AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_ecoli_reg_300.orf -o00760_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yabB 300 orf, hypothetical protein #2 murC 53 L-alanine adding enzyme, UDP-N-acetyl-muramate:alanine ligase #3 ftsZ 60 cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase #4 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #5 nadC 87 quinolinate phosphoribosyltransferase #6 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #7 pncB 265 nicotinate phosphoribosyltransferase #8 pntA 300 pyridine nucleotide transhydrogenase, alpha subunit #9 nadE 201 NAD synthetase, prefers NH3 over glutamine #10 gatZ 28 putative tagatose 6-phosphate kinase 1 #11 gatY 197 tagatose-bisphosphate aldolase 1 #12 BIME96 27 BIME #13 b2097 184 orf, hypothetical protein #14 agaZ 248 putative tagatose 6-phosphate kinase 2 #15 metA 156 homoserine transsuccinylase #16 aceB 268 malate synthase A #17 aceA 29 isocitrate lyase #18 BIME206 22 BIME #19 aceK 27 isocitrate dehydrogenase kinase/phosphatase #20 deoC 257 2-deoxyribose-5-phosphate aldolase #21 deoA 83 thymidine phosphorylase #22 deoB 51 phosphopentomutase #23 deoD 56 purine-nucleoside phosphorylase Motif number 1 ACCCGTTGCTACTGAAACGACAAGCGACAGCGG 9 137 0 ACAAACGAAA 0.97932 -65 ACCCCTCCAGACAGAAAAGACAAAACTTCCTTA 9 176 0 ACAAAAGAAA 0.840975 -26 GATAACGATCACAAAAACGACAATATGAAAATT 11 116 0 ACAAACGAAA 0.97932 -82 TTGAAATCGAAAACAAACGACAGGAT 11 182 1 AAAAACGAAG 0.97932 -16 GGCAAAACGAAATGAAACGAAAGTTTTACGAAA 14 20 0 AAAAACGAAG 0.97932 -229 AATGAAAGTCACTGAAACGAGAGTAGCTTGCGT 14 100 0 ACAAACGAAG 0.991069 -149 GTGAGATAAAAATAAAACGAAAGATAATGGTTT 14 159 0 AAAAACGAAG 0.97932 -90 TATCAACTGAAACAAAACGAAAGATTAATATCG 14 202 1 AAAAACGAAG 0.97932 -47 TATAAGAATGACTAAAAGGAGAGAAA 15 4 0 ACAAAGGAAG 0.971265 -153 TTGTTATGTCACAAAAAGGATAAAACA 23 40 1 ACAAAGGAAA 0.935168 -17 ** ****** ** Masking position 7 Map Score: 16.5082 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 23 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 AATTTCTAATCTGGATGCAGATTTATCTTC 6 123 1 CTGGATGCAG 0.795679 -95 TTTATCTTCACCGGACGCAGACTTGTCTAT 6 144 1 CCGGACGCAG 0.970464 -74 TCAGTCTATTCCTGTTGCGTAAATCGCGCT 7 46 1 CCTGTTGCGT 0.76206 -220 CCTTAGAACGCCGGATAAAGACTGATAATT 8 63 0 CCGGATAAAG 0.808261 -238 TTGTGTGGCTCCTGACACAGGCAAACCATC 8 253 1 CCTGACACAG 0.830775 -48 TGTTTTTATGCCGGATGCGGTGTAAACATA 11 25 0 CCGGATGCGG 0.967988 -173 TTTATCTCACCATGACGCAGTATCAACTGA 14 182 1 CATGACGCAG 0.84355 -67 