AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ifhlA_pyro_opreg_100.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0879 300 367aa long hypothetical hydrogenase expression/formation protein hypD #2 PH1353 66 679aa long hypothetical formate dehydrogenase #3 PH1354 28 196aa long hypothetical protein #4 PH1429 288 147aa long hypothetical protein #5 PH1433 59 118aa long hypothetical protein #6 PH1437 45 427aa long hypothetical NADH-ubiquinone oxidoreductase subunit #7 PH1439 300 321aa long hypothetical NADH-ubiquinone oxidoreductase subunit #8 PH1454 265 241aa long hypothetical protein #9 PH1581 75 139aa long hypothetical protein Motif number 1 ATTTCAAGAACCTTTCCTGGGACGGCAAGACACAT 1 83 0 CCTTCCGGAG 0.958361 -218 TCACTCACCTCCAAGGGCTGAGAAAACTTC 1 281 0 CACTCCAGGG 0.983393 -20 ATAATATTTGCTGCTCTTATGGTTGCTCTTAGTCC 4 40 1 CTCTCTAGGG 0.955712 -249 AAAACCGTTGCTTCTCCAATGGTATCGTAACCTCT 4 208 0 CTCTCCAGGT 0.968378 -81 AGAAGAGCTACAGCTCCGGCTATTGCCGTGAATAA 4 241 0 CACTCCGTAG 0.801687 -48 TCCTCTCCCTCCTCCAGGGCCTTAGAAGAGCTA 4 266 0 CTCTCCGGCT 0.890027 -23 TTACCTCCCCTCCTCAGGAGATAGGGATGACCTG 6 22 0 CTCTCAGGAG 0.969785 -24 TAGGGATGGTCCCGTCAGATGGAAGATGAGGGAAC 7 21 1 CCGTCAAGGG 0.95882 -280 AAAGGGGATCCCACTCCCGCGGGAGTAGGATGCAT 7 262 1 CCCTCCGGGG 0.99589 -39 CTGACCGCGGCCATTCCCACGGTAGCAGCTAGCAA 8 88 0 CCTTCCAGGG 0.983727 -178 CCGCTCAGGGCCGCTCCTATGGCCGCTTCCGTCAT 8 172 0 CCCTCCAGGG 0.99715 -94 ATATATAAATCTTGTCAGGTGATGGTAAC 9 57 1 CTGTCAGGAG 0.895677 -19 ** **** * ** * Masking position 5 Map Score: 14.9552 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 245 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 AGTTGATTTTGGAGGTGTGAAAAGGGAGGT 1 136 1 GGAGGTGTGA 0.826335 -165 GTGTGAAAAGGGAGGTTAGACTTGACCTTC 1 150 1 GGAGGTTAGA 0.863553 -151 ACATCGGTTAGAAGGTCAAGTCTAACCTCC 1 160 0 GAAGGTCAAG 0.874343 -141 CTCAGCCCTTGGAGGTGAGTGA 1 289 1 GGAGGTGAGT 0.958842 -12 ATTTGGTCTAGGCGGTGAAGATTGGAAAAG 4 90 1 GGCGGTGAAG 0.952595 -199 GGCCCTGGAGGAGGGAGAGGA 4 278 1 GAGGGAGAGG 0.942691 -11 TATCTCCTGAGGAGGGGAGGTAA 6 33 1 GGAGGGGAGG 0.994048 -13 GGAAGAAGGGTAGGGATGGTCCCG 7 5 1 GAAGGGTAGG 0.941437 -296 CCGTCAGATGGAAGATGAGGGAACCAACTT 7 32 1 GAAGATGAGG 0.973529 -269 GGATGCATTAGGGGGTGAGGAT 7 289 1 GGGGGTGAGG 0.994048 -12 TTTTAATGGCGAAGATGAAGACAGCACCGC 8 203 0 GAAGATGAAG 0.922253 -63 GTATGAAAGCGAGGAGGAAGAGAAACCTGG 8 243 1 GAGGAGGAAG 0.823113 -23 ********** Masking position 4 Map Score: 14.7145 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 682 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 AAATTAAAGGAAACATCGGGATAGTTGATTT 1 114 1 AAACATGGGA 0.920365 -187 AACCGATGTAAGAGCTGGTGATTACGTTATA 1 181 1 AGAGCTGTGA 0.761282 -120 CGACGAGGAAAAAGCTAAGGAAATACTTGAA 1 241 1 AAAGCTAGGA 0.95525 -60 GGAAATACTTGAAGCTTGGGAGGAAGTTTTC 1 259 1 GAAGCTGGGA 0.991779 -42 AAATATGACCAAAAATGGGGAAC 