AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_mjan_reg_100.orf -o294_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 RMJ07952 220 M_jannaschii_chromosome #2 RMJ10405 122 M_jannaschii_chromosome #3 RMJ01297 29 M_jannaschii_chromosome #4 RMJ01220 226 M_jannaschii_chromosome #5 RMJ11540 84 M_jannaschii_chromosome Motif number 1 GCCCAACTTACATTATATGTATAATA 1 6 1 ACTTCATTAT 0.810423 -215 ATATTCAAATATTTCTATTAATATGCACAAA 1 56 0 ATTTTATTAA 0.949182 -165 AAACTATTTTAATTCCATTTAGTTCTAAATA 1 84 0 AATTCATTTA 0.901975 -137 TGTGTGCCTTATTTATCTTAATAATGTTTTG 1 119 0 ATTTTCTTAA 0.904115 -102 TAGGTAATTTAATTACCTTAAAAATGATTAA 2 29 0 AATTCCTTAA 0.961171 -94 TAAATTACCTAATTATATAAAATTTGTGTTA 2 49 1 AATTTATAAA 0.921923 -74 ATTATATAAAATTTGTGTTAAACAAAATTGA 2 60 1 ATTTTGTTAA 0.778637 -63 ATAGTATAATATTTTCATTAAAAATTTATTA 2 100 1 ATTTCATTAA 0.957806 -23 TTTTCATTAAAAATTTATTAAA 2 111 1 AAATTATTAA 0.883329 -12 AGAGAATTGCATAAATTATTGGTGA 3 5 1 AATTCATAAA 0.934856 -25 TCTTCCTTTTAATTCCATAATACCACTTTTA 4 17 0 AATTCATAAT 0.857124 -210 CGGAGGTGTAAATTTTCTTATGATTGAGGGA 4 201 1 AATTTCTTAT 0.894897 -26 GATTTATTTTAATTTTATTTTATCGATAAAT 5 37 1 AATTTATTTT 0.759903 -48 TTTTATCGATAAATCTATTAAAAACTTTTTT 5 54 1 AAATTATTAA 0.883329 -31 **** ****** Masking position 1 Map Score: 15.5499 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 816 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 2 ATGGAATTAAAATAGTTTTTTGCAAAACAT 1 97 1 AATAGTTTTT 0.962 -124 TATTTATCTTAATAATGTTTTGCAAAAAAC 1 111 0 AATAATGTTT 0.782296 -110 TAGCCCTATTTATAGTTTTTTGCAAAAGGT 1 195 0 TATAGTTTTT 0.768906 -26 GCCTATCCCTAATCAATCTTAATCATTTTT 2 11 1 AATCAATCTT 0.92325 -112 AATCAATCTTAATCATTTTTAAGGTAATTA 2 21 1 AATCATTTTT 0.944438 -102 TATCAAATGTCATCAATTTTGTTTAACACA 2 73 0 CATCAATTTT 0.738113 -50 TTTAATAAATTTTTAATGAAAAT 2 110 0 AATAAATTTT 0.952806 -13 AGTTTCACCAATAATTTATGCAATTCTCT 3 11 0 AATAATTTAT 0.786047 -19 TATGCTTTGAAATACTTCTTCCTTTTAATT 4 34 0 AATACTTCTT 0.856279 -193 AAATAAAAATCATTCTTTTATTAGAAG 5 8 1 AATCATTCTT 0.945314 -77 ATAAAATTAAAATAAATCTTCTAATAAAAG 5 25 0 AATAAATCTT 0.941562 -60 AAAAGTTTTTAATAGATTTATCGATAAAAT 5 53 0 AATAGATTTA 0.661867 -32 TTATCACCAAAAAAGTTTTTAATAGATTTA 5 63 0 AAAAGTTTTT 0.674755 -22 ********** Masking position 2 Map Score: 13.3695 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 639 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 3 GAGTATAGCAATAGAGGCTTTGCCTCTATGCTTT 4 56 0 AAGGGCTGCC 0.998964 -171 GCTATACTCCAGAGCGGGGTTGCCAGAGGCAACC 4 81 1 AAGGGGTGCC 0.999289 -146 CCCCAGATAGAAAGTGGGGTTGCCTCTGGCAACC 4 98 0 AAGGGGTGCC 0.999289 -129 GTATCCCAATAGAGGGGCAAAGCCCTTCTATAGT 4 133 1 AAGGGCAGCC 0.9966 -94 AAGCCCTTCTATAGTGAGGATACCTCTTAACACT 4 152 1 