AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -itrpR_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0470 97 oligoendopeptidase F (pepF) #2 HP0471 300 glutathione-regulated potassium-efflux system protein (kefB) #3 HP1279 300 anthranilate isomerase (trpC) #4 HP1282 222 anthranilate synthase component I (trpE) Motif number 1 TAAAATATGCTTGTATTTTAACATAACACTCACAAT 1 43 0 TTTATTTTAA 0.82192 -55 AAGGCAAACTTTCTATTTATGAAAAAGATTTTTGAA 2 55 0 TTTATTTAAA 0.979988 -246 GCGTTTTAATTTTTATTTTACTAAAATAGAGCGTTT 2 108 1 TTTATTTAAA 0.958298 -193 ATGGGTTTAGTAAGATTTAAATAATAAATTACTTAT 2 161 1 TAGATTTATA 0.623289 -140 AATAAATTACTTATATATATTTGATAGATATTATTT 2 183 1 TTTATATATA 0.783248 -118 ATTTGATAGATATTATTTTGTTCAATAGTGTTATTT 2 201 1 TATATTTAAT 0.769702 -100 ATAGTTTCGCTTTTATTTCTTTAAAACAAATTGATT 2 256 1 TTTATTTAAA 0.937882 -45 TTTGCCCCCCTATGATTTGAAAGAATTACAGATTGA 3 66 1 TAGATTTAAT 0.733007 -235 TCAAGCGTGTTTAGATATTTTAGAAAATAAAGGCAA 3 120 1 TTGATATAAA 0.917783 -181 GGCGAGTTTGTTGTATTTAAGCCATAAAGCTAAAGA 3 189 1 TTTATTTATA 0.931314 -112 GCGCTTTGGTTTTTAAATGCTCTAAAGTCATGCTCA 3 239 0 TTTAAATAAA 0.702305 -62 GGCTTAGCCTTATGATTTTTTGCAAATGCGCATAAG 3 275 0 TAGATTTAAA 0.940342 -26 GCAGAATGTCTTGGAATTTTTGAAAACGCTCACTCA 4 128 1 TTGAATTAAA 0.878121 -95 TTGCCCATTTATCTATTTCTTGTAAAATACGAGTTT 4 176 1 ATTATTTAAA 0.822315 -47 AAATACGAGTTTATTTTTAGCGTAAAGAAATTG 4 200 1 TTTTTTTAAA 0.822313 -23 ** ***** *** Masking position 8 Map Score: 13.9991 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 540 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 TGGCGCAAAAACCAAATGATAAGTTT 1 7 1 AAAAACCAAA 0.890138 -91 ACACTCACAATACAAGCAAACTTATCATTT 1 24 0 TACAAGCAAA 0.895748 -74 ATTTTAACATAACACTCACAATACAAGCAA 1 35 0 AACACTCACA 0.781934 -63 TATGTTAAAATACAAGCATATTTTAACTCC 1 54 1 TACAAGCATA 0.867077 -44 TTCATCCAATTAAACCCTAACCGACTCTTG 2 14 1 TAAACCCTAA 0.856646 -287 AATAAAAATTAAAACGCTAGGATTATACTG 2 95 0 AAAACGCTAG 0.766006 -206 AACCCATATTCAAACGCAAACACCAAACGC 2 138 0 CAAACGCAAA 0.924329 -163 TAAATCTTACTAAACCCATATTCAAACGCA 2 150 0 TAAACCCATA 0.90623 -151 TTTAAAGAAATAAAAGCGAAACTATCCTAT 2 251 0 TAAAAGCGAA 0.79782 -50 TTACAGATTGAAAACGCACAAGAAAGCACT 3 91 1 AAAACGCACA 0.963212 -210 AAAATATCTAAACACGCTTGAGTGCTTTCT 3 111 0 AACACGCTTG 0.630979 -190 TAGAGCATTTAAAAACCAAAGCGCCTTATG 3 251 1 AAAAACCAAA 0.890138 -50 CGCATTTGCAAAAAATCATAAGGCTAAGCC 3 281 1 AAAAATCATA 0.706303 -20 CTTTAGATTGTAAAAGCATAAAAAGGAATT 4 43 1 TAAAAGCATA 0.904591 -180 CTTCTTTTCGCACAACCACATTTTTAAGAG 4 97 1 CACAACCACA 0.637649 -126 GGAATTTTTGAAAACGCTCACTCATTAGCG 4 140 1 AAAACGCTCA 0.924771 -83 ATGGGCAATAAATACGCTAATGAGTGAGCG 4 154 0 AATACGCTAA 0.613924 -69 ACGCTAAAAATAAACTCGTATTTTACAAGA 4 193 0 TAAACTCGTA 0.543818 -30 ********** Masking position 4 Map Score: 14.1718 Number of sites scoring better than the average of aligned sites = 2189 Number in coding regions = 1951 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 3 GAAATCCCCTTTTTATATCAATT 1 85 0 GAAACCTTTT 0.983311 -13 