GTCGAGCCTGCATGTTGAAGGTGAGAAAGT 15 61 0 CATGTTGAAG 0.439544 -96 AATTTATTCACCTGCTGAGGTACGTTTCGG 16 82 0 CCTGCTGAGG 0.874938 -187 TTTTCGGATCCATGACGAGGAGCTGCACG 16 250 1 CATGACGAGG 0.843546 -19 ATTCTCTGCTCCTGATGAGGGCGCTAA 19 11 1 CCTGATGAGG 0.967205 -17 TCACTTTGATCCTGATGCGTTTGCCACCAC 20 66 1 CCTGATGCGT 0.93991 -192 TACCCGTAGGCCGGATAAGGCGTAGACGCA 21 21 1 CCGGATAAGG 0.883002 -63 GCGGCTTTTGCCGGATGCGTCTACGCCTTA 21 36 0 CCGGATGCGT 0.949841 -48 ********** Masking position 1 Map Score: 14.8421 Number of sites scoring better than the average of aligned sites = 2866 Number in coding regions = 2275 Number in noncoding regions = 591 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 3 GAGGGATTTTTTCTTACAGCTATTCATAACG 1 107 1 TTCTTCAGCT 0.605796 -194 AACATCGGGTTTTTTACCTCGGTATGCCTTG 1 191 1 TTTTTCCTCG 0.966648 -110 CTCCGTAAACTCCTTTCAGTGGGAAATTGTG 1 249 1 TCCTTCAGTG 0.745882 -52 GTAGCGATGCCTTTTGCATCGTATGAATTTA 2 13 1 CTTTTCATCG 0.868898 -41 ATAAGATCATTCTTTACATCGCAACCCTGAA 6 25 0 TCTTTCATCG 0.966648 -193 GATATTCCCTTCCATCGGTTTTATTGA 8 284 0 CCCTTCATCG 0.822145 -17 GTTTTTTCCTTGTTAAATGGCA 10 17 0 TTTTTCCTTG 0.920111 -12 GGAGGCCGTTTTTTTGCCTTTCACTCCTCGA 11 83 1 TTTTTCCTTT 0.768015 -115 CTTTTGGATGTTTTTTCAGCGTTTTCTGTTG 13 133 0 TTTTTCAGCG 0.913722 -52 TACGGGCGAGTTTTTCCATCTTTTGGATGTT 13 152 0 TTTTTCATCT 0.857755 -33 TCTAACGTAGTCTTTTCCTTGAAACTTTCTC 15 38 1 TCTTTCCTTG 0.940872 -119 CTTCTTTTCCTTTTATGCCGAAG 20 3 1 TCTTTCCTTT 0.820594 -255 CGCCTCATACTCTTTTCCTCGGGAGGTTACC 21 63 1 TCTTTCCTCG 0.975636 -21 ***** ***** Masking position 5 Map Score: 8.70342 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 586 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 AAGCCAGTCACAAGGCATACCGAGGTAAAA 1 202 0 CAAGGCATAC 0.873203 -99 TTCCTTCAGACGACGCATACAGGTATGTTA 6 74 0 CGACGCATAC 0.969847 -144 GAAGTCTCAACGCCGAATACAGAATTTCTA 6 101 1 CGCCGAATAC 0.907204 -117 TCTATGATGTCGCGTCATACTATTTTTCAA 6 169 1 CGCGTCATAC 0.96406 -49 AATTGCGAAACAAGGTATACTCCAGCAGTT 7 191 1 CAAGGTATAC 0.660223 -75 TGGTGGTTAAAACGTCATACAGGAATCCTC 9 101 0 AACGTCATAC 0.602903 -101 CGTATGTTTACACCGCATCCGGCATAAAAA 11 23 1 CACCGCATCC 0.952709 -175 TACGCCTTATACGAACAACACC 12 3 1 CGCCTTATAC 0.928508 -25 GATGCGTCTACGCCTTATCCGGCCTACGGG 21 23 0 CGCCTTATCC 0.890524 -61 GATAAGGCGTAGACGCATCCGGCAAAAGCC 21 34 1 AGACGCATCC 0.756308 -50 CGGCAAAAGCCGCCTCATACTCTTTTCCTC 21 53 1 CGCCTCATAC 0.978737 -31 ********** Masking position 7 Map Score: 8.25302 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 