AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_Lysine_Biosynthesis_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 lysA 121 diaminopimelate decarboxylase #2 dapF 300 diaminopimelate epimerase #3 HI0727 260 diaminopimelate decarboxylase (lysA) #4 HI0750 143 diaminopimelate epimerase (dapF) Motif number 1 CACATCATAAAAAGAATAAAAAATATCGATTTA 1 63 0 AAAGTAAAAA 0.941333 -59 TAAATCTGATAAAATGCGGCAAATTATAAAGCC 3 25 1 AAAACGGAAA 0.973831 -236 CCGCCTTTCACAAGCTTGAGAAAGGCTTTATAA 3 48 0 CAAGTGAAAA 0.959888 -213 AGTGAGAAAGAAAAAATGAAAAAATTACTATTA 3 92 1 AAAATGAAAA 0.906018 -169 TGAAAAAGATCAAGCTCAACAAACTCAATAATC 3 193 1 CAAGCAAAAA 0.939058 -68 AGGAATGAATAAAGTGCGGTAAAAATTTACGGT 4 21 1 AAAGCGGAAA 0.994736 -123 TAGTATAAGCAAAGTGCGGTAAAAATACCGTAA 4 47 0 AAAGCGGAAA 0.994736 -97 TTTGCATTATAAAGAGCAGCAAAAATCATGGCA 4 92 0 AAAGCAGAAA 0.984111 -52 GAATTTATACAAAGGATGGAAAA 4 131 1 AAAGTGGAAA 0.989711 -13 **** *** *** Masking position 3 Map Score: 13.9536 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 222 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 TTTTTATGATGTGGCGTAATCATAAAAAAG 1 83 1 GTGGCGTAAT 0.871083 -39 ATCGCAGGAGAAGACGTAAAAG 2 3 0 AAGACGTAAA 0.829027 -298 AATACAGTGAGTGCCTTAAACACGTTTTTC 2 76 0 GTGCCTTAAA 0.939997 -225 TTTTATCTGCAGGCGGGAAATAGAGCGGAC 2 144 0 AGGCGGGAAA 0.824156 -157 CAAACCGGTAGAGACGCAAACGCAATCCAC 2 190 1 GAGACGCAAA 0.914558 -111 GCAATCCACGGTGCCGGATAAAAACGATCG 2 211 1 GTGCCGGATA 0.925146 -90 ATCTGATAAAATGCGGCAAATTATAAAGCC 3 28 1 ATGCGGCAAA 0.966908 -233 GCTACAGGATGTGGCGTAAAAGGTTCTTTA 3 155 1 GTGGCGTAAA 0.983153 -106 AATGAATAAAGTGCGGTAAAAATTTACGGT 4 24 1 GTGCGGTAAA 0.992202 -120 TGCGGTAAAAATACCGTAAATTTTTACCGC 4 36 0 ATACCGTAAA 0.834772 -108 TATAAGCAAAGTGCGGTAAAAATACCGTAA 4 47 0 GTGCGGTAAA 0.992202 -97 GCATTATAAAGAGCAGCAAAAATCATGGCA 4 92 0 GAGCAGCAAA 0.87365 -52 ********** Masking position 8 Map Score: 13.5086 Number of sites scoring better than the average of aligned sites = 1998 Number in coding regions = 1854 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 3 GACATAAATCGATATTTTTTATTCTTTTTA 1 59 1 GATATTTTTT 0.799165 -63 GATATTTTTTATTCTTTTTATGATGTGGCG 1 69 1 ATTCTTTTTA 0.637269 -53 CTCCAGATAAGTGCTTTTTTATGATTACGC 1 96 0 GTGCTTTTTT 0.960112 -26 GTCGGCGGCGGTGCGTTTTTATCTGCAGGC 2 160 0 GTGCGTTTTT 0.902324 -141 CCAGTGGCGCGATCGTTTTTATCCGGCACC 2 220 0 GATCGTTTTT 0.908373 -81 AAAATTAATAGTAATTTTTTCATTTTTTCT 3 100 0 GTAATTTTTT 0.705648 -161 GGCGTAAAAGGTTCTTTATATTTTCCTGAA 3 167 1 GTTCTTTATA 0.929311 -94 TGTTGAGCTTGATCTTTTTCAGGAAAATAT 3 184 0 GATCTTTTTC 0.872782 -77 AATTTTTACCGCACTTTATTCATTCCTTGG 4 18 0 GCACTTTATT 0.838589 -126 TTATACTAGAGTTCTTTATTTGCCATGATT 4 72 1 GTTCTTTATT 0.966704 -72 GATTTTTGCTGCTCTTTATAATGCAAAAAT 4 98 1 GCTCTTTATA 0.881579 -46 ********** Masking position 6 Map Score: 7.56415 Number of sites scoring better than the average of aligned sites = 973 Number in coding regions = 768 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 4 ATGGATTACCGGATTGCGAGAGAGCGCTA 1 10 0 GGATTGCGAG 0.97221 -112 TTTTCATTATGGATTGCCTGTAAAGTTCAT 2 51 0 GGATTGCCTG 0.994071 -250 AGTAATACAGTGAGTGCCTTAAACACGTTT 2 79 0 TGAGTGCCTT 0.972716 -222 CCGGCACCGTGGATTGCGTTTGCGTCTCTA 2 198 0 GGATTGCGTT 0.980801 -103 GTTGTGTGCCTGTTTTAGTTAT 3 249 0 TGTGTGCCTG 0.960653 -12 ********** Masking position 5 Map Score: 