AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_mjan_reg_100.orf -o321_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 RMJ00843 201 M_jannaschii_chromosome #2 RMJ04712 278 M_jannaschii_chromosome Motif number 1 TCACCAACTTATTAGGAATTTATAATGATTA 1 16 1 ATTAGGATTT 0.920037 -186 CAAAAGTTATAAATAAGATTTATCATTATTA 1 45 0 AAATAAGTTT 0.819578 -157 CGGGTATCCCAATAGGGGTTTTCCCCATGGC 1 95 0 AATAGGGTTT 0.981354 -107 ACCTCACTTTAATAAAGATTTGAGAGCATAT 1 144 1 AATAAAGTTT 0.939342 -58 AGTTATACATCCAAGGGTTTTGCTCCTATTG 1 175 0 CCAAGGGTTT 0.887702 -27 CAAAAAAGTTATACATCCAAGG 1 190 0 AAAAAAGTAT 0.704236 -12 GTCCTTTGTCAATAGGGTTTTCCC 2 4 0 AATAGGGTTT 0.98133 -275 ACCCTATTGACAAAGGACTTTACAGCTTTTT 2 17 1 CAAAGGATTT 0.947087 -262 TTTATACCATATAAGGAATTTTGATGCCAAA 2 45 1 ATAAGGATTT 0.947365 -234 CTTTCACAGAAATAAAATTTTATGATTGAAT 2 85 0 AATAAAATTT 0.879687 -194 GTTAGGGTATCACAGGACTTTCACAGAAATA 2 102 0 CACAGGATTT 0.807025 -177 AAAAAGATTTATAAAAATTTTGGAGAAAATA 2 192 0 ATAAAAATTT 0.841131 -87 GAGTATTTATAAAAAAGATTTATAAAAATTT 2 203 0 AAAAAAGTTT 0.960164 -76 TAAAGCATATATATGAGGTTTGATAGAGTAT 2 228 0 ATATGAGTTT 0.816808 -51 ******* *** Masking position 9 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 TCATTATTAATCATTATAAATTCCTAATAA 1 24 0 TCATTATAAA 0.856178 -178 ATAAGATTTATCATTATTAATCATTATAAA 1 34 0 TCATTATTAA 0.970607 -168 TAATGATAAATCTTATTTATAACTTTTGGT 1 48 1 TCTTATTTAT 0.928199 -154 TGCTCTCAAATCTTTATTAAAGTGAGGTTG 1 142 0 TCTTTATTAA 0.970781 -60 GCCAAAGGCATCTTTATTCAATCATAAAAT 2 70 1 TCTTTATTCA 0.898303 -209 TTTTTATAAATCTTTTTTATAAATACTCTA 2 206 1 TCTTTTTTAT 0.953998 -73 CTATCAAACCTCATATATATGCTTTAATAG 2 233 1 TCATATATAT 0.698434 -46 ATTAGATGCTTCATAATTATCCCTATTAAA 2 255 0 TCATAATTAT 0.953994 -24 ********** Masking position 4 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 0.962521 -142 AATAGGCTTATATTGCCATGGGGAAAACCCCT 1 81 1 TATCCATGGG 0.9901 -121 CTCGCTCGGGTATCCCAATAGGGGTTTTCCCC 1 100 0 TATCAATAGG 0.975844 -102 GATTTGAGAGCATATCAATAGGAGCAAAACCC 1 160 1 CATCAATAGG 0.914709 -42 AAAAAAGTTATACATCCAAGGGTTTTGCTCCT 1 179 0 TACCCAAGGG 0.975652 -23 GGGAAAACCCTATTGACAAAGGACTTTACAGC 2 11 1 TATACAAAGG 0.962521 -268 TAAGGAATTTTGATGCCAAAGGCATCTTTATT 2 56 1 TGACCAAAGG 0.926909 -223 ACCTCCTCGCTATGCCCGGAGGTGTAAATTAG 2 133 1 TATCCGGAGG 0.964934 -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 GGGATACCCGAGCGAGGTTGCCAAGACAAC 1 116 1 AGCGAGGTTG 0.997652 -86 TCTTTATTAAAGTGAGGTTGTCTTGGCAAC 1 132 0 AGTGAGGTTG 0.99362 -70 CTCCGGGCATAGCGAGGAGGTGTTAGGGTA 2 124 0 AGCGAGGAGG 0.995086 -155 ********** Masking position 5 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 0.980804 -48 TTACAGCTTTTTATACCATATAAGGAATTT 2 36 1 TTATACCATA 0.952454 -243 TAAAATTTTATGATTGAATAAAGATGCCTT 2 74 0 TGATTGAATA 0.904354 -205 GAAAGTCCTGTGATACCCTAACACCTCCTC 2 111 1 TGATACCCTA 0.963907 -168 ATATGAGGTTTGATAGAGTATTTATAAAAA 2 219 0 TGATAGAGTA 0.945251 -60 ATTATCCCTATTAAAGCATATATATGAGGT 2 240 0 TTAAAGCATA 0.920943 -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 TAAATTCCTAATAAGTTGGTGATGCTT 1 8 0 ATAAGTTGGT 0.857334 -194 ACTTTTGGTGATAATAGGCTTATATTGCCA 1 69 1 ATAATAGGCT 0.937372 -133 TTTGCTCCTATTGATATGCTCTCAAATCTT 1 158 0 TTGATATGCT 0.938622 -44 ATCAAAATTCCTTATATGGTATAAAAAGCT 2 40 0 CTTATATGGT 0.902409 -239 TTTCAAGATAATAATTTGCTAATTTACACC 2 153 0 ATAATTTGCT 0.95487 -126 TCAAACCTCATATATATGCTTTAATAGGGA 2 236 1 TATATATGCT 0.844065 -43 TGATATTAGATGCTTCATAATTAT 2 265 0 ATTAGATGCT 0.970347 -14 ********** Masking position 4 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 0.979643 -120 AGTGAGGTTGTCTTGGCAACCTCGCTCGGG 1 122 0 TCTTGGCAAC 0.979312 -80 CTGTAAAGTCCTTTGTCAATAGGGTTTTCC 2 12 0 CTTTGTCAAT 0.951883 -267 ATAAAGATGCCTTTGGCATCAAAATTCCTT 2 57 0 CTTTGGCATC 0.979642 -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