AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00472_hpyl_reg_300.orf -o00472_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 Purged sequences: HP1350 209 protease Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #4 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #5 HP1352 300 adenine specific DNA methyltransferase (HINFIM) Motif number 1 ATTATATTGATTTAGCGTTACTT 1 1 0 TTTAGCTATT 0.820795 -257 GGTGTTTGTTTTAAGACGCTATGACTATCTTTA 1 74 0 TTAAGAGTTG 0.6615 -184 ATTGGCATGATTTAAGAGTAATGGGTGTTTGTT 1 97 0 TTTAAGGATG 0.907013 -161 GGTAGTTTTTTTTAAGTTGTGTTATTATTTTCA 1 153 0 TTTAAGTTTT 0.931721 -105 GATTGATTTTTTTAAGGGTAGTTTTTTTTAAGT 1 169 0 TTTAAGGATT 0.961456 -89 ATTTAAGAATTTTAGATTGATTTTTTTAAGGGT 1 183 0 TTTAGATATT 0.886471 -75 ATTTTGAGTTTTTAGGAGCAGTTTTT 2 4 0 TTTAGGGATT 0.988475 -211 GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 2 23 0 TTTAGGTATT 0.979131 -192 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAA 2 51 0 TTAAGGATTT 0.74644 -164 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAA 2 95 0 TTTAGGTTTT 0.979131 -120 ATTTACATTTTTTAAACGCTATTAGATATAATA 2 156 1 TTTAAAGTTT 0.805875 -59 TGGACCTAGCTGTAGGGTTAATTAAAATTATTT 3 37 0 TGTAGGTATT 0.856116 -107 CAATTTCAATTTTAGGGGGTTTTGTTTGGTATT 3 94 0 TTTAGGGTTT 0.988475 -50 AAAGGCATTCTTAAGGGGTTCTGTCTCATTAAG 4 17 0 TTAAGGGTTG 0.921522 -72 AATGCCTTTATTTAAGAGCATTTGTGATAGAAT 4 41 1 TTTAAGGATT 0.961456 -48 CACAAGCGTTTTAAGGTTATCTTAATGTTTAAT 5 237 0 TTAAGGTTTT 0.942618 -64 ****** * * ** Masking position 4 Map Score: 23.1396 Number of sites scoring better than the average of aligned sites = 1453 Number in coding regions = 1225 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 TTCACACTCTTTAGACTTGAAATTTGAAAATAATA 1 129 1 TTGATTATTT 0.973751 -129 ATAGCTATATTTTAATTTAAGAATTTTAGATTGAT 1 195 0 TTAATTAATT 0.959337 -63 CGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGT 2 15 0 TTATTTATTT 0.935415 -200 TTCTACTACATTTGAAATAATTTTTCTTATAAACA 2 74 1 TTGAATATTT 0.9116 -141 CAATAGCCCCTTTGAATTGAATTTTTTCTCAATTT 2 115 0 TTGATTATTT 0.973751 -100 GGGCTATTGTTTAAAATTTACATTTTTTAAACGCT 2 141 1 TTAATTATTT 0.981169 -74 GTAGGGTTAATTAAAATTATTTATTGAGTTGAATT 3 24 0 TTAATTTATT 0.768499 -120 ATTTTCAGACTTCAATTTCAATTTTAGGGGGTTTT 3 104 0 TTAATTATTT 0.981169 -40 TTCCCTTTATTTAAAAATCACCATTCTATCACAAA 4 61 0 TTAAATAATT 0.867692 -28 ATCTTAATGTTTAATCTTTAGCTTTGTTCTCATCA 5 217 0 TTATTTATTT 0.935415 -84 ** ** ** * *** Masking position 8 Map Score: 11.0381 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 99 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 TGAGAGAAAGGTTTGGGTTTAGGGTTTGAA 1 33 0 GTTTGGGTTT 0.815882 -225 AGAGTAATGGGTGTTTGTTTTAAGACGCTA 1 86 0 GTGTTTGTTT 0.891462 -172 AGTGTGAATTGGCATGATTTAAGAGTAATG 1 107 0 GGCATGATTT 0.58593 -151 TTTAAGTTGTGTTATTATTTTCAAATTTCA 1 146 0 GTTATTATTT 0.784477 -112 TTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 166 0 GGTAGTTTTT 0.675141 -92 TTGAAACCTTGAGATTGTTTTAGTGTATTA 1 229 0 GAGATTGTTT 0.683032 -29 GTAGAATTAAGGCAGTGTTTTTGCGTCAAG 2 50 0 GGCAGTGTTT 0.937102 -165 TCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 94 0 GGTTTTGTTT 0.974046 -121 ATTCAAAGGGGCTATTGTTTAAAATTTACA 2 133 1 GCTATTGTTT 0.952179 -82 AATTTTAGGGGGTTTTGTTTGGTATTTTAC 3 90 0 GGTTTTGTTT 0.974046 -54 CCTTAAGAATGCCTTTATTTAAGAGCATTT 4 34 1 GCCTTTATTT 0.761296 -55 GGAGTTATGCGTTTTTGTTGTATCGTTTAA 5 133 1 GTTTTTGTTG 0.766309 -168 ACCTTAAAACGCTTGTGTTAAAATGGCTAG 5 253 1 GCTTGTGTTA 0.662376 -48 ********** Masking position 8 Map Score: 6.84165 