AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_hpyl_reg_300.orf -o00720_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 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 0.921424 -135 CCAACCGCTACTTTTAAACACGCATTCAAAA 1 107 1 CTTTTAAACC 0.968813 -92 ACTATATAACCCTTAAAAATCTTTTTTTGAA 1 131 0 CCTTAAAAAC 0.868453 -68 TATTACTAAGCTTTTTAATAAGAGGGTGTAT 2 80 0 CTTTTTAATA 0.679564 -107 TCATTAAGTTTCTTAAAACAAAAATATAACA 2 148 0 TCTTAAAACA 0.758576 -39 AAAACTCCCTTAAAATGATCATTAAGTT 2 169 0 CCTTAAAATA 0.879504 -18 ATAGTTACCACCTATAAAATAAGGATCGTTC 3 12 0 CCTATAAAAA 0.803026 -203 AAATTTACATTTTTTAAACGCTATTAGATAT 3 51 0 TTTTTAAACC 0.854417 -164 AAAAATGTAAATTTTAAACAATAGCCCCTTT 3 68 1 ATTTTAAACA 0.580658 -147 AATAATTTTTCTTATAAACAAAACCTAAATT 3 116 0 CTTATAAACA 0.895827 -99 AAAAACTGCTCCTAAAAACTCAAAATTAACC 3 194 0 CCTAAAAACC 0.834563 -21 TTCTCCTTTTTAAATCGCATTATTGA 4 112 0 CTTTTTAAAC 0.657709 -16 AGTATCCCTCCCTTTAAAAGAGTGTGAGTTT 5 129 1 CCTTTAAAAA 0.924984 -69 CGTTTTGACCTTTACATTAAGATAACAAG 6 9 1 CCTTTACATA 0.806706 -166 ATTTCCACAATTTTTACACAAAAGAGGGTTA 6 64 0 TTTTTACACA 0.589892 -111 AAACCCTAATTTTTTAAACACCATTTCCACA 6 86 0 TTTTTAAACC 0.854474 -89 ATACCTTCTACTTAAAAACCCTAATTTTTTA 6 101 0 CTTAAAAACC 0.801529 -74 GATTTTAAAACCTTAAAAAAATAGCATAAAC 6 136 0 CCTTAAAAAA 0.862926 -39 TTTTTTAAGGTTTTAAAATCAAATTTCAAAG 6 147 1 TTTTAAAATA 0.525235 -28 TTTATAACTCCTTTAAATCCCCTCTAATGT 7 10 1 CCTTTAAATC 0.944642 -192 TATCCATTTGCTTATTAATAATTGGTTGTTA 7 59 0 CTTATTAATA 0.381265 -143 TGGTTTTACTCTTTTACACAATGAAATTGTT 7 98 0 CTTTTACACA 0.883706 -104 GTTAATCCTTTAAATAATAGTGTCAGT 7 185 0 CCTTTAAATA 0.942055 -17 ********* * Masking position 3 Map Score: 25.2158 Number of sites scoring better than the average of aligned sites = 2747 Number in coding regions = 2387 Number in noncoding regions = 360 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 2 ACTCAAACTTTAGAAAAAGGATAAACA 1 182 1 TAAAAAGGAT 0.946592 -17 GGTATTTTTGAATAGAAAGGGTGGTT 2 5 0 AAGAAAGGGT 0.945398 -182 AAAATCATAAACCAAAAAGAATACACCCTCTT 2 60 1 AAAAAAGAAT 0.826757 -127 AAGCTTTTTAATAAGAGGGTGTATTCTTTTTG 2 72 0 AAGAGGGTGT 0.602966 -115 TTACCACCTATAAAATAAGGATCGTTCA 3 7 0 TAATAAGGAT 0.57289 -208 GCTATTAGATATAATAAGGGATAGTTACCACC 3 31 0 AATAAGGGAT 0.72011 -184 ACCATGCGATACAAAAAAGGATTTTAA 4 6 0 AAAAAAGGAT 0.976241 -122 CTTAACTAAAAGTAAAAAGAGTTTTGTTATCA 4 56 1 AAAAAAGAGT 0.796552 -72 AATAATGCGATTTAAAAAGGAGAA 4 114 1 TAAAAAGGAG 0.805315 -14 ACATTATGACTACAAAAAGGGTGAT 5 4 0 TAAAAAGGGT 0.935655 -194 CACGATGAAACCTAAAGGGGATATTAGCGTTA 5 54 0 CAAAGGGGAT 0.723992 -144 ATTGAGACTGATAAAAAAGGAAATAGCACGAT 5 80 0 AAAAAAGGAA 0.778552 -118 CCACACAGAAAGAAAAAAGTATCCCTCCCTTT 5 112 1 AAAAAAGTAT 0.899031 -86 ATCCCTCCCTTTAAAAGAGTGTGAGTTTGGAT 5 132 1 TAAAGAGTGT 0.667194 -66 GCTTAAAACCATGAAAAAGGAGATGCG 5 181 1 AAAAAAGGAG 0.905567 -17 CAATTTTTACACAAAAGAGGGTTATTATCCGT 6 56 