AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_mjan_reg_300.orf -o060_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 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 CCTATACATCTGTATAAAAAACACTACAGG 1 19 0 TGTATAAAAA 0.946109 -77 GATATATATGATTATAAATATTATATACCT 1 51 1 ATTATAAATA 0.980533 -45 TTAAAAATTAATAGAAAAATAATAAAA 2 8 1 TTAATAGAAA 0.615887 -28 TAATAGAAAAATAATAAAAAAGGATAA 2 19 1 ATAATAAAAA 0.945799 -17 GGTAGTTGCCAAAATAAATATACTTTTCTG 3 30 1 AAAATAAATA 0.884339 -271 TGAGGGAATAAATATAAAACCTATTTGAGG 3 58 1 AATATAAAAC 0.874016 -243 TATTTGAGGTTTTATAAATACCTTTTTATG 3 79 1 TTTATAAATA 0.924294 -222 TTACTTTTTTATTATAAATATAATCTGCTG 3 121 0 ATTATAAATA 0.980533 -180 ATCCATTAGGATTATAAAAACATTTTTATA 3 161 1 ATTATAAAAA 0.98678 -140 ATATAGAAGAAGTATAAAAATGTTTTTATA 3 173 0 AGTATAAAAA 0.978298 -128 AATACCTAAAAATATAGAAGAAGTATAAAA 3 184 0 AATATAGAAG 0.748606 -117 GTATTGTTTATGTATAAAAACAAAAGATGG 3 216 0 TGTATAAAAA 0.946109 -85 ATACATAAACAATACAAATAATATGGCGGA 3 231 1 AATACAAATA 0.798666 -70 ACTTAAATAAAATATATAAAGTTATCCGCC 3 255 0 AATATATAAA 0.796488 -46 CCAGAATGTTATTATAAAAACTTAAATAAA 3 274 0 ATTATAAAAA 0.98678 -27 TAGTTGATGCAATATAAATGATGTAGGCTA 4 12 0 AATATAAATG 0.89192 -72 ACTCGCATTATTTATAAATAGTTGATGCAA 4 30 0 TTTATAAATA 0.924294 -54 GCGAGTAATAATTCTAAAAATTAAGAAAAT 4 54 1 ATTCTAAAAA 0.898115 -30 ********** Masking position 6 Map Score: 32.2007 Number of sites scoring better than the average of aligned sites = 1349 Number in coding regions = 916 Number in noncoding regions = 433 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 2 TTTTTTATACAGATGTATAGGAAGATATATATGATTATAA 1 28 1 AGATATATAT 0.954742 -68 TATCCCTCATAAAATTATTTAAAGGTATATAATATTTATA 1 63 0 AAATATATAT 0.967962 -33 TTAAAAATTAATAGAAAAATAATAAAAAAGGAT 2 4 1 AAATAATAAT 0.8651 -32 AATAAATATAAAACCTATTTGAGGTTTTATAAATACCTTT 3 64 1 AAATATTTAT 0.985417 -237 TTTATAATAAAAAAGTAAATAGTAATTTATCCATTAGGAT 3 133 1 AAATAATTAT 0.943617 -168 AAAATATAGAAGAAGTATAAAAATGTTTTTATAATCCTAA 3 166 0 AGATATTTTT 0.819831 -135 TAAAATATATAAAGTTATCCGCCATATTATTTGTATTGTT 3 238 0 AAATATTTAT 0.985414 -63 TGTTATTATAAAAACTTAAATAAAATATATAAAGTTATCC 3 258 0 AAATTAATAT 0.708868 -43 CTTAATTTTTAGAATTATTACTCGCATTATTTATAAATAG 4 39 0 AGATATTTAT 0.979635 -45 AATAATTCTAAAAATTAAGAAAATCTTTATGGTG 4 60 1 AAATAATTAT 0.967211 -24 *** *** **** Masking position 6 Map Score: 11.846 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 290 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 TTAAATAATTTTATGAGGGATATTA 1 81 1 TTATGAGGGA 0.962787 -15 TATCACCAATATTTTAGGTAGTTGCCAAAA 3 14 1 ATTTTAGGTA 0.934555 -287 AAATATACTTTTCTGAGGGAATAAATATAA 3 45 1 TTCTGAGGGA 0.986019 -256 TATAAAACCTATTTGAGGTTTTATAAATAC 3 70 1 ATTTGAGGTT 0.957719 -231 TTCTTCTATATTTTTAGGTATTGTCCATCT 3 192 1 TTTTTAGGTA 0.963822 -109 TATAATAACATTCTGGGGTTACA 3 288 1 TTCTGGGGTT 0.943444 -13 ********** Masking position 4 Map Score: 4.17757 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 114 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ATAGGAAGATATATATGATTATAAATATTA 1 44 1 ATATATGATT 0.883664 -52 ATTTAAAGGTATATAATATTTATAATCATA 1 57 0 ATATAATATT 0.921674 -39 TTTTGACAGCAGATTATATTTATAATAAAA 3 115 1 AGATTATATT 0.947921 -186 ATAACTTTATATATTTTATTTAAGTTTTTA 3 260 1 ATATTTTATT 0.960255 -41 CACCATAAAGATTTTCTTAATTTTTAGA 4 66 0 AGATTTTCTT 0.921565 -18 ********** Masking position 4 Map Score: 0.967825 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 313 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 ********** 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 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