AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_hpyl_reg_300.orf -o117_hpyl_300.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 RHP01243 241 AE000511 #3 RHP01245 116 AE000511 #4 RHP00648 31 AE000511 #5 RHP00649 116 AE000511 Motif number 1 AATGATTATCTTAAAATTAGAAAGTTTCTT 1 14 0 TTAAAATTAG 0.932124 -287 AACACCCCAAATAAAATTAAGCGAGCATTA 1 106 0 ATAAAATTAA 0.845796 -195 ATTCCTGAGATTATAATTAATTATGGGTAA 1 256 0 TTATAATTAA 0.89954 -45 TAACTTTAAATTGAGATTAAATCCACATTA 2 153 0 TTGAGATTAA 0.720865 -89 TGAGTATTTGCTAAAATGTAACTTTAAATT 2 171 0 CTAAAATGTA 0.820034 -71 CAAATACTCACTATAATAAGCGTTTATTTT 2 191 1 CTATAATAAG 0.725502 -51 AACGCTCTTTTTAAAATAAACGCTTATTAT 2 203 0 TTAAAATAAA 0.907522 -39 AATAAAATATTTATAATTTAGATCTCTATC 3 67 1 TTATAATTTA 0.836744 -50 AAACTAAGATAAATTAAAATATT 4 4 1 CTAAGATAAA 0.797898 -28 AATTAAAATATTAAAATTAG 4 22 1 TTAAAATTAG 0.932124 -10 CCTTAAATGCCTAAAATTTAGAAAAAATCA 5 16 1 CTAAAATTTA 0.960082 -101 TTGATCTTATCTAAAATTTGCTAAGAATAC 5 49 1 CTAAAATTTG 0.941017 -68 TAAGAATACACTAAAATTTAGTTTTAATTT 5 70 1 CTAAAATTTA 0.960082 -47 CGCACCACGCTTGAAATTAAAACTAAATTT 5 83 0 TTGAAATTAA 0.898671 -34 ********** Masking position 6 Map Score: 15.8366 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 480 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 GATGCTTTTTTGAAACGCTTAATAGCAAATTA 1 46 0 TGAAACCTAA 0.895124 -255 CAAAAAAGCATCAAATTGACATCTTTTAAGCA 1 66 1 TCAAATGCAT 0.685591 -235 GGTCAGGGGTTCGAACCCCCTACACTCCACCA 1 172 1 TCGAACCCTA 0.86738 -129 TCTTTATGGATCAAACCCGTTTTCTTGCTAGT 1 223 1 TCAAACCTTT 0.965994 -78 GCTCAAACTCCCTTGATGAAAAAC 1 287 0 TCAAACCCTT 0.970507 -14 GATCAAATCCTTATTGGTTTTTTA 2 3 1 TCAAATCTAT 0.946526 -239 AAGCTTATTTTGGAATACTTTTAGCTTGTTTG 2 36 0 TGGAATCTTT 0.815436 -206 TAAATTGAGATTAAATCCACATTAAAAGAATT 2 145 0 TTAAATCCAT 0.912561 -97 TCTTTTTAAAATAAACGCTTATTATAGTGAGT 2 196 0 ATAAACCTAT 0.69678 -46 TCCTTAAAAATTGAACGCTCTTTTTAAAATAA 2 214 0 TTGAACCCTT 0.90349 -28 TAGGTGTTTGTGAAACACCTATAAACGCAATA 3 39 1 TGAAACCTAT 0.960057 -78 TGATTCCTTAAATGCCTAAAATTTAGAAA 5 8 1 TTAAATCTAA 0.762024 -109 ****** * *** Masking position 5 Map Score: 8.13769 Number of sites scoring better than the average of aligned sites = 1248 Number in coding regions = 1096 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 3 TCTTAATTTGCTATTAAGCGTTTCAAAAAA 1 43 1 CTATTAAGCG 0.915066 -258 AAATTGACATCTTTTAAGCAAAATGTTATA 1 78 1 CTTTTAAGCA 0.97736 -223 CACTCCACCATTATTACGCTTATTCTCTTT 1 194 1 TTATTACGCT 0.743879 -107 CTCGCAATTGTTATTAAGCTTATTTTGGAA 2 53 0 TTATTAAGCT 0.871041 -189 ATAAAAAATTCTTTTAATGTGGATTTAATC 2 139 1 CTTTTAATGT 0.753815 -103 GAGCGTTCAATTTTTAAGGAATAGAA 2 226 1 TTTTTAAGGA 0.924134 -16 TTTAATTAACCTTTAAAGGTTACC 3 5 0 CTTTAAAGGT 0.940723 -112 ACAACAAATTCTATAAAGGATAGAGATCTA 3 