AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iiclR_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 PH0198 300 168aa long hypothetical protein #2 PH0583 100 318aa long hypothetical protein #3 PH0803 56 110aa long hypothetical protein #4 PH1150 89 236aa long hypothetical arylmalonate decarboxylase Motif number 1 CTTGGGTTGCTAGATAGGGAGGTACTTTAA 1 46 0 TAGATAGGGA 0.992722 -255 TTAGGGAAGATGGTGAGGAACTTGGGTTGC 1 66 0 TGGTGAGGAA 0.943414 -235 GGTAGGATCAGAGTTAGGGAAGATGGTGAG 1 79 0 GAGTTAGGGA 0.989602 -222 GTCTTAACTCCAGTTAAGGATATTTCAATA 1 127 0 CAGTTAAGGA 0.899383 -174 CTATAAATTTTAGTGAGGGGAGGCTTGAAG 1 156 0 TAGTGAGGGG 0.982424 -145 CTAGGTTTGCTAGATAAGGAAGGTTTTTGT 1 208 0 TAGATAAGGA 0.959312 -93 AAGTGAGGGACCGAGGGTTG 1 291 0 AAGTGAGGGA 0.982345 -10 GTAACTTCTTGGGGGAGGGAAG 2 3 0 GGGGGAGGGA 0.975316 -98 ATAGCAGGGATGGAGAGGGATCAGA 2 86 1 TGGAGAGGGA 0.993585 -15 AAATCCCTATTACATAGGGATTTTAAACTA 4 58 0 TACATAGGGA 0.946397 -32 ********** Masking position 6 Map Score: 17.2627 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 606 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 TAGGGAGGTACTTTAATACTTAAGCAAAAGGTT 1 29 0 CTAAACTTAA 0.974099 -272 GTTAAGGATATTTCAATAATCACAGAGATAAGA 1 112 0 TTAAAATCAC 0.831275 -189 TGAGGGGAGGCTTGAAGTCTTAACTCCAGTTAA 1 140 0 CTAATCTTAA 0.922388 -161 TGTCAAGGAGTTGGAATACTCAAGGCTATAAAT 1 178 0 TTAAACTCAA 0.982238 -123 ATTGCTAAGCTTAGAAAAATCAAAGTACCGGAC 1 244 1 TTAAAATCAA 0.959379 -57 AGGTACTAAACCGAAATACTTAACATCTATTGA 2 34 0 CCAAACTTAA 0.963999 -67 CGGTTTAGTACCTAAAGACTTAATAAGGGGAAA 2 54 1 CCAAACTTAA 0.964 -47 TTCCCATTATCAAATAAAGCATA 3 1 1 TTCATATCAA 0.762453 -56 GGTTATCAAACTTAACTTTACCCTA 3 42 0 TTCAACTTAA 0.9372 -15 TTTATAATGTTCCCAAAGATCAAGGAGGTTAG 4 10 0 TCAAGATCAA 0.817106 -80 ** ** ****** Masking position 6 Map Score: 6.98794 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 244 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TGAGGAACTTGGGTTGCTAGATAGGGAGGT 1 53 0 GGGTTGCTAG 0.993148 -248 ACAGAGATAAGATTTGGTAGGATCAGAGTT 1 94 0 GATTTGGTAG 0.970156 -207 TTTACTTCTAGGTTTGCTAGATAAGGAAGG 1 215 0 GGTTTGCTAG 0.995969 -86 TAAGTATTTCGGTTTAGTACCTAAAGACTT 2 45 1 GGTTTAGTAC 0.923815 -56 TATGTAATAGGGATTTCTAGGTGACAGC 4 72 1 GGATTTCTAG 0.96096 -18 ********** Masking position 5 Map Score: 3.72254 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 50 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AAGGTTTTTGTCAAGGAGTTGGAATACTCA 1 189 0 TCAAGGAGTT 0.990579 -112 ATCTAGCAAACCTAGAAGTAAATTGCTAAG 1 223 1 CCTAGAAGTA 0.942758 -78 CTTCCCTCCCCCAAGAAGTTACCTCAATAG 2 11 1 CCAAGAAGTT 0.990579 -90 TTCCCAAAGATCAAGGAGGTTAG 4 4 0 TCAAGGAGGT 0.984045 -86 ********** Masking position 4 Map Score: 1.65706 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 69 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AAAAGGTTTATTAAATATATGAAACC 1 7 0 TTAAATATAT 0.881427 -294 ATATATTTAATAAACCTTTTGCTTAAGTAT 1 17 1 TAAACCTTTT 0.766336 -284 AACCTTTTGCTTAAGTATTAAAGTACCTCC 1 29 1 TTAAGTATTA 0.756251 -272 TTAACTCCAGTTAAGGATATTTCAATAATC 1 124 0 TTAAGGATAT 0.816671 -177 CTCCCCTCACTAAAATTTATAGCCTTGAGT 1 164 1 TAAAATTTAT 0.793028 -137 TCAATAGATGTTAAGTATTTCGGTTTAGTA 2 34 1 TTAAGTATTT 0.957622 -67 TTTCCCCTTATTAAGTCTTTAGGTACTAAA 2 57 0 TTAAGTCTTT 0.8746 -44 CATTATCAAATAAAGCATATAAAACGTTAG 3 15 1 TAAAGCATAT 0.873005 -42 GTTATCAAACTTAACTTTACCCTAACGTTT 3 36 0 TTAACTTTAC 0.622996 -21 GGGAACATTATAAAATTTTTTGAATAAAAT 4 29 1 TAAAATTTTT 0.820317 -61 ATAGGGATTTTAAACTATTTTATTCAAAAA 4 45 0 TAAACTATTT 0.921405 -45 ********** Masking position 4 Map Score: 5.9655 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 387 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 6 ********** No masking Map Score: -1.04207e-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: -1.04207e-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: -1.04207e-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