AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_mjan_reg_300.orf -o321_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 RMJ00843 201 M_jannaschii_chromosome #2 RMJ04712 278 M_jannaschii_chromosome Motif number 1 TAATCATTATAAATTCCTAATAAGTTGGTGA 1 16 0 AAATCCTAAT 0.920358 -186 TAATAATGATAAATCTTATTTATAACTTTTG 1 45 1 AAACTTATTT 0.820222 -157 GCCATGGGGAAAACCCCTATTGGGATACCCG 1 95 1 AAACCCTATT 0.981434 -107 ATATGCTCTCAAATCTTTATTAAAGTGAGGT 1 144 0 AAACTTTATT 0.939591 -58 CAATAGGAGCAAAACCCTTGGATGTATAACT 1 175 1 AAACCCTTGG 0.888138 -27 CCTTGGATGTATAACTTTTTTG 1 190 1 ATACTTTTTT 0.705144 -12 GGGAAAACCCTATTGACAAAGGAC 2 4 1 AAACCCTATT 0.981409 -275 AAAAAGCTGTAAAGTCCTTTGTCAATAGGGT 2 17 0 AAATCCTTTG 0.947306 -262 TTTGGCATCAAAATTCCTTATATGGTATAAA 2 45 0 AAATCCTTAT 0.947583 -234 ATTCAATCATAAAATTTTATTTCTGTGAAAG 2 85 1 AAATTTTATT 0.880149 -194 TATTTCTGTGAAAGTCCTGTGATACCCTAAC 2 102 1 AAATCCTGTG 0.807705 -177 TATTTTCTCCAAAATTTTTATAAATCTTTTT 2 192 1 AAATTTTTAT 0.841714 -87 AAATTTTTATAAATCTTTTTTATAAATACTC 2 203 1 AAACTTTTTT 0.96033 -76 ATACTCTATCAAACCTCATATATATGCTTTA 2 228 1 AAACTCATAT 0.817462 -51 *** ******* Masking position 3 Map Score: 16.1054 Number of sites scoring better than the average of aligned sites = 1794 Number in coding regions = 1528 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 TTATTAGGAATTTATAATGATTAATAATGA 1 24 1 TTTATAATGA 0.878326 -178 TTTATAATGATTAATAATGATAAATCTTAT 1 34 1 TTAATAATGA 0.975569 -168 ACCAAAAGTTATAAATAAGATTTATCATTA 1 48 0 ATAAATAAGA 0.94007 -154 CAACCTCACTTTAATAAAGATTTGAGAGCA 1 142 1 TTAATAAAGA 0.975781 -60 ATTTTATGATTGAATAAAGATGCCTTTGGC 2 70 0 TGAATAAAGA 0.914649 -209 TAGAGTATTTATAAAAAAGATTTATAAAAA 2 206 0 ATAAAAAAGA 0.961779 -73 CTATTAAAGCATATATATGAGGTTTGATAG 2 233 0 ATATATATGA 0.73753 -46 TTTAATAGGGATAATTATGAAGCATCTAAT 2 255 1 ATAATTATGA 0.961774 -24 ********** Masking position 7 Map Score: 7.8672 Number of sites scoring better than the average of aligned sites = 666 Number in coding regions = 550 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 ATAAGCCTATTATCACCAAAAGTTATAAATAA 1 60 0 TATCCAAAAG 0.957548 -142 AATAGGCTTATATTGCCATGGGGAAAACCCCT 1 81 1 TATCCATGGG 0.988744 -121 CTCGCTCGGGTATCCCAATAGGGGTTTTCCCC 1 100 0 TATCAATAGG 0.972588 -102 GATTTGAGAGCATATCAATAGGAGCAAAACCC 1 160 1 CATCAATAGG 0.904033 -42 AAAAAAGTTATACATCCAAGGGTTTTGCTCCT 1 179 0 TACCCAAGGG 0.972371 -23 GGGAAAACCCTATTGACAAAGGACTTTACAGC 2 11 1 TATACAAAGG 0.957548 -268 TAAGGAATTTTGATGCCAAAGGCATCTTTATT 2 56 1 TGACCAAAGG 0.917614 -223 ACCTCCTCGCTATGCCCGGAGGTGTAAATTAG 2 133 1 TATCCGGAGG 0.960267 -146 *** ******* Masking position 12 Map Score: 4.72753 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 221 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 GTTGTCTTGGCAACCTCGCTCGGGTATCCC 1 116 0 CAACCTCGCT 0.997662 -86 GTTGCCAAGACAACCTCACTTTAATAAAGA 1 132 1 CAACCTCACT 0.993648 -70 TACCCTAACACCTCCTCGCTATGCCCGGAG 2 124 1 CCTCCTCGCT 0.995107 -155 ********** Masking position 6 Map Score: 3.06216 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 AATAAAGATTTGAGAGCATATCAATAGGAG 1 154 1 TGAGAGCATA 0.979896 -48 TTACAGCTTTTTATACCATATAAGGAATTT 2 36 1 TTATACCATA 0.950273 -243 TAAAATTTTATGATTGAATAAAGATGCCTT 2 74 0 TGATTGAATA 0.900198 -205 GAAAGTCCTGTGATACCCTAACACCTCCTC 2 111 1 TGATACCCTA 0.962231 -168 ATATGAGGTTTGATAGAGTATTTATAAAAA 2 219 0 TGATAGAGTA 0.942759 -60 ATTATCCCTATTAAAGCATATATATGAGGT 2 240 0 TTAAAGCATA 0.917442 -39 ********** Masking position 3 Map Score: 1.62238 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 155 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AAGCATCACCAACTTATTAGGAATTTA 1 8 1 ACCAACTTAT 0.845214 -194 TGGCAATATAAGCCTATTATCACCAAAAGT 1 69 0 AGCCTATTAT 0.93151 -133 AAGATTTGAGAGCATATCAATAGGAGCAAA 1 158 1 AGCATATCAA 0.932868 -44 AGCTTTTTATACCATATAAGGAATTTTGAT 2 40 1 ACCATATAAG 0.893645 -239 GGTGTAAATTAGCAAATTATTATCTTGAAA 2 153 1 AGCAAATTAT 0.95056 -126 TCCCTATTAAAGCATATATATGAGGTTTGA 2 236 0 AGCATATATA 0.831041 -43 ATAATTATGAAGCATCTAATATCA 2 265 1 AGCATCTAAT 0.967465 -14 ********** Masking position 1 Map Score: 1.54034 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 425 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 GGGGTTTTCCCCATGGCAATATAAGCCTAT 1 82 0 CCATGGCAAT 0.980637 -120 AGTGAGGTTGTCTTGGCAACCTCGCTCGGG 1 122 0 TCTTGGCAAC 0.980322 -80 CTGTAAAGTCCTTTGTCAATAGGGTTTTCC 2 12 0 CTTTGTCAAT 0.95417 -267 ATAAAGATGCCTTTGGCATCAAAATTCCTT 2 57 0 CTTTGGCATC 0.980636 -222 ********** Masking position 4 Map Score: 0.0692681 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 65 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: 4.35863e-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: 4.35863e-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 10 ********** No masking Map Score: 4.35863e-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