AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dapB 166 dihydrodipicolinate reductase #2 usg 65 putative PTS system enzyme II A component #3 pdxB 98 erythronate-4-phosphate dehyrogenase #4 dapA 79 dihydrodipicolinate synthase #5 lysC 300 aspartokinase III, lysine sensitive Motif number 1 CCAGCGCATCGCTACGCCGCCAGCCAAAAACGCTG 1 98 0 GCAGCGCCCC 0.996456 -69 TCCAGAAATAGCAAAGCTCCCTGCCAATGTTACAG 2 31 0 GCAGCCCCCC 0.994819 -35 CGTTACTTGGGCAACGCGCCTCTTCTGGCCTGCGC 5 20 0 GCAGCCCTTC 0.994078 -281 AATCACCTCGGCGATGCACCCCCTCAGGTGTTATC 5 77 0 GCAGCCCCTC 0.999022 -224 TCCACCACTTGCGAAACGCCCGACTGCGAACGCTT 5 171 0 GCAACCCCCT 0.987299 -130 GCGAAGTATCGCTCTGCGCCCACCCGTCTTCCGCT 5 228 1 GCCGCCCCCC 0.999091 -73 ** * ** *** ** Masking position 7 Map Score: 12.9844 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 62 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 TCACATGTTATTGGCATGCAGTCATTCATC 1 15 1 TTGGCATGCA 0.894349 -152 ATCAGCGTTTTTGGCTGGCGGCGTAGCGAT 1 96 1 TTGGCTGGCG 0.977207 -71 GGCGTAGCGATGCGCTGGTTACTCTGAAAA 1 115 1 TGCGCTGGTT 0.869509 -52 TGCTGTAACATTGGCAGGGAGCTTTGCTAT 2 29 1 TTGGCAGGGA 0.876772 -37 ACCTGAAATCTTCGCAAGTATGCCTGGCCG 3 24 1 TTCGCAAGTA 0.96592 -75 TCTTCTGGCCTGCGCTAGCGCAGG 5 5 0 TGCGCTAGCG 0.97739 -296 AGAGGCGCGTTGCCCAAGTAACGGTGTTGG 5 32 1 TGCCCAAGTA 0.890004 -269 ATGATGAACGTGGCCAGCCGTTCAATCACC 5 105 0 TGGCCAGCCG 0.800622 -196 ACCAGAAGCGTTCGCAGTCGGGCGTTTCGC 5 166 1 TTCGCAGTCG 0.909739 -135 AGTCGGGCGTTTCGCAAGTGGTGGAGCACT 5 181 1 TTCGCAAGTG 0.981787 -120 AGAGCGATACTTCGCTACTATTTTCACCCA 5 213 0 TTCGCTACTA 0.830686 -88 TCTTCCGCTCTTCCCTTGTGCCAAGGCTGA 5 254 1 TTCCCTTGTG 0.855347 -47 ********** Masking position 1 Map Score: 9.80911 Number of sites scoring better than the average of aligned sites = 5469 Number in coding regions = 5241 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 3 GCGAGATTATGGCACACTTGTCCGGTTAAC 3 53 1 GGCACACTTG 0.801376 -46 GCTAGCGCAGGCCAGAAGAGGCGCGTTGCC 5 16 1 GCCAGAAGAG 0.895035 -285 TGTTGGAGGAGCCAGTCCTGTGATAACACC 5 56 1 GCCAGTCCTG 0.856164 -245 GCGATGCACCCCCTCAGGTGTTATCACAGG 5 72 0 CCCTCAGGTG 0.917608 -229 GGGGGTGCATCGCCGAGGTGATTGAACGGC 5 89 1 CGCCGAGGTG 0.9036 -212 TTCATCATCGGCTACAGGGGCTGAATCCCC 5 127 1 GCTACAGGGG 0.934234 -174 GACTGCGAACGCTTCTGGTGACAACCCAGG 5 155 0 GCTTCTGGTG 0.661561 -146 CAGAAGCGTTCGCAGTCGGGCGTTTCGCAA 5 168 1 CGCAGTCGGG 0.946242 -133 CGGGCGTTTCGCAAGTGGTGGAGCACTTCT 5 184 1 GCAAGTGGTG 0.916066 -117 ACTATTTTCACCCAGAAGTGCTCCACCACT 5 197 0 CCCAGAAGTG 0.960528 -104 AGGGAAGAGCGGAAGACGGGTGGGCGCAGA 5 240 0 GGAAGACGGG 0.919797 -61 TTTCAGCCTTGGCACAAGGGAAGAGCGGAA 5 256 0 GGCACAAGGG 0.958653 -45 ********** Masking position 10 Map Score: 6.57822 Number of