AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_hpyl_reg_300.orf -o00920_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 HP0106 24 cystathionine gamma-synthase (metB) #2 HP0107 38 cysteine synthetase (cysK) #3 HP1210 300 serine acetyltransferase (cysE) Motif number 1 AAATTCAATAAAAAAGGAAAAAC 1 2 1 AATCATAAAA 0.983726 -23 TCTCCTATAACAAACAATAAAATTCAATTTTG 2 16 0 CAACATAAAA 0.849072 -23 CATTTTTATTTTTTCATTAAAATAGTTTTATT 3 40 1 TTTCATAAAA 0.918114 -261 TCGGCATTTATTTGGAATAAAACTATTTTAAT 3 55 0 TTTGATAAAA 0.960314 -246 AATCCTTTAAAAAGGCTTAAAAACTCACTAGT 3 98 0 AAAGCTAAAA 0.94068 -203 ATCCTTTCAAATTCGCTTAAACAATCCTTTAA 3 120 0 ATTGCTAAAC 0.927838 -181 AGCGAATTTGAAAGGATTAAAAGAGAGAGCGT 3 135 1 AAAGATAAAA 0.976369 -166 GTAAAAAATTAATAGAGTAAAACGCTCTCTCT 3 156 0 AATGATAAAA 0.990452 -145 CACTCCTTTAAATGGAGTAAAAAATTAATAGA 3 172 0 AATGATAAAA 0.990451 -129 TTTCTCACCCATTCCAATAAAACTTGATGCAA 3 232 0 ATTCATAAAA 0.98072 -69 GTTGGAATATATTTGAATCAACATGAGCAGAT 3 266 0 ATTGATCAAC 0.863183 -35 *** ** ***** Masking position 10 Map Score: 17.8224 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 458 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 AATTCAATAAAAAAGGAAAAACC 1 12 1 AAAAGGAAAA 0.878026 -13 TATTGTTTGTTATAGGAGAA 2 29 1 TATAGGAGAA 0.895778 -10 ATGCAGATTGAAAAAGATTACTATTAACTA 3 13 0 AAAAAGATTA 0.877975 -288 AAATGCCGAATAAATGATAGACTAGTGAGT 3 78 1 TAAATGATAG 0.792375 -223 CAATCCTTTAAAAAGGCTTAAAAACTCACT 3 101 0 AAAAGGCTTA 0.884004 -200 TAAGCCTTTTTAAAGGATTGTTTAAGCGAA 3 111 1 TAAAGGATTG 0.986909 -190 AAGCGAATTTGAAAGGATTAAAAGAGAGAG 3 134 1 GAAAGGATTA 0.955414 -167 AGTAAAAAATTAATAGAGTAAAACGCTCTC 3 159 0 TAATAGAGTA 0.788647 -142 TTACTCCATTTAAAGGAGTGTGAGTTTAGG 3 184 1 TAAAGGAGTG 0.986662 -117 CATCAAGTTTTATTGGAATGGGTGAGAAAA 3 235 1 TATTGGAATG 0.717246 -66 ********** Masking position 2 Map Score: 7.3907 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 920 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 3 TCGCAAAATTGAATTTTATTGTTTGTTATA 2 13 1 GAATTTTATT 0.874293 -26 TTTTCAATCTGCATTTTTATTTTTTCATTA 3 29 1 GCATTTTTAT 0.95367 -272 CATTTATTCGGCATTTATTTGGAATAAAAC 3 64 0 GCATTTATTT 0.978065 -237 AAAACTTGATGCAAATTTTTCTTGTCATTA 3 216 0 GCAAATTTTT 0.961342 -85 ATCAACATGAGCAGATTTTTTCTCACCCAT 3 252 0 GCAGATTTTT 0.974033 -49 TCTCCGGTTGGAATATATTTGAATCAACAT 3 274 0 GAATATATTT 0.917521 -27 ********** Masking position 6 Map Score: 5.1062 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 316 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TTTCCTTTTTTATTGAATTT 1 1 0 TATTGAATTT 0.939842 -24 AATCGCAAAATTGAATTTTATTGTTTGT 2 9 1 AATTGAATTT 0.956994 -30 AATGATAGACTAGTGAGTTTTTAAGCCTTT 3 90 1 TAGTGAGTTT 0.974569 -211 AGGATTGTTTAAGCGAATTTGAAAGGATTA 3 124 1 AAGCGAATTT 0.981906 -177 ATTTAAAGGAGTGTGAGTTTAGGTATAATG 3 191 1 GTGTGAGTTT 0.945268 -110 ATAAAACTTGATGCAAATTTTTCTTGTCAT 3 218 0 ATGCAAATTT 0.819973 -83 ********** Masking position 6 Map Score: 3.66833 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 477 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 ********** No masking Map Score: -3.31523e-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: -3.31523e-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: -3.31523e-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