GGTTGGGGTTCAAAAATCTTTTTCATAAATAGA 2 47 1 CAAACTTTTT 0.872081 -254 TGCGTTAAGGCAAACTTTCTATTTATGAAAAAG 2 64 0 CAAATCTATT 0.947406 -237 ACGCAAACACCAAACGCTCTATTTTAGTAAAAT 2 122 0 CAAATCTATT 0.947336 -179 AAATAAAAGCGAAACTATCCTATTAAATTGATC 2 241 0 GAAATCCTAT 0.772625 -60 AAGTCATGCTCACACCCTCTTTTAAATCTTTAG 3 218 0 CACATCTTTT 0.930161 -83 ATTTAAAAACCAAAGCGCCTTATGCGCATTTGC 3 257 1 CAAACCTTAT 0.958536 -44 GTGGTGGTTAGAAAATTCCTTTTTATGCTTTTA 4 53 0 GAAACCTTTT 0.983012 -170 CCACCAAATTGAAAGCTTCTTTTCGCACAACCA 4 82 1 GAAATCTTTT 0.974796 -141 **** ****** Masking position 4 Map Score: 7.73968 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 373 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 ATTTTAGAGTATGACTTGAGCGCTAAAGATT 3 31 1 ATGACTTAGC 0.976789 -270 GGGCAAATCAAAATCTTTAGCGCTCAAGTCA 3 42 0 AAATCTTAGC 0.972105 -259 ACCCTCTTTTAAATCTTTAGCTTTATGGCTT 3 207 0 AAATCTTAGC 0.972105 -94 GGGTGTGAGCATGACTTTAGAGCATTTAAAA 3 234 1 ATGACTTAGA 0.919873 -67 TTGCGTTATAAGTTTTTAGAGGATAACTTC 4 10 1 AAGTTTTAGA 0.757971 -213 TTTTTAGAGGATAACTTCAGCTTTAGATTGT 4 23 1 ATAACTTAGC 0.972105 -200 AAATACGAGTTTATTTTTAGCGTAAAGAAAT 4 200 1 TTATTTTAGC 0.719881 -23 ******* *** Masking position 9 Map Score: 3.31345 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 348 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CGGAATTTTAGAGTATGACTTGAGCGCTAAA 3 27 1 GAGATGACTT 0.995031 -274 AAGAGGGTGTGAGCATGACTTTAGAGCATTT 3 230 1 GAGATGACTT 0.995284 -71 TAAGTTTTTAGAGGATAACTTCAGCTTTAGA 4 19 1 GAGATAACTT 0.981596 -204 TTTAAGAGAGCAGAATGTCTTGGAATTTTTG 4 119 1 CAGATGTCTT 0.968962 -104 *** ******* Masking position 6 Map Score: 2.70681 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 16 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 CCCTTTTTATATCAATTTGGAGTTAAAATA 1 72 0 ATCAATTTGG 0.97999 -26 GTGTTTGCGTTTGAATATGGGTTTAGTAAG 2 145 1 TTGAATATGG 0.887569 -156 CCCCAGTAGAATCAATTTGTTTTAAAGAAA 2 271 0 ATCAATTTGT 0.955934 -30 CTTGTGCGTTTTCAATCTGTAATTCTTTCA 3 83 0 TTCAATCTGT 0.948144 -218 AAAAGAAGCTTTCAATTTGGTGGTGGTTAG 4 75 0 TTCAATTTGG 0.985959 -148 ********** Masking position 5 Map Score: 2.49977 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 75 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TGGCGCAAAAACCAAATGATAAGT 1 5 1 GCAAAAACCA 0.930334 -93 ATATTCAAACGCAAACACCAAACGCTCTAT 2 133 0 GCAAACACCA 0.985854 -168 CACATTCGCCACAACCACCATTGTATGCGA 3 160 0 ACAACCACCA 0.993172 -141 GAATTTTCTAACCACCACCAAATTGAAAGC 4 68 1 ACCACCACCA 0.984968 -155 TTCTTTTCGCACAACCACATTTTTAAGAGA 4 98 1 ACAACCACAT 0.894423 -125 ********** Masking position 4 Map Score: 3.02304 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 129 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 8 ********** No masking Map Score: 6.56131e-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 9 ********** No masking Map Score: 6.56131e-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 10 ********** No masking Map Score: 6.56131e-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