AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_cell_division_mjan_reg_300.orf -o248_mjan_300.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 TTGTAATCCCTCCTATGCCGATATA 1 123 0 ATCCCTCCTA 0.933665 -15 GCTAAGGAAGCTCCAAGCTTTAGCTCGGAG 2 19 1 CTCCAAGCTT 0.980664 -282 TCTGAATCCTCTCCGAGCTAAAGCTTGGAG 2 29 0 CTCCGAGCTA 0.985602 -272 TTCATTAACTCTCCTTGCTACGCTCGAAGA 2 74 1 CTCCTTGCTA 0.987867 -227 TTTGTCTCGCCGCCTCCCTATCTTCGAGCG 2 94 0 CGCCTCCCTA 0.969846 -207 TGCCCGATGACACCAACCTGCCCTGTGACC 2 181 1 CACCAACCTG 0.948754 -120 CAACACGGAACACCCTGCTACTTATCGTCG 2 217 0 CACCCTGCTA 0.982065 -84 GTGTTGGAACCTCCACCCTTTAGGTGGAGA 2 241 1 CTCCACCCTT 0.982088 -60 ********** Masking position 9 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 AATTACGAACAATATTTATATGTAATCTCT 1 43 0 AATATTTATA 0.937736 -95 TATTGTTCGTAATTTTATTATATTAAAATT 1 59 1 AATTTTATTA 0.951734 -79 TTGTTAAAGTAATTTTAATATAATAAAATT 1 69 0 AATTTTAATA 0.977248 -69 ATAAATATTAAATTTGAATAAAGCATTGTT 1 94 0 AATTTGAATA 0.973825 -44 ATTCAAATTTAATATTTATATATCGGCATA 1 105 1 AATATTTATA 0.937736 -33 AAATCCTTCGAATTTCATTAACTCTCCTTG 2 61 1 AATTTCATTA 0.898902 -240 ATATACTTGAAATTAGTATAATGCTTTATT 2 134 1 AATTAGTATA 0.855609 -167 ********** Masking position 2 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 0.959015 -284 CATCTGAATCCTCTCCGAGCTAAAGCTTGG 2 31 0 CTCTCCGAGC 0.995212 -270 ATTTCATTAACTCTCCTTGCTACGCTCGAA 2 72 1 CTCTCCTTGC 0.953923 -229 CCGCCTCCCTATCTTCGAGCGTAGCAAGGA 2 85 0 ATCTTCGAGC 0.928839 -216 TAATGTTTGTCTCGCCGCCTCCCTATCTTC 2 99 0 CTCGCCGCCT 0.954306 -202 CCGTGTTGGAACCTCCACCCTTTAGGTGGA 2 239 1 ACCTCCACCC 0.965532 -62 AACTGATCTTCTCTCCACCTAAAGGGTGGA 2 252 0 CTCTCCACCT 0.977358 -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 AATATTTATATGTAATCTCTGTTCTGTTTG 1 33 0 TGTAATCTCT 0.949417 -105 TTTATTATATTAAAATTACTTTAACAATGC 1 72 1 TAAAATTACT 0.838116 -66 TTGTAATCCCTCCTATGCCGA 1 127 0 TGTAATCCCT 0.989999 -11 AGGATTCAGATGAAATCCTTCGAATTTCAT 2 49 1 TGAAATCCTT 0.97118 -252 TTGAAATTAGTATAATGCTTTATTGAGGGT 2 140 1 TATAATGCTT 0.889009 -161 GAAGATCAGTTAAAATTCCTAAATACTCCC 2 271 1 TAAAATTCCT 0.965136 -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 TCCCTCCTATGCCGATATATAAATATTAAA 1 112 0 GCCGATATAT 0.882639 -26 TGCTACGCTCGAAGATAGGGAGGCGGCGAG 2 89 1 GAAGATAGGG 0.966182 -212 AGGTCACAGGGCAGGTTGGTGTCATCGGGC 2 182 0 GCAGGTTGGT 0.93179 -119 ACTTATCGTCGCCGATAGGTCACAGGGCAG 2 198 0 GCCGATAGGT 0.990134 -103 ACCTATCGGCGACGATAAGTAGCAGGGTGT 2 208 1 GACGATAAGT 0.982005 -93 TAGGTGGAGAGAAGATCAGTTAAAATTCCT 2 261 1 GAAGATCAGT 0.939833 -40 ********** Masking position 6 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