AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipdhR_ecoli_hinf_300.orf -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 pdhR 300 transcriptional regulator for pyruvate dehydrogenase complex #2 aceE 160 pyruvate dehydrogenase (decarboxylase component) #3 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #4 metA 156 homoserine transsuccinylase #5 aceB 268 malate synthase A #6 aceA 29 isocitrate lyase #7 aceK 182 isocitrate dehydrogenase kinase/phosphatase #8 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #9 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #10 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) Motif number 1 TTAACAACTTGACATATATAACGTTTCAAAGTT 1 148 0 GACTATAACG 0.761726 -153 GTAAAATACCGACGGATAGAACGACCCGGTGGT 3 103 1 GACGATAACG 0.970246 -198 CTGACTGTAGGCCGGATAAGGCGTTCACGCCGC 7 27 1 GCCGATAGCG 0.998025 -156 TGCACCGATTGCCGGATGCGGCGTGAACGCCTT 7 44 0 GCCGATGGCG 0.998465 -139 GGTGCACGATGCCTGATGCGACGCTTGCGCGTC 7 71 1 GCCGATGGCG 0.998465 -112 ACGGCTGTAGGCATGATAAGACGCGCAAGCGTC 7 90 0 GCAGATAGCG 0.982586 -93 CCGAACGTAGGCTGGATAAGGCGTTTACGCCGC 7 125 1 GCTGATAGCG 0.982586 -58 GCAGAGAATTGCCGGATGCGGCGTAAACGCCTT 7 142 0 GCCGATGGCG 0.998465 -41 TTAAAACAAAGCCCGATGGAATGCAATATTTTA 10 46 1 GCCGATGATG 0.954341 -254 *** **** * ** Masking position 7 Map Score: 18.6949 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 351 Number in noncoding regions = 596 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 AGACCAATTGACTTCGGCAAGTGGCTTAAG 1 271 1 ACTTCGGCAA 0.879122 -30 CGCATATAAAAGCGCGGCAACTAAACGTAG 2 55 1 AGCGCGGCAA 0.949817 -106 ATATTTATCTCCGGCGGTCATACCCGTCGT 3 269 0 CCGGCGGTCA 0.949958 -32 AAGCGTATGTAGTGAGGTAATCAGGTT 4 140 1 AGTGAGGTAA 0.952212 -17 CCCGAAGGTGCCTGAGGTAAGGTGCTGAAT 5 38 0 CCTGAGGTAA 0.879122 -231 ATCCAGCCTACGTTCGGCAACGGCTGTAGG 7 112 0 CGTTCGGCAA 0.886577 -71 GCTCCTGATGAGGGCGCTAA 7 173 1 AGGGCGCTAA 0.866563 -10 AGACCGTAAAAGTGCGGTCAATATTTTTAA 8 76 1 AGTGCGGTCA 0.9918 -38 TTGATGAAAACTGCGGTCAAAAAACATTG 9 10 1 ACTGCGGTCA 0.986012 -53 TTCCTTTTAAAGTGCGGTCATAAAACACAA 9 37 0 AGTGCGGTCA 0.9918 -26 ATTATTTGAAAGTGCGGTAATTTTTTTGTG 10 104 0 AGTGCGGTAA 0.992328 -196 ********** Masking position 10 Map Score: 14.9383 Number of sites scoring better than the average of aligned sites = 827 Number in coding regions = 787 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 AGCGCATATAAAAGCGCGGCAACTAAACGT 2 53 1 AAAGCGCGGC 0.981812 -108 AAAGACCGTAAAAGTGCGGTCAATATTTTT 8 74 1 AAAGTGCGGT 0.996241 -40 TTGATGAAAACTGCGGTCAAAAAACAT 9 8 1 AAACTGCGGT 0.986958 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 9 39 0 AAAGTGCGGT 0.996241 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 10 106 0 AAAGTGCGGT 0.996241 -194 ********** Masking position 3 Map Score: 10.2279 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 ATTGAATTAAAAATCACAAAATTGGTAAGTGAA 1 33 1 AAACAAAATT 0.725279 -268 TAACGATTATTAAACTATAAAAATCCGAATTGA 1 71 0 TAACTAAAAA 0.941932 -230 TATAGTTTAATAATCGTTAAAAAACTCCTTTCC 1 85 1 TAACTAAAAA 0.941932 -216 TGGATAATTTTTACCAGAAAAATCA 2 3 0 TTACAAAAAT 0.852227 -158 ATTCATGAGATTACCAGAAAAAAGC 3 3 0 TTACAAAAAA 0.917488 -298 TAGCTGAAGATAACCAGAAAATTTGCCAATGTC 4 88 0 TAACAAAATT 0.784224 -69 TTAAAATGCAAAATCAAAAACAATTTCCATTTT 5 154 0 AAACAAACAA 0.795922 -115 TTACCTCGTAAAAACGTTAAAAATATTGACCGC 8 89 0 AAACTAAAAA 0.921772 -25 TTTTTGAAAAAAATCTGAAAAAACTTTAAAACA 10 21 1 AAACAAAAAA 0.957839 -279 TTCGCTAAAATAACCAGTAAAATