AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_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 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 #6 HI0255 100 dihydrodipicolinate synthetase (dapA) #7 HI1303 147 riboflavin synthase, beta chain (ribH) #8 HI1433 58 usg-1 protein (usg1) Motif number 1 TTTTTGGCTGGCGGCGTAGCGATGCGCTGGTTACT 1 103 1 GGGGTGCGGC 0.944524 -64 GCGCAGGCCAGAAGAGGCGCGTTGCCCAAGTAACG 5 20 1 GAGGGGCGGC 0.997304 -281 AGTAACGGTGTTGGAGGAGCCAGTCCTGTGATAAC 5 48 1 TGGGGGCCTC 0.972344 -253 GATAACACCTGAGGGGGTGCATCGCCGAGGTGATT 5 77 1 GGGGGGCAGC 0.992978 -224 AGAAGCGTTCGCAGTCGGGCGTTTCGCAAGTGGTG 5 169 1 GAGCGGCGTC 0.976643 -132 CGTTTCGCAAGTGGTGGAGCACTTCTGGGTGAAAA 5 188 1 GGGGGGCATC 0.992795 -113 AGCGGAAGACGGGTGGGCGCAGAGCGATACTTCGC 5 228 0 GGTGGGCAGC 0.994878 -73 TAAAAATATAGTGTTGGTGCGGGTTATGAACAATA 7 53 1 GGTGGGCGTT 0.965887 -95 * ** ** *** ** Masking position 9 Map Score: 12.2673 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 412 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 CCTGTCACATGTTATTGGCATGCA 1 2 1 CTGTCCTGTA 0.968115 -165 TCACTGATATCCCTCCCTGTTTATCATTAATTT 1 57 1 CCCTCCGTTA 0.925785 -110 CTTCTTCATGCTCTCTGCTGTAACATTGGCAGG 2 14 1 CTCTCGTGTA 0.99417 -52 GCGATGCACCCCCTCAGGTGTTATCACAGGACT 5 69 0 CCCTCGTGTA 0.997169 -232 GGGCTGAATCCCCTGGGTTGTCACCAGAAGCGT 5 144 1 CCCTGGTGTA 0.985446 -157 ATAACCTCCGTCGGTTTTTAATTTTATTAT 6 81 0 CCGTCGTTTA 0.975927 -20 TTTTCTCTCCGCTGTAAAATAATCAGC 8 42 0 CTCTCGTGTA 0.99417 -17 ***** * *** * Masking position 13 Map Score: 7.94596 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 58 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 TTTGCATAGACCGTTTTCAGAGTAACCAGCGCATCGC 1 121 0 CCTTGGAACC 0.992843 -46 GGGAGCTTTGCTATTTCTGGAGTAAACCACC 2 45 1 CTTCGGAAAC 0.980786 -21 GGGCCATCCTCTGTGCAAACAAGTGTCTCA 4 60 0 CCTTGGAAAC 0.988629 -20 TCCTCCAACACCGTTACTTGGGCAACGCGCCTCTTCT 5 29 0 CCTCGGAACG 0.995378 -272 CAGAAGTGCTCCACCACTTGCGAAACGCCCGACTGCG 5 178 0 CCCCGGAACG 0.983039 -123 CCATTTTCAGCCTTGGCACAAGGGAAGAGCGGAAGAC 5 253 0 CCTCAGGAAG 0.892988 -48 ATTTTAGCGACTATAACAAGTGAAACCAAATAATAAA 6 52 1 CTTCGGAACC 0.987835 -49 TGGAAAATTTCCTTCATTAAGGTAAACTATCGGCAAT 7 16 0 CCTTAGAAAC 0.952142 -132 ** * * * * **** Masking position 15 Map Score: 6.50273 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 288 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 ACATGTTATTGGCATGCAGTCATTCATCGACT 1 17 1 GGCTGCAGCA 0.921903 -150 CGCATCGCTACGCCGCCAGCCAAAAACGCTGA 1 97 0 CGCGCCAGCA 0.996908 -70 GAAATAGCAAAGCTCCCTGCCAATGTTACAGC 2 30 0 AGCCCCTGCA 0.941608 -36 GCCATAATCTCGCGGCCAGGCATACTTGCGAA 3 34 0 CGCGCCAGCA 0.997166 -65 TGGCATTAAAAGCAAGCAGACAGAACCGTTCT 4 13 0 AGCAGCAGCA 0.952882 -67 ACGGTGTTGGAGGAGCCAGTCCTGTGATAACA 5 52 1 AGGGCCAGCC 0.935207 -249 CGATGATGAACGTGGCCAGCCGTTCAATCACC 5 105 0 CGTGCCAGCG 0.984766 -196 TCACCAGAAGCGTTCGCAGTCGGGCGTTTCGC 5 164 1 CGTCGCAGCG 0.953515 -137 *** ***** ** Masking position 7 Map Score: 5.53454 Number of sites scoring better than the average of aligned sites = 1616 Number in coding regions = 1567 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 AAAAAACTCCTTTAATGAAAAAAA 6 2 1 AAAAACCTTA 0.937125 -99 TATAGTCGCTAAAATAACGTTAATTTGCAAATT 6 34 0 AAAATCGTTA 0.982048 -67 ATAAAATTGCCGATAGTTTACCTTA 7 3 1 AAAATCCGAA 0.944382 -145 ATTTTTATGGAAAATTTCCTTCATTAAGGTAAA 7 27 0 AAAATCCTTA 0.986274 -121 TATGAACAATAAAATCGCCTTAAAAATGAGTCC 7 77 1 