AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_pyro_reg_300.orf -o060_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 RPH00271 204 Pyrococcus_OT3 #2 RPH00270 138 Pyrococcus_OT3 #3 RPH00072 223 Pyrococcus_OT3 Motif number 1 AAAGCTTAGAAAAAGGACAAAACTTAAAA 1 8 0 AAAAGCAAAA 0.909343 -197 CTTCACTGACAATTTGGAAAAGCTTAGAAAAA 1 26 0 AATTTAAAAG 0.760027 -179 AAATGAGTATAAAATTCAAGAATCTAATGAAG 1 102 1 AAAATAAGAA 0.924202 -103 AAACAAGAAAAAAATAGAAAGATTTATTATAG 1 145 1 AAAATAAAGA 0.936758 -60 TTACCTAAACAAAATTAAAAAATTTTGTAACT 2 29 1 AAAATAAAAA 0.986116 -110 GGGAATAAGGAAAGTTACAAAATTTTTTAATT 2 41 0 AAAGTCAAAA 0.924159 -98 AACTAGTGCGAAAATATAAATAAAGCTTATCC 3 27 1 AAAATAAATA 0.946301 -197 GATCAAATTGAAAATTTAAAAGTGGATAAGCT 3 50 0 AAAATAAAAG 0.960961 -174 TGAAATAAAGAATTTCTCAAAAATTGTATATT 3 86 0 AATTTCAAAA 0.882612 -138 TTAATAACATAAAATTGAAATAAAGAATTTCT 3 101 0 AAAATAAATA 0.946301 -123 AATCCTAAAAAATATGTCAAAAAATATATAAA 3 172 1 AATATCAAAA 0.968056 -52 TATGTCAAAAAATATATAAAAATCGTGAGCTT 3 184 1 AATATAAAAA 0.97357 -40 ***** ***** Masking position 9 Map Score: 14.9916 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 212 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 2 AGTTAACCTCCTTTCGCTATAATAAATCTT 1 163 0 CTTTCGCTAT 0.929259 -42 CACCCATGTTCATTCCCCCTGGAGTTAACC 1 185 0 CATTCCCCCT 0.985078 -20 GCTATCCCCTTAGGGTAATTA 2 2 1 CTATCCCCTT 0.966997 -137 AATTTTGTAACTTTCCTTATTCCCAAAGCC 2 49 1 CTTTCCTTAT 0.898616 -90 TTTCACTGAGCTTTCCCTCGTTTTAAATAG 2 106 0 CTTTCCCTCG 0.982547 -33 AACTTTCCCCCCATTTCACTGA 2 127 0 CTTTCCCCCC 0.991473 -12 CTTCCCCCTTAAATTCATAA 3 214 0 CTTCCCCCTT 0.977491 -10 ********** Masking position 5 Map Score: 6.90811 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 423 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 CTAAACCTTCACTGACAATTTGGAAAAGCT 1 34 0 ACTGACAATT 0.777571 -171 GTTGAAATGAGTATAAAATTCAAGAATCTA 1 98 1 GTATAAAATT 0.872817 -107 CTAAACAAAATTAAAAAATTTTGTAACTTT 2 33 1 TTAAAAAATT 0.822391 -106 CTGAGATCAAATTGAAAATTTAAAAGTGGA 3 56 0 ATTGAAAATT 0.943284 -168 TGATCTCAGAATATACAATTTTTGAGAAAT 3 77 1 ATATACAATT 0.934881 -147 TAAAATTGAAATAAAGAATTTCTCAAAAAT 3 94 0 ATAAAGAATT 0.886383 -130 ATTTTTAATAACATAAAATTGAAATAAAGA 3 107 0 ACATAAAATT 0.92663 -117 ATTTTATGTTATTAAAAATTATCTCAAATT 3 118 1 ATTAAAAATT 0.952519 -106 ATTTTTTAGGATTAAAAATTCCTATTAGGA 3 155 0 ATTAAAAATT 0.952519 -69 GTCAAAAAATATATAAAAATCGTGAGCTTA 3 187 1 ATATAAAAAT 0.805094 -37 ********** Masking position 5 Map Score: 8.9427 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 65 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TTTATTCAATATATCACCTACAAGTATAGT 1 70 1 ATATCACCTA 0.969818 -135 TTTTATACTCATTTCAACTATACTTGTAGG 1 86 0 ATTTCAACTA 0.977091 -119 TAATGAAGAAATATCAATTAAACAAGAAAA 1 126 1 ATATCAATTA 0.964998 -79 CTTTCCCCCCATTTCACTGAGCTTTCCCTC 2 117 0 ATTTCACTGA 0.950528 -22 GAAATTCTTTATTTCAATTTTATGTTATTA 3 102 1 ATTTCAATTT 0.923123 -122 ********** Masking position 6 Map Score: 2.4928 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 58 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TAGCTGTCATTTATTCAATATATCACCTAC 1 61 1 TTATTCAATA 0.907698 -144 TAATTGATATTTCTTCATTAGATTCTTGAA 1 116 0 TTCTTCATTA 0.849597 -89 GTAACTTTCCTTATTCCCAAAGCCCAGGTT 2 55 1 TTATTCCCAA 0.957908 -84 TTTAAATAGATTATTCATACATTCCTGGGC 2 85 0 TTATTCATAC 0.919806 -54 CAATTTTATGTTATTAAAAATTATCTCAAA 3 116 1 TTATTAAAAA 0.623068 -108 TCAAATTGTTTTATTCCTAATAGGAATTTT 3 141 1 TTATTCCTAA 0.969859 -83 ATAGGAATTTTTAATCCTAAAAAATATGTC 3 160 1 TTAATCCTAA 0.913264 -64 ********** Masking position 5 Map Score: 3.43567 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 195 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ********** No masking Map Score: 1.72962e-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: 1.72962e-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: 1.72962e-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