AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ilexA_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 PH0120 50 211aa long hypothetical protein #2 PH0697 300 641aa long hypothetical protein #3 PH1932 188 192aa long hypothetical protein Motif number 1 TCAATATGAGTATTGGGAAGGTATTTGAGATGA 2 20 0 TATGGAGGTA 0.977035 -281 CCAATACTCATATTGAGTAAGTCTTCAATCTTA 2 37 1 TATGGAAGTC 0.968465 -264 TCAGCATATTTAATGAGAAGGGCCTTTAGATAA 2 72 1 TATGGAGGGC 0.990154 -229 GTTGAAATTCTCCTCAGGAGGTCAAAAGACTAT 2 182 0 TCTCGAGGTC 0.986495 -119 GGTCGAATAGTAATCGGTAGGTTTTTAGCCTTG 2 252 1 TATCGAGGTT 0.986847 -49 CCTAGCAGGATAGGGCGCCGGCCTTCTAAGCCG 3 47 1 TAGGGCGGCC 0.96532 -142 GCCGGCCTTCTAAGCCGGAGGTCGCGGGTTCGA 3 63 1 TAGCGAGGTC 0.99362 -126 AGAGCGTTAAAATTCTGGAGGCTGAAAAGG 3 169 1 AATCGAGGCT 0.900473 -20 ** ** * ***** Masking position 7 Map Score: 6.91527 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 89 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 GAGATATAACTTAAAAGTTGTGG 1 4 0 TTAAAAGTTG 0.880438 -47 AGGGCCTTTAGATAAAGCTGAAGCCTTTGC 2 90 1 GATAAAGCTG 0.933893 -211 TACACATCTTGCAAACGTTGCTTTTAAAGA 2 153 0 GCAAACGTTG 0.98319 -148 AATGCACTATGAAGAAGTTGAAATTCTCCT 2 201 0 GAAGAAGTTG 0.982835 -100 CTCTGTAAAAGAAAACGTTGGCGGGCCCGG 3 102 0 GAAAACGTTG 0.992355 -87 TTTTACAGAGGAAAAAGTTATATTGGAAAA 3 122 1 GAAAAAGTTA 0.960356 -67 ********** Masking position 5 Map Score: 5.01706 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 293 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CGGTTAAGCCTCCAAGACATTT 1 39 0 GTTAAGCCTC 0.972715 -12 TGATCTAAGATTGAAGACTTACTCAATATG 2 45 0 TTGAAGACTT 0.912365 -256 TTAGATAAAGCTGAAGCCTTTGCTCTGCAA 2 97 1 CTGAAGCCTT 0.952074 -204 ATCGGTAGGTTTTTAGCCTTGGAATTTAAT 2 264 1 TTTTAGCCTT 0.952196 -37 TGATAAATGTTTTAACGCTTTTCCAATATA 3 140 0 TTTAACGCTT 0.946828 -49 CCTCCAGAATTTTAACGCTCTGATAAATGT 3 160 0 TTTAACGCTC 0.955563 -29 CCTTTTCAGCCTCCAGAATTTTA 3 176 0 TTTCAGCCTC 0.972715 -13 ********** Masking position 5 Map Score: 4.41113 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 339 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 CTCCAAGACATTTTTCTCGAGATATAACTTA 1 21 0 TTTTTTCGAG 0.890356 -30 ATAGCAATTTTTCTTGCAGAGCAAAGGCTTC 2 109 0 TTCTTCAGAG 0.986672 -192 CCGATTACTATTCGACCAGAGATATTATATG 2 238 0 TTCGACAGAG 0.943175 -63 TTCTCTCGGAGTTTTTAATTA 2 290 0 TTCTCCGGAG 0.977856 -11 ATTTCATAACTTTTCTCCGAGTGGGCCCGTA 3 15 1 TTTTCCCGAG 0.985419 -174 CCAACGTTTTCTTTTACAGAGGAAAAAGTTA 3 111 1 CTTTTCAGAG 0.962661 -78 GCGTTAAAACATTTATCAGAGCGTTAAAATT 3 152 1 ATTTACAGAG 0.928409 -37 ***** ***** Masking position 10 Map Score: 4.40871 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 112 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TTAATGAGAAGGGCCTTTAGATAAAGCTGA 2 81 1 GGGCCTTTAG 0.989665 -220 TTCTCCGAGTGGGCCCGTAGCCTAGCAGGA 3 27 1 GGGCCCGTAG 0.998593 -162 AAACGTTGGCGGGCCCGGCGGGATTCGAAC 3 90 0 GGGCCCGGCG 0.99793 -99 ********** Masking position 5 Map Score: 1.96252 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AGTTATATCTCGAGAAAAATGTCTTGGAGG 1 23 1 CGAGAAAAAT 0.980832 -28 CTTTGCTCTGCAAGAAAAATTGCTATGTCA 2 114 1 CAAGAAAAAT 0.970658 -187 TGCTTTTAAAGAAGGAAAGTATGACATAGC 2 135 0 GAAGGAAAGT 0.967758 -166 GGGCCCACTCGGAGAAAAGTTATGAAATTG 3 13 0 GGAGAAAAGT 0.987524 -176 ********** Masking position 6 Map Score: 1.66438 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 87 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 ********** No masking Map Score: -4.80737e-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: -4.80737e-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: -4.80737e-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