AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_pyro_reg_300.orf -o00460_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 PH0066 227 328aa long hypothetical L-asparaginase #2 PH0067 59 184aa long hypothetical protein #3 PH0231 95 303aa long hypothetical protein #4 PH0232 53 305aa long hypothetical L-asparaginase #5 PH1463 40 438aa long hypothetical L-asparaginase #6 PH1654 185 427aa long hypothetical serine hydroxymethyltransferase Motif number 1 TTTCGAACACCATAAACCTTCTAACGAGGGGA 1 102 0 CATAAACTTT 0.945682 -126 ATCTTGACACTTTAACCACCCTTTTATAAATC 1 144 1 TTTAACCCCT 0.860178 -84 ATAAGTAAGATTTAGAATTTTTGGCAAATACT 1 184 0 TTTAGAATTT 0.67832 -44 TAACCAATTACTTAAGCATTTTCATTAACAAA 2 21 0 CTTAAGCTTT 0.890199 -39 AGTAATTGGTTATTAACGCTTTCTGGGGG 2 41 1 TATTAACCTT 0.631476 -19 TAGATAATCTTATAAACGCTATGATATCGATA 3 18 0 TATAAACCTT 0.945682 -78 TCTAATCGGACTTAAAAATTATTATTTACTGT 3 46 1 CTTAAAATTT 0.846956 -50 CCATAATTCTTTTAACCTTTCGATATCCTTTC 4 16 1 TTTAACCTTG 0.871196 -38 GGTTTATATCCCCTCTCTTAACATTT 5 5 1 TATATCCCTT 0.843489 -36 TATCCCCTCTCTTAACATTTTTCTGGGGGTAT 5 17 1 CTTAACATTT 0.884337 -24 TGTTCAGTTACATAACCTTTTTAAGGAAGTAT 6 38 0 CATAACCTTT 0.960085 -148 ATTGTGGAGTTTTATCCTCTGTGAGTTTTCAA 6 89 1 TTTATCCCTT 0.904298 -97 GGGCAATCCTTTTAGACGTTTTGAAAACTCAC 6 109 0 TTTAGACTTT 0.92083 -77 TTAACTTAAATTTAAACCTTGTGCATTTTTGG 6 139 0 TTTAAACTTT 0.971065 -47 ******* ** * Masking position 3 Map Score: 11.8184 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 690 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 GTAAGATTTAGAATTTTTGGCAAATACTAT 1 182 0 GAATTTTTGG 0.990621 -46 TTACTTATTAGAATTTGAGTTGGTGGTCAA 1 208 1 GAATTTGAGT 0.801036 -20 AAGGTTAAAAGAATTATGGAAACG 4 5 0 GAATTATGGA 0.801036 -49 GATATCCTTTCAATTTTGGGATGGGCA 4 37 1 CAATTTTGGG 0.961758 -17 TTAAGGCAACCAAATTTTGGCGAGGGAT 6 9 0 CAAATTTTGG 0.930823 -177 ACAATTTCTTGAATTATTGTCGAATGTTCA 6 64 0 GAATTATTGT 0.913417 -122 AATAATTCAAGAAATTGTGGAGTTTTATCC 6 76 1 GAAATTGTGG 0.956327 -110 TAAACCTTGTGCATTTTTGGGCAATCCTTT 6 129 0 GCATTTTTGG 0.965502 -57 ********** Masking position 3 Map Score: 5.82108 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 270 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TTCATAGTATTTGCCAAAAATTCTAAATCT 1 179 1 TTGCCAAAAA 0.94954 -49 CCCCCAGAAAGCGTTAATAA 2 50 0 CCCCCAGAAA 0.986413 -10 TGCCCATCCCAAAATTGAAAGGATA 4 39 0 ATCCCAAAAT 0.884222 -15 GAATACCCCCAGAAAAATGTTAAGA 5 26 0 CCCCCAGAAA 0.986413 -15 ATCCCTCGCCAAAATTTGGTTGCCT 6 6 1 TCGCCAAAAT 0.957851 -180 CTAAAAGGATTGCCCAAAAATGCACAAGGT 6 126 1 TGCCCAAAAA 0.968013 -60 ********** Masking position 6 Map Score: 4.42355 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 86 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 GATTTGGATAGAGCTCCCACTTAATTCCCTGAGGA 1 69 0 GACTCCTTAT 0.942279 -159 GCTCTATCCAAATCCCCTCGTTAGAAGGTTTATGG 1 90 1 AACCCCTTAA 0.981966 -138 TTGACACTTTAACCACCCTTTTATAAATCTCTTTC 1 147 1 AACACCTTAA 0.991795 -81 TTGACCACCAACTCAAATTCTAATAAG 1 211 0 GACACCTCAA 0.988106 -17 ATTAAATCACCAGATCATATAGAGGAGAA 3 77 0 AACACCTCAA 0.989807 -19 TAAGAATCACCATGCTAATATTTGCTTAA 6 167 0 AACACCCTAT 0.959481 -19 ** **** *** * Masking position 13 Map Score: 1.76401 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 GTGGGAGCTCTATCCAAATCCCCTCGTTAG 1 84 1 TATCCAAATC 0.934463 -144 TTTGAAGTTATTTCGAACACCATAAACCTT 1 114 0 TTTCGAACAC 0.949009 -114 GTTTGATTATCGATATCATAGCGTTTA 3 8 1 TATCGATATC 0.96464 -88 CGTTTCCATAATTCTTTTAACC 4 3 1 TTTCCATAAT 0.804523 -51 TCTTTTAACCTTTCGATATCCTTTCAATTT 4 23 1 TTTCGATATC 0.980732 -31 CTTTTAGACGTTTTGAAAACTCACAGAGGA 6 103 0 TTTTGAAAAC 0.887288 -83 ********** Masking position 6 Map Score: 1.39977 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 132 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 GAGCCTAGATCCCAGGGAAGGTGGGCTCTA 1 18 1 CCCAGGGAAG 0.978815 -210 ACCGAAGTTCCTCAGGGAATTAAGTGGGAG 1 61 1 CTCAGGGAAT 0.974093 -167 AAACCTTCTAACGAGGGGATTTGGATAGAG 1 91 0 ACGAGGGGAT 0.975568 -137 AAAATGTTAAGAGAGGGGATATAAACC 5 8 0 GAGAGGGGAT 0.974529 -33 TTTGAAAACTCACAGAGGATAAAACTCCAC 6 92 0 CACAGAGGAT 0.966246 -94 ********** Masking position 4 Map Score: 0.403217 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 246 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -1.39734e-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: -1.39734e-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 9 ********** No masking Map Score: -1.39734e-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