AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifur_mjan_opreg_300.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0165 32 conserved hypothetical protein #2 MJ0167 122 molybdenum cofactor biosynthesis protein (moaB) #3 MJ0168 230 archaeal histone A1 Motif number 1 ATTCCCTCCAAAACTTTTAGAAAAAACAT 1 7 0 AAATTTAAAA 0.985262 -26 ATAAAAATTAAAAATTTTAAAAATAAAAT 2 7 0 AAATTTAAAA 0.985262 -116 GAAGGAAGTAAAATATTAATAATAAAAATTAAA 2 28 0 AAATTAAAAT 0.925541 -95 ACTTCCTTCCAAAACTTTAGAATTCTTTTGTTA 2 52 1 AAATTTAAAT 0.966484 -71 ATTAATGAATATAAATTAAAATAACAAAAGAAT 2 73 0 ATATTAAATA 0.890734 -50 AAATAAATATATAAATTAATGAATATAAATTAA 2 87 0 ATATTAAGAA 0.884399 -36 ATTAATTTATATATTTATTTAAACGGTGGAAAT 2 100 1 ATATATTAAA 0.75509 -23 ATAGATAAACATAAATTAATAGAGTTTAATT 3 9 0 ATATTAAAGA 0.827045 -222 AATTTAAAATATAATTTTATGAAAGATAGATAA 3 34 0 ATATTTAGAA 0.946628 -197 AATGTATGTCACAAATTTAAAATATAATTTTAT 3 47 0 ACATTTAAAT 0.933754 -184 AATTTGTGACATACATTATAAATAGTGTTTTTT 3 63 1 ATATTATAAT 0.791596 -168 GTGTGACACTAAAATTATAAAAAACACTATTTA 3 81 0 AAATATAAAA 0.9098 -150 TTTTAGTGTCACACTTTTTAATACCTTCTTTAT 3 100 1 ACATTTTATA 0.686032 -131 TATGTGTGGGAAAATTTTCCAAAGACTTTCACA 3 130 1 AAATTTCAAA 0.950991 -101 AAAATGACCGAAAAGTTTAAATAAAGGATTTTA 3 170 1 AAATTTAATA 0.943261 -61 TTTCCAATAAATACTGTTATAAAATCCTTTATT 3 189 0 ATAGTTAAAA 0.900465 -42 CCACCTCACAATAGATTTCCAATAAATACTGTT 3 204 0 ATATTTCAAT 0.904896 -27 *** **** *** Masking position 3 Map Score: 22.6971 Number of sites scoring better than the average of aligned sites = 2961 Number in coding regions = 2120 Number in noncoding regions = 841 Number of orfs with sites within 600 bp upstream = 509 Fraction of orfs with sites within 600 bp upstream = 0.0817539 Motif number 2 ATGTTTTTTCTAAAAGTTTTGGAGGG 1 7 1 TTTCTAAAAG 0.778962 -26 ATTTTATTTTTAAAATTTTTAATTTT 2 7 1 TTTTTAAAAT 0.939119 -116 GGAAGTAAAATATTAATAATAAAAATTAAA 2 28 0 TATTAATAAT 0.870297 -95 ATTCTTTTGTTATTTTAATTTATATTCATT 2 73 1 TATTTTAATT 0.837629 -50 TTTAAATAAATATATAAATTAATGAATATA 2 93 0 TATATAAATT 0.745163 -30 TTTATATATTTATTTAAACGGTGGAAAT 2 105 1 TATTTAAACG 0.95342 -18 CATAAAATTATATTTTAAATTTGTGACATA 3 46 1 TATTTTAAAT 0.942046 -185 TAAAAAACACTATTTATAATGTATGTCACA 3 67 0 TATTTATAAT 0.963236 -164 TAAATAGTGTTTTTTATAATTTTAGTGTCA 3 81 1 TTTTTATAAT 0.911693 -150 ATAAAGAAGGTATTAAAAAGTGTGACACTA 3 103 0 TATTAAAAAG 0.911636 -128 TAAAATCCTTTATTTAAACTTTTCGGTCAT 3 173 0 TATTTAAACT 0.970021 -58 ********** Masking position 8 Map Score: 14.0234 Number of sites scoring better than the average of aligned sites = 1792 Number in coding regions = 1306 Number in noncoding regions = 486 Number of orfs with sites within 600 bp upstream = 384 Fraction of orfs with sites within 600 bp upstream = 0.0616768 Motif number 3 ATGTTTTTTCTAAAAGTTTTG 1 2 1 TGTTTTTTCT 0.624311 -31 ATTTTATTTTTAAAATTTTTA 2 2 1 TTTTATTTTT 0.966925 -121 TTTTAAAATTTTTAATTTTTATTATTAATA 2 18 1 TTTAATTTTT 0.92936 -105 AGAATTCTTTTGTTATTTTAATTTATATTC 2 70 1 TGTTATTTTA 0.915243 -53 ATTTATATTCATTAATTTATATATTTATTT 2 90 1 ATTAATTTAT 0.839942 -33 TAATTTATATATTTATTTAAACGGTGGAAA 2 102 1 ATTTATTTAA 0.885346 -21 ATTAAACTCTATTAATTTATGTTTATCTAT 3 12 1 ATTAATTTAT 0.839942 -219 TTTCATAAAATTATATTTTAAATTTGTGAC 3 43 1 TTATATTTTA 0.685916 -188 TTATAAATAGTGTTTTTTATAATTTTAGTG 3 78 1 TGTTTTTTAT 0.819648 -153 TTTCGGTCATTTTCATTTTTTGTGAAAGTC 3 153 0 TTTCATTTTT 0.885934 -78 TTATAAAATCCTTTATTTAAACTTTTCGGT 3 176 0 CTTTATTTAA 0.82074 -55 ********** Masking position 6 Map Score: 8.35222 Number of sites scoring better than the average of aligned sites = 3273 Number in coding regions = 2369 Number in noncoding regions = 904 Number of orfs with sites within 600 bp upstream = 539 Fraction of orfs with sites within 600 bp upstream = 0.0865724 Motif number 4 ATGTTTTTTCTAAAAGTTTTGGAGG 1 6 1 TTTTCTAAAA 0.668094 -27 TCAATTCCCTCCAAAACTTTTAGA 1 19 0 TTCCCTCCAA 0.943911 -14 AATATTTTACTTCCTTCCAAAACTTTAGAA 2 44 1 TTCCTTCCAA 0.72245 -79 ATTTCCACCGTTTAAATAAATATATAAATT 2 103 0 TTTAAATAAA 0.567511 -20 TTTATCTATCTTTCATAAAATTATATTTTA 3 33 1 TTTCATAAAA 0.838661 -198 TTGGAAAATTTTCCCACACATAAAGAAGGT 3 122 0 TTCCCACACA 0.930501 -109 GTGGGAAAATTTTCCAAAGACTTTCACAAA 3 135 1 TTTCCAAAGA 0.874197 -96 TCCAAAGACTTTCACAAAAAATGAAAATGA 3 147 1 TTCACAAAAA 0.938797 -84 GACCGAAAAGTTTAAATAAAGGATTTTATA 3 175 1 TTTAAATAAA 0.567511 -56 CACAATAGATTTCCAATAAATACTGTTATA 3 201 0 TTCCAATAAA 0.946237 -30 ********** Masking position 2 Map Score: 3.76628 Number of sites scoring better than the average of aligned sites = 1697 Number in coding regions = 1515 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 5 ********** No masking Map Score: 4.64285e-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 6 ********** No masking Map Score: 4.64285e-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: 4.64285e-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