AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i312_mixed26_hpyl_reg_100.orf -o312_hpyl_100.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 RHP00817 253 AE000511 #2 RHP00960 126 AE000511 Motif number 1 GATGACTCCTTTAATTGAAATTTAAATTCT 1 9 1 CTTAATTAAA 0.881036 -245 AGCTAATGAGCTAGAATTTAAATTTCAATTAA 1 21 0 CTGAATTAAA 0.954716 -233 TTGGTTAGATTTTGCATTATAAAATGAAATCC 1 54 0 TTGCATTTAA 0.74151 -200 GTATTAAAAATTAGTATTAAAATCTTTTTCGT 1 92 0 TTGTATTAAA 0.819674 -162 TCAATTAACGCTCGTATTAAAAATTAGTATTA 1 105 0 CTGTATTAAA 0.98574 -149 ATTATAGCTTTTTTCATTCAAAGATGTTAGTA 1 157 0 TTTCATTAAA 0.566542 -97 TAATAAAGAAGTTGCATTAAAAAGGAAAGACA 1 185 1 GTGCATTAAA 0.961819 -69 TTTATTGGATTTAGTATTTTCACTATTATAGC 2 13 1 TTGTATTTCA 0.900516 -114 ATAATGATTTTTGGAATTGTAACATAAAACCC 2 86 0 TTGAATTTAA 0.896066 -41 ** ***** *** Masking position 6 Map Score: 13.3661 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 322 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 TGAGCTAGAATTTAAATTTCAATTAAAGGAGT 1 15 0 TTTATTTCAA 0.878518 -239 TAGCTAGGATTTCATTTTATAATGCAAAATCT 1 48 1 TTCATTATAA 0.962086 -206 TTAAAATCTTTTTCGTTAATAATTGGTTAGAT 1 76 0 TTTCTAATAA 0.920252 -178 GGGATTTGTCTTTCCTTTTTAATGCAACTTCT 1 191 0 TTTCTTTTAA 0.960255 -63 AAATCCCCTTTTTAAGGTATAATATGAGGAAT 1 216 1 TTTAGTATAA 0.961861 -38 AGAGGCGGGTTTTATGTTACAATTCCAAAAAT 2 80 1 TTTATTACAA 0.982267 -47 GACTATCCTTTATTTTATAATAATGATTTT 2 107 0 TTTATTATAA 0.987978 -20 **** ****** Masking position 11 Map Score: 6.57524 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 95 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 AGCTAATGAGCTAGAATTTAAATTTCAATT 1 23 0 CTAGAATTTA 0.818715 -231 TAATAATTGGTTAGATTTTGCATTATAAAA 1 62 0 TTAGATTTTG 0.923296 -192 TATTAACGAAAAAGATTTTAATACTAATTT 1 87 1 AAAGATTTTA 0.968136 -167 TTTTTCATTCAAAGATGTTAGTAGTTTTGA 1 150 0 AAAGATGTTA 0.954874 -104 CTTCTTTATTATAGCTTTTTTCATTCAAAG 1 166 0 ATAGCTTTTT 0.827649 -88 AAGCTATAATAAAGAAGTTGCATTAAAAAG 1 179 1 AAAGAAGTTG 0.902486 -75 CTTACACCTATAAGATTTTATCATCAAGCT 2 52 0 TAAGATTTTA 0.934858 -75 ATTTTATAATAATGATTTTTGGAATTGTAA 2 96 0 AATGATTTTT 0.837667 -31 ********** Masking position 8 Map Score: 5.2345 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 844 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 4 AATTTAAATTTCAATTAAAGGAGTCATC 1 9 0 TCAATTAAAG 0.917918 -245 TTTTGCATTATAAAATGAAATCCTAGCTAA 1 47 0 TAAAATGAAA 0.895215 -207 AATACGAGCGTTAATTGAAGCACTTCTATT 1 119 1 TTAATTGAAG 0.779437 -135 TATAGCTTTTTTCATTCAAAGATGTTAGTA 1 157 0 TTCATTCAAA 0.772221 -97 TGAAAAAAGCTATAATAAAGAAGTTGCATT 1 173 1 TATAATAAAG 0.910784 -81 ATAAAGAAGTTGCATTAAAAAGGAAAGACA 1 187 1 TGCATTAAAA 0.853579 -67 CCTCATATTATACCTTAAAAAGGGGATTTG 1 215 0 TACCTTAAAA 0.922276 -39 AAATACTAAATCCAATAAAAA 2 2 0 TCCAATAAAA 0.927264 -125 TATAAGATTTTATCATCAAGCTATCTTTTG 2 44 0 TATCATCAAG 0.757576 -83 TTTGGAATTGTAACATAAAACCCGCCTCTT 2 79 0 TAACATAAAA 0.916302 -48 ATCATTATTATAAAATAAAGGATAGTC 2 110 1 TAAAATAAAG 0.95913 -17 ********** Masking position 8 Map Score: 7.76348 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 751 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 5 CTAGCTAATGAGCTAGAATTTAAATTTCAA 1 25 0 AGCTAGAATT 0.952516 -229 GAATGAAAAAAGCTATAATAAAGAAGTTGC 1 170 1 AGCTATAATA 0.993108 -84 CCCCTTTTTAAGGTATAATATGAGGAATTT 1 220 1 AGGTATAATA 0.976427 -34 AGCTATCTTTTGCTATAATAGTGAAAATAC 2 26 0 TGCTATAATA 0.97767 -101 CGCCTCTTACACCTATAAGATTTTATCATC 2 57 0 ACCTATAAGA 0.945061 -70 ********** Masking position 5 Map Score: 4.71037 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 57 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ********** No masking Map Score: 2.36911e-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: 2.36911e-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: 2.36911e-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