AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_hpyl_reg_100.orf -o00720_hpyl_100.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 HP0027 198 isocitrate dehydrogenase (icd) #2 HP0121 186 phosphoenolpyruvate synthase (ppsA) #3 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #4 HP0779 127 aconitase B (acnB) #5 HP1045 197 acetyl-CoA synthetase (acoE) #6 HP1325 174 fumarase (fumC) #7 HP1398 201 alanine dehydrogenase (ald) Motif number 1 TAAATGATTTCTTTTAAAAACATTGCGTTTT 1 64 1 CTTTTAAAAC 0.904106 -135 CCAACCGCTACTTTTAAACACGCATTCAAAA 1 107 1 CTTTTAAACC 0.970152 -92 ACTATATAACCCTTAAAAATCTTTTTTTGAA 1 131 0 CCTTAAAAAC 0.912686 -68 TCATTAAGTTTCTTAAAACAAAAATATAACA 2 148 0 TCTTAAAACA 0.891422 -39 AAAACTCCCTTAAAATGATCATTAAGTT 2 169 0 CCTTAAAATA 0.912371 -18 ATAGTTACCACCTATAAAATAAGGATCGTTC 3 12 0 CCTATAAAAA 0.80591 -203 AAATTTACATTTTTTAAACGCTATTAGATAT 3 51 0 TTTTTAAACC 0.881475 -164 AAAAATGTAAATTTTAAACAATAGCCCCTTT 3 68 1 ATTTTAAACA 0.646898 -147 AATAATTTTTCTTATAAACAAAACCTAAATT 3 116 0 CTTATAAACA 0.88965 -99 AAAAACTGCTCCTAAAAACTCAAAATTAACC 3 194 0 CCTAAAAACC 0.899485 -21 AGTATCCCTCCCTTTAAAAGAGTGTGAGTTT 5 129 1 CCTTTAAAAA 0.942208 -69 TAAAAAATGCGCTTAAAACCATGAAAAAGGA 5 171 1 GCTTAAAACA 0.750135 -27 CGTTTTGACCTTTACATTAAGATAACAAG 6 9 1 CCTTTACATA 0.825796 -166 ATTTCCACAATTTTTACACAAAAGAGGGTTA 6 64 0 TTTTTACACA 0.67855 -111 AAACCCTAATTTTTTAAACACCATTTCCACA 6 86 0 TTTTTAAACC 0.881589 -89 ATACCTTCTACTTAAAAACCCTAATTTTTTA 6 101 0 CTTAAAAACC 0.834804 -74 GATTTTAAAACCTTAAAAAAATAGCATAAAC 6 136 0 CCTTAAAAAA 0.91236 -39 TTTTTTAAGGTTTTAAAATCAAATTTCAAAG 6 147 1 TTTTAAAATA 0.574196 -28 TTTATAACTCCTTTAAATCCCCTCTAATGT 7 10 1 CCTTTAAATC 0.943638 -192 TGGTTTTACTCTTTTACACAATGAAATTGTT 7 98 0 CTTTTACACA 0.901999 -104 GTTAATCCTTTAAATAATAGTGTCAGT 7 185 0 CCTTTAAATA 0.943418 -17 ********* * Masking position 3 Map Score: 25.0131 Number of sites scoring better than the average of aligned sites = 2231 Number in coding regions = 1943 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 2 ACCCTTAAAAATCTTTTTTTGAATGCGTGTTT 1 122 0 ATCTTTTTTA 0.780561 -77 TGTTTATCCTTTTTCTAAAGTTTGAGT 1 182 0 ATCCTTTTTA 0.974466 -17 AACCACCCTTTCTATTCAAAAATACC 2 5 1 ACCCTTTCTT 0.853377 -182 AAGAGGGTGTATTCTTTTTGGTTTATGATTTT 2 60 0 ATTCTTTTTT 0.860641 -127 AAGAATACACCCTCTTATTAAAAAGCTTAGTA 2 76 1 CCTCTTATTA 0.492694 -111 TGAACGATCCTTATTTTATAGGTGGTAA 3 7 1 ATCCTTATTA 0.898244 -208 GTGGTAACTATCCCTTATTATATCTAATAGCG 3 32 1 TCCCTTATTA 0.703928 -183 TTTAAAATTTACATTTTTTAAACGCTATTAGA 3 54 0 ACATTTTTTA 0.480682 -161 TTAAAATCCTTTTTTGTATCGCATGGT 4 6 1 ATCCTTTTTT 0.971481 -122 TGATAACAAAACTCTTTTTACTTTTAGTTAAG 4 56 0 ACTCTTTTTT 0.898621 -72 TTCTCCTTTTTAAATCGCATTATT 4 114 0 CTCCTTTTTA 0.941642 -14 ATCACCCTTTTTGTAGTCATAATGT 5 4 1 ACCCTTTTTA 0.982071 -194 ATCGTGCTATTTCCTTTTTTATCAGTCTCAAT 5 80 1 TTCCTTTTTT 0.864722 -118 AAAGGGAGGGATACTTTTTTCTTTCTGTGTGG 