AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_hpyl_reg_300.orf -o00272_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 HP0133 180 serine transporter (sdaC) #4 HP0885 167 virulence factor mviN protein (mviN) #5 HP1210 300 serine acetyltransferase (cysE) Motif number 1 GTTTTTCCTTTTTTATTGAATTT 1 3 0 TTTTATTGAT 0.937758 -22 CAAAATTGAATTTTATTGTTTGTTATAGGAG 2 16 1 TTTTATTGTT 0.955098 -23 TATAATCCTTTATTAATCTTTTTTTAAGCGT 3 14 1 TATTAATCTT 0.747162 -167 ATTAATCTTTTTTTAAGCGTTATTATAGCTT 3 25 1 TTTTAAGCTT 0.96973 -156 AGCATAAAGCTTTTTATGATTGGGGTTTTTT 3 117 0 TTTTTATGTT 0.871551 -64 TTTTTAATCCTTAAATGGTATA 4 2 1 TTTTAATCTT 0.97503 -166 ATTTTCAGTGTTTTTTTGTTAGCATATTTCT 4 51 0 TTTTTTTGTA 0.647225 -117 AAAAATATTTTTTTTAGCATACTGGTTGTAT 4 92 0 TTTTTAGCTA 0.734267 -76 AGCTTAGGGATTTTATGCTCTAGGATTTTTG 4 130 1 TTTTATGCCT 0.803497 -38 ATTTTTGGCTTTTTACGGGATTTG 4 154 1 TTTTACGGAT 0.910762 -14 AATAAAACTATTTTAATGAAAAAATAAAAAT 5 41 0 TTTTAATGAA 0.896523 -260 ATTAAAATAGTTTTATTCCAAATAAATGCCG 5 55 1 TTTTATTCAA 0.882105 -246 ACTAGTGAGTTTTTAAGCCTTTTTAAAGGAT 5 98 1 TTTTAAGCTT 0.96973 -203 TTTAAGCCTTTTTAAAGGATTGTTTAAGCGA 5 109 1 TTTAAAGGTT 0.660856 -192 ACGCTCTCTCTTTTAATCCTTTCAAATTCGC 5 136 0 TTTTAATCTT 0.97503 -165 AGAGAGAGCGTTTTACTCTATTAATTTTTTA 5 156 1 TTTTACTCAT 0.939312 -145 TCTATTAATTTTTTACTCCATTTAAAGGAGT 5 172 1 TTTTACTCAT 0.939312 -129 TTGCATCAAGTTTTATTGGAATGGGTGAGAA 5 232 1 TTTTATTGAA 0.857431 -69 ******** ** Masking position 3 Map Score: 25.4832 Number of sites scoring better than the average of aligned sites = 1509 Number in coding regions = 1215 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 2 TTCTATAATCCTTTATTAATCTTTT 3 6 1 TAATCCTTTA 0.986577 -175 AATCCTTTATTAATCTTTTTTTAAGCGTTA 3 17 1 TAATCTTTTT 0.961758 -164 TTTTTAATCCTTAAATGGTATAAT 4 5 1 TAATCCTTAA 0.923666 -163 TAGTTAATAGTAATCTTTTTCAATCTGCAT 5 13 1 TAATCTTTTT 0.961758 -288 AGTGAGTTTTTAAGCCTTTTTAAAGGATTG 5 101 1 TAAGCCTTTT 0.947195 -200 TTCGCTTAAACAATCCTTTAAAAAGGCTTA 5 111 0 CAATCCTTTA 0.947159 -190 CTCTCTCTTTTAATCCTTTCAAATTCGCTT 5 134 0 TAATCCTTTC 0.971879 -167 GAGAGCGTTTTACTCTATTAATTTTTTACT 5 159 1 TACTCTATTA 0.794961 -142 ATTAATTTTTTACTCCATTTAAAGGAGTGT 5 175 1 TACTCCATTT 0.922219 -126 ********** Masking position 8 Map Score: 11.9283 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 150 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 TCGCAAAATTGAATTTTATTGTTTGTTATA 2 13 1 GAATTTTATT 0.735225 -26 TTTTGGGCACGCATTTATTTTCTAAAATCC 3 72 0 GCATTTATTT 0.965695 -109 TTTTTTGTTAGCATATTTCTTTTTTCAAAT 