894 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 5 TTGTGCCTGTCGCCTGAGGCCGTAATCATCGT 3 25 0 CGCCTAGCCG 0.909996 -36 TTGTACTAAACGCTCCTGTACGAGGACGCTAC 7 235 1 CGCTCTGACG 0.975119 -31 AACGAGACATCGCCCCGGCACGAATCACTACT 8 12 0 CGCCCGGACG 0.985735 -289 GTGGGATAAACACCTTAGAACGCCGGATAAAG 8 73 0 CACCTAGACG 0.809737 -228 TAGTAACAAACGCCCTATAACGTACTGAAAAT 8 179 0 CGCCCATACG 0.976882 -122 CCACACAAGCTGCTCATGTACGAGCTAAATGT 8 229 0 TGCTCTGACG 0.942302 -72 CGCTTTTTCAAGCCCGTGAACGAAACGGCTCC 9 62 1 AGCCCTGACG 0.970442 -140 CATTTCGTTTTGCCTATTAACGCCTTTCTATT 14 39 1 TGCCTTTACG 0.899219 -210 AAGCCCACCTTGCCCATTGACGCAAGCTACTC 14 81 1 TGCCCTTACG 0.964469 -168 ***** ** *** Masking position 3 Map Score: 4.91134 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 447 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 CTTTATATTTGCTGTGGAAAATAGTGAGTCA 1 55 1 GCTGTGAAAA 0.844171 -246 TTTTAAAACGGTGATGACGATGAGGGATTTT 1 86 1 GTGATGCGAT 0.519268 -215 CGTCCAACGTGCGAAGCAAATTAACGTTATG 1 131 0 GCGAAGAAAT 0.871395 -170 AGTTTACGGAGCTGAGGAAAAGCTTGTCAAG 1 229 0 GCTGAGAAAA 0.714929 -72 TTTCAGGGTTGCGATGTAAAGAATGATCTTA 6 24 1 GCGATGAAAG 0.868306 -194 CGTAAATCGCGCTATGCAGAATCTTCATCTT 7 63 1 GCTATGAGAA 0.595307 -203 TATGCCGGATGCGGTGTAAACATACGTGGCA 11 18 0 GCGGTGAAAC 0.977355 -180 TGTAAGGTACGCGATGACAATACCACTTAAT 13 36 1 GCGATGCAAT 0.914875 -149 AAATACCTTTGCGGTGAAAACTTGACCGCGC 13 77 1 GCGGTGAAAC 0.977355 -108 GAATGCGTCAGTGGTGGCAAACGCATCAGGA 20 75 0 GTGGTGCAAA 0.799112 -183 TCGCATTACAGTGATGCAAACTTGTAAGTAG 20 133 1 GTGATGAAAC 0.822124 -125 GAAGTGTGTTGCGGAGTAGATGTTAGAATAC 20 188 1 GCGGAGAGAT 0.864116 -70 CATAACAAAGGCGGAGTCAACGCTCCGCCCA 23 17 0 GCGGAGCAAC 0.936185 -40 ****** **** Masking position 10 Map Score: 6.29408 Number of sites scoring better than the average of aligned sites = 2094 Number in coding regions = 1890 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 7 GAAGCAAATTAACGTTATGAATAGCTGTAAG 1 119 0 AACGTATGAA 0.951559 -182 ACCTGATTTCAACGTGTTGAAAAATAGTATG 6 184 0 AACGTTTGAA 0.734357 -34 AACGCCCTATAACGTACTGAAAATTATGCCT 8 172 0 AACGTCTGAA 0.80382 -129 TCACAAAAACGACAATATGAAAATTATTCGA 11 110 0 GACAAATGAA 0.769016 -88 TCGATTTCAAAATATAATGAAATTATTTGTT 11 161 0 AATATATGAA 0.763959 -37 TAATAGGCAAAACGAAATGAAACGAAAGTTT 14 27 0 AACGAATGAA 0.942965 -222 TCACAAAAGAAACATAATGAAAGTCACTGAA 14 117 0 AACATATGAA 0.954551 -132 GTGAGATAAAAATAAAACGAAAGATAATGGT 14 161 0 AATAAACGAA 0.630433 -88 TATCAACTGAAACAAAACGAAAGATTAATAT 14 202 1 AACAAACGAA 0.917168 -47 ACTTGTTGATAACAATATGAATAAAATTTAT 16 105 0 AACAAATGAA 0.946462 -164 GATCAAAGTGAACATCACGAAACTTCTTACA 20 46 0 AACATACGAA 0.929358 -212 ***** ***** Masking position 2 Map Score: 7.77844 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 106 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 GATATGTCCTAAAATGCCGCTCGCGTCGCAAAC 1 17 1 AAAATGCCCG 0.959431 -284 CTCGCGTCGCAAACTGACACTTTATATTTGCTG 1 36 1 AAACTGCCTT 0.744236 -265 TCACCGTTTTAAAATGACTCACTATTTTCCACA 1 67 0 AAAATGCCCT 0.946302 -234 CATACGATGCAAAAGGCATCGCTACAA 2 5 0 AAAAGGACCT 0.635481 -49 TCTTTGTGCTAAACTGGCCCGCCGAATGTATAG 4 39 1 AAACTGCCCC 0.961704 -62 CCCGTGAACGAAACGGCTCCGCTTTCAGAGGAT 9 74 1 AAACGGTCCT 0.713298 -128 TCCGGCATAAAAACACGCGCACTTTGCTACGGC 11 40 1 AAACACCCCT 0.843004 -158 AAAGGCAAAAAAACGGCCTCCCGATAGGGAAGC 11 71 0 AAACGGCCCG 0.976945 -127 TTTGCGGTGAAAACTTGACCGCGCTAACATTTT 13 84 1 AAACTTACCG 0.671942 -101 CAAAAGATGGAAAAACTCGCCCGTAACGACCAG 13 158 1 AAAAACCCCG 0.741163 -27 CTTTTCCTTGAAACTTTCTCACCTTCAACATGC 15 49 1 AAACTTCCCC 0.861506 -108 TTCGGAAATAAAAAAGGCACCCGAAGGTGCCTG 16 54 0 AAAAAGCCCG 0.914592 -215 ATGGATCCGAAAACTTCCCCACTGTGAACGAAG 16 230 0 AAACTTCCCT 0.916563 -39 ****** * * ** Masking position 3 Map Score: 6.03666 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 523 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 GGAAAAGCTTGTCAAGCCAGTCACAAGGCA 1 215 0 GTCAAGCCAG 0.977608 -86 CGACATCATAGACAAGTCTGCGTCCGGTGA 6 151 0 GACAAGTCTG 0.944985 -67 CAGCGTGTTAGATAAGCCTGGAATACATTG 9 30 1 GATAAGCCTG 0.944985 -172 ATTTGCCAATGTCGAGCCTGCATGTTGAAG 15 71 0 GTCGAGCCTG 0.965731 -86 TTTTATTGGCGACAAGCCAGGAGAATGAA 20 239 1 GACAAGCCAG 0.984266 -19 ********** Masking position 5 Map Score: 1.75441 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 71 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 GATTCGTTAGCTATCTGGAGTTTTAAC 5 71 1 CTATCTGGAG 0.989115 -17 TTTGTCTTTTCTGTCTGGAGGGGTTCA 9 185 1 CTGTCTGGAG 0.981608 -17 TACGGCTTCCCTATCGGGAGGCCGTTTTTT 11 67 1 CTATCGGGAG 0.980915 -131 TTATCTTCAGCTATCTGGATGTCTAAACGT 15 108 1 CTATCTGGAT 0.958233 -49 ********** Masking position 4 Map Score: 1.68909 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 15 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TTAAAACGGTGATGACGATGAGGGATTTTT 1 88 1 GATGACGATG 0.698242 -213 TTTTTATGAGGCCGACGATGATTACGGCCT 3 11 1 GCCGACGATG 0.958276 -50 AAACTGGCCCGCCGAATGTATAGTACACTT 4 49 1 GCCGAATGTA 0.660278 -52 GTCTGCGTCCGGTGAAGATAAATCTGCATC 6 136 0 GGTGAAGATA 