Number of sites scoring better than the average of aligned sites = 992 Number in coding regions = 846 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 TGCGAGATATATGAGAGAAAGGTTTGGGTTT 1 43 0 ATGAGAAAAG 0.969988 -215 AAAACCTAAATTGAGAAAAAATTCAATTCAA 2 108 1 TTGAGAAAAA 0.953605 -107 TTGATGCTTAATGAGACAGAACCCCTTAAGA 4 11 1 ATGAGAAGAA 0.982229 -78 TTAAGAGCATTTGTGATAGAATGGTGATTTT 4 52 1 TTGTGAAGAA 0.912826 -37 TCTATCGCAAATGAGAGCGAGATTAGGCAAT 5 29 0 ATGAGACGAG 0.978222 -272 TCGCTCTCATTTGCGATAGAGGCTCTAAAGT 5 40 1 TTGCGAAGAG 0.949353 -261 GATGCATTTGATGAGAACAAAGCTAAAGATT 5 209 1 ATGAGACAAA 0.947396 -92 ****** **** Masking position 6 Map Score: 5.19087 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 76 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 5 AAAGAGTGTGAATTGGCATGATTTAAGAGT 1 111 0 AATTGGCATG 0.854741 -147 AATTAACCTAAAATCGCTTGACGCAAAAAC 2 34 1 AAATCGCTTG 0.979625 -181 ATTCACATGCAAATCGCAAAGCATGTTCGT 5 96 0 AAATCGCAAA 0.886354 -205 CGATACAACAAAAACGCATAACTCCCCGAT 5 128 0 AAAACGCATA 0.886227 -173 AGATAACCTTAAAACGCTTGTGTTAAAATG 5 248 1 AAAACGCTTG 0.973159 -53 GCTTGTGTTAAAATGGCTAGAGTAGCAGAT 5 263 1 AAATGGCTAG 0.96592 -38 TAGCAGATATAAAAGGTTAGTTAATC 5 285 1 AAAAGGTTAG 0.738447 -16 ********** Masking position 2 Map Score: 3.02175 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 738 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 TTCTTAAATTAAAATATAGCTATAATACAC 1 207 1 AAAATATAGC 0.89346 -51 TCAAGGTTTCAAAATTTAGCC 1 247 1 AAAATTTAGC 0.893469 -11 AAAATTATTTCAAATGTAGTAGAATTAAGG 2 68 0 CAAATGTAGT 0.958771 -147 ATAATAGCGCAAAATGTAGTAAAATACCAA 3 72 1 AAAATGTAGT 0.93666 -72 GCATCAAATGCAAATGCATCAAATGATAGA 5 184 0 CAAATGCATC 0.950688 -117 TTGTTCTCATCAAATGCATCAAATGCAAAT 5 199 0 CAAATGCATC 0.950688 -102 ********** Masking position 5 Map Score: 1.93239 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 88 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AACTTAAAAAAAACTACCCTTAAAAAAATC 1 168 1 AAACTACCCT 0.934938 -90 TAAAAACTCAAAATTAACCTAAAATCGCTT 2 23 1 AAATTAACCT 0.892198 -192 TTATAGGTGGTAACTATCCCTTATTATATC 2 180 0 TAACTATCCC 0.980453 -35 TAAATAATTTTAATTAACCCTACAGCTAGG 3 36 1 TAATTAACCC 0.960452 -108 TGATAGAAGCTATCTATCCCCACCTATTTT 5 161 0 TATCTATCCC 0.925231 -140 GATTAACTAACCTTTTATATCTG 5 288 0 TAACTAACCT 0.978591 -13 ********** Masking position 5 Map Score: 3.65891 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 37 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ATTAAAATATAGCTATAATACACTAAAACA 1 214 1 AGCTATAATA 0.814806 -44 TTTTGCGTCAAGCGATTTTAGGTTAATTTT 2 32 0 AGCGATTTTA 0.857489 -183 ATTTTTTAAACGCTATTAGATATAATAAGG 2 162 1 CGCTATTAGA 0.893565 -53 GGTAACTATCCCTTATTATATCTAATAGCG 2 172 0 CCTTATTATA 0.851018 -43 TGAACGATCCTTATTTTATAGGTGGTAA 2 197 0 CCTTATTTTA 0.822585 -18 CTACATTTTGCGCTATTATATTGGACCTAG 3 61 0 CGCTATTATA 0.972923 -83 ATCTATCCCCACCTATTTTAAACGATACAA 5 150 0 ACCTATTTTA 0.948157 -151 CTGCTACTCTAGCCATTTTAACACAAGCGT 5 261 0 AGCCATTTTA 0.857489 -40 GATTAACTAACCTTTTATATCTGCTACTC 5 282 0 ACCTTTTATA 0.780317 -19 ********** Masking position 6 Map Score: 3.59013 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 250 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 ********** No masking Map Score: 2.12695e-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 10 ********** No masking Map Score: 2.12695e-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 11 ********** No masking Map Score: 2.12695e-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