4 41 0 GCATATTTCT 0.946176 -127 TGTTGGTTAAAAATATTTTTTTTAGCATAC 4 101 0 AAATATTTTT 0.589195 -67 TTTTCAATCTGCATTTTTATTTTTTCATTA 5 29 1 GCATTTTTAT 0.905942 -272 CATTTATTCGGCATTTATTTGGAATAAAAC 5 64 0 GCATTTATTT 0.965695 -237 AAAACTTGATGCAAATTTTTCTTGTCATTA 5 216 0 GCAAATTTTT 0.921783 -85 ATCAACATGAGCAGATTTTTTCTCACCCAT 5 252 0 GCAGATTTTT 0.946176 -49 TCTCCGGTTGGAATATATTTGAATCAACAT 5 274 0 GAATATATTT 0.88755 -27 ********** Masking position 6 Map Score: 8.08542 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 414 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 TTATAGCTTGTGCGGGTTAAATCGTGGATTT 3 47 1 TGCGGTTAAA 0.982344 -134 GAGCTTTCATTGTAGCATAAAGCTTTTTATG 3 130 0 TGTGCATAAA 0.950113 -51 ATCCCTAAGCTGTTGGTTAAAAATATTTTTT 4 110 0 TGTGGTTAAA 0.97875 -58 AAAATAAAAATGCAGATTGAAAAAGATTACT 5 21 0 TGCGATTGAA 0.960834 -280 TCGGCATTTATTTGGAATAAAACTATTTTAA 5 56 0 TTTGAATAAA 0.846994 -245 TCCAAATAAATGCCGAATAAATGATAGACTA 5 71 1 TGCGAATAAA 0.98097 -230 AATCTGCTCATGTTGATTCAAATATATTCCA 5 265 1 TGTGATTCAA 0.953106 -36 *** ******* Masking position 10 Map Score: 5.43335 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 103 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 GATTAATAAAGGATTATAGAA 3 2 0 GGATTATAGA 0.963638 -179 GTTAAATCGTGGATTTTAGAAAATAAATGC 3 62 1 GGATTTTAGA 0.988661 -119 TTATGATTGGGGTTTTTTGAGATTAAGGGG 3 105 0 GGTTTTTTGA 0.955576 -76 AACAGCTTAGGGATTTTATGCTCTAGGATT 4 127 1 GGATTTTATG 0.960668 -41 TTATGCTCTAGGATTTTTGGCTTTTTACGG 4 142 1 GGATTTTTGG 0.986354 -26 CCTTTTTAAAGGATTGTTTAAGCGAATTTG 5 115 1 GGATTGTTTA 0.929933 -186 ********** Masking position 5 Map Score: 6.36709 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 146 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ACCCGCACAAGCTATAATAACGCTTAAAAAA 3 33 0 GCTATAATAC 0.812385 -148 AAAGCTTTATGCTACAATGAAAGCTCTTTAA 3 135 1 GCTACAATGA 0.918201 -46 ATAAAAGGGCGGTTTAATAGC 3 170 1 GGTTTAATAC 0.833646 -11 ATCCTTAAATGGTATAATATAAGAATTTGAA 4 17 1 GGTATAATAA 0.96194 -151 TGTGAGTTTAGGTATAATGACAAGAAAAATT 5 202 1 GGTATAATGC 0.973182 -99 ********* * Masking position 6 Map Score: 0.925712 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 17 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 ********** No masking Map Score: 1.57984e-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 8 ********** No masking Map Score: 1.57984e-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 9 ********** No masking Map Score: 1.57984e-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