAAAGGGCA 1 39 0 AAATTTTGCC 0.972266 -165 GCATAAATCAAAAATTAAACTGGATTAAAAA 1 82 1 AAATTAAACT 0.867549 -122 ATTTTTGGATAATTTCAAGTCGTAGCATACC 1 167 0 AATTCAAGTC 0.923977 -37 CCTAACTTTAAAAATCAAGCCTTCAAAAACC 3 11 0 AAATCAAGCC 0.992038 -93 TTTAACATAAAAGATTAAGCCTAACTTTAAA 3 30 0 AAATTAAGCC 0.994627 -74 AACTTTAAACCTAAAACCTAA 3 93 0 AATTTAAACC 0.974635 -11 ** ******** Masking position 2 Map Score: 8.72273 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 441 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TTAATTTTTGATTTATGCTTATAATACTAT 1 70 0 ATTTATGCTT 0.908819 -134 TAAAAAGACGATCAATCGTTCTCATTAAAA 1 107 1 ATCAATCGTT 0.968391 -97 AAAAGAGCGAATGTAACCTTAAATGGTTTT 1 135 0 ATGTAACCTT 0.944428 -69 AAAATGATTCCTTTTTATTTTTG 1 191 0 ATGATTCCTT 0.937927 -13 AACTTTAAAAATCAAGCCTTCAAAAACC 3 9 0 ATCAAGCCTT 0.983714 -95 AACATAAAAGATTAAGCCTAACTTTAAAAA 3 28 0 ATTAAGCCTA 0.920765 -76 TATATTTTATATTTATCGTTAGGTTTTAGG 3 75 1 ATTTATCGTT 0.956283 -29 ********** Masking position 1 Map Score: 5.02722 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 344 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 AAATTTCATCATAGTAAGGCTGTGTT 1 6 0 ATGTAAGGCT 0.987615 -198 TTATAATACTATAATGCGGTTTAAAATTTTG 1 51 0 ATATGCGGTT 0.943607 -153 CTTTTAGGGTATGCTACGACTTGAAATTATC 1 160 1 ATCTACGACT 0.939638 -44 CTTGATTTTTAAAGTTAGGCTTAATCTTTTA 3 23 1 AAGTTAGGCT 0.949897 -81 TTATGTTAAAATTCTGAGATTTTATATATTT 3 51 1 ATCTGAGATT 0.916118 -53 TTTTATATTTATCGTTAGGTTTTAGGTTTAA 3 79 1 ATGTTAGGTT 0.957513 -25 ** ******** Masking position 5 Map Score: 1.3353 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 135 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CCTTAAATGGTTTTTTAATGAGAACGATTG 1 119 0 TTTTTTAATG 0.98499 -85 TTCCTTTTTATTTTTGGATAATTTCAAGTC 1 177 0 TTTTTGGATA 0.889102 -27 GACTTTTCTTTTTTCATGGCTTGTCT 2 9 0 TTTTTTCATG 0.974862 -18 GGTTTTTGAAGGCTTGATTTTT 3 3 1 TTTTTGAAGG 0.976563 -101 TGAAGGCTTGATTTTTAAAGTTAGGCTTAA 3 17 1 ATTTTTAAAG 0.887914 -87 ********** Masking position 5 Map Score: 1.65577 Number of sites scoring better than the average of aligned sites = 885 Number in coding regions = 772 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 ********** No masking Map Score: -4.38104e-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: -4.38104e-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: -4.38104e-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