AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i061_Glutamate_Synthase_pyro_reg_300.orf -o061_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 RPH00254 247 Pyrococcus_OT3 #2 RPH01722 125 Pyrococcus_OT3 Motif number 1 AAAATGTCTAAAAATATTGGTAAGCACTTCT 1 25 0 AAAATATGGT 0.976184 -223 GATAGGTTGAAAACTTTTGGTTTTAAAAATG 1 50 0 AAACTTTGGT 0.992696 -198 AGAGGGTTTTAAACTAATGGTTTTAAAAACC 1 162 1 AAACTATGGT 0.984428 -86 TATAACGGATAAAATTATTTTAATGAACAAA 1 217 1 AAAATTTTTT 0.498467 -31 AACTTATTGTAAACTATTGGTTGGATAATAA 2 37 0 AAACTATGGT 0.991016 -89 TTGTTTTTATAAACTTATTGTAAACTATTGG 2 48 0 AAACTTTTGT 0.971971 -78 CTAGGTTCTGAACATTTTGTTTTTATAAACT 2 64 0 AACATTTGTT 0.711651 -62 AAATGTTCAGAACCTAGTGTAATGTCCAAAA 2 78 1 AACCTATGTA 0.845212 -48 CGAGTTCGTGAACATTTTTGGACATTACACT 2 93 0 AACATTTTGG 0.835436 -33 ****** **** Masking position 5 Map Score: 13.8685 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 155 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 GAAAACTTTTGGTTTTAAAAATGTCTAAAA 1 43 0 GGTTTTAAAA 0.98876 -205 TAAGGGGATAGGTTGAAAACTTTTGGTTTT 1 57 0 GGTTGAAAAC 0.945984 -191 CCTTTTAGAGGGTTTTAAACTAATGGTTTT 1 156 1 GGTTTTAAAC 0.984387 -92 TTAAACTAATGGTTTTAAAAACCGCTATAA 1 170 1 GGTTTTAAAA 0.98876 -78 AATGAACAAAGGTGGTACAC 1 238 1 GGTGGTACAC 0.943397 -10 GTAAACTATTGGTTGGATAATAAATAAAAG 2 30 0 GGTTGGATAA 0.935406 -96 TGAACATTTTGTTTTTATAAACTTATTGTA 2 57 0 GTTTTTATAA 0.813015 -69 CATTACACTAGGTTCTGAACATTTTGTTTT 2 72 0 GGTTCTGAAC 0.943936 -54 ********** Masking position 9 Map Score: 9.83495 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 134 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 TTAGACATTTTTAAAACCAAAAGTTTTCAA 1 45 1 TTAAAACCAA 0.984036 -203 AACCATTAGTTTAAAACCCTCTAAAAGGAA 1 154 0 TTAAAACCCT 0.989623 -94 ATAGCGGTTTTTAAAACCATTAGTTTAAAA 1 168 0 TTAAAACCAT 0.991381 -80 TAAAAACCGCTATAAACCCTGAATTCCAGG 1 185 1 TATAAACCCT 0.926521 -63 CCTTTGTTCATTAAAATAATTTTATCCGTT 1 220 0 TTAAAATAAT 0.857397 -28 AATAAGTTTATAAAAACAAAATGTTCAGAA 2 60 1 TAAAAACAAA 0.917797 -66 ********** Masking position 5 Map Score: 6.49432 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 133 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TTCCCTTTTGGGATAAGGGGATAGGTTGAA 1 70 0 GGATAAGGGG 0.987098 -178 TGCTTATCCTGGAGTAGAGTAGAAAATGCT 1 109 0 GGAGTAGAGT 0.880131 -139 TATAGGCCTGGAATTCAGGGTTTATAGCGG 1 191 0 GAATTCAGGG 0.973715 -57 TTATTTTAATGAACAAAGGTGGTACAC 1 231 1 GAACAAAGGT 0.857086 -17 ATAAATAAAAGGATGCGAGGAGTGTATCGA 2 11 0 GGATGCGAGG 0.971565 -115 AAATGTTCACGAACTCGGGGGTGTTCATT 2 107 1 GAACTCGGGG 0.991621 -19 ********** Masking position 3 Map Score: 1.52609 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 428 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TACCAATATTTTTAGACATTTTTAAAACCA 1 34 1 TTTAGACATT 0.977103 -214 TTCCTTTCCTTTTAGAGGGTTTTAAACTAA 1 149 1 TTTAGAGGGT 0.927722 -99 ATTCAGGGTTTATAGCGGTTTTTAAAACCA 1 179 0 TATAGCGGTT 0.903366 -69 TTAAAATAATTTTATCCGTTATAGGCCTGG 1 210 0 TTTATCCGTT 0.960779 -38 GTGTACCACCTTTGTTCATTAAAATAATTT 1 228 0 TTTGTTCATT 0.825599 -20 CGTGAACATTTTTGGACATTACACTAGGTT 2 88 0 TTTGGACATT 0.972099 -38 ********** Masking position 3 Map Score: 0.890116 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 244 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 AATATTGGTAAGCACTTCTTAATGGTGAAG 1 14 0 AGCACTTCTT 0.922247 -234 ATGCTCCGACAACATTCCCTTTTGGGATAA 1 84 0 AACATTCCCT 0.979405 -164 ATGTTGTCGGAGCATTTTCTACTCTACTCC 1 99 1 AGCATTTTCT 0.944975 -149 AAGCATGAAAAACGCTTCCTTTCCTTTTAG 1 134 1 AACGCTTCCT 0.953347 -114 CCATTAGTTTAAAACCCTCTAAAAGGAAAG 1 152 0 AAAACCCTCT 0.750153 -96 CTAGGTTCTGAACATTTTGTTTTTATAAAC 2 65 0 AACATTTTGT 0.875244 -61 CGAGTTCGTGAACATTTTTGGACATTACAC 2 94 0 AACATTTTTG 0.825382 -32 AATGAACACCCCCGAGTTCGTGAA 2 112 0 AACACCCCCG 0.960313 -14 ********** Masking position 1 Map Score: 2.82745 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 722 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 7 ********** No masking Map Score: 3.93231e-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: 3.93231e-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: 3.93231e-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