85 0 CTATAAAGGA 0.930337 -32 AAATTTTAGGCATTTAAGGAATCA 5 5 0 CATTTAAGGA 0.858669 -112 ACCACCGCCTTTAACGCACCACGCTTGA 5 99 0 CTTTAACGCA 0.893697 -18 ********** Masking position 6 Map Score: 7.2916 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 734 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TAAAATTAAGCGAGCATTATAACATTTTGC 1 95 0 CGAGCATTAT 0.935751 -206 CTCAACGCTGCCAGCGTTGCGCTCTCCCAG 1 143 0 CCAGCGTTGC 0.954821 -158 CCCCTACACTCCACCATTATTACGCTTATT 1 188 1 CCACCATTAT 0.947762 -113 ATTATAATCTCAGGAATTGTTTTTCATCAA 1 269 1 CAGGAATTGT 0.747438 -32 CCATTATTAACCCGCATTGTCCCACTCAAA 2 86 0 CCCGCATTGT 0.96747 -156 CCCATTTAACCCGCCATTATTAACCCGCAT 2 99 0 CCGCCATTAT 0.924293 -143 TAGATAAGATCAAGCGTGATTTTTTCTAAA 5 32 0 CAAGCGTGAT 0.932348 -85 GTTTTAATTTCAAGCGTGGTGCGTTAAAGG 5 90 1 CAAGCGTGGT 0.956253 -27 ********** Masking position 7 Map Score: 2.60121 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 254 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 GAAACGCTTAATAGCAAATTAAGAATGATT 1 37 0 ATAGCAAATT 0.95587 -264 AGCGAGCATTATAACATTTTGCTTAAAAGA 1 87 0 ATAACATTTT 0.861824 -214 AATAAGCTTAATAACAATTGCGAGTGGTTT 2 59 1 ATAACAATTG 0.870689 -183 GTTATTTTGAATAAAAAATTCTTTTAATGT 2 129 1 ATAAAAAATT 0.928482 -113 AAGTTACATTTTAGCAAATACTCACTATAA 2 177 1 TTAGCAAATA 0.726127 -65 TTCTATTCCTTAAAAATTGAACGCTCTTT 2 223 0 TTAAAAATTG 0.66247 -19 TATAAACGCAATAAAATATTTATAATTTAG 3 58 1 ATAAAATATT 0.85462 -59 GCCAGTCTCCACAACAAATTCTATAAAGGA 3 95 0 ACAACAAATT 0.863841 -22 CTAAGATAAATTAAAATATTAAAATTAG 4 14 1 TTAAAATATT 0.80061 -18 TAGTGTATTCTTAGCAAATTTTAGATAAGA 5 53 0 TTAGCAAATT 0.936688 -64 ********** Masking position 6 Map Score: 4.47152 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 293 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 TGAGCTAACACCCCAAATAAAATTAAGCGA 1 112 0 CCCCAAATAA 0.932123 -189 CTAAAAGTATTCCAAAATAAGCTTAATAAC 2 44 1 TCCAAAATAA 0.956181 -198 TTCAAAATAACCCCATTTAACCCGCCATTA 2 110 0 CCCCATTTAA 0.853949 -132 GAATTTTTTATTCAAAATAACCCCATTTAA 2 120 0 TTCAAAATAA 0.944278 -122 TGAGATTAAATCCACATTAAAAGAATTTTT 2 142 0 TCCACATTAA 0.896455 -100 TGGATTTAATCTCAATTTAAAGTTACATTT 2 158 1 CTCAATTTAA 0.902638 -84 TTAGCAAATACTCACTATAATAAGCGTTTA 2 187 1 CTCACTATAA 0.848375 -55 GAACGCTCTTTTTAAAATAAACGCTTATTA 2 204 0 TTTAAAATAA 0.6543 -38 CGCACCACGCTTGAAATTAAAACTAAATTT 5 83 0 TTGAAATTAA 0.694654 -34 ********** Masking position 8 Map Score: 3.58733 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 433 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 ********** No masking Map Score: 1.55142e-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: 1.55142e-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: 1.55142e-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