AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00473_hpyl_reg_300.orf -o00473_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 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 AACCTTTAATTTTTGAGAGAATTTAAAAGTTATCAT 1 18 1 TTTTAATTTA 0.991064 -129 TAAGGCTTAATTTTAAGCACGTTTTAGTATGATAAC 1 46 0 TTTTACTTTA 0.950118 -101 GAAAATCGCTTTTTAATGCAAATAAAATGCTAAAAT 1 90 1 TTTTAAATAA 0.928483 -57 AATGCCATGATTTAAAAAGAATTTAAGGCAATGA 1 123 1 TTTAAATTTA 0.919425 -24 TTTTAAGAAAATTCAAAAGCCTTTTT 2 1 1 TTTTAATTCA 0.957964 -77 CAAAAGCCTTTTTTTAGGTAAATATAGATAGACTTT 2 24 1 TTTTAAATAA 0.948046 -54 ATTGCAATCGTTTTTAGGGAGTTTGATC 2 60 1 TTTTAATTTA 0.991068 -18 CTTTTGAGCATTTTTACAGACACTCATTGCCACTAA 5 34 0 TTTTAAACTA 0.890128 -267 TTAGGCTTTGTTGTCATCAATTTTAAAGCTACCACT 5 110 0 TTGTAATTTA 0.950064 -191 CTTAAACGGGTTTTGTTTGAGTTTTAGGCTTTGTTG 5 133 0 TTTTTATTTA 0.957737 -168 TATTGTATATTTTTTACCCATATTTAGAAATTCTTA 5 165 0 TTTTAAATTA 0.980902 -136 ACGCCATGAATTTTCATCTTATTATAAGGTATTGTA 5 194 0 TTTTATTTAA 0.820423 -107 CATTTTTTATTTCTTTATTAATTTGATTGCATAATA 5 238 1 TTCTTATTTA 0.795513 -63 **** * * *** * Masking position 16 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 TTTCTTAAACAATAAGGCTTAATTTTAAGC 1 64 0 AATAAGGCTT 0.935995 -83 TATTTGCATTAAAAAGCGATTTTCTTAAAC 1 84 0 AAAAAGCGAT 0.959883 -63 ATAAAATGCTAAAATGCCATGATTTAAAAA 1 111 1 AAAATGCCAT 0.925281 -36 GCCATGATTTAAAAAGAATTTAAGGCAATG 1 126 1 AAAAAGAATT 0.89891 -21 ATTTACCTAAAAAAAGGCTTTTGAATTTTC 2 17 0 AAAAAGGCTT 0.986231 -61 CAAACTCCCTAAAAACGATTGCAATAAAGT 2 55 0 AAAAACGATT 0.849773 -23 CTAGGGTTTAAAAAAGAAATTCC 3 4 0 AAAAAGAAAT 0.850369 -37 AAAAACTCCTTAATAAACTAG 3 30 0 AAAACTCCTT 0.858448 -11 TAAAAATGCTCAAAAGCATTTTCTATAATA 5 54 1 CAAAAGCATT 0.876906 -247 CATTTTCTATAATAAGCCATAATAAAAGGG 5 70 1 AATAAGCCAT 0.941329 -231 AAGCCATAATAAAAGGGCTTGCAAGCGAGT 5 83 1 AAAAGGGCTT 0.943619 -218 AAACTCAAACAAAACCCGTTTAAGAATTTC 5 145 1 AAAACCCGTT 0.834437 -156 AAATGAGCGCAAAACGCCATGAATTTTCAT 5 213 0 AAAACGCCAT 0.980079 -88 ********** Masking position 4 Map Score: 14.835 Number of sites scoring better than the average of aligned sites = 2867 Number in coding regions = 2515 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 3 AAAAAGCGATTTTCTTAAACAATAAGGCTT 1 74 0 TTTCTTAAAC 0.947081 -73 GCTTTTGAATTTTCTTAAAA 2 1 0 TTTCTTAAAA 0.857996 -77 GGAATTTCTTTTTTAAACCCTAGTTTAT 3 9 1 TTTTTTAAAC 0.818139 -32 TAAACCCTAGTTTATTAAGGAGTTTTT 3 24 1 TTTATTAAGG 0.951225 -17 TTTATTAAAGGGACTATCAG 4 1 1 TTTATTAAAG 0.968806 -21 TTTATTATGGCTTATTATAGAAAATGCTTT 5 66 0 CTTATTATAG 0.912247 -235 TGCAAGCCCTTTTATTATGGCTTATTATAG 5 76 0 TTTATTATGG 0.919995 -225 ATATTTAGAAATTCTTAAACGGGTTTTGTT 5 152 0 ATTCTTAAAC 0.903747 -149 GAATTTTCATCTTATTATAAGGTATTGTAT 5 193 0 CTTATTATAA 0.739311 -108 ATGCAATCAAATTAATAAAGAAATAAAAAA 5 240 0 ATTAATAAAG 0.674577 -61 TATGTCAGCTATTATTATGCAATCAAATTA 5 256 0 ATTATTATGC 0.829637 -45 ********** Masking position 7 Map Score: 10.674 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 414 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 ATGCTAAAATGCCATGATTTAAAAAGAATT 1 116 1 GCCATGATTT 0.972578 -31 TCATTGCCTTAAATTCTTTTTAAAT 1 132 0 GCCTTAAATT 0.826396 -15 AAATTCAAAAGCCTTTTTTTAGGTAAATAT 2 19 1 GCCTTTTTTT 0.714045 -59 AGACTTTATTGCAATCGTTTTTAGGGAGTT 2 53 1 GCAATCGTTT 0.858637 -25 TTGCGGCTTTGCCCTCTTTTAGTGGCAATG 5 16 1 GCCCTCTTTT 0.967509 -285 AGGCTTTGTTGTCATCAATTTTAAAGCTAC 5 114 0 GTCATCAATT 0.945444 -187 AGCGCAAAACGCCATGAATTTTCATCTTAT 5 208 0 GCCATGAATT 0.972578 -93 ATGGCGTTTTGCGCTCATTTTTTATTTCTT 5 223 1 GCGCTCATTT 0.903803 -78 CTATTATTATGCAATCAAATTAATAAAGAA 5 248 0 GCAATCAAAT 0.735282 -53 GATGTGTTATGTCAGCTATTATTATGCAAT 5 263 0 GTCAGCTATT 0.654675 -38 ********** Masking position 10 Map Score: 4.018 Number of sites scoring better than the average of aligned sites = 874 Number in coding regions = 811 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 AGGCTTAATTTTAAGCACGTTTTAGTATGAT 1 49 0 TTAAGCACTT 0.971052 -98 ATCATGGCATTTTAGCATTTTATTTGCATTA 1 103 0 TTTAGCATTT 0.923653 -44 GATTGCGGCTTTGCCCTCTTTTAGTGGCAAT 5 14 1 TTGCCCTCTT 0.97084 -287 GAAAATGCTTTTGAGCATTTTTACAGACACT 5 46 0 TTGAGCATTT 0.97962 -255 TGTATATTTTTTACCCATATTTAGAAATTCT 5 167 0 TTACCCATTT 0.946043 -134 TCATGGCGTTTTGCGCTCATTTTTTATTTCT 5 221 1 TTGCGCTCTT 0.984543 -80 ******** ** Masking position 2 Map Score: 3.29781 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 203 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 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 Motif number 8 ********** 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