2 3 0 AAAAATGGGA 0.932205 -64 TCTAGGCGGTGAAGATTGGAAAAGATATCGC 4 96 1 GAAGATGGAA 0.906794 -193 CCCCTCCTCAGGAGATAGGGATGACCTGCAT 6 19 0 GGAGATGGGA 0.979542 -27 CCGTCAGATGGAAGATGAGGGAACCAACTTT 7 32 1 GAAGATAGGG 0.867596 -269 TTCAATTCAGAAAACTCGGGAAATAAATCCA 7 225 1 AAAACTGGGA 0.937096 -76 TTTTAATGGCGAAGATGAAGACAGCACCGCT 8 202 0 GAAGATAAGA 0.754918 -64 ****** **** Masking position 6 Map Score: 5.94906 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 749 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 ACCTTCTAACCGATGTAAGAGCTGGTGATTAC 1 174 1 CGATGAAAGC 0.96617 -127 AAAAACTCGACGAGGAAAAAGCTAAGGAAATA 1 234 1 CGAGGAAAGC 0.978402 -67 GTTACGATACCATTGGAGAAGCAACGGTTTTA 4 212 1 CATTGAGAGC 0.956395 -77 CGGTTTTATTCACGGCAATAGCCGGAGCTGTA 4 236 1 CACGGAAAGC 0.984828 -53 TCTTCTAAGGCCCTGGAGGAGGGAGAGGA 4 270 1 CCCTGAGAGG 0.930895 -19 CCGATGTCGTCGTTGCAATAGCCTCTATAGAT 7 110 1 CGTTGAAAGC 0.96617 -191 ATCCCACTCCCGCGGGAGTAGGATGCATTAGG 7 269 1 CGCGGAGAGG 0.986882 -32 CGGCCATTCCCACGGTAGCAGCTAGCAAATCC 8 84 0 CACGGAGAGC 0.990381 -182 ***** ** *** Masking position 7 Map Score: 8.45772 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 66 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ACCATTAAGAAGTGCTTACCAATATTTTTA 1 46 0 AGTGCTTACC 0.816789 -255 CTCACCTCCAAGGGCTGAGAAAACTTCCTC 1 278 0 AGGGCTGAGA 0.952598 -23 CTCAGGAGATAGGGATGACCTGCATTCTTT 6 14 0 AGGGATGACC 0.984045 -32 GAAGAAGGGTAGGGATGGTCCCGTCAGATG 7 12 1 AGGGATGGTC 0.927905 -289 ACAATAGCGAAGGGATTGGAAGGAAATCAA 7 76 1 AGGGATTGGA 0.953494 -225 CGTTGAATGGAGGGATTTGCTAGCTGCTAC 8 72 1 AGGGATTTGC 0.939485 -194 TAAAAATGAAAGGGATTACATTTATAATGG 9 20 0 AGGGATTACA 0.961134 -56 ********** Masking position 1 Map Score: 2.64071 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 202 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TTGGGAGGAAGTTTTCTCAGCCCTTGGAGGTG 1 274 1 GTTTCTCACC 0.934418 -27 TCGGTATAGCGATATCTTTTCCAATCTTCACC 4 103 0 GTATCTTTCC 0.978281 -186 CTTCTCCAATGGTATCGTAACCTCTGTAGTCA 4 201 0 GTATCGTACC 0.87214 -88 GGGATGACCTGCATTCTTTACC 6 1 0 GATTCTTTCC 0.946075 -45 TCGGCTAGTTGATTTCCTTCCAATCCCTTCGC 7 82 0 GTTTCCTTCA 0.842266 -219 AGGCAAGAAGATTATCCTAACCGAAAAAGATC 7 183 1 ATATCCTACC 0.694522 -118 TTTACTTCTGGATTTATTTCCCGAGTTTTCTG 7 232 0 GTTTATTTCC 0.91626 -69 GATTATATCCGCAATACTTTCCGTTGAATGGA 8 51 1 GAATACTTCC 0.7334 -215 CAACCAGGTTTCTCTTCCTCCTCGCTTT 8 248 0 GTTTCTCTCC 0.96376 -18 * ******* ** Masking position 5 Map Score: 1.49521 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 437 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 CTTGACCTTCTAACCGATGTAAGAGCTGGT 1 170 1 TAACCGATGT 0.938668 -131 AATGGTATCGTAACCTCTGTAGTCAAACAC 4 196 0 TAACCTCTGT 0.925126 -93 GGAAATCAACTAGCCGATGTCGTCGTTGCA 7 97 1 TAGCCGATGT 0.978399 -204 GTCGTTGCAATAGCCTCTATAGATCCATGC 7 118 1 TAGCCTCTAT 0.908885 -183 ACCGATAGGGTAGCCGTAGTGAAAGAAGGC 7 157 1 TAGCCGTAGT 0.93228 -144 CTAATGATTATATCCGCAATACTTTCCGTT 8 46 1 TATCCGCAAT 0.789716 -220 ACCGTGGGAATGGCCGCGGTCAGCCTATTT 8 100 1 TGGCCGCGGT 0.948928 -166 ********** Masking position 1 Map Score: 0.898909 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 112 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TAATCACCAGCTCTTACATCGGTTAGAAGGTC 1 173 0 CTCTTAACGG 0.935352 -128 TTTGGCATTTCTCTCATTGATGATAATATTTG 4 18 1 CTCTCATATG 0.891932 -271 CTTATGGTTGCTCTTAGTCCAGGGTACGGAAT 4 55 1 CTCTTATCAG 0.955556 -234 TTCTTGCCTTCTTTCACTACGGCTACCCTATC 7 160 0 CTTTCATCGG 0.982722 -141 TCTGCTAAAACTTTCAATTCAGAAAACTCGGG 7 213 1 CTTTCATCAG 0.973525 -88 GTGGGATCCCCTTTTACTTCTGGATTTATTTC 7 244 0 CTTTTATCTG 0.962283 -57 TTCCTCCTCGCTTTCATACCTGTACGTCCTTT 8 230 0 CTTTCAACTG 0.958183 -36 ****** * *** Masking position 6 Map Score: 3.35394 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 46 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 CATTTTTAAAACCAAAAGTTTTCAACCTATCC 1 12 0 ACCAAATTTT 0.975792 -289 AGAAGTGCTTACCAATATTTTTAGACATTTTT 1 37 0 ACCAATTTTT 0.924478 -264 CCATAAGAGCAGCAAATATTATCATCAATGAG 4 30 0 AGCAAATTAT 0.955754 -259 CACCGCCTAGACCAAATTTTATTCCGTACCCT 4 75 0 ACCAAATTAT 0.955519 -214 CCATTGGAGAAGCAACGGTTTTATTCACGGCA 4 221 1 AGCAACTTTT 0.947806 -68 TGAAAGTTTTAGCAGATCTTTTTCGGTTAGGA 7 197 0 AGCAGATTTT 0.936385 -104 ****** **** Masking position 4 Map Score: 0.171366 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 43 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 ********** No masking Map Score: -3.21633e-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 11 CCTTTCCTGGGACGGCAAGACACATTAGCTT 1 77 0 GAGGCAAGAC 0.945886 -224 TGTTTCCTTTAATTTCAAGAACCTTTCCTGG 1 98 0 AATTCAAGAA 0.730902 -203 CATCGGTTAGAAGGTCAAGTCTAACCTCCCT 1 158 0 AAGTCAAGTC 0.732298 -143 CTTCCTCCCAAGCTTCAAGTATTTCCTTAGC 1 254 0 AGTTCAAGTA 0.672954 -47 ACCTCCAAAAAGAGGAAAGAAA 3 2 0 AGGGAAAGAA 0.933603 -27 CGAAGACGTGGGTGGAATGAACATAGTTACG 4 159 1 GGGGAATGAA 0.839686 -130 GATACCAGCTGCAAGAAATCTCTGGGA 5 7 1 AGTGCAAGAA 0.933603 -53 CTCCCATAAGGGTCATGACGTAACTTGTA 5 41 0 AGGTCATGAC 0.838784 -19 CGTAGTGAAAGAAGGCAAGAAGATTATCCTA 7 171 1 GAGGCAAGAA 0.965411 -130 CCCTCCATTCAACGGAAAGTATTGCGGATAT 8 55 0 AAGGAAAGTA 0.746493 -211 TTGCAACGTCGGGGGCCTGAAGCAGGAAAAA 8 142 0 GGGGCCTGAA 0.799279 -124 ** ******** Masking position 9 Map Score: 2.08867 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 539 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 ********** No masking Map Score: -3.21633e-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 13 ********** No masking Map Score: -3.21633e-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 14 ********** No masking Map Score: -3.21633e-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