AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i159_glycolate_Oxidase_hpyl_reg_100.orf -o159_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01426 203 AE000511 #2 RHP00088 297 AE000511 #3 RHP00089 82 AE000511 #4 RHP00098 37 AE000511 Motif number 1 TACGGATTGATTAAAAAGAAAATACCCAACGCTA 1 17 1 TAAAAGAAAA 0.975939 -187 AAAACGCGCTTCATAAAGCTATAAAAACAAGGCC 1 95 1 TATAAGCTAA 0.985989 -109 AGCCATTAAAGAAAAACGATACAAGTTTAAAGCC 1 130 0 GAAAAGATAA 0.928335 -74 ATAGCATAAATGATAATGAAAAAGTAAATGAGAG 2 49 1 TATAAGAAAG 0.929081 -249 GCTAATGGCTTGATAAAGCTTAGATTTTATCATA 2 126 1 TATAAGCTTA 0.907836 -172 TTCTTAAATCTAAAAATGCTACAATGTTTATCTT 2 251 1 TAAAAGCTAA 0.98928 -47 ATGTTTATCTTTAAAACGAAAGGGCAATTTAACC 2 274 1 TAAAAGAAAG 0.939641 -24 TAATCATTCTTAAAAACGCTAAAAATTA 3 5 0 TAAAAGCTAA 0.988043 -78 TGATTAGTTATAATAACGCTACTAACAACACTCA 3 33 1 TATAAGCTAA 0.984989 -50 AGCTAAAATCTATTAAGGAAATCAGT 3 67 1 TTTAAGAAAA 0.812603 -16 ACAATCAGCTTAAAAAGGATATAAA 4 23 1 TAAAAGATAA 0.985507 -15 * **** **** * Masking position 6 Map Score: 17.3127 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 312 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 GCATGGTGGTTTCTCATAAATGGTTTTATCT 1 58 0 TTTCATAAAT 0.909553 -146 GAGAAACCACCATGCATCAATAAAACGCGCT 1 74 1 CAGCATCAAT 0.842423 -130 AAAACAAGGCCAGGCTTTAAACTTGTATCGT 1 118 1 CAGCTTTAAA 0.888203 -86 CTTGTATCGTTTTTCTTTAATGGCTTATGTT 1 139 1 TTTCTTTAAT 0.879571 -65 GATTTGATTGAAGGCATTAAACAACTGC 1 186 1 AAGCATTAAA 0.75669 -18 TCCCATAATTATAGCATAAATGATAATGAAA 2 39 1 ATGCATAAAT 0.814518 -259 AGCTTAGATTTTATCATAAAAATCTATTTAA 2 142 1 TTTCATAAAA 0.920895 -156 TTTTACCTAATTCTCATTAAATAGATTTTTA 2 158 0 TTTCATTAAA 0.907458 -140 AAAAAAGGGGTTGGCATCAATAGGGGGTTAA 2 187 1 TTGCATCAAT 0.887239 -111 ATGTAAAAAGCATTCTTAAATCTAAAAATGC 2 239 1 CATCTTAAAT 0.855041 -59 GCTACAATGTTTATCTTTAAAACGAAAGGGC 2 268 1 TTTCTTTAAA 0.894342 -30 TATAACTAATCATTCTTAAAAACGCTAAAAA 3 14 0 CATCTTAAAA 0.872337 -69 TTGGATACAATCAGCTTAAAAAGGATATAAA 4 17 1 TCGCTTAAAA 0.786835 -21 ** ******** Masking position 9 Map Score: 10.0661 Number of sites scoring better than the average of aligned sites = 1392 Number in coding regions = 1175 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 TATAAGACGAGATAAAACCATTTATGAGAA 1 49 1 GATAAAACCA 0.893588 -155 TTCATAAAGCTATAAAAACAAGGCCAGGCT 1 104 1 TATAAAAACA 0.741722 -100 AAAGAAAAACGATACAAGTTTAAAGCCTGG 1 127 0 GATACAAGTT 0.765657 -77 TATCATTTATGCTATAATTATGGGACAACT 2 34 0 GCTATAATTA 0.731944 -264 AGATTTTTATGATAAAATCTAAGCTTTATC 2 137 0 GATAAAATCT 0.950803 -161 TTACATATTATATAAAAATATCCCCTTTTA 2 215 0 TATAAAAATA 0.550662 -83 ATCTAAAAATGCTACAATGTTTATCTTTAA 2 258 1 GCTACAATGT 0.843796 -40 TCTTAAAAACGCTAAAAATTA 3 2 0 GCTAAAAATT 0.899837 -81 TTATAATAACGCTACTAACAACACTCAAGC 3 40 1 GCTACTAACA 0.77496 -43 CAACACTCAAGCTAAAATCTATTAAGGAAA 3 58 1 GCTAAAATCT 0.962874 -25 ACGAAATTGGATACAATCAGCTTAAAAAG 4 10 1 GATACAATCA 0.961362 -28 ********** Masking position 4 Map Score: 5.40301 Number of sites scoring better than the average of aligned sites = 1376 Number in coding regions = 1198 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 4 AAACCAACACAAAGGAGATACT 2 3 0 AAAGGAGATA 0.986581 -295 TAGGTAAAAAAAAGGGGTTGGCATCAATAG 2 180 1 AAAGGGGTTG 0.981159 -118 TTGGCATCAATAGGGGGTTAAAAGGGGATA 2 197 1 TAGGGGGTTA 0.940567 -101 TAGGGGGTTAAAAGGGGATATTTTTATATA 2 207 1 AAAGGGGATA 0.993999 -91 ATCAGCTTAAAAAGGATATAAA 4 26 1 AAAGGATATA 0.933728 -12 ********** Masking position 2 Map Score: 3.44833 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 197 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 ********** No masking Map Score: -9.14168e-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 6 ********** No masking Map Score: -9.14168e-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: -9.14168e-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