0 AAAAGAGGGT 0.95545 -119 AGGGTTTTTAAGTAGAAGGTATAAGAGTTTAT 6 110 1 AAGAAGGTAT 0.744217 -65 AGAATAGAACATTAGAGGGGATTTAAAGGAGT 7 17 0 AAGAGGGGAT 0.8952 -185 * ********* Masking position 4 Map Score: 17.1405 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 725 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 ATTATAAGCCAAAAAATTAAATGATTTCTTTT 1 47 1 AAAAAATAAT 0.948237 -152 AAATAACTTGAAAAAACGCAATGTTTTTAAAA 1 75 0 AAAAAACAAT 0.962776 -124 TATACTAGCGCAAAAATACTATATAACCCTTA 1 147 0 CAAAAATTAT 0.536295 -52 ACCGCCCATTATACAATAAAATCATAAACCAA 2 43 1 ATACAATAAT 0.615641 -144 CAATAAAATCATAAACCAAAAAGAATACACCC 2 56 1 ATAAACCAAA 0.783611 -131 TTTTTGTTTTAAGAAACTTAATGATCATTTTA 2 155 1 AAGAAACAAT 0.766358 -32 AATAGCGTTTAAAAAATGTAAATTTTAAACAA 3 57 1 AAAAAATAAA 0.820026 -158 CTAAATTGAGAAAAAATTCAATTCAAAGGGGC 3 91 0 AAAAAATAAT 0.948237 -124 TTCTTATAAACAAAACCTAAATTGAGAAAAAA 3 107 0 CAAAACCAAT 0.942075 -108 AACTGCTCCTAAAAACTCAAAATTAACCTAAA 3 190 0 AAAAACTAAA 0.879905 -25 TGAGACTGATAAAAAAGGAAATAGCACGATGA 5 78 0 AAAAAAGAAT 0.810634 -120 CCTTCTACTTAAAAACCCTAATTTTTTAAACA 6 97 0 AAAAACCAAT 0.976521 -78 AAAAAATAGCATAAACTCTTATACCTTCTACT 6 120 0 ATAAACTTAT 0.621946 -55 ATGTTCTATTCTAAACCAAAATTAACAACCAA 7 37 1 CTAAACCAAT 0.850618 -165 TTTTTCTATCAAAAACTTGAATGGTTTTACTC 7 118 0 AAAAACTAAT 0.96715 -84 TTTGATAGAAAAACACCCCAATAGTCTTATTG 7 137 1 AAACACCAAT 0.912165 -65 ******* *** Masking position 5 Map Score: 15.113 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 750 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 GAAAAAACGCAATGTTTTTAAAAGAAATCA 1 68 0 AATGTTTTTA 0.789927 -131 CTTTTTGGTTTATGATTTTATTGTATAATG 2 49 0 TATGATTTTA 0.913578 -138 ATCATGCTATCATTGTTATATTTTTGTTTT 2 135 1 CATTGTTATA 0.71794 -52 ATTGTTATATTTTTGTTTTAAGAAACTTAA 2 146 1 TTTTGTTTTA 0.762616 -41 TTAAAATTTACATTTTTTAAACGCTATTAG 3 55 0 CATTTTTTAA 0.614811 -160 TCAAAGGGGCTATTGTTTAAAATTTACATT 3 71 0 TATTGTTTAA 0.819918 -144 CAATTTAGGTTTTGTTTATAAGAAAAATTA 3 115 1 TTTGTTTATA 0.520085 -100 GCGCATTTTTTATTATTATATCCAAACTCA 5 153 0 TATTATTATA 0.739013 -45 TCTCCTTTTTCATGGTTTTAAGCGCATTTT 5 174 0 CATGGTTTTA 0.904114 -24 TAAAAACCCTAATTTTTTAAACACCATTTC 6 90 0 AATTTTTTAA 0.50374 -85 GAGTTTATGCTATTTTTTTAAGGTTTTAAA 6 134 1 TATTTTTTTA 0.882243 -41 TCCTTTGAAATTTGATTTTAAAACCTTAAA 6 150 0 TTTGATTTTA 0.739833 -25 CAAAAACTTGAATGGTTTTACTCTTTTACA 7 111 0 AATGGTTTTA 0.857072 -91 TAGTGTCAGTTATGATTATATTCGCTCAAT 7 165 0 TATGATTATA 0.799491 -37 TAACTGACACTATTATTTAAAGGATTAAC 7 183 1 TATTATTTAA 0.740593 -19 ********** Masking position 10 Map Score: 9.70597 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 708 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 5 TAGGAGTTGAATGCTATCAAAACTTAAGGA 1 17 0 ATGCTATCAA 0.877211 -182 AAGCTCTATCATGCTATCATTGTTATATTT 2 128 1 ATGCTATCAT 0.926942 -59 CATTTTTTAAACGCTATTAGATATAATAAG 3 45 0 ACGCTATTAG 