AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i160_Porphyrin_Biosynthesis_hpyl_reg_300.orf -o160_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 RHP00037 163 AE000511 #2 RHP00038 117 AE000511 #3 RHP00039 44 AE000511 #4 RHP00040 65 AE000511 Motif number 1 AATAAAGAAAATTTATACCAAATCTTATTGC 1 6 0 ATTTATATTT 0.939191 -158 AAATTTTCTTTATTATAGCCCATTTTCATGCTCCTT 1 28 1 TATTATATTT 0.85534 -136 TTTCATGCTCCTTTAAATTTTGCTTTTAAAACAAAG 1 51 1 CTTTAAACTT 0.883614 -113 AAGTTTGAAATTTTAAAGGGCTTTGTTTTAAAAGCA 1 71 0 TTTTAAATGT 0.970144 -93 CCTTTGGGTTTTTTATAACAAGGAGTTACAACA 1 141 1 TTTTATAGGT 0.906725 -23 TTTTAAGAAAGGTGTTTGTATGGGGC 2 1 1 TTTTAAGTTT 0.979281 -117 GGGGCTAACGCTTTAAGCGTTGGCTTTTTGCTTTAA 2 32 1 CTTTAAGGTT 0.911187 -86 TTTTGCTTTAATTTTTACTTCTTTTTTAATAAAATA 2 57 1 ATTTTTATTT 0.832175 -61 ATAAAATACTCTTTTTGATTCCTTTTTATTATAGGC 2 85 1 CTTTTTGTTT 0.89135 -33 TTTTTAGATTTTTCTTAATCTTAAGC 3 1 1 TTTTTAGTTT 0.938173 -44 ATCTTAAGCCTTTTAAAAGGCGTTTTA 3 28 1 TTTTAAATTT 0.984702 -17 CATAGTTGTTTTTTAAAATGAATATT 4 1 0 TTTTAAATTT 0.984702 -65 TAATTATGGTTTTTATACTCCATAGTTGTTTTTTAA 4 21 0 TTTTATATGT 0.965575 -45 ******* * ** Masking position 4 Map Score: 15.0386 Number of sites scoring better than the average of aligned sites = 1901 Number in coding regions = 1466 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 2 TTTCTTTATTATAGCCCATTTTCATGCTCC 1 32 1 ATAGCCCATT 0.898761 -132 CTTTTAAAACAAAGCCCTTTAAAATTTCAA 1 73 1 AAAGCCCTTT 0.608933 -91 GGTTGGAACTATAATCGGTTAAAGTTTGAA 1 98 0 ATAATCGGTT 0.910013 -66 TTTTAAGAAAGGTGTTTGTATGGGGCT 2 8 1 AAAGGTGTTT 0.902299 -110 GGCTAACGCTTTAAGCGTTGGCTTTTTGCT 2 34 1 TTAAGCGTTG 0.828575 -84 CCTTTTTATTATAGGCGGTTATT 2 105 1 ATAGGCGGTT 0.989422 -13 TTTCTTAATCTTAAGCCTTTTAAAAGGCGT 3 21 1 TTAAGCCTTT 0.910625 -24 AAGCCTTTTAAAAGGCGTTTTA 3 33 1 AAAGGCGTTT 0.611442 -12 TTTATACTCCATAGTTGTTTTTTAAAATGA 4 16 0 ATAGTTGTTT 0.914701 -50 ********** Masking position 3 Map Score: 8.18069 Number of sites scoring better than the average of aligned sites = 1378 Number in coding regions = 1243 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 TGGGCTATAATAAAGAAAATTTATACCAAA 1 20 0 TAAAGAAAAT 0.968874 -144 GCTTTGTTTTAAAAGCAAAATTTAAAGGAG 1 58 0 AAAAGCAAAA 0.96269 -106 AAGTAAAAATTAAAGCAAAAAGCCAACGCT 2 47 0 TAAAGCAAAA 0.979642 -71 TACTTCTTTTTTAATAAAATACTCTTTTTG 2 72 1 TTAATAAAAT 0.913129 -46 ATAACCGCCTATAATAAAAAGGAATCAAAA 2 97 0 ATAATAAAAA 0.913129 -21 AGGCTTAAGATTAAGAAAAATCTAAAAA 3 9 0 TTAAGAAAAA 0.982981 -36 ********** Masking position 4 Map Score: 6.05827 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 653 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 AAATGGGCTATAATAAAGAAAATTTATACC 1 23 0 TAATAAAGAA 0.788583 -141 GGGCTTTGTTTTAAAAGCAAAATTTAAAGG 1 60 0 TTAAAAGCAA 0.938997 -104 ATAGTTCCAACCAAAAGCAAGGATGCCTTT 1 116 1 CCAAAAGCAA 0.95599 -48 TTATAAAAAACCCAAAGGCATCCTTGCTTT 1 129 0 CCCAAAGGCA 0.814695 -35 GGGTTTTTTATAACAAGGAGTTACAACA 1 146 1 TAACAAGGAG 0.90407 -18 AAAATTAAAGCAAAAAGCCAACGCTTAAAG 2 42 0 CAAAAAGCCA 0.942838 -76 AGTATTTTATTAAAAAAGAAGTAAAAATTA 2 65 0 TAAAAAAGAA 0.963648 -53 TAAAAAGGAATCAAAAAGAGTATTTTATTA 2 83 0 TCAAAAAGAG 0.931948 -35 CCGCCTATAATAAAAAGGAATCAAAAAGAG 2 93 0 TAAAAAGGAA 0.98633 -25 CTTAAGCCTTTTAAAAGGCGTTTTA 3 30 1 TTAAAAGGCG 0.911984 -15 ATATTCATTTTAAAAAACAACTATGGAGTA 4 12 1 TAAAAAACAA 0.939202 -54 ********** Masking position 5 Map Score: 14.2356 Number of sites scoring better than the average of aligned sites = 983 Number in coding regions = 812 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 ********** No masking Map Score: 4.92707e-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 6 ********** No masking Map Score: 4.92707e-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: 4.92707e-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