0.69692 -82 TCCAGCAGTTCCTGAAGATGTTTATTGTAC 7 211 1 CCTGAAGATG 0.917466 -55 GAGCCTGCATGTTGAAGGTGAGAAAGTTTC 15 58 0 GTTGAAGGTG 0.859046 -99 CATCCAGATAGCTGAAGATAACCAGAAAAT 15 99 0 GCTGAAGATA 0.922846 -58 AAAAAAGGCACCCGAAGGTGCCTGAGGTAA 16 48 0 CCCGAAGGTG 0.94852 -221 TTCCTTTTATGCCGAAGGTGATGCGCCATT 20 17 1 GCCGAAGGTG 0.983738 -241 ********** Masking position 5 Map Score: 2.49699 Number of sites scoring better than the average of aligned sites = 1468 Number in coding regions = 1394 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 12 GGCCGACGATGATTACGGCCTCAGGCGACA 3 20 1 GATTACGGCC 0.958593 -41 GTTTCTCTCCGATTTGTGCCTGTCGCCTGA 3 40 0 GATTTGTGCC 0.936398 -21 AAGTAGTGATTCGTGCCGGGGCGATGT 8 8 1 GATTCGTGCC 0.896224 -293 CAAAAATCAGTATTTCGGCGTGAACTCGCA 8 130 0 TATTTCGGCG 0.797743 -171 CTCCAGTTCAGATTACTGCGATATTAATCT 14 223 0 GATTACTGCG 0.936398 -26 CTCTGCTCCTGATGAGGGCGCTAA 19 14 1 GATGAGGGCG 0.924753 -14 TGGATTTGGGCGGAGCGTTGAC 23 3 1 GATTTGGGCG 0.975574 -54 ********** Masking position 2 Map Score: 1.33473 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 176 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AAAATATTAACGATTCAGCCGTGATAGTGG 8 101 0 CGATTCAGCC 0.989353 -200 GTTTTAACCACCATTCAGCCCGCTGTCGCT 9 118 1 CCATTCAGCC 0.972015 -84 TCTGTTGGCTCGATTCATCAGAAAAAATGT 13 110 0 CGATTCATCA 0.937802 -75 GATCGTTAAGCGATTCAGCACCTTACCTCA 16 26 1 CGATTCAGCA 0.983638 -243 ********** Masking position 5 Map Score: 1.06272 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 17 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 GGGTATTAGCACCACATATAAGGAGATCCTGC 5 11 0 ACACATTAAG 0.945092 -77 TCTGGTAATAATCACAAATAAGATCATTCTTT 6 41 0 ACACAATAAG 0.982648 -177 CGAGATAACGATCACAAAAACGACAATATGAA 11 120 0 ACACAAAACG 0.885764 -78 CTTTTCGTTCAGCACAACTAAGACTACTCATT 16 186 0 ACACAATAAG 0.982648 -83 TTCGATACACATCACAATTAAGGAAATCTACT 20 159 0 ACACAATAAG 0.982648 -99 * ***** **** Masking position 6 Map Score: 0.834877 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 GAGTCATTTTAAAACGGTGATGACGATGAG 1 80 1 AAAACGGTGA 0.953742 -221 CGTAAAATAAACAACGCTGATATTAGCCGT 1 160 1 ACAACGCTGA 0.960227 -141 ACTATTTTTCAACACGTTGAAATCAGGTCA 6 187 1 AACACGTTGA 0.937581 -31 AGGCTTATCTAACACGCTGATAAACAAGAG 9 19 0 AACACGCTGA 0.983529 -183 GAGCCAACAGAAAACGCTGAAAAAACATCC 13 129 1 AAAACGCTGA 0.982201 -56 ********** Masking position 4 Map Score: 2.49239 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 50 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802