AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_mthe_reg_100.orf -o00660_mthe_100.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 MTH563 140 succinyl-CoA synthetase, alpha subunit #2 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #3 MTH1444 64 acetolactate synthase, large subunit #4 MTH1602 63 acetolactate synthase, large subunit homolog Motif number 1 CATATTATCCTTAATTGTGAAGGGCTCTTC 1 41 1 TTAATTGTGA 0.960557 -100 GGAGAAGTGTTTAATTATGATAGAGTTCTG 1 70 0 TTAATTATGA 0.987522 -71 TCTGAAATATTTAATTATGCTCATGAAGAG 1 107 0 TTAATTATGC 0.95459 -34 GTAAACCATGAAATGGAGAAT 2 2 1 TAAACCATGA 0.953714 -228 CAGATTATAATAAATTATCAGGGTGTTCCC 2 135 0 TAAATTATCA 0.929074 -95 ATTTAAATAATTAATCAAGAATAATATTAT 2 173 0 TTAATCAAGA 0.932896 -57 ATTAATTATTTAAATTCTGAAGGCAAAGCT 2 188 1 TAAATTCTGA 0.960557 -42 GCCAACTATTTAAATCATGAATTAAAAAAA 4 27 0 TAAATCATGA 0.987273 -37 ********** Masking position 4 Map Score: 10.3012 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 39 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 TTATCCTTAATTGTGAAGGGCTCTTCAGAA 1 45 1 TTGTGAAGGG 0.983203 -96 TATGATAGAGTTCTGAAGAGCCCTTCACAA 1 55 0 TTCTGAAGAG 0.988607 -86 TAAACACTTCTCCTGAACGGCTCTTCATGA 1 87 1 TCCTGAACGG 0.980324 -54 TTAATTATGCTCATGAAGAGCCGTTCAGGA 1 97 0 TCATGAAGAG 0.955207 -44 GCCCCGGAAAACCTGAAAACCGGAATATAC 2 54 1 ACCTGAAAAC 0.80554 -176 CAGGGCATTTTGCTGAAAACCTCTGGTGAA 2 105 1 TGCTGAAAAC 0.940722 -125 TGAAAACCTCTGGTGAAGGGAACACCCTGA 2 118 1 TGGTGAAGGG 0.984456 -112 ATTATTTAAATTCTGAAGGCAAAGCTAAGA 2 192 1 TTCTGAAGGC 0.988253 -38 ********** Masking position 6 Map Score: 10.2884 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 591 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 ATGAGCATAATTAAATATTTCAGACCACAA 1 113 1 TTAAATATTT 0.969221 -28 CAGTCCCGGGGTAAAGATGTGTATATTCCG 2 74 0 GTAAAGATGT 0.93088 -156 CCTTCAGAATTTAAATAATTAATCAAGAAT 2 181 0 TTAAATAATT 0.885967 -49 TTATTTGAAAGTATATATTTTATAGGAAAT 3 11 1 GTATATATTT 0.930982 -54 ATATTTTATAGGAAATATGTCATTAATAAT 3 25 1 GGAAATATGT 0.930877 -40 CCCCCTTCTGTTAATATTTTTTTAATTCA 4 10 1 GTTAATATTT 0.931051 -54 AATTCATGATTTAAATAGTTGGCAGAATAT 4 34 1 TTAAATAGTT 0.920098 -30 ********** Masking position 5 Map Score: 4.37857 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 18 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TTTTTTCAGTGACCTCCACCGATGT 1 3 1 TTTTCAGGCT 0.98835 -138 TGTGAAGGGCTCTTCAGAACTCTATCATAATTA 1 56 1 TCTTCAGACT 0.919621 -85 CCTTTCTTTTGTGGTCTGAAATATTTA 1 124 0 TCTTTTGGCT 0.909454 -17 GGTTTTCAGGTTTTCCGGGGCCTATGTAAATCA 2 42 0 TTTTCCGGCT 0.974503 -188 GGTGTTCCCTTCACCAGAGGTTTTCAGCAAAAT 2 111 0 TCACCAGGTT 0.864271 -119 TTATAATAAATTATCAGGGTGTTCCCTTCACCA 2 128 0 TTATCAGGTT 0.957572 -102 TAATTTATTATAATCTGAGTTCTGAATAATATT 2 148 1 TAATCTGGCT 0.973619 -82 ATCGTGGTTCTTATCTTAGCTTTGCCTTCAGAA 2 202 0 TTATCTTGTT 0.688725 -28 CACCCATCTATATTCTGCCAACTATTTAAATCA 4 40 0 TATTCTGCCT 0.882712 -24 ******* * ** Masking position 1 Map Score: 3.25589 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 765 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 CCCTTCACAATTAAGGATAATATGACTCCA 1 35 0 TTAAGGATAA 0.736539 -106 CAGAACTCTATCATAATTAAACACTTCTCC 1 70 1 TCATAATTAA 0.800253 -71 TTAATTATGCTCATGAAGAGCCGTTCAGGA 1 97 0 TCATGAAGAG 0.735342 -44 ATTCTCCATTTCATGGTTTAC 2 2 0 TCATGGTTTA 0.838822 -228 ACTCAGATTATAATAAATTATCAGGGTGTT 2 138 0 TAATAAATTA 0.646368 -92 ATAATCTGAGTTCTGAATAATATTATTCTT 2 157 1 TTCTGAATAA 0.734485 -73 AAATAATTAATCAAGAATAATATTATTCAG 2 169 0 TCAAGAATAA 0.96495 -61 CTTCAGAATTTAAATAATTAATCAAGAATA 2 180 0 TAAATAATTA 0.396422 -50 AGGAAATATGTCATTAATAATAATGACAGA 3 34 1 TCATTAATAA 0.821226 -31 ACTATTTAAATCATGAATTAAAAAAATATT 4 23 0 TCATGAATTA 0.971684 -41 ********** Masking position 1 Map Score: 1.93108 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 497 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 ********** No masking Map Score: 5.21128e-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: 5.21128e-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: 5.21128e-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