AAAATCCTTA 0.986272 -71 AGTCCTAAATAAAATAGGGTAAAGCCTTATTAA 7 105 1 AAAATGGTAA 0.889829 -43 AAAATCGCGTATATTCAATATTA 7 135 0 AAAATCGTAA 0.976749 -13 ***** **** * Masking position 4 Map Score: 5.26597 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 58 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TCACTGATATCCCTCCCTGTTTATCATTAA 1 57 1 CCCTCCCTGT 0.905201 -110 TTCTTCATGCTCTCTGCTGTAACATTGGCA 2 15 1 TCTCTGCTGT 0.877404 -51 GGGCCATCCTCTGTGCAAACAAGT 4 66 0 CATCCTCTGT 0.935905 -14 GGGCAACGCGCCTCTTCTGGCCTGCGCTAG 5 17 0 CCTCTTCTGG 0.97239 -284 CGGCGATGCACCCCCTCAGGTGTTATCACA 5 74 0 CCCCCTCAGG 0.886519 -227 CCAGGGGATTCAGCCCCTGTAGCCGATGAT 5 130 0 CAGCCCCTGT 0.957809 -171 ACAGGGGCTGAATCCCCTGGGTTGTCACCA 5 140 1 AATCCCCTGG 0.909712 -161 CCGACTGCGAACGCTTCTGGTGACAACCCA 5 157 0 ACGCTTCTGG 0.904005 -144 TATTTCGTTCCTGGTTTTGGTGTA 8 5 1 TCGTTCCTGG 0.787234 -54 TTTTCTCTCCGCTGTAAAATAATCA 8 44 0 TCTCCGCTGT 0.943725 -15 ********** Masking position 7 Map Score: 4.55382 Number of sites scoring better than the average of aligned sites = 2652 Number in coding regions = 2401 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 7 CGGCCAGGCATACTTGCGAAGATTTCAGGT 3 24 0 TACTTGCGAA 0.980471 -75 TTCTGGCCTGCGCTAGCGCAGG 5 3 0 CGCTAGCGCA 0.959888 -298 CCAACACCGTTACTTGGGCAACGCGCCTCT 5 32 0 TACTTGGGCA 0.956048 -269 AGTGCTCCACCACTTGCGAAACGCCCGACT 5 181 0 CACTTGCGAA 0.987493 -120 TGGGTGAAAATAGTAGCGAAGTATCGCTCT 5 213 1 TAGTAGCGAA 0.920081 -88 TCAGCCTTGGCACAAGGGAAGAGCGGAAGA 5 254 0 CACAAGGGAA 0.91056 -47 ********** Masking position 10 Map Score: 2.61844 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 192 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 TTCTCTTTTGTTAATTTGCATAGACCGTTT 1 142 0 TTAATTTGCA 0.963581 -25 AATTTGCAAATTTTTTTTCATTAAAGGAGT 6 16 0 TTTTTTTTCA 0.887313 -85 TAAAATAACGTTAATTTGCAAATTTTTTTT 6 28 0 TTAATTTGCA 0.963581 -73 TAAGGCGATTTTATTGTTCATAACCCGCAC 7 69 0 TTATTGTTCA 0.921075 -79 ATAATCAGCATTATTTTACACCAAAACCAG 8 21 0 TTATTTTACA 0.969621 -38 ATAATGCTGATTATTTTACAGCGGAGAGAA 8 37 1 TTATTTTACA 0.969621 -22 ********** Masking position 5 Map Score: 4.84728 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 64 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 ATGACTGCATGCCAATAACATGTGACAGG 1 10 0 GCCAATAACA 0.798566 -157 TACGCCGCCAGCCAAAAACGCTGATAATTA 1 91 0 GCCAAAAACG 0.979514 -76 CGCTGGTTACTCTGAAAACGGTCTATGCAA 1 127 1 TCTGAAAACG 0.906678 -40 AGCCCCTGTAGCCGATGATGAACGTGGCCA 5 119 0 GCCGATGATG 0.955046 -182 CAAGGGAAGAGCGGAAGACGGGTGGGCGCA 5 242 0 GCGGAAGACG 0.977659 -59 TTGTGCCAAGGCTGAAAATGGATCCCCTGA 5 269 1 GCTGAAAATG 0.954997 -32 ********** Masking position 5 Map Score: 0.200935 Number of sites scoring better than the average of aligned sites = 1444 Number in coding regions = 1354 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 10 GAAATCTTCGCAAGTATGCCTGGCCGCGAG 3 28 1 CAAGTATGCC 0.987317 -71 GTTAACCGGACAAGTGTGCCATAATCTCGC 3 53 0 CAAGTGTGCC 0.995312 -46 TCTGTGCAAACAAGTGTCTCAATGGTACGT 4 51 0 CAAGTGTCTC 0.976905 -29 ********** Masking position 3 Map Score: 0.0208514 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 6 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ********** No masking Map Score: -2.17893e-12 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: -2.17893e-12 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: -2.17893e-12 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