AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_mjan_reg_100.orf -o320_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 RMJ01269 211 M_jannaschii_chromosome #2 RMJ02550 225 M_jannaschii_chromosome Motif number 1 TTTCATTAACATATACATACCGAATAAGGTA 1 29 0 ATATACATAC 0.926886 -183 TTTATATAGAATTTCATTAACATATACATAC 1 40 0 ATTTCATTAC 0.892349 -172 AGTTGATTCAACATCAATAACTGTAAATATA 1 89 1 ACATCAATAC 0.938978 -123 AACTGTAAATATATAAATACTTATATCTTAC 1 107 1 ATATAAATAT 0.974437 -105 TGTTTTTTGTAAATAAATAGCAAAGCTATCT 1 168 0 AAATAAATAC 0.905507 -44 TATTGCTCATATATAAAAAATGAAATTGCCA 2 80 0 ATATAAAAAT 0.913705 -146 ATCTCGAAAAATTTAAATATTGCTCATATAT 2 97 0 ATTTAAATAT 0.913756 -129 ACCAACAATATTATCATTATTTTTAATAACT 2 135 1 TTATCATTAT 0.724614 -91 TTTTGATATTATATAATTACTATTATTATTA 2 194 0 ATATAATTAT 0.945235 -32 TAATTATATAATATCAAAAGCGGGATAGTT 2 206 1 ATATCAAAAC 0.948206 -20 ********* * Masking position 4 Map Score: 8.39277 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 593 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 AATTCTATATAAACCTTTCGGTTTTGTGTA 1 58 1 AAACCTTTCG 0.978881 -154 GCTATCTTATAAATCTTTGTTTCATCAGCA 1 145 0 AAATCTTTGT 0.947608 -67 AATAAATAGCAAAGCTATCTTATAAATCTT 1 158 0 AAAGCTATCT 0.981347 -54 ACAAAAAACAAAACGTATTTAAGGATGATA 1 189 1 AAACGTATTT 0.801939 -23 AGCAATATTTAAATTTTTCGAGATAGATTT 2 104 1 AAATTTTTCG 0.869149 -122 ATTGTTGGTTAAATCTATCTCGAAAAATTT 2 114 0 AAATCTATCT 0.978936 -112 CTAATACTTTAAAGCTTTTTGATACGGAAG 2 164 0 AAAGCTTTTT 0.95859 -62 ********** Masking position 3 Map Score: 4.62942 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 475 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 3 CGAATAAGGTAACAATCTGAGGTGAGAAG 1 10 0 AACAATCTGA 0.904113 -202 TTGATGTTGAATCAACTTTACACAAAACCG 1 76 0 ATCAACTTTA 0.856627 -136 ATCTTACAAAATTATGCTGATGAAACAAAG 1 131 1 ATTATGCTGA 0.842928 -81 CACTATCATCCTTAAATACGTTTT 1 198 0 ATCATCCTTA 0.959224 -14 TAATAGGGCAATTATTCTTTTAATGGTATC 2 36 1 ATTATTCTTT 0.769226 -190 AAATTGCCATAACATTTTGAGGTGATACCA 2 59 0 AACATTTTGA 0.896939 -167 AGATTTAACCAACAATATTATCATTATTTT 2 128 1 AACAATATTA 0.794349 -98 CAATATTATCATTATTTTTAATAACTTCCG 2 140 1 ATTATTTTTA 0.911014 -86 TATAATTACTATTATTATTACTAATACTTT 2 184 0 ATTATTATTA 0.877222 -42 ********** Masking position 4 Map Score: 3.31724 Number of sites scoring better than the average of aligned sites = 862 Number in coding regions = 698 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 4 TGAATCAACTTTACACAAAACCGAAAGGTT 1 69 0 TTACACAAAA 0.939352 -143 TACTTATATCTTACAAAATTATGCTGATGA 1 124 1 TTACAAAATT 0.87146 -88 AAACAAAGATTTATAAGATAGCTTTGCTAT 1 153 1 TTATAAGATA 0.892573 -59 TGCTATTTATTTACAAAAAACAAAACGTAT 1 177 1 TTACAAAAAA 0.976052 -35 TATTGCTCATATATAAAAAATGAAATTGCC 2 81 0 ATATAAAAAA 0.879084 -145 GATACGGAAGTTATTAAAAATAATGATAAT 2 144 0 TTATTAAAAA 0.868425 -82 ATAATAGTAATTATATAATATCAAAAGCGG 2 199 1 TTATATAATA 0.86908 -27 ********** Masking position 3 Map Score: 3.59273 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 355 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 CTTCTCACCTCAGATTGTTACC 1 3 1 TCTCACCTCA 0.991231 -209 CCTATGAGAATAGCCCCCCAATAATAGGGC 2 15 1 TAGCCCCCCA 0.987612 -211 CTTTTAATGGTATCACCTCAAAATGTTATG 2 52 1 TATCACCTCA 0.992619 -174 ********** Masking position 10 Map Score: 0.130061 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ********** No masking Map Score: -8.6443e-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: -8.6443e-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: -8.6443e-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