AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00473_hpyl_reg_100.orf -o00473_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 HP0737 146 conserved hypothetical integral membrane protein #2 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #3 HP0942 40 D-alanine glycine permease (dagA) #4 HP0943 21 D-amino acid dehydrogenase (dadA) #5 HP0944 300 translation initiation inhibitor, putative Motif number 1 ATGATAACTTTTAAATTCTCTCAAAAATTAAAGGTT 1 18 0 TAAATTAAAA 0.991268 -129 GTTATCATACTAAAACGTGCTTAAAATTAAGCCTTA 1 46 1 TAAAGTAAAA 0.951208 -101 ATTTTAGCATTTTATTTGCATTAAAAAGCGATTTTC 1 90 0 TTATTTAAAA 0.92915 -57 TCATTGCCTTAAATTCTTTTTAAATCATGGCATT 1 123 0 TAAATTTAAA 0.921019 -24 AAAAAGGCTTTTGAATTTTCTTAAAA 2 1 0 TGAATTAAAA 0.958863 -77 AAAGTCTATCTATATTTACCTAAAAAAAGGCTTTTG 2 24 0 TTATTTAAAA 0.949178 -54 GATCAAACTCCCTAAAAACGATTGCAAT 2 60 0 TAAATTAAAA 0.991271 -18 TTAGTGGCAATGAGTGTCTGTAAAAATGCTCAAAAG 5 34 1 TAGTTTAAAA 0.892381 -267 AGTGGTAGCTTTAAAATTGATGACAACAAAGCCTAA 5 110 1 TAAATTACAA 0.951153 -191 CAACAAAGCCTAAAACTCAAACAAAACCCGTTTAAG 5 133 1 TAAATAAAAA 0.958668 -168 TAAGAATTTCTAAATATGGGTAAAAAATATACAATA 5 165 1 TAATTTAAAA 0.981333 -136 TACAATACCTTATAATAAGATGAAAATTCATGGCGT 5 194 1 TTAAATAAAA 0.823822 -107 TATTATGCAATCAAATTAATAAAGAAATAAAAAATG 5 238 0 TAAATAAGAA 0.799269 -63 * *** * * **** Masking position 15 Map Score: 17.0188 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 699 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 CCTTTAATTTTTGAGAGAATTTAAAAGTTATC 1 20 1 TAGAGAATTT 0.920473 -127 TTATTTGCATTAAAAAGCGATTTTCTTAAACA 1 83 0 TAAAGCGATT 0.824431 -64 TTCTTTTTAAATCATGGCATTTTAGCATTTTA 1 112 0 AATGGCATTT 0.794304 -35 TGCCATGATTTAAAAAGAATTTAAGGCAATGA 1 125 1 TAAAGAATTT 0.942049 -22 TTAAGAAAATTCAAAAGCCTTTTTTTAGGTAA 2 13 1 TAAAGCCTTT 0.972695 -65 TAGGTAAATATAGATAGACTTTATTGCAATCG 2 38 1 TATAGACTTT 0.921106 -40 TGCAATCGTTTTTAGGGAGTTTGATC 2 62 1 TAGGGAGTTT 0.976893 -16 ACCCTAGTTTATTAAGGAGTTTTT 3 27 1 AAAGGAGTTT 0.923823 -14 TTTATTAAAGGGACTATCAGC 4 6 1 TAGGGACTAT 0.784116 -16 GTAAAAATGCTCAAAAGCATTTTCTATAATAA 5 53 1 TAAAGCATTT 0.957373 -248 ACCACTCGCTTGCAAGCCCTTTTATTATGGCT 5 84 0 TAAGCCCTTT 0.866047 -217 AAGATGAAAATTCATGGCGTTTTGCGCTCATT 5 210 1 TATGGCGTTT 0.973785 -91 TAACACATCATCATAGGAGTTTCAATC 5 284 1 TTAGGAGTTT 0.863365 -17 * ********* Masking position 12 Map Score: 13.5397 Number of sites scoring better than the average of aligned sites = 1992 Number in coding regions = 1789 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 3 TGCTTAAAATTAAGCCTTATTGTTTAAGAAA 1 63 1 TAAGCCTATT 0.863231 -84 AAAATGCTAAAATGCCATGATTTAAAAAGAA 1 113 1 AATGCCTGAT 0.941635 -34 TCATTGCCTTAAATTCTTTTTAA 1 134 0 ATTGCCTAAA 0.800522 -13 AGAAAATTCAAAAGCCTTTTTTTAGGTAAAT 2 16 1 AAAGCCTTTT 0.800398 -62 GATCAAACTCCCTAAAAACGATTGCA 2 62 0 AACTCCTAAA 0.946316 -16 AAAAACTCCTTAATAAACTAGGGT 3 27 0 AACTCCTAAT 0.954436 -14 AAAAGAGGGCAAAGCCGCAATCTGT 5 5 0 AAAGCCCAAT 0.954689 -296 TTTTCTATAATAAGCCATAATAAAAGGGCTT 5 72 1 TAAGCCTAAT 0.962175 -229 TGATGACAACAAAGCCTAAAACTCAAACAAA 5 127 1 AAAGCCAAAA 0.923894 -174 CCATATTTAGAAATTCTTAAACGGGTTTTGT 5 153 0 AAATTCTAAA 0.627405 -148 ATGAGCGCAAAACGCCATGAATTTTCATCTT 5 210 0 AACGCCTGAA 0.968352 -91 ****** **** Masking position 6 Map Score: 7.9474 Number of sites scoring better than the average of aligned sites = 1935 Number in coding regions = 1786 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 AATGCCATGATTTAAAAAGAATTTAAGGCA 1 123 1 TTTAAAAAGA 0.701691 -24 TATATTTACCTAAAAAAAGGCTTTTGAATT 2 20 0 TAAAAAAAGG 0.940109 -58 TTTTTTTAGGTAAATATAGATAGACTTTAT 2 32 1 TAAATATAGA 0.913049 -46 AAACTAGGGTTTAAAAAAGAAATTCC 3 7 0 TTAAAAAAGA 0.956716 -34 AAACCCTAGTTTATTAAGGAGTTTTT 3 25 1 TTATTAAGGA 0.823887 -16 TTTATTAAAGGGACTATCAGC 4 2 1 TTATTAAAGG 0.909336 -20 TTATTATGGCTTATTATAGAAAATGCTTTT 5 65 0 TTATTATAGA 0.885972 -236 TAATAAGCCATAATAAAAGGGCTTGCAAGC 5 79 1 TAATAAAAGG 0.90934 -222 AGTGGTAGCTTTAAAATTGATGACAACAAA 5 110 1 TTAAAATTGA 0.777971 -191 TAAGAATTTCTAAATATGGGTAAAAAATAT 5 165 1 TAAATATGGG 0.768676 -136 AATAAAGAAATAAAAAATGAGCGCAAAACG 5 227 0 TAAAAAATGA 0.825589 -74 TGCAATCAAATTAATAAAGAAATAAAAAAT 5 239 0 TTAATAAAGA 0.950082 -62 TTTGATTGCATAATAATAGCTGACATAACA 5 259 1 TAATAATAGC 0.645424 -42 ********** Masking position 6 Map Score: 14.971 Number of sites scoring better than the average of aligned sites = 935 Number in coding regions = 718 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 5 ********** No masking Map Score: -1.12023e-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 6 ********** No masking Map Score: -1.12023e-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 7 ********** No masking Map Score: -1.12023e-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