AAGGAGTACC 0.980982 -75 * ** *** **** Masking position 3 Map Score: 8.31861 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 3 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 AAAGCATAGAGGCAAAGCCTCTATTGCTATA 4 56 1 GGCAAAGCCC 0.994865 -171 GGTTGCCTCTGGCAACCCCGCTCTGGAGTAT 4 84 0 GGCAACCCCC 0.998287 -143 GGTTGCCAGAGGCAACCCCACTTTCTATCTG 4 98 1 GGCAACCCCC 0.998287 -129 CCCCTCTATTGGGATACTCCCCAGATAGAAA 4 119 0 GGGATACTCC 0.940064 -108 CCAATAGAGGGGCAAAGCCCTTCTATAGTGA 4 138 1 GGCAAAGCCT 0.967713 -89 AGTGTTAAGAGGTATCCTCACTATAGAAGGG 4 155 0 GGTATCCTCC 0.952881 -72 ********* * Masking position 4 Map Score: 7.79639 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 20 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 CTACACCTTTTTATTTTTTGTGCATATTAA 1 40 1 TTATTTTTTG 0.93464 -181 GGAATTAAAATAGTTTTTTGCAAAACATTA 1 99 1 TAGTTTTTTG 0.986445 -122 TTTATCTTAATAATGTTTTGCAAAAAACTA 1 109 0 TAATGTTTTG 0.954942 -112 GCCCTATTTATAGTTTTTTGCAAAAGGTAT 1 193 0 TAGTTTTTTG 0.986445 -28 ATCTATTAAAAACTTTTTTGGTGATAATT 5 66 1 AACTTTTTTG 0.92319 -19 ********** Masking position 6 Map Score: 3.72766 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 70 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CATTATATGTATAATATCACTACACCTTTT 1 21 1 ATAATATCAC 0.909548 -200 TAATATGCACAAAAAATAAAAAGGTGTAGT 1 39 0 AAAAAATAAA 0.861878 -182 TGCAAAAGGTATAAATTAAATATGAATATT 1 175 0 ATAAATTAAA 0.861717 -46 CTTTTGCAAAAAACTATAAATAGGGCTATT 1 197 1 AAACTATAAA 0.797093 -24 AAATTACCTAATTATATAAAATTTGTGTTA 2 50 1 ATTATATAAA 0.803269 -73 TGAAAATATTATACTATCAAATGTCATCAA 2 87 0 ATACTATCAA 0.909593 -36 ATAATTTAAAAGTGGTATTA 4 1 1 ATAATTTAAA 0.90071 -226 TTTTAATTCCATAATACCACTTTTAAATTA 4 12 0 ATAATACCAC 0.677252 -215 TAAAATAAAATTAAAATAAATCTTCTAATA 5 29 0 TTAAAATAAA 0.753821 -56 AGATTTATCGATAAAATAAAATTAAAATAA 5 40 0 ATAAAATAAA 0.957081 -45 ********** Masking position 9 Map Score: 4.90329 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1314 Number in noncoding regions = 477 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 7 TAATAGAAATATTTGAATATTTAGAACTAA 1 67 1 ATTTGAATAT 0.920465 -154 TATAAATTAAATATGAATATTTGAACGCCC 1 166 0 ATATGAATAT 0.896887 -55 TCCCTCAATCATAAGAAAATTTACACCTCC 4 202 0 ATAAGAAAAT 0.919978 -25 TCATTCTTTTATTAGAAGATTTATTTTAAT 5 20 1 ATTAGAAGAT 0.947497 -65 ********** Masking position 6 Map Score: 0.128808 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 60 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 ********** No masking Map Score: 1.80068e-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: 1.80068e-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: 1.80068e-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