AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_mthe_reg_300.orf -o321_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 RTH01701 256 M.thermo #2 RTH00023 76 M.thermo #3 RTH01134 56 M.thermo #4 RTH00011 154 M.thermo Motif number 1 TCCTTCAGTGATTTTTTTAATGTGTGTCTTT 1 21 1 ATTTTTTTAT 0.969646 -236 ATAAACATGAAATTTTTTAATTAGTGATCCT 1 65 0 AATTTTTTAT 0.930811 -192 AAAAAATTTCATGTTTATATTATTTTTCCGT 1 78 1 ATGTTTATAT 0.808984 -179 GTTAACCTAAATTTTCTTATGCAGAAGACAT 1 107 1 ATTTTCTTAG 0.803026 -150 TGCAGAAGACATTTATATATTTATTCGCCGT 1 126 1 ATTTATATAT 0.908944 -131 TATAAGATTCAGCTTTTTAATAGATGACGGC 1 152 0 AGCTTTTTAT 0.83985 -105 TATGGTCATGAGTATTATAAGATTCAGCTTT 1 167 0 AGTATTATAG 0.762181 -90 AGGCAGCAAGATTAATATATGGTCATGAGTA 1 184 0 ATTAATATAG 0.776803 -73 GTCAGTTAATATTAATTTAATTAATACGATT 2 21 0 ATTAATTTAT 0.763581 -56 ATTATTTAGGATTATTTTAGTGATAA 4 6 0 ATTATTTTAT 0.937962 -149 TCAGACACAGAATTATTTAGGATTATTTTAG 4 17 0 AATTATTTAG 0.826593 -138 TGGAGGACATAACTTTATAATGCTTCAGACA 4 41 0 AACTTTATAT 0.756313 -114 GTAGGGGAAGATTTTTTTACTCTTCCTGATA 4 123 1 ATTTTTTTAT 0.9712 -32 ********* * Masking position 9 Map Score: 12.2101 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 82 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 TTAATGTGTGTCAGCAGGATCACTAATTAA 1 50 1 TCAGCAGGAT 0.993023 -207 TAATATATGGTCATGAGTATTATAAGATTC 1 173 0 TCATGAGTAT 0.793136 -84 TACGGCGCAGGCAGCAAGATTAATATATGG 1 193 0 GCAGCAAGAT 0.961827 -64 AAAATTATGATCAGGTAGATTTGAA 2 62 1 TCAGGTAGAT 0.958024 -15 GATCTTCTCCTCCGCTGGAGGACATAACTT 4 57 0 TCCGCTGGAG 0.958344 -98 CGTGGTTAATCCATCAGGAGCCGGGAAAAG 4 86 0 CCATCAGGAG 0.944883 -69 GGTTAATCTATCAGGAAGAGTAAAAAAATC 4 132 0 TCAGGAAGAG 0.984461 -23 ********** Masking position 9 Map Score: 4.42234 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 826 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 ATAAGAAAATTTAGGTTAACGGAAAAATAAT 1 96 0 TTGGTTAACG 0.988199 -161 ATTTAATTAATACGATTAACGGTCCTA 2 7 0 TAGATTAACG 0.981863 -70 CAGTGATTGATATGGATAACGTCTACATACC 3 33 0 TAGGATAACG 0.946701 -24 CCGGCTCCTGATGGATTAACCACGATCCTCG 4 92 1 ATGATTAACC 0.973798 -63 ACTCTTCCTGATAGATTAACCATC 4 141 1 ATGATTAACC 0.973798 -14 ** ******** Masking position 7 Map Score: 2.29406 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 CACATTAAAAAAATCACTGAAGGAAGGTAG 1 15 0 AAATCACTGA 0.918893 -242 ACACACATTAAAGACACACATTAAAAAAAT 1 31 0 AAGACACACA 0.972959 -226 AGTGATCCTGCTGACACACATTAAAGACAC 1 44 0 CTGACACACA 0.961 -213 TTATCCATATCAATCACTGATT 3 45 1 CAATCACTGA 0.962302 -12 TATAATGCTTCAGACACAGAATTATTTAGG 4 27 0 CAGACACAGA 0.991603 -128 ********** Masking position 6 Map Score: 2.15775 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 107 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AACTCTCTAAGACCTGATCATGGAATATGG 1 222 1 GACCTGATCA 0.99595 -35 AATATTAACTGACCGGATGAACAAAAATTA 2 39 1 GACCGGATGA 0.991176 -38 TTCAAATCTACCTGATCATAATTTTTGT 2 59 0 TACCTGATCA 0.989031 -18 ********** Masking position 7 Map Score: 1.51192 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ATATAAACATGAAATTTTTTAATTAGTGAT 1 68 0 GAAATTTTTT 0.869521 -189 TTCTTATGCAGAAGACATTTATATATTTAT 1 120 1 GAAGACATTT 0.957651 -137 CAGCGGAGGAGAAGATCTTTTCCCGGCTCC 4 70 1 GAAGATCTTT 0.847574 -85 CTCGGTAGGGGAAGATTTTTTTACTCTTCC 4 119 1 GAAGATTTTT 0.942619 -36 ********** Masking position 3 Map Score: 0.653386 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 36 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 1.74326e-12 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: 1.74326e-12 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 9 ********** No masking Map Score: 1.74326e-12 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