AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_hpyl_reg_100.orf -o00272_hpyl_100.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 AAATTCAATAAAAAAGGAAAAAC 1 3 1 ATCAATAAAA 0.929246 -22 CTCCTATAACAAACAATAAAATTCAATTTTG 2 16 0 AACAATAAAA 0.948817 -23 ACGCTTAAAAAAAGATTAATAAAGGATTATA 3 14 0 AAGATTAATA 0.72031 -167 AAGCTATAATAACGCTTAAAAAAAGATTAAT 3 25 0 AAGCTTAAAA 0.965421 -156 AAAAAACCCCAATCATAAAAAGCTTTATGCT 3 117 1 AACATAAAAA 0.855351 -64 TATACCATTTAAGGATTAAAAA 4 2 0 AAGATTAAAA 0.971453 -166 AGAAATATGCTAACAAAAAAACACTGAAAAT 4 51 1 TACAAAAAAA 0.615225 -117 ATACAACCAGTATGCTAAAAAAAATATTTTT 4 92 1 TAGCTAAAAA 0.706583 -76 CAAAAATCCTAGAGCATAAAATCCCTAAGCT 4 130 0 AGGCATAAAA 0.780873 -38 CAAATCCCGTAAAAAGCCAAAAAT 4 154 0 ATCCGTAAAA 0.898935 -14 ATTTTTATTTTTTCATTAAAATAGTTTTATT 5 41 1 TTCATTAAAA 0.883619 -260 CGGCATTTATTTGGAATAAAACTATTTTAAT 5 55 0 TTGAATAAAA 0.867047 -246 ATCCTTTAAAAAGGCTTAAAAACTCACTAGT 5 98 0 AAGCTTAAAA 0.965421 -203 TCGCTTAAACAATCCTTTAAAAAGGCTTAAA 5 109 0 AACCTTTAAA 0.629384 -192 GCGAATTTGAAAGGATTAAAAGAGAGAGCGT 5 136 1 AAGATTAAAA 0.971453 -165 TAAAAAATTAATAGAGTAAAACGCTCTCTCT 5 156 0 ATGAGTAAAA 0.930981 -145 ACTCCTTTAAATGGAGTAAAAAATTAATAGA 5 172 0 ATGAGTAAAA 0.930981 -129 TTCTCACCCATTCCAATAAAACTTGATGCAA 5 232 0 TTCAATAAAA 0.839791 -69 ** ******** Masking position 9 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 AAAAGATTAATAAAGGATTATAGAA 3 6 0 TAAAGGATTA 0.98643 -175 TAACGCTTAAAAAAAGATTAATAAAGGATT 3 17 0 AAAAAGATTA 0.961314 -164 ATTATACCATTTAAGGATTAAAAA 4 5 0 TTAAGGATTA 0.922815 -163 ATGCAGATTGAAAAAGATTACTATTAACTA 5 13 0 AAAAAGATTA 0.961314 -288 CAATCCTTTAAAAAGGCTTAAAAACTCACT 5 101 0 AAAAGGCTTA 0.946591 -200 TAAGCCTTTTTAAAGGATTGTTTAAGCGAA 5 111 1 TAAAGGATTG 0.946555 -190 AAGCGAATTTGAAAGGATTAAAAGAGAGAG 5 134 1 GAAAGGATTA 0.971549 -167 AGTAAAAAATTAATAGAGTAAAACGCTCTC 5 159 0 TAATAGAGTA 0.793003 -142 ACACTCCTTTAAATGGAGTAAAAAATTAAT 5 175 0 AAATGGAGTA 0.921352 -126 ********** Masking position 3 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 0.766553 -26 TTTTGGGCACGCATTTATTTTCTAAAATCC 3 72 0 GCATTTATTT 0.970819 -109 TTTTTTGTTAGCATATTTCTTTTTTCAAAT 4 41 0 GCATATTTCT 0.954095 -127 TGTTGGTTAAAAATATTTTTTTTAGCATAC 4 101 0 AAATATTTTT 0.607577 -67 TTTTCAATCTGCATTTTTATTTTTTCATTA 5 29 1 GCATTTTTAT 0.919289 -272 CATTTATTCGGCATTTATTTGGAATAAAAC 5 64 0 GCATTTATTT 0.970819 -237 AAAACTTGATGCAAATTTTTCTTGTCATTA 5 216 0 GCAAATTTTT 0.932885 -85 ATCAACATGAGCAGATTTTTTCTCACCCAT 5 252 0 GCAGATTTTT 0.954095 -49 TCTCCGGTTGGAATATATTTGAATCAACAT 5 274 0 GAATATATTT 0.893365 -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 0.981942 -134 GAGCTTTCATTGTAGCATAAAGCTTTTTATG 3 130 0 TGTGCATAAA 0.949035 -51 ATCCCTAAGCTGTTGGTTAAAAATATTTTTT 4 110 0 TGTGGTTAAA 0.978269 -58 AAAATAAAAATGCAGATTGAAAAAGATTACT 5 21 0 TGCGATTGAA 0.959963 -280 TCGGCATTTATTTGGAATAAAACTATTTTAA 5 56 0 TTTGAATAAA 0.844001 -245 TCCAAATAAATGCCGAATAAATGATAGACTA 5 71 1 TGCGAATAAA 0.980538 -230 AATCTGCTCATGTTGATTCAAATATATTCCA 5 265 1 TGTGATTCAA 0.952071 -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 TTCTATAATCCTTTATTAATC 3 2 1 TCTATAATCC 0.960008 -179 GCATTTATTTTCTAAAATCCACGATTTAAC 3 62 0 TCTAAAATCC 0.987497 -119 CCCCTTAATCTCAAAAAACCCCAATCATAA 3 105 1 TCAAAAAACC 0.951182 -76 AATCCTAGAGCATAAAATCCCTAAGCTGTT 4 127 0 CATAAAATCC 0.956756 -41 CCGTAAAAAGCCAAAAATCCTAGAGCATAA 4 142 0 CCAAAAATCC 0.984957 -26 CAAATTCGCTTAAACAATCCTTTAAAAAGG 5 115 0 TAAACAATCC 0.923207 -186 ********** Masking position 6 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