5 112 0 ATACTTTTTT 0.860641 -86 ATCCAAACTCACACTCTTTTAAAGGGAGGGAT 5 132 0 ACACTCTTTA 0.698585 -66 CGCATCTCCTTTTTCATGGTTTTAAGC 5 181 0 CTCCTTTTTT 0.935075 -17 ACGGATAATAACCCTCTTTTGTGTAAAAATTG 6 56 1 ACCCTCTTTT 0.919425 -119 ********* * Masking position 5 Map Score: 18.7368 Number of sites scoring better than the average of aligned sites = 1323 Number in coding regions = 1045 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 3 CTCCTAATTATAAGCCAAAAAATTAAATGA 1 41 1 TAAGCCAAAA 0.921775 -158 AATAAAATCATAAACCAAAAAGAATACACC 2 57 1 TAAACCAAAA 0.98261 -130 ACAAACTAGCTAAAACTAAAGCTCTATCAT 2 110 1 TAAAACTAAA 0.958916 -77 TTAAGTTTCTTAAAACAAAAATATAACAAT 2 146 0 TAAAACAAAA 0.940978 -41 TCTTATAAACAAAACCTAAATTGAGAAAAA 3 108 0 AAAACCTAAA 0.963155 -107 AAACTCAAAATTAACCTAAAATCGCTTGAC 3 180 0 TTAACCTAAA 0.92073 -35 ACAACTTAACTAAAAGTAAAAAGAGTTTTG 4 52 1 TAAAAGTAAA 0.751369 -76 ATAGCACGATGAAACCTAAAGGGGATATTA 5 60 0 GAAACCTAAA 0.956468 -138 ATTTGATTTTAAAACCTTAAAAAAATAGCA 6 141 0 AAAACCTTAA 0.786242 -34 TGTTCTATTCTAAACCAAAATTAACAACCA 7 38 1 TAAACCAAAA 0.98261 -164 ********** Masking position 3 Map Score: 12.0841 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 274 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 ATTATAAGCCAAAAAATTAAATGATTTCTTTT 1 47 1 AAAAAATAAT 0.954083 -152 AAATAACTTGAAAAAACGCAATGTTTTTAAAA 1 75 0 AAAAAACAAT 0.961909 -124 ACCGCCCATTATACAATAAAATCATAAACCAA 2 43 1 ATACAATAAT 0.642135 -144 CAATAAAATCATAAACCAAAAAGAATACACCC 2 56 1 ATAAACCAAA 0.617495 -131 TTTTTGTTTTAAGAAACTTAATGATCATTTTA 2 155 1 AAGAAACAAT 0.774074 -32 AATAGCGTTTAAAAAATGTAAATTTTAAACAA 3 57 1 AAAAAATAAA 0.887871 -158 CTAAATTGAGAAAAAATTCAATTCAAAGGGGC 3 91 0 AAAAAATAAT 0.954083 -124 TTTCTTATAAACAAAACCTAAATTGAGAAAAA 3 108 0 ACAAAACAAA 0.752495 -107 AACTGCTCCTAAAAACTCAAAATTAACCTAAA 3 190 0 AAAAACTAAA 0.86673 -25 TGAGACTGATAAAAAAGGAAATAGCACGATGA 5 78 0 AAAAAAGAAT 0.8292 -120 CCTTCTACTTAAAAACCCTAATTTTTTAAACA 6 97 0 AAAAACCAAT 0.954004 -78 TAAAACCTTAAAAAAATAGCATAAACTCTTAT 6 130 0 AAAAAATCAT 0.738167 -45 TTACTCTTTTACACAATGAAATTGTTCTATTT 7 92 0 ACACAATAAT 0.735138 -110 TTTTTCTATCAAAAACTTGAATGGTTTTACTC 7 118 0 AAAAACTAAT 0.944644 -84 TTTGATAGAAAAACACCCCAATAGTCTTATTG 7 137 1 AAACACCAAT 0.89764 -65 ******* *** Masking position 5 Map Score: 14.5151 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 607 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 5 TTTTTGGTTTATGATTTTATTGTATAATGGG 2 47 0 ATATTTTATT 0.69714 -140 TCATGCTATCATTGTTATATTTTTGTTTTAA 2 136 1 ATGTTATATT 0.9271 -51 ATTCAATTCAAAGGGGCTATTGTTTAAAATT 3 77 0 AAGGGCTATT 0.909141 -138 TTGTAGTCATAATGTTCTACTATATTAGCAT 5 21 1 AAGTTCTACT 0.869059 -177 ATGAAACCTAAAGGGGATATTAGCGTTAATA 5 51 0 AAGGGATATT 0.796476 -147 TTTAGGTTTCATCGTGCTATTTCCTTTTTTA 5 70 1 ATGTGCTATT 0.968191 -128 TTTACACAAAAGAGGGTTATTATCCGTTCGC 6 52 0 AGGGGTTATT 0.697022 -123 