0.950735 -170 TAGCGTTAATATGCTAATATAGTAGAACAT 5 32 0 ATGCTAATAT 0.944519 -166 TAGCATATTAACGCTAATATCCCCTTTAGG 5 46 1 ACGCTAATAT 0.957997 -152 ATAAGAGTTTATGCTATTTTTTTAAGGTTT 6 130 1 ATGCTATTTT 0.900371 -45 ATCATAACTGACACTATTATTTAAAGGATT 7 179 1 ACACTATTAT 0.872197 -23 ********** Masking position 6 Map Score: 3.43801 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 88 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 ATAACCCTTAAAAATCTTTTTTTGAATGCGT 1 126 0 AAATCTTTTT 0.726373 -73 TGTTTATCCTTTTTCTAAAGTTT 1 186 0 TTATCCTTTT 0.915694 -13 CCAAAAAGAATACACCCTCTTATTAAAAAGC 2 71 1 TAACCCTCTT 0.812157 -116 AAGAAACTTAATGATCATTTTAAGGGAGTTT 2 165 1 ATATCATTTT 0.671508 -22 TTAAAATCCTTTTTTGTATCGCA 4 3 1 AAATCCTTTT 0.935572 -125 CCATGATAACAAAACTCTTTTTACTTTTAGT 4 60 0 AAACTCTTTT 0.816912 -68 ATCACCCTTTTTGTAGTCATA 5 1 1 ATACCCTTTT 0.981168 -197 TATTAACGCTAATATCCCCTTTAGGTTTCAT 5 51 1 AAATCCCCTT 0.643056 -147 TCATCGTGCTATTTCCTTTTTTATCAGTCTC 5 78 1 ATTCCTTTTT 0.621122 -120 CGCATCTCCTTTTTCATGGTTTTA 5 184 0 ATTCCTTTTT 0.621122 -14 CGAACGGATAATAACCCTCTTTTGTGTAAAA 6 53 1 ATACCCTCTT 0.956573 -122 TTTATAACTCCTTTAAATCCCCTC 7 4 1 ATACTCCTTT 0.715658 -198 TGTTCTATTTATTATCCATTTGCTTATTAAT 7 71 0 ATATCCATTT 0.752054 -131 CTTGAATGGTTTTACTCTTTTACACAATGAA 7 104 0 TTACTCTTTT 0.767676 -98 GTTAATCCTTTAAATAATAGTG 7 190 0 TTATCCTTTA 0.498575 -12 ** ******** Masking position 10 Map Score: 8.48883 Number of sites scoring better than the average of aligned sites = 1594 Number in coding regions = 1352 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 7 TCATGCTATCATTGTTATATTTTTGTTTTAA 2 136 1 ATGTTATATT 0.908318 -51 ATTCAATTCAAAGGGGCTATTGTTTAAAATT 3 77 0 AAGGGCTATT 0.952711 -138 TTGTAGTCATAATGTTCTACTATATTAGCAT 5 21 1 AAGTTCTACT 0.953622 -177 ATGAAACCTAAAGGGGATATTAGCGTTAATA 5 51 0 AAGGGATATT 0.846106 -147 TTTAGGTTTCATCGTGCTATTTCCTTTTTTA 5 70 1 ATGTGCTATT 0.972683 -128 AATCCCCTCTAATGTTCTATTCTAAACCAAA 7 26 1 AAGTTCTATT 0.972934 -176 ACACAATGAAATTGTTCTATTTATTATCCAT 7 83 0 ATGTTCTATT 0.973196 -119 AAAAACTTGAATGGTTTTACTCTTTTACACA 7 109 0 ATGTTTTACT 0.760902 -93 ** ******** Masking position 9 Map Score: 4.9377 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 35 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ATAATGGGCGGTTAGTTAGGTATTTTTGAA 2 25 0 GTTAGTTAGG 0.959579 -162 GCGATTTTAGGTTAATTTTGAGTTTTTAGG 3 185 1 GTTAATTTTG 0.947943 -30 TAGGGCATTAGTCAATAATGCGATTTAAAA 4 101 1 GTCAATAATG 0.829064 -27 TTAAAAGAGTGTGAGTTTGGATATAATAAT 5 142 1 GTGAGTTTGG 0.933003 -56 ATAATTGGTTGTTAATTTTGGTTTAGAATA 7 43 0 GTTAATTTTG 0.947943 -159 AAATAATAGTGTCAGTTATGATTATATTCG 7 171 0 GTCAGTTATG 0.968665 -31 ********** Masking position 6 Map Score: 1.26624 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 50 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 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