AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_mjan_reg_100.orf -o060_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 RMJ03246 95 M_jannaschii_chromosome #2 RMJ04234 35 M_jannaschii_chromosome #3 RMJ09126 300 M_jannaschii_chromosome #4 RMJ06483 83 M_jannaschii_chromosome Motif number 1 CCTGTAGTGTTTTTTATACAGATGTATAGG 1 19 1 TTTTTATACA 0.9469 -77 AGGTATATAATATTTATAATCATATATATC 1 51 0 TATTTATAAT 0.98437 -45 TTATCCTTTTTTATTATTTTTCTATTA 2 19 0 TTTTTATTAT 0.931293 -17 CAGAAAAGTATATTTATTTTGGCAACTACC 3 30 0 TATTTATTTT 0.87183 -271 CCTCAAATAGGTTTTATATTTATTCCCTCA 3 58 0 GTTTTATATT 0.879203 -243 CATAAAAAGGTATTTATAAAACCTCAAATA 3 79 0 TATTTATAAA 0.929231 -222 CAGCAGATTATATTTATAATAAAAAAGTAA 3 121 1 TATTTATAAT 0.98437 -180 TATAAAAATGTTTTTATAATCCTAATGGAT 3 161 0 TTTTTATAAT 0.987146 -140 TATAAAAACATTTTTATACTTCTTCTATAT 3 173 1 TTTTTATACT 0.98131 -128 CCATCTTTTGTTTTTATACATAAACAATAC 3 216 1 TTTTTATACA 0.9469 -85 TCCGCCATATTATTTGTATTGTTTATGTAT 3 231 0 TATTTGTATT 0.842369 -70 GGCGGATAACTTTATATATTTTATTTAAGT 3 255 1 TTTATATATT 0.789085 -46 TTTATTTAAGTTTTTATAATAACATTCTGG 3 274 1 TTTTTATAAT 0.987146 -27 TAGCCTACATCATTTATATTGCATCAACTA 4 12 1 CATTTATATT 0.851107 -72 TTGCATCAACTATTTATAAATAATGCGAGT 4 30 1 TATTTATAAA 0.929231 -54 ATTTTCTTAATTTTTAGAATTATTACTCGC 4 54 0 TTTTTAGAAT 0.913939 -30 ********** Masking position 5 Map Score: 32.4853 Number of sites scoring better than the average of aligned sites = 777 Number in coding regions = 525 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 2 AAAGGTATATAATATTTATAATCATATATATCTTCCT 1 46 0 AATTTAATAT 0.869253 -50 ACCTTTAAATAATTTTATGAGGGATATTA 1 77 1 AATTAGATAT 0.98836 -19 TTAAAAATTAATAGAAAAATAATAAAAAAG 2 4 1 AAATAGAAAT 0.971873 -32 CAACTACCTAAAATATTGGTGATATAT 3 1 0 AAATTGATAT 0.978791 -300 AATAAATATAAAACCTATTTGAGGTTTTATAAATACC 3 64 1 AAATAGGTTT 0.876252 -237 ATGTTTTTATAATCCTAATGGATAAATTACTATTTAC 3 147 0 AATTAGAAAT 0.959329 -154 CAATACCTAAAAATATAGAAGAAGTATAAAAATGTTT 3 178 0 AAATAGGTAT 0.981134 -123 TAAAATATATAAAGTTATCCGCCATATTATTTGTATT 3 241 0 AAATAGATAT 0.992022 -60 GTTATTATAAAAACTTAAATAAAATATATAAAGTTAT 3 260 0 AAATAAATAT 0.953292 -41 ATTATTTATAAATAGTTGATGCAATATAAATGATGTA 4 17 0 AATTTGATAT 0.974658 -67 *** ** * **** Masking position 6 Map Score: 13.6609 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 265 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TATATCTTCCTATACATCTGTATAAAAAACACT 1 24 0 TATACTTTAT 0.973142 -72 TATAGGAAGATATATATGATTATAAATATTATA 1 43 1 TATATTATAT 0.795537 -53 ATAAATATTATATACCTTTAAATAATTTTATGA 1 64 1 TATACTTAAT 0.92084 -32 ATCCTTTTTTATTATTTTTCTATTAATTTTTAA 2 11 0 ATTATTTTAT 0.94301 -25 TTCCCTCAGAAAAGTATATTTATTTTGGCAACT 3 33 0 AAAGTTTTAT 0.628459 -268 AGGTTTTATAAATACCTTTTTATGTCAAACTTT 3 85 1 AATACTTTAT 0.980339 -216 TAAATTACTATTTACTTTTTTATTATAAATATA 3 129 0 TTTACTTTAT 0.95859 -172 TAGGATTATAAAAACATTTTTATACTTCTTCTA 3 167 1 AAAACTTTAT 0.910596 -134 AAAGATGGACAATACCTAAAAATATAGAAGAAG 3 191 0 AATACTAAAT 0.765848 -110 TATTATTTGTATTGTTTATGTATAAAAACAAAA 3 221 0 ATTGTTTTAT 0.841074 -80 TAATATGGCGGATAACTTTATATATTTTATTTA 3 249 1 GATAATTTAT 0.751877 -52 ATATATTTTATTTAAGTTTTTATAATAACATTC 3 268 1 TTTAATTTAT 0.84094 -33 TATTACTCGCATTATTTATAAATAGTTGATGCA 4 31 0 ATTATTTAAT 0.843005 -53 ***** * * *** Masking position 12 Map Score: 10.7733 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 686 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 4 ACAGATGTATAGGAAGATATATATGATTAT 1 36 1 AGGAAGATAT 0.898204 -60 ATAAAATTATTTAAAGGTATATAATATTTA 1 65 0 TTAAAGGTAT 0.588919 -31 AATATCCCTCATAAAATTATTTAAAGGTAT 1 75 0 ATAAAATTAT 0.687953 -21 AAAAATTAATAGAAAAATAATAAAAAAGGA 2 13 1 AGAAAAATAA 0.927855 -23 AAAATAATAAAAAAGGATAA 2 26 1 AAAAGGATAA 0.789484 -10 TTATTCCCTCAGAAAAGTATATTTATTTTG 3 39 0 AGAAAAGTAT 0.939166 -262 TTCTGAGGGAATAAATATAAAACCTATTTG 3 55 1 ATAAATATAA 0.805263 -246 AGTTTGACATAAAAAGGTATTTATAAAACC 3 86 0 AAAAAGGTAT 0.94003 -215 CTTTTTTATTATAAATATAATCTGCTGTCA 3 118 0 ATAAATATAA 0.805263 -183 TATTTATAATAAAAAAGTAAATAGTAATTT 3 131 1 AAAAAAGTAA 0.869113 -170 AAAATATAGAAGAAGTATAAAAATGTTTTT 3 176 0 AGAAGTATAA 0.662129 -125 AATAAAATATATAAAGTTATCCGCCATATT 3 250 0 ATAAAGTTAT 0.834776 -51 TAAAAACTTAAATAAAATATATAAAGTTAT 3 260 0 AATAAAATAT 0.558973 -41 TGTAACCCCAGAATGTTATTATAAAAACT 3 282 0 AGAATGTTAT 0.554311 -19 TCTAAAAATTAAGAAAATCTTTATGGTG 4 66 1 AAGAAAATCT 0.319289 -18 ********** Masking position 4 Map Score: 6.37651 Number of sites scoring better than the average of aligned sites = 3401 Number in coding regions = 2748 Number in noncoding regions = 653 Number of orfs with sites within 600 bp upstream = 465 Fraction of orfs with sites within 600 bp upstream = 0.0746868 Motif number 5 TAAATAATTTTATGAGGGATATTA 1 82 1 TATGAGGGAA 0.928482 -14 ATCACCAATATTTTAGGTAGTTGCCAAAATA 3 15 1 TTTTAGGTAT 0.977961 -286 AATATACTTTTCTGAGGGAATAAATATAAAA 3 46 1 TCTGAGGGAT 0.98445 -255 ATAAAACCTATTTGAGGTTTTATAAATACCT 3 71 1 TTTGAGGTTT 0.968142 -230 TCTTCTATATTTTTAGGTATTGTCCATCTTT 3 193 1 TTTTAGGTAT 0.977961 -108 ********* * Masking position 5 Map Score: 1.68917 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 114 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ********** No masking Map Score: -8.36008e-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: -8.36008e-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: -8.36008e-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