AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i244_regulatory1_mthe_reg_300.orf -o244_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH00046 176 M.thermo #2 RTH00235 158 M.thermo #3 RTH01020 117 M.thermo Motif number 1 ACTTCCCGCATTAACAGTATCAGC 1 5 1 CCCGCATTAA 0.996738 -172 AGGGATGTTGCCGGCTTTAACAGTGAA 2 8 0 CCGGCTTTAA 0.993931 -151 GGGAGAGATGCCGGCCTTTAATGTTCCATG 2 39 0 CCGGCCTTTA 0.978448 -120 CGGCATCTCTCCCACCTCAAGTTTATTGAT 2 56 1 CCCACCTCAA 0.98591 -103 CACGGGGGGACGGGCATCAATTTTTAAGTG 2 93 1 CGGGCATCAA 0.98389 -66 TTGAACACCCGAATGAAAGTTAACTGG 2 142 0 CCCGAATGAA 0.93892 -17 ATTCAACACTCCCACTTCAAAATATTTATT 3 12 1 CCCACTTCAA 0.978372 -106 CACTAATCATCCGGCATTAATAAATATTTT 3 30 0 CCGGCATTAA 0.996738 -88 ********** Masking position 10 Map Score: 15.1745 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 113 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 CCGCATTAACAGTATCAGCTGGAGGGTTCC 1 16 1 AGTATCAGCT 0.749585 -161 TCAGCTGGAGGGTTCCAGTTCAACATAAAA 1 30 1 GGTTCCAGTT 0.953802 -147 TGACATCCGGGTTTCCAGTCACTGACTGCA 1 97 0 GTTTCCAGTC 0.91549 -80 TGGAAACCCGGATGTCAGCTGGTAAAGAAA 1 110 1 GATGTCAGCT 0.94799 -67 CCGCTGCCTCAGTGGCAGTTTTTTCTTTAC 1 131 0 AGTGGCAGTT 0.888837 -46 ATGAAGGGATGTTGCCGGCTTTAACAGTGA 2 12 0 GTTGCCGGCT 0.98873 -147 AGGTGGGAGAGATGCCGGCCTTTAATGTTC 2 43 0 GATGCCGGCC 0.991984 -116 CTTAAAAATTGATGCCCGTCCCCCCGTGCA 2 91 0 GATGCCCGTC 0.956578 -68 TCAATTTTTAAGTGCCAGCACGATATAGTT 2 109 1 AGTGCCAGCA 0.948068 -50 AATATTTATTAATGCCGGATGATTAGTGTG 3 32 1 AATGCCGGAT 0.902837 -86 TTTTTAATAAATTACCGGTCATGTATCACA 3 58 0 ATTACCGGTC 0.860549 -60 ********** Masking position 3 Map Score: 10.6279 Number of sites scoring better than the average of aligned sites = 1035 Number in coding regions = 966 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 ATTAACAGTATCAGCTGGAGGGTTCCAGTTC 1 20 1 TCAGCTGGGG 0.99339 -157 TATTTTATGTTGAACTGGAACCCTCCAGCTG 1 31 0 TGAACTGGAC 0.958105 -146 AACCCGGATGTCAGCTGGTAAAGAAAAAACT 1 114 1 TCAGCTGGAA 0.976587 -63 AAACTGCCACTGAGGCAGCGGATTGACCTGA 1 140 1 TGAGGCAGGG 0.915478 -37 TCAATAAACTTGAGGTGGGAGAGATGCCGGC 2 54 0 TGAGGTGGAG 0.99557 -105 ATAAATATTTTGAAGTGGGAGTGTTGAATT 3 10 0 TGAAGTGGAG 0.98395 -108 GGTAAGTATCGGAGCTGGTGATGG 3 104 1 GGAGCTGGGA 0.973609 -14 ******** ** Masking position 3 Map Score: 6.50693 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 708 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 CAGCTGGTAAAGAAAAAACTGCCACTGAGG 1 125 1 AGAAAAAACT 0.987569 -52 CGGATTGACCTGAAAAATCTCGTCGGGGG 1 158 1 TGAAAAATCT 0.968722 -19 CCCCCCGTGCAGAAAAATCAATAAACTTGA 2 72 0 AGAAAAATCA 0.968722 -87 GTAATTTATTAAAAAAAACTCATGGTCATC 3 73 1 AAAAAAAACT 0.952929 -45 ********** Masking position 5 Map Score: 2.81505 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ACTTCCCGCATTAACAGTATCAGCTGGA 1 9 1 CATTAACAGT 0.959374 -168 GCAGTTTTTTCTTTACCAGCTGACATCCGG 1 117 0 CTTTACCAGC 0.990982 -60 ATGTTGCCGGCTTTAACAGTGAA 2 4 0 CTTTAACAGT 0.959374 -155 AGGCCGGCATCTCTCCCACCTCAAGTTTAT 2 52 1 CTCTCCCACC 0.975294 -107 AATTCAACACTCCCACTTCAAAATATT 3 8 1 CACTCCCACT 0.961694 -110 CCATCACCAGCTCCGATACTT 3 107 0 CATCACCAGC 0.975717 -11 ********** Masking position 8 Map Score: 5.02071 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 128 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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: -1.88842e-14 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