AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_mjan_pyro_100.orf -o248_mjan_pyro_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ11895 137 M_jannaschii_chromosome #2 RMJ05430 300 M_jannaschii_chromosome #3 RPH01533 194 Pyrococcus_OT3 #4 RPH01651 62 Pyrococcus_OT3 Motif number 1 TTGTAATCCCTCCTATGCCGATATA 1 123 0 ATCCCTCCTA 0.896995 -15 GCTAAGGAAGCTCCAAGCTTTAGCTCGGAG 2 19 1 CTCCAAGCTT 0.960493 -282 TCTGAATCCTCTCCGAGCTAAAGCTTGGAG 2 29 0 CTCCGAGCTA 0.967663 -272 TTCATTAACTCTCCTTGCTACGCTCGAAGA 2 74 1 CTCCTTGCTA 0.978882 -227 TTTGTCTCGCCGCCTCCCTATCTTCGAGCG 2 94 0 CGCCTCCCTA 0.945676 -207 TGCCCGATGACACCAACCTGCCCTGTGACC 2 181 1 CACCAACCTG 0.940342 -120 CAACACGGAACACCCTGCTACTTATCGTCG 2 217 0 CACCCTGCTA 0.978108 -84 GTGTTGGAACCTCCACCCTTTAGGTGGAGA 2 241 1 CTCCACCCTT 0.970166 -60 TTCTACCACCATCCTAAGATTCTGGG 3 179 0 CACCATCCTA 0.985245 -16 ********** Masking position 9 Map Score: 9.91089 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 111 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 ACAGAGATTACATATAAATATTGTTCGTAATT 1 41 1 CATATAAATT 0.909728 -97 GTAATTTTATTATATTAAAATTACTTTAACAA 1 67 1 TATATAAATT 0.967386 -71 TTAACAATGCTTTATTCAAATTTAATATTTAT 1 92 1 TTTATCAATT 0.963606 -46 CCTATGCCGATATATAAATATTAAATTTGAAT 1 105 0 TATATAAATT 0.975431 -33 GATGTTTACATTTGTCAACATTTAAAGCTTTT 3 27 1 TTTGTAAATT 0.935604 -168 CGTTGTTTCTTTTTTGAACATTAATGTCCATC 3 62 0 TTTTTAAATT 0.907219 -133 TATTTGAAAGTTTATCAAAATTTTCGAGCATT 3 109 1 TTTATAAATT 0.982038 -86 AATTAACCTTTTTATCCAAATCATCTTCCATA 3 141 0 TTTATCAATC 0.862044 -54 CAGGATAATTTATATAAGAATTCCTGGGTTCA 4 24 1 TATATAGATT 0.912092 -39 ***** ** *** Masking position 5 Map Score: 9.69485 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 137 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 TATAAATATTGTTCGTAATTTTATTATATT 1 53 1 GTTCGTAATT 0.886807 -85 TGCTAAGGAAGCTCCAAGCTTTAGCTCGGA 2 18 1 GCTCCAAGCT 0.914097 -283 CCAAGCTTTAGCTCGGAGAGGATTCAGATG 2 31 1 GCTCGGAGAG 0.950356 -270 TCCTTGCTACGCTCGAAGATAGGGAGGCGG 2 85 1 GCTCGAAGAT 0.985243 -216 GTAGCAGGGTGTTCCGTGTTGGAACCTCCA 2 226 1 GTTCCGTGTT 0.826739 -75 CTCCCATTTTGCTCGTTGTTTCTTTTTTGA 3 77 0 GCTCGTTGTT 0.969662 -118 TTCCATAAATGCTCGAAAATTTTGATAAAC 3 118 0 GCTCGAAAAT 0.963097 -77 AAGATTCTGGGTTCGTTAATTAACCTTTTT 3 160 0 GTTCGTTAAT 0.864113 -35 ********** Masking position 3 Map Score: 4.98443 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 29 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AGCTTTAGCTCGGAGAGGATTCAGATGAAA 2 34 1 CGGAGAGGAT 0.946039 -267 CTCGAAGATAGGGAGGCGGCGAGACAAACA 2 96 1 GGGAGGCGGC 0.956129 -205 TGTGACCTATCGGCGACGATAAGTAGCAGG 2 204 1 CGGCGACGAT 0.865056 -97 TCCACCTAAAGGGTGGAGGTTCCAACACGG 2 239 0 GGGTGGAGGT 0.981773 -62 CCTTTAGGTGGAGAGAAGATCAGTTAAAAT 2 257 1 GAGAGAAGAT 0.913039 -44 GTAAACATCAGAGTGGGGATGATAA 3 6 0 GAGTGGGGAT 0.932801 -189 CGAGCAAAATGGGAGGATATTTGAAAGTTT 3 92 1 GGGAGGATAT 0.911269 -103 GAGCATTTATGGAAGATGATTTGGATAAAA 3 134 1 GGAAGATGAT 0.879915 -61 CAGAATCTTAGGATGGTGGTAGAA 3 181 1 GGATGGTGGT 0.880982 -14 ********** Masking position 5 Map Score: 3.45011 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 435 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 CAAACAGAACAGAGATTACATATAAATATT 1 33 1 AGAGATTACA 0.859847 -105 AAATATTGTTCGTAATTTTATTATATTAAA 1 56 1 CGTAATTTTA 0.816177 -82 GCATTGTTAAAGTAATTTTAATATAATAAA 1 72 0 AGTAATTTTA 0.934183 -66 TCGGCATAGGAGGGATTACAA 1 127 1 AGGGATTACA 0.961156 -11 ATGAAATTCGAAGGATTTCATCTGAATCCT 2 49 0 AAGGATTTCA 0.898292 -252 AAAGCATTATACTAATTTCAAGTATATAAA 2 131 0 ACTAATTTCA 0.872922 -170 GGGAGTATTTAGGAATTTTAACTGATCTTC 2 271 0 AGGAATTTTA 0.957939 -30 ********** Masking position 5 Map Score: 1.45072 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 384 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 ATTAAAATTACTTTAACAATGCTTTATTCAAA 1 80 1 CTTAACATGC 0.926855 -58 CTTCGAATTTCATTAACTCTCCTTGCTACGCT 2 66 1 CTTAACCTCC 0.9723 -235 TCAGAGCTACCCTCAATAAAGCATTATACTAA 2 146 0 CTCAATAAGC 0.862595 -155 AGTTAAAATTCCTAAATACTCCCGTAGTGGAG 2 278 1 CTAAATCTCC 0.979429 -23 AATCATCTTCCATAAATGCTCGAAAATTTTGA 3 123 0 CTAAATCTCG 0.887388 -72 ATTCTGGGTTCGTTAATTAACCTTTTTATCCA 3 155 0 CTTAATAACC 0.850622 -40 GGAATTCTTATATAAATTATCCTGCTATTAAC 4 16 0 TTAAATATCC 0.84434 -47 TATTACACCACTTTAGTGAACCCAGGAATTCT 4 40 0 CTTAGTAACC 0.912729 -23 * ***** **** Masking position 5 Map Score: 1.30901 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 248 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 ********** No masking Map Score: -1.80235e-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: -1.80235e-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: -1.80235e-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