2.9761 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 276 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 ATGCAAAAATGATATGGATTACCGGATTGC 1 23 0 GATATGGATT 0.886433 -99 AATATCGATTTATGTCGAGTCTATGCAAAA 1 45 0 TATGTCGAGT 0.953271 -77 TTCTTTTTATGATGTGGCGTAATCATAAAA 1 80 1 GATGTGGCGT 0.994309 -42 AAAAAGCACTTATCTGGAGTTTGTT 1 107 1 TATCTGGAGT 0.964017 -15 TTCGCTACAGGATGTGGCGTAAAAGGTTCT 3 152 1 GATGTGGCGT 0.994309 -109 ********** Masking position 5 Map Score: 2.94816 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 83 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AAAGCGATGAACTTTACAGGCAATCCATAA 2 45 1 ACTTTACAGG 0.920806 -256 GGTGCGTTTTTATCTGCAGGCGGGAAATAG 2 151 0 TATCTGCAGG 0.921087 -150 TGCGTTTGCGTCTCTACCGGTTTGGTCGGC 2 184 0 TCTCTACCGG 0.9896 -117 AACGCAATCCACGGTGCCGGATAAAAACGA 2 208 1 ACGGTGCCGG 0.964668 -93 AAAGTCAGTTTCTGTACCCGCGTGATTGGA 2 277 1 TCTGTACCCG 0.953523 -24 GCTTGTATATTCGCTACAGGATGTGGCGTA 3 143 1 TCGCTACAGG 0.980436 -118 ********** Masking position 5 Map Score: 2.17911 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 776 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CTTTTACGTCTTCTCCTGCGATGATAGA 2 9 1 TCTTCTCCTG 0.980247 -292 GACTTTTAGTAATTCACCTGGGATGGACCA 2 253 0 AATTCACCTG 0.970999 -48 AAAATTTTCCTGTTTAAATCTG 3 3 1 AATTTTCCTG 0.982044 -258 AGGTTCTTTATATTTTCCTGAAAAAGATCA 3 175 1 TATTTTCCTG 0.982044 -86 ********** Masking position 4 Map Score: 1.85954 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 72 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TTTACGTCTTCTCCTGCGATGATAGAAAGCA 2 13 1 CCCTGCGATG 0.993907 -288 CCGGTTTGGTCGGCGGCGGTGCGTTTTTATC 2 167 0 CGCGGCGGTG 0.906115 -134 TTTTATCCGGCACCGTGGATTGCGTTTGCGT 2 203 0 CCCGTGGATT 0.925362 -98 ACGATCGCGCCACTGGCGATGGTCCATCCCA 2 234 1 CCTGGCGATG 0.97346 -67 TTTAGTAATTCACCTGGGATGGACCATCGCC 2 248 0 CCCTGGGATG 0.991838 -53 * ********* Masking position 10 Map Score: 2.18876 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 745 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 ATGAAAAACGTGTTTAAGGCACTCACTGTA 2 74 1 TGTTTAAGGC 0.805551 -227 CGGGCTGCGGTCTGAAAGGTCCGCTCTATT 2 126 1 TCTGAAAGGT 0.927175 -175 TTCACAAGCTTGAGAAAGGCTTTATAATTT 3 45 0 TGAGAAAGGC 0.98765 -216 TTCTCAAGCTTGTGAAAGGCGGATTTACCG 3 59 1 TGTGAAAGGC 0.990488 -202 TACCGATAAGTGAGAAAGAAAAAATGAAAA 3 84 1 TGAGAAAGAA 0.845942 -177 CAGGATGTGGCGTAAAAGGTTCTTTATATT 3 159 1 CGTAAAAGGT 0.873186 -102 TATATTTTCCTGAAAAAGATCAAGCTCAAC 3 183 1 TGAAAAAGAT 0.824196 -78 ********** Masking position 6 Map Score: 2.04253 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 528 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 10 AGAAACTGACTTTTAGTAATTCACCTGGGA 2 260 0 TTTTAGTAAT 0.976041 -41 GTACTAAAATTAATAGTAATTTTTTCATTT 3 105 0 TAATAGTAAT 0.864531 -156 TTACTATTAATTTTAGTACTTAGTTCAGCT 3 116 1 TTTTAGTACT 0.959838 -145 TGTGTGCCTGTTTTAGTTATTTTGGGAATG 3 239 0 TTTTAGTTAT 0.941604 -22 ********** Masking position 5 Map Score: 0.0359116 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ********** No masking Map Score: -6.939e-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 12 ********** No masking Map Score: -6.939e-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 13 ********** No masking Map Score: -6.939e-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