AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i070_Threonine_Biosynthesis_pyro_reg_100.orf -o070_pyro_100.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 RPH00272 300 Pyrococcus_OT3 #2 RPH00072 223 Pyrococcus_OT3 Motif number 1 AAACTCATCGTTCCTCCTTATTCAGGAGATGT 1 92 1 TTCCCCTTTT 0.946085 -209 GCAACCTACTATCCTCCTTTAAAGTGCTATGT 1 132 0 ATCCCCTTAA 0.98629 -169 ATCACCCTTCTTCCTACTTCATTCTTGGAAAT 1 173 0 TTCCACTTAT 0.982653 -128 CAATTACCCGTCCCAACTTCAAAACTCCCAAA 1 251 0 TCCCACTTAA 0.971525 -50 TTTGCACCCTCCATTAACTTTTCTTGG 1 284 0 ACCCCCATAA 0.847172 -17 AATAAAGCTTATCCACTTTTAAATTTTCAATT 2 45 1 ATCCCTTTAA 0.959282 -179 ACTTTTAAATTTTCAATTTGATCTCAGAATAT 2 59 1 TTTCATTTAT 0.778875 -165 AAATTCTTTATTTCAATTTTATGTTATTAAAA 2 103 1 TTTCATTTAT 0.785071 -121 CTTCCCCCTTAAATTCATAAGCT 2 211 0 TTCCCCTTAA 0.99276 -13 **** **** ** Masking position 9 Map Score: 8.54393 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 648 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 AGGAATTTTTCTTTCCTTCTAGAGCGAACC 1 60 0 CTTTCCTTCT 0.974015 -241 GGAAACTCATCGTTCCTCCTTATTCAGGAG 1 90 1 CGTTCCTCCT 0.984794 -211 TAAAGTGCTATGTTCTTCATAACATCTCCT 1 115 0 TGTTCTTCAT 0.810035 -186 TAGCAACCTACTATCCTCCTTTAAAGTGCT 1 136 0 CTATCCTCCT 0.947449 -165 CCTAAATCACCCTTCTTCCTACTTCATTCT 1 180 0 CCTTCTTCCT 0.972902 -121 AGTGGATAAGCTTTATTTATATTTTCGCAC 2 32 0 CTTTATTTAT 0.793078 -192 TTGAGAAATTCTTTATTTCAATTTTATGTT 2 98 1 CTTTATTTCA 0.7542 -126 TCTCAAATTGTTTTATTCCTAATAGGAATT 2 139 1 TTTTATTCCT 0.951134 -85 TAATAGGAATTTTTAATCCTAAAAAATATG 2 158 1 TTTTAATCCT 0.827642 -66 ********** Masking position 4 Map Score: 6.3076 Number of sites scoring better than the average of aligned sites = 1541 Number in coding regions = 1413 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 CTCAGAATATACAATTTTTGAGAAATTCTT 2 81 1 ACAATTTTTG 0.974353 -143 ACAATTTGAGATAATTTTTAATAACATAAA 2 120 0 ATAATTTTTA 0.97024 -104 ATTTTTTGACATATTTTTTAGGATTAAAAA 2 167 0 ATATTTTTTA 0.957903 -57 CGATTTTTATATATTTTTTGACATATTTTT 2 179 0 ATATTTTTTG 0.960882 -45 TCATAAGCTCACGATTTTTATATATTTTTT 2 190 0 ACGATTTTTA 0.940673 -34 ********** Masking position 5 Map Score: 3.70312 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 39 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GAACGATGAGTTTCCAGGAATTTTTCTTTC 1 75 0 TTTCCAGGAA 0.956988 -226 TAGTTCCTGATTTCCAAGAATGAAGTAGGA 1 164 1 TTTCCAAGAA 0.985108 -137 TCATGACCTTTCTCCAAGACAAGTACCACT 1 213 0 TCTCCAAGAC 0.988439 -88 ACTTCAAAACTCCCAAAGACGTCTTTCATG 1 238 0 TCCCAAAGAC 0.928642 -63 GACGGGTAATTGACCAAGAAAAGTTAATGG 1 271 1 TGACCAAGAA 0.969082 -30 CTAAAAAATATGTCAAAAAATATATAAAAA 2 176 1 TGTCAAAAAA 0.843517 -48 ********** Masking position 6 Map Score: 2.9384 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 221 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TGCTATGTTCTTCATAACATCTCCTGAATA 1 110 0 TTCATAACAT 0.98695 -191 AAAGACGTCTTTCATGACCTTTCTCCAAGA 1 224 0 TTCATGACCT 0.985686 -77 GAGATAATTTTTAATAACATAAAATTGAAA 2 113 0 TTAATAACAT 0.950247 -111 CCCCCTTAAATTCATAAGCTCACGATTTTT 2 201 0 TTCATAAGCT 0.977622 -23 ********** Masking position 5 Map Score: 2.0435 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 30 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TATACTAAGGTTCGCTCTAGAAGGAAAGAA 1 52 1 TTCGCTCTAG 0.962117 -249 GAAGGGTGATTTAGGACTAGTGGTACTTGT 1 195 1 TTAGGACTAG 0.97904 -106 TATTTATATTTTCGCACTAGTTAGGTTCGG 2 19 0 TTCGCACTAG 0.987668 -205 AAAATTCCTATTAGGAATAAAACAATTTGA 2 141 0 TTAGGAATAA 0.920479 -83 GACATATTTTTTAGGATTAAAAATTCCTAT 2 160 0 TTAGGATTAA 0.920479 -64 ********** Masking position 8 Map Score: 2.93551 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 40 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: -9.07063e-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: -9.07063e-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 9 ********** No masking Map Score: -9.07063e-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