AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_hpyl_reg_300.orf -o00020_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0026_HP0027 198 HP0026: citrate synthase (gltA), HP0027: isocitrate dehydrogenase (icd) #2 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #3 HP0779 127 aconitase B (acnB) #4 HP1325 174 fumarase (fumC) Motif number 1 TTTTTAAGGGTTATATAGTATTTTTGCGCTAGTATA 1 41 0 TTATTTTTTG 0.700934 -158 TATATAACCCTTAAAAATCTTTTTTTGAATGCGTGT 1 60 1 TTAATTTTTT 0.980945 -139 ATTTCTTTTAAAAACATTGCGTTTTTTCAAGTTATT 1 114 0 AAAAGTTTTT 0.680802 -85 AGCCAAAAAATTAAATGATTTCTTTTAAAAACATTG 1 131 0 TTAATCTTTT 0.964664 -68 TGAACGATCCTTATTTTATAGGTGGT 2 1 1 TGAATTATTT 0.733158 -214 GCTATTGTTTAAAATTTACATTTTTTAAACGCTATT 2 57 0 AAAATTTTTT 0.914496 -158 AATAGCCCCTTTGAATTGAATTTTTTCTCAATTTAG 2 87 1 TTGATTTTTT 0.904797 -128 GGTTTTGTTTATAAGAAAAATTATTTCAAATGTAGT 2 122 1 ATAATTATTT 0.907646 -93 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGCG 2 152 1 TTAAGTTTTT 0.964733 -63 CGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGTT 2 186 1 TTAAGTTTTT 0.964776 -29 TTAAAATCCTTTTTTGTATCGCATGG 3 1 1 TTAATTTTTG 0.964536 -127 TTGCCCCATGATAACAAAACTCTTTTTACTTTTAGT 3 60 0 ATAATCTTTT 0.938942 -68 TTCTCCTTTTTAAATCGCATTATTGACTAATGCCC 3 103 0 TTAATTATTG 0.871989 -25 TTGCGAACGGATAATAACCCTCTTTTGTGTAAAAAT 4 50 1 ATAATCTTTT 0.938942 -125 CTTCTACTTAAAAACCCTAATTTTTTAAACACCATT 4 92 0 AAAATTTTTT 0.84093 -83 GGTATAAGAGTTTATGCTATTTTTTTAAGGTTTTAA 4 127 1 TTTATTTTTT 0.865093 -48 **** ****** Masking position 14 Map Score: 18.032 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1069 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 2 CGCATTCAAAAAAAGATTTTTAAGGGTTATAT 1 61 0 AAGATTTTTA 0.891373 -138 CTTTTTTTGAATGCGTGTTTAAAAGTAGCGGT 1 78 1 ATGTGTTTAA 0.950045 -121 TGAAAAAACGCAATGTTTTTAAAAGAAATCAT 1 121 1 CAGTTTTTAA 0.846162 -78 TATTATATCTAATAGCGTTTAAAAAATGTAAA 2 47 1 AAGCGTTTAA 0.915841 -168 TTTTTGCGTCAAGCGATTTTAGGTTAATTTTG 2 173 1 AAGATTTTAG 0.957408 -42 TAGGTTAATTTTGAGTTTTTAGGAGCAGTTTT 2 192 1 TTGTTTTTAG 0.700393 -23 GCGATACAAAAAAGGATTTTAA 3 1 0 AAGATTTTAA 0.975732 -127 ACTAAAAGTAAAAAGAGTTTTGTTATCATGGG 3 60 1 AAGAGTTTTG 0.823876 -68 TTAGTCAATAATGCGATTTAAAAAGGAGAA 3 108 1 ATGATTTAAA 0.732202 -20 AAATTGTGGAAATGGTGTTTAAAAAATTAGGG 4 82 1 AAGTGTTTAA 0.967493 -93 TTTAAAAAATTAGGGTTTTTAAGTAGAAGGTA 4 99 1 TAGTTTTTAA 0.867446 -76 AGTAGAAGGTATAAGAGTTTATGCTATTTTTT 4 120 1 ATGAGTTTAT 0.786249 -55 ATCCTTTGAAATTTGATTTTAAAACCTTAAAA 4 149 0 ATGATTTTAA 0.962536 -26 ** ******** Masking position 8 Map Score: 12.7552 Number of sites scoring better than the average of aligned sites = 1141 Number in coding regions = 955 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 ATAGTTACTCAAACTTTAGAAAAAGGATAAAC 1 12 0 AAACTTTAGA 0.965692 -187 TATAAGCCAAAAAATTAAATGATTTCTTTTAA 1 139 0 AAAATTAAAA 0.902254 -60 AATGCTATCAAAACTTAAGGAAGTCAA 1 182 1 AAACTTAAGA 0.979026 -17 GCTATTGTTTAAAATTTACATTTTTTAAACGC 2 61 0 AAAATTTACT 0.632365 -154 CAAATGTAGTAGAATTAAGGCAGTGTTTTTGC 2 148 1 AGAATTAAGA 0.863894 -67 CTAAAAACTCAAAATTAACCTAAAATCGCTTG 2 182 0 AAAATTAACA 0.954114 -33 AAGTTGTAAGAAACTTTAGCTACCATGCGATA 3 27 0 AAACTTTAGA 0.965327 -101 AAGTTTCTTACAACTTAACTAAAAGTAAAAAG 3 43 1 CAACTTAACA 0.905111 -85 TTGATTTTAAAACCTTAAAAAAATAGCATAAA 4 137 0 AACCTTAAAA 0.809077 -38 ********* * Masking position 6 Map Score: 4.99112 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 156 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 TGTTTATCCTTTTTCTAAAGTTT 1 4 1 TTATCCTTTT 0.981093 -195 TTAAAATCCTTTTTTGTATCGCA 3 4 1 AAATCCTTTT 0.92731 -124 ACTAATGCCCTAATCGTTTGCCCCATGATA 3 83 0 TAATCGTTTG 0.927597 -45 TTCTCCTTTTTAAATCGCAT 3 118 0 TTCTCCTTTT 0.949937 -10 AAGAGGGTTATTATCCGTTCGCAACAAGAA 4 44 0 TTATCCGTTC 0.917562 -131 GCTAATCCTTTGAAATTTGATT 4 163 0 TAATCCTTTG 0.982457 -12 ********** Masking position 4 Map Score: 3.11437 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 139 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 CAACCGCTACTTTTAAACACGCATTCAAAA 1 82 0 TTTTAAACAC 0.980606 -117 AATTTACATTTTTTAAACGCTATTAGATAT 2 51 0 TTTTAAACGC 0.930783 -164 AAAATGTAAATTTTAAACAATAGCCCCTTT 2 69 1 TTTTAAACAA 0.980404 -146 TGAATTGAATTTTTTCTCAATTTAGGTTTT 2 98 1 TTTTTCTCAA 0.653156 -117 ATAATTTTTCTTATAAACAAAACCTAAATT 2 116 0 TTATAAACAA 0.901947 -99 TTTCCACAATTTTTACACAAAAGAGGGTTA 4 64 0 TTTTACACAA 0.980488 -111 TTTAAACACCATTTCCACAATTTTTACACA 4 75 0 ATTTCCACAA 0.736266 -100 AACCCTAATTTTTTAAACACCATTTCCACA 4 86 0 TTTTAAACAC 0.980606 -89 ********** Masking position 4 Map Score: 8.72584 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 131 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 ********** No masking Map Score: -2.32047e-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: -2.32047e-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: -2.32047e-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