AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_mjan_reg_300.orf -o180_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 RMJ11220 100 M_jannaschii_chromosome #2 RMJ12405 146 M_jannaschii_chromosome #3 RMJ01295 229 M_jannaschii_chromosome Motif number 1 ATTAATTAAAGTATATAAAT 1 1 0 GTATATAAAT 0.937786 -100 GGGAAATTAATTATAAAAAAGCTACGTAAT 1 39 0 TTATAAAAAA 0.965079 -62 AAAATTAAGGTTTTAAAAATAGAATTGGGA 1 65 0 TTTTAAAAAT 0.898244 -36 ATTTTAAATATTATAATAAATCATAATTAA 2 45 0 TTATAATAAA 0.953258 -102 TATAAACCCTATATAAACATAACTGAACAA 2 84 0 ATATAAACAT 0.919421 -63 TATATAGGGTTTATATTAAAATTATGAAAG 2 99 1 TTATATTAAA 0.900135 -48 TGATTAATGAGTTTAAAAAATCTTTCATAA 2 120 0 GTTTAAAAAA 0.905033 -27 ATTTTTATAAATATATTCATATATGTAAGT 3 33 0 ATATATTCAT 0.771791 -197 ATGAATATATTTATAAAAATGATTTATATA 3 43 1 TTATAAAAAT 0.978296 -187 CGAAAGTTCTATATATAAATCATTTTTATA 3 54 0 ATATATAAAT 0.810885 -176 CCAAATACCTTTTTAAAAATATAAGTTGCG 3 82 0 TTTTAAAAAT 0.898244 -148 TACAATAACATTATAATCATTGCCGAATAA 3 171 0 TTATAATCAT 0.94169 -59 GTAGTATTTGGTTTAATAAAGTAGTGGTGA 3 206 1 GTTTAATAAA 0.870585 -24 ********** Masking position 5 Map Score: 19.3883 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 840 Number in noncoding regions = 366 Number of orfs with sites within 600 bp upstream = 334 Fraction of orfs with sites within 600 bp upstream = 0.053646 Motif number 2 TTTTAGATTAATTAAAGTATATAAAT 1 7 0 ATTAAAGTAT 0.831435 -94 ATTAATTATAAAAAAGCTACGTAATGATTT 1 34 0 AAAAAGCTAC 0.799698 -67 CTACTAAAAAATTAAGGTTTTAAAAATAGA 1 72 0 ATTAAGGTTT 0.893196 -29 ATCATAATTAATTAAGCAACTGGGAGATTG 2 26 0 ATTAAGCAAC 0.714066 -121 AATGAGTTTAAAAAATCTTTCATAATTTTA 2 115 0 AAAAATCTTT 0.859798 -32 TTTTAAACTCATTAATCATTGAACT 2 132 1 ATTAATCATT 0.844963 -15 GATAATCACCAATAAACTTTAAACTTACAT 3 11 1 AATAAACTTT 0.939766 -219 AGTTCTATATATAAATCATTTTTATAAATA 3 50 0 ATAAATCATT 0.848542 -180 TGATTTATATATAGAACTTTCGCAACTTAT 3 62 1 ATAGAACTTT 0.863251 -168 TTATATTTTTAAAAAGGTATTTGGATGCCT 3 88 1 AAAAAGGTAT 0.798125 -142 TCAATATTCAATAAAACATTTTATTCCTGC 3 125 1 ATAAAACATT 0.929045 -105 AATAAACTATATAGAACTTTCGCAGGAATA 3 146 0 ATAGAACTTT 0.863251 -84 ATCATTGCCGAATAAACTATATAGAACTTT 3 156 0 AATAAACTAT 0.90881 -74 ********** Masking position 5 Map Score: 11.4373 Number of sites scoring better than the average of aligned sites = 2028 Number in coding regions = 1656 Number in noncoding regions = 372 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 3 TTATATACTTTAATTAATCTAAAATCATTA 1 13 1 TAATTAATCT 0.770577 -88 AAAAGCTACGTAATGATTTTAGATTAATTA 1 23 0 TAATGATTTT 0.963393 -78 AGCTTTTTTATAATTAATTTCCCAATTCTA 1 46 1 TAATTAATTT 0.535161 -55 TTTAAAACCTTAATTTTTTAGTAGTGAGTA 1 78 1 TAATTTTTTA 0.79385 -23 TAATAAATCATAATTAATTAAGCAACTGGG 2 32 0 TAATTAATTA 0.497187 -115 TTAAATATTATAATAAATCATAATTAATTA 2 42 0 TAATAAATCA 0.545152 -105 GTTCAATGATTAATGAGTTTAAAAAATCTT 2 126 0 TAATGAGTTT 0.912102 -21 ATATTTATAAAAATGATTTATATATAGAAC 3 49 1 AAATGATTTA 0.878867 -181 CGCAGGAATAAAATGTTTTATTGAATATTG 3 126 0 AAATGTTTTA 0.786061 -104 GCAATGATTATAATGTTATTGTATAATTGT 3 178 1 TAATGTTATT 0.65537 -52 ********** Masking position 4 Map Score: 6.30888 Number of sites scoring better than the average of aligned sites = 1071 Number in coding regions = 834 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 4 AAAAATAGAATTGGGAAATTAATTATAAAA 1 51 0 TTGGGAAATT 0.984626 -50 AATTAAGCAACTGGGAGATTGTAATGTGTG 2 17 0 CTGGGAGATT 0.983082 -130 AAAATATAAGTTGCGAAAGTTCTATATATA 3 67 0 TTGCGAAAGT 0.990007 -163 CATTTTATTCCTGCGAAAGTTCTATATAGT 3 141 1 CTGCGAAAGT 0.993516 -89 ********** Masking position 6 Map Score: 3.48251 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 19 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 CTTAATTTTTTAGTAGTGAGTAAGT 1 86 1 TATAGTGATA 0.969083 -15 GTTGCTTAATTAATTATGATTTATTATAATAT 2 36 1 TATTATGATT 0.855184 -111 GTTTAAAGTTTATTGGTGATTATC 3 3 0 TATGGTGATA 0.984382 -227 TTTTATTGAATATTGATGCCTAAAGGCATCCA 3 109 0 TATGATGCTA 0.963901 -121 TTTAATAAAGTAGTGGTGATTAA 3 217 1 TATGGTGATA 0.984382 -13 ** ****** ** Masking position 7 Map Score: 2.67679 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 37 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ********** No masking Map Score: -6.51267e-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: -6.51267e-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: -6.51267e-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