sites scoring better than the average of aligned sites = 4932 Number in coding regions = 4587 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 281 Fraction of orfs with sites within 600 bp upstream = 0.0451333 Motif number 4 TCGATGAATGACTGCATGCCAATAACATGT 1 17 0 ACTGCATGCC 0.97327 -150 TCTCTTCTTCATGCTCTCTGCTGTA 2 6 1 TCTTCATGCT 0.867645 -60 AACGGTTCTGTCTGCTTGCTTTTAATGCCA 4 15 1 TCTGCTTGCT 0.968869 -65 GCAACGCGCCTCTTCTGGCCTGCGCTAGCG 5 15 0 TCTTCTGGCC 0.984681 -286 AGGTGATTGAACGGCTGGCCACGTTCATCA 5 104 1 ACGGCTGGCC 0.991477 -197 GTGGTGGAGCACTTCTGGGTGAAAATAGTA 5 198 1 ACTTCTGGGT 0.944752 -103 AGAGCGGAAGACGGGTGGGCGCAGAGCGAT 5 235 0 ACGGGTGGGC 0.904182 -66 ********** Masking position 8 Map Score: 5.00988 Number of sites scoring better than the average of aligned sites = 1692 Number in coding regions = 1621 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 TCGACTCATGCCTTTCACTGATATCCCTCC 1 43 1 CCTTTCACTG 0.836442 -124 TTTGCATAGACCGTTTTCAGAGTAACCAGC 1 128 0 CCGTTTTCAG 0.985541 -39 GGGCCATCCTCTGTGCAAACAAG 4 67 0 CCATCCTCTG 0.977848 -13 TGGGCAACGCGCCTCTTCTGGCCTGCGCTA 5 18 0 GCCTCTTCTG 0.928391 -283 GTCACCAGAAGCGTTCGCAGTCGGGCGTTT 5 163 1 GCGTTCGCAG 0.927048 -138 CTGCGCCCACCCGTCTTCCGCTCTTCCCTT 5 241 1 CCGTCTTCCG 0.979712 -60 GTCAGGGGATCCATTTTCAGCCTTGGCACA 5 270 0 CCATTTTCAG 0.968021 -31 ********** Masking position 4 Map Score: 2.96919 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 762 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 AGCGATGCGCTGGTTACTCTGAAAACGGTCT 1 120 1 TGGTACTCTG 0.98471 -47 ATCACAGGACTGGCTCCTCCAACACCGTTAC 5 49 0 TGGTCCTCCA 0.973259 -252 CTACAGGGGCTGAATCCCCTGGGTTGTCACC 5 138 1 TGATCCCCTG 0.990063 -163 AGGCTGAAAATGGATCCCCTGACACGAGGTA 5 277 1 TGGTCCCCTG 0.997456 -24 *** ******* Masking position 5 Map Score: 1.08023 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 52 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 7 CCTGTCACATGTTATTGGCAT 1 1 1 CCTGCACATG 0.974476 -166 GCAAGTATGCCTGGCCGCGAGATTATGGCAC 3 37 1 CTGGCGCGAG 0.981643 -62 CGAGAGTTAACCGGACAAGTGTGCCATAATC 3 57 0 CCGGCAAGTG 0.983155 -42 GATTGAACGGCTGGCCACGTTCATCATCGGC 5 108 1 CTGGCACGTT 0.973746 -193 CATTTTCAGCCTTGGCACAAGGGAAGAGCGG 5 258 0 CTTGCACAAG 0.90459 -43 AAATGGATCCCCTGACACGAGGTAGTT 5 284 1 CCTGCACGAG 0.995044 -17 **** ****** Masking position 6 Map Score: 6.22871 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 162 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ********** No masking Map Score: -7.50743e-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: -7.50743e-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: -7.50743e-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