AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_Iron_Transport_pyro_reg_300.orf -o101_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH00338 102 Pyrococcus_OT3 #2 RPH00337 40 Pyrococcus_OT3 #3 RPH00336 19 Pyrococcus_OT3 #4 RPH01136 73 Pyrococcus_OT3 #5 RPH01137 59 Pyrococcus_OT3 #6 RPH01139 48 Pyrococcus_OT3 #7 RPH01525 213 Pyrococcus_OT3 #8 RPH01532 194 Pyrococcus_OT3 Motif number 1 CCACCCCTGCAAAAATGATTGCAACCTAGACAA 1 76 0 AAAAAGTTCA 0.880296 -27 TTAAACCCCAATAAAAGAGCAAATTTATGCCTT 2 17 0 ATAAAGGCAA 0.954705 -24 TAAAACTTTTAAAAATTGTTAAAAGCTGTAACA 4 27 1 AAAAATTTAA 0.895251 -47 CCAATTTCAGAAAAAGTGTTACAGCTTTTAACA 4 43 0 AAAAATTTCA 0.729863 -31 AGTTTTTAAAATAAAAGGTTAAAAA 5 3 0 ATAAAGTTAA 0.984635 -57 CCCGAGATTTATTAAGGATTAACACTTGATTTT 6 16 0 ATTAAGTTAC 0.768015 -33 AAATTAATGGATAAAAAGTCCAAGTAA 7 5 0 ATAAAATCAA 0.929255 -209 CTTTTTATCCATTAATTTTTTAAACAACGATCC 7 20 1 ATTAATTTAA 0.878766 -194 GATGATTTGGATAAAAAGGTTAATTAACGAACC 8 35 0 ATAAAAGTAA 0.802615 -160 ATCATCTTCCATAAATGCTCGAAAATTTTGATA 8 62 1 ATAAAGTCAA 0.985232 -133 GAAAATTTTGATAAACTTTCAAATATCCTCCCA 8 82 1 ATAAATTCAA 0.960747 -113 GTAGATGGACATTAATGTTCAAAAAAGAAACAA 8 124 0 ATTAAGTCAA 0.955387 -71 ATGTCCATCTACAAAAGCTTTAAATGTTGACAA 8 145 1 ACAAAGTTAA 0.931733 -50 ***** * ** ** Masking position 5 Map Score: 12.8956 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 302 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 CTCTTCCACCTCCTTATTTCCA 1 3 1 CTTCCACCTC 0.931774 -100 CCCACCACCCCTGCAAAAATG 1 92 0 CCACCACCCC 0.967743 -11 GAGGTTAATTGTACCCCTATTCCTAGCTAT 7 94 1 GTACCCCTAT 0.90096 -120 CACCCACTAACTAGCACTATTATAGCTAGG 7 115 0 CTAGCACTAT 0.902724 -99 GGATCTTCTACTACCCCCACCACTACCACC 7 149 1 CTACCCCCAC 0.997228 -65 ACCCCCACCACTACCACCACTCCCCAAACA 7 161 1 CTACCACCAC 0.997283 -53 CAAACACAATCTACCCATACCATAACTAAG 7 185 1 CTACCCATAC 0.940139 -29 TTCTACCACCATCCTAAGATTC 8 3 1 CTACCACCAT 0.993079 -192 ********** Masking position 5 Map Score: 10.712 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 157 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 AGGTATATATAGGATTTTTGTCTTAAATATA 1 33 0 AGGATTTTGT 0.985429 -70 AAGGGCTTTTAGGAGTTTTTAAAATAAAAGG 5 18 0 AGGAGTTTTA 0.960064 -42 GACGATCTTTGAAAAATAGAAA 5 48 0 ACGATTTTGA 0.947285 -12 CCAAATAATTAGGATCGTTGTTTAAAAAATT 7 33 0 AGGATGTTGT 0.974563 -181 GAATAATCCAAGGAGGTTCTAACATGAAGAG 7 66 1 AGGAGTTCTA 0.941778 -148 GTGGGTGCATAGGATCTTCTACTACCCCCAC 7 138 1 AGGATTTCTA 0.966175 -76 CCAGAATCTTAGGATGGTGGTAGAA 8 5 0 AGGATGTGGT 0.933397 -190 GCAAAATGGGAGGATATTTGAAAGTTTATCA 8 90 0 AGGATTTTGA 0.990876 -105 ***** ***** Masking position 4 Map Score: 9.19909 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 228 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 GATTTGGATAAATATGCCA 3 9 0 ATTTGGATAA 0.935624 -11 ACCTAAAGTTGAAAACTAAAACTTT 4 6 1 AAGTTGAAAA 0.664902 -68 AAAACTAAAACTTTTAAAAATTGTTAAAAG 4 22 1 CTTTTAAAAA 0.860284 -52 AGTGTTACAGCTTTTAACAATTTTTAAAAG 4 32 0 CTTTTAACAA 0.861416 -42 TTAACCTTTTATTTTAAAAACTCCTAAAAG 5 14 1 ATTTTAAAAA 0.904371 -46 GACGATCTTTGAAAAATAGAAAAGGG 5 44 0 CTTTGAAAAA 0.857559 -16 GATCCTAATTATTTGGACGAATAATCCAAG 7 48 1 ATTTGGACGA 0.811469 -166 ATGGAAGATGATTTGGATAAAAAGGTTAAT 8 44 0 ATTTGGATAA 0.935624 -151 ATGCTCGAAAATTTTGATAAACTTTCAAAT 8 76 1 ATTTTGATAA 0.939534 -119 ATGGACATTAATGTTCAAAAAAGAAACAAC 8 123 0 ATGTTCAAAA 0.742829 -72 AAAGCTTTAAATGTTGACAAATGTAAACAT 8 158 1 ATGTTGACAA 0.938412 -37 ********** Masking position 7 Map Score: 9.27036 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 209 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 CTCTTCCACCTCCTTATTTCCATATATTTA 1 11 1 TCCTTATTTC 0.960476 -92 CAAGTGTTAATCCTTAATAAATCTCGGGAG 6 21 1 TCCTTAATAA 0.826671 -28 ATAATTAGGATCGTTGTTTAAAAAATTAAT 7 30 0 TCGTTGTTTA 0.972525 -184 GATTCTGGGTTCGTTAATTAACCTTTTTAT 8 28 1 TCGTTAATTA 0.957931 -167 CCCATTTTGCTCGTTGTTTCTTTTTTGAAC 8 111 1 TCGTTGTTTC 0.974498 -84 ********** Masking position 5 Map Score: 1.6308 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 72 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ********** No masking Map Score: -1.51813e-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 7 ********** No masking Map Score: -1.51813e-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: -1.51813e-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