AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ifnr_pyro_opreg_300.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 PH0538 78 290aa long hypothetical protein #2 PH1391 56 348aa long hypothetical protein #3 PH1463 40 438aa long hypothetical L-asparaginase #4 PH1509 300 440aa long hypothetical NADH oxidase Motif number 1 GAAATGGTTTTAACTTGTGGGGGTGCAAGTAACTT 1 17 0 TAAGTGGGTG 0.975714 -62 ATGGATAGGTAAATAATTTTGGGTGGATGC 2 6 0 AAATTGGGTG 0.962019 -51 CCATTGTATTTAAAGTGAGTGGGATAAAGC 2 37 1 TAAGAGGGAT 0.929454 -20 TACCCCCAGAAAAATGTTAAGAGAGGGGATATAAA 3 13 0 AAATTGAGAG 0.974928 -28 AGCGAGCTTCTCAGCTTTTCGGGAGTCAATCCTCT 4 25 0 TCATTGGGAG 0.989774 -276 GATAATGGATAAAGCAGTATGAGCTAGCATTCGAT 4 69 1 AAAGTGAGCT 0.757379 -232 CAACAAAATGTCAACATTTGGAGATCTTTGCGCGA 4 138 1 TCATTGAGAT 0.938181 -163 CTTTGCGCGATAAAGATAATCGGAGAGATGCTCCT 4 163 1 TAATACGGAG 0.817452 -138 AATTTTTCCTTCATATTTCAGTGAGTTTTTTGTCT 4 205 0 TCATTGTGAG 0.926227 -96 TAAGAGATATTAAAATGTTGGGGAGAAAATGAGGG 4 250 0 TAAGTGGGAG 0.993129 -51 CCCAAGAGAGAAAGGGTTAAGAGATATTAAAATGT 4 267 0 AAATTGAGAT 0.934583 -34 *** ** ***** Masking position 3 Map Score: 10.467 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 551 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 GTTTTAACTTGTGGGGGTGCAAGTAACTTG 1 16 0 GTGGGGGTGC 0.976778 -63 AAATAATTTTGGGTGGATGC 2 1 0 GGGTGGATGC 0.983354 -56 TAAATACAATGGATAGGTAAATAATTTTGG 2 19 0 GGATAGGTAA 0.767231 -38 TGTTAAGAGAGGGGATATAAACC 3 4 0 GGGGATATAA 0.915598 -37 ACATTTTTCTGGGGGTATTC 3 31 1 GGGGGTATTC 0.941573 -10 AAGCTCGCTATGAGGGATGATAATGGATAA 4 51 1 TGAGGGATGA 0.866401 -250 CATTCGATAAGGAGAGGTTTATCGAAATAA 4 96 1 GGAGAGGTTT 0.801773 -205 AAAGATAATCGGAGAGATGCTCCTGAACTC 4 174 1 GGAGAGATGC 0.992619 -127 TTAAAATGTTGGGGAGAAAATGAGGGCATT 4 246 0 GGGGAGAAAA 0.898273 -55 TCTCTCTTGGGTGGAGATGC 4 291 1 GTGGAGATGC 0.981988 -10 ********** Masking position 8 Map Score: 8.8842 Number of sites scoring better than the average of aligned sites = 1301 Number in coding regions = 1157 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 ATGGTTTTAACTTGTGGGGGTGCAAGTAAC 1 19 0 CTTGTGGGGG 0.98884 -60 GGTAAATAATTTTGGGTGGATGC 2 4 0 TTTGGGTGGA 0.967636 -53 TCTTAACATTTTTCTGGGGGTATTC 3 26 1 TTTCTGGGGG 0.888162 -15 AGCTTCTCAGCTTTTCGGGAGTCAATCCTC 4 26 0 CTTTTCGGGA 0.973345 -275 AAAATGTCAACATTTGGAGATCTTTGCGCG 4 142 1 CATTTGGAGA 0.813652 -159 ATTTGGAGATCTTTGCGCGATAAAGATAAT 4 153 1 CTTTGCGCGA 0.915105 -148 CAGTGAGTTTTTTGTCTAGAGTTCAGGAGC 4 192 0 TTTGTCTAGA 0.823885 -109 ATATTAAAATGTTGGGGAGAAAATGAGGGC 4 249 0 GTTGGGGAGA 0.954373 -52 CCCTTTCTCTCTTGGGTGGAGATGC 4 286 1 CTTGGGTGGA 0.987095 -15 ********** Masking position 3 Map Score: 6.93396 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 686 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TTATAAGAGTTTTGGAAATGGTTTTAACTT 1 36 0 TTTGGAAATG 0.931526 -43 CTTTAAATACAATGGATAGGTAAATAATTT 2 22 0 AATGGATAGG 0.844993 -35 CAGAAAAATGTTAAGAGAGGGGATATAAAC 3 12 0 TTAAGAGAGG 0.926612 -29 TAGCATTCGATAAGGAGAGGTTTATCGAAA 4 93 1 TAAGGAGAGG 0.986279 -208 TCGAAATAAGGAAGGAAAGGCCAACAAAAT 4 117 1 GAAGGAAAGG 0.976759 -184 AATGTCAACATTTGGAGATCTTTGCGCGAT 4 144 1 TTTGGAGATC 0.823017 -157 CTCCACCCAAGAGAGAAAGGGTTAAGAGAT 4 277 0 GAGAGAAAGG 0.849367 -24 TTCTCTCTTGGGTGGAGATGC 4 290 1 GGTGGAGATG 0.952159 -11 ********** Masking position 6 Map Score: 3.05437 Number of sites scoring better than the average of aligned sites = 1702 Number in coding regions = 1597 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 ********** No masking Map Score: -6.37056e-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 6 ********** No masking Map Score: -6.37056e-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 7 ********** No masking Map Score: -6.37056e-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