AATCCCCTCTAATGTTCTATTCTAAACCAAA 7 26 1 AAGTTCTATT 0.949883 -176 ACACAATGAAATTGTTCTATTTATTATCCAT 7 83 0 ATGTTCTATT 0.970175 -119 AAAAACTTGAATGGTTTTACTCTTTTACACA 7 109 0 ATGTTTTACT 0.85167 -93 AAACACCCCAATAGTCTTATTGAGCGAATAT 7 147 1 ATGTCTTATT 0.814827 -55 AGTGTCAGTTATGATTATATTCGCTCAATAA 7 163 0 ATATTATATT 0.63868 -39 ** ******** Masking position 9 Map Score: 5.87543 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 173 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 6 AGGAGTTGAATGCTATCAAAACTTAAGGAA 1 16 0 TGCTATCAAA 0.92426 -183 ATTAAATGATTTCTTTTAAAAACATTGCGT 1 62 1 TTCTTTTAAA 0.857625 -137 TTTTTTCAAGTTATTTCCAACCGCTACTTT 1 91 1 TTATTTCCAA 0.896877 -108 AACCACCCTTTCTATTCAAAAATACCTAA 2 10 1 TTCTATTCAA 0.835961 -177 CTATCCCTTATTATATCTAATAGCGTTTAA 3 39 1 TTATATCTAA 0.72101 -176 GAAATAATTTTTCTTATAAACAAAACCTAA 3 119 0 TTCTTATAAA 0.599141 -96 ATAAGAAAAATTATTTCAAATGTAGTAGAA 3 132 1 TTATTTCAAA 0.924323 -83 GTTTGCCCCATGATAACAAAACTCTTTTTA 4 68 0 TGATAACAAA 0.692898 -60 TTTTTTATTATTATATCCAAACTCACACTC 5 148 0 TTATATCCAA 0.911712 -50 CTTTGAAATTTGATTTTAAAACCTTAAAAA 6 148 0 TGATTTTAAA 0.737633 -27 TGGGGTGTTTTTCTATCAAAAACTTGAATG 7 127 0 TTCTATCAAA 0.95116 -75 ********** Masking position 9 Map Score: 8.09018 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 360 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 TAATTAGGAGTTGAATGCTATCAAAACTTAA 1 20 0 TTGAATCTAT 0.917966 -179 TTTTTAAGGGTTATATAGTATTTTTGCGCTA 1 143 1 TTATATGTAT 0.853248 -56 TGGTTTATGATTTTATTGTATAATGGGCGGT 2 43 0 TTTTATGTAT 0.58922 -144 TTTACATTTTTTAAACGCTATTAGATATAAT 3 48 0 TTAAACCTAT 0.788908 -167 AATAGCCCCTTTGAATTGAATTTTTTCTCAA 3 87 1 TTGAATGAAT 0.803086 -128 AAATCCTTTTTTGTATCGCATGGTAGCTAAA 4 14 1 TTGTATGCAT 0.905989 -114 TTCTCCTTTTTAAATCGCATTATTGACTAA 4 108 0 TTAAATGCAT 0.942959 -20 CCCTAATTTTTTAAACACCATTTCCACAATT 6 83 0 TTAAACCCAT 0.827928 -92 TATAACTCCTTTAAATCCCCTCTAATGTTCT 7 13 1 TTAAATCCCT 0.723335 -189 TATCAAAAACTTGAATGGTTTTACTCTTTTA 7 113 0 TTGAATGTTT 0.722687 -89 ****** **** Masking position 5 Map Score: 0.388826 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 239 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 CTAGCTAAAACTAAAGCTCTATCATGCTAT 2 115 1 CTAAAGCTCT 0.963871 -72 GCATTATTGACTAATGCCCTAATCGTTTGC 4 92 0 CTAATGCCCT 0.975334 -36 TTTTGTAGTCATAATGTTCTACTATATTAG 5 19 1 ATAATGTTCT 0.91631 -179 TAAATCCCCTCTAATGTTCTATTCTAAACC 7 24 1 CTAATGTTCT 0.977558 -178 ********** Masking position 4 Map Score: 0.164334 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 20 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 9 ********** No masking Map Score: 2.51122e-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 10 ********** No masking Map Score: 2.51122e-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 11 ********** No masking Map Score: 2.51122e-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