AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_hpyl_reg_100.orf -o117_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01199 300 AE000511 #2 RHP01245 116 AE000511 #3 RHP00648 31 AE000511 #4 RHP00649 116 AE000511 Motif number 1 AATGATTATCTTAAAATTAGAAAGTTTCTT 1 14 0 TTAAAATTAG 0.938973 -287 AACACCCCAAATAAAATTAAGCGAGCATTA 1 106 0 ATAAAATTAA 0.892145 -195 ATTCCTGAGATTATAATTAATTATGGGTAA 1 256 0 TTATAATTAA 0.947156 -45 AATAAAATATTTATAATTTAGATCTCTATC 2 67 1 TTATAATTTA 0.948164 -50 AATTTTAATATTTTAATTTATCTTAGTTT 3 10 0 TTTTAATTTA 0.742623 -22 AATTAAAATATTAAAATTAG 3 22 1 TTAAAATTAG 0.938973 -10 CCTTAAATGCCTAAAATTTAGAAAAAATCA 4 16 1 CTAAAATTTA 0.970123 -101 TTGATCTTATCTAAAATTTGCTAAGAATAC 4 49 1 CTAAAATTTG 0.95896 -68 TAAGAATACACTAAAATTTAGTTTTAATTT 4 70 1 CTAAAATTTA 0.970123 -47 CGCACCACGCTTGAAATTAAAACTAAATTT 4 83 0 TTGAAATTAA 0.903263 -34 ********** Masking position 5 Map Score: 15.3454 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 202 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 AAATGTTATAATGCTCGCTTAATTTTATTTGG 1 98 1 ATCCGCTTAA 0.958817 -203 ACTAGCAAGAAAACGGGTTTGATCCATAAAGA 1 223 0 AACGGTTTGA 0.955671 -78 GCTCAAACTCCCTTGATGAAAAACAA 1 285 0 AACCCCTTGA 0.994361 -16 GGTGTTTGTGAAACACCTATAAACGCAATAAA 2 41 1 AACCCTATAA 0.895639 -76 ATTTAGAAAAAATCACGCTTGATCTTATCTAA 4 31 1 AACCGCTTGA 0.995701 -86 GCCTTTAACGCACCACGCTTGAAATTAAAACT 4 89 0 CACCGCTTGA 0.993625 -28 ACCACCGCCTTTAACGCACCACGC 4 103 0 CACCCTTTAA 0.965298 -14 ** * ******* Masking position 12 Map Score: 6.79115 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 353 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 ATGCTTTTTTGAAACGCTTAATAGCAAATT 1 47 0 GAAACGCTTA 0.977937 -254 TAGGGGGTTCGAACCCCTGACCTCAACGCT 1 164 0 GAACCCCTGA 0.975856 -137 TCAGGGGTTCGAACCCCCTACACTCCACCA 1 174 1 GAACCCCCTA 0.995077 -127 AGGTGTTTCACAAACACCTAAAGGTTTAAT 2 29 0 CAAACACCTA 0.971739 -88 AGGTGTTTGTGAAACACCTATAAACGCAAT 2 40 1 GAAACACCTA 0.991807 -77 ********** Masking position 3 Map Score: 4.44494 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 65 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TTTTTTGAAACGCTTAATAGCAAATTAAGA 1 43 0 CGCTTAATAG 0.942187 -258 GTCAATTTGATGCTTTTTTGAAACGCTTAA 1 56 0 TGCTTTTTTG 0.840033 -245 TATAACATTTTGCTTAAAAGATGTCAATTT 1 78 0 TGCTTAAAAG 0.983089 -223 GGTTTAATTAACCTTTAAAGGTTACC 2 7 0 ACCTTTAAAG 0.934298 -110 TAGATCTCTATCCTTTATAGAATTTGTTGT 2 85 1 TCCTTTATAG 0.977909 -32 TGATTCCTTAAATGCCTAAAATTT 4 5 1 TCCTTAAATG 0.950633 -112 TCAAGCGTGGTGCGTTAAAGGCGGTGGT 4 99 1 TGCGTTAAAG 0.958841 -18 ********** Masking position 5 Map Score: 5.1604 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 325 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 GCGTTGCGCTCTCCCAGCTGAGCTAACACC 1 130 0 CTCCCAGCTG 0.970226 -171 GCTGGGAGAGCGCAACGCTGGCAGCGTTGA 1 142 1 CGCAACGCTG 0.994302 -159 AACCCCTGACCTCAACGCTGCCAGCGTTGC 1 153 0 CTCAACGCTG 0.993852 -148 GTAGGGGGTTCGAACCCCTGACCTCAACGC 1 165 0 CGAACCCCTG 0.921258 -136 ACCCCCTACACTCCACCATTATTACGCTTA 1 186 1 CTCCACCATT 0.874151 -115 GCCTTTAACGCACCACGCTTGAAATTAAAA 4 91 0 CACCACGCTT 0.971416 -26 ********** Masking position 9 Map Score: 3.05362 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 296 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ********** No masking Map Score: 7.69818e-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: 7.69818e-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 8 ********** No masking Map Score: 7.69818e-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