AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_cell_division_mjan_reg_100.orf -o248_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ11895 137 M_jannaschii_chromosome #2 RMJ05430 300 M_jannaschii_chromosome Motif number 1 TATATCGGCATAGGAGGGATTACAA 1 123 1 TAGGAGGGAT 0.919593 -15 CTCCGAGCTAAAGCTTGGAGCTTCCTTAGC 2 19 0 AAGCTTGGAG 0.976321 -282 CTCCAAGCTTTAGCTCGGAGAGGATTCAGA 2 29 1 TAGCTCGGAG 0.982342 -272 TCTTCGAGCGTAGCAAGGAGAGTTAATGAA 2 74 0 TAGCAAGGAG 0.985114 -227 CGCTCGAAGATAGGGAGGCGGCGAGACAAA 2 94 1 TAGGGAGGCG 0.963146 -207 GGTCACAGGGCAGGTTGGTGTCATCGGGCA 2 181 0 CAGGTTGGTG 0.937731 -120 CGACGATAAGTAGCAGGGTGTTCCGTGTTG 2 217 1 TAGCAGGGTG 0.978028 -84 TCTCCACCTAAAGGGTGGAGGTTCCAACAC 2 241 0 AAGGGTGGAG 0.978048 -60 ********** Masking position 2 Map Score: 8.86328 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 136 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 AGAGATTACATATAAATATTGTTCGTAATT 1 43 1 TATAAATATT 0.937458 -95 AATTTTAATATAATAAAATTACGAACAATA 1 59 0 TAATAAAATT 0.951513 -79 AATTTTATTATATTAAAATTACTTTAACAA 1 69 1 TATTAAAATT 0.977152 -69 AACAATGCTTTATTCAAATTTAATATTTAT 1 94 1 TATTCAAATT 0.973705 -44 TATGCCGATATATAAATATTAAATTTGAAT 1 105 0 TATAAATATT 0.937458 -33 CAAGGAGAGTTAATGAAATTCGAAGGATTT 2 61 0 TAATGAAATT 0.898463 -240 AATAAAGCATTATACTAATTTCAAGTATAT 2 134 0 TATACTAATT 0.855027 -167 ********** Masking position 8 Map Score: 7.1993 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 287 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 TTGCTAAGGAAGCTCCAAGCTTTAGCTCGG 2 17 1 AGCTCCAAGC 0.957889 -284 CATCTGAATCCTCTCCGAGCTAAAGCTTGG 2 31 0 CTCTCCGAGC 0.995075 -270 ATTTCATTAACTCTCCTTGCTACGCTCGAA 2 72 1 CTCTCCTTGC 0.952664 -229 CCGCCTCCCTATCTTCGAGCGTAGCAAGGA 2 85 0 ATCTTCGAGC 0.926946 -216 TAATGTTTGTCTCGCCGCCTCCCTATCTTC 2 99 0 CTCGCCGCCT 0.953056 -202 CCGTGTTGGAACCTCCACCCTTTAGGTGGA 2 239 1 ACCTCCACCC 0.964578 -62 AACTGATCTTCTCTCCACCTAAAGGGTGGA 2 252 0 CTCTCCACCT 0.976723 -49 ********** Masking position 6 Map Score: 3.91914 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 131 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 CAAACAGAACAGAGATTACATATAAATATT 1 33 1 AGAGATTACA 0.945492 -105 GCATTGTTAAAGTAATTTTAATATAATAAA 1 72 0 AGTAATTTTA 0.827548 -66 TCGGCATAGGAGGGATTACAA 1 127 1 AGGGATTACA 0.989171 -11 ATGAAATTCGAAGGATTTCATCTGAATCCT 2 49 0 AAGGATTTCA 0.968809 -252 ACCCTCAATAAAGCATTATACTAATTTCAA 2 140 0 AAGCATTATA 0.880679 -161 GGGAGTATTTAGGAATTTTAACTGATCTTC 2 271 0 AGGAATTTTA 0.962376 -30 ********** Masking position 5 Map Score: 3.38516 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 336 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TTTAATATTTATATATCGGCATAGGAGGGA 1 112 1 ATATATCGGC 0.887608 -26 CTCGCCGCCTCCCTATCTTCGAGCGTAGCA 2 89 0 CCCTATCTTC 0.967744 -212 GCCCGATGACACCAACCTGCCCTGTGACCT 2 182 1 ACCAACCTGC 0.934835 -119 CTGCCCTGTGACCTATCGGCGACGATAAGT 2 198 1 ACCTATCGGC 0.990143 -103 ACACCCTGCTACTTATCGTCGCCGATAGGT 2 208 0 ACTTATCGTC 0.98285 -93 AGGAATTTTAACTGATCTTCTCTCCACCTA 2 261 0 ACTGATCTTC 0.942539 -40 ********** Masking position 5 Map Score: 3.32381 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 36 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: -3.81261e-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: -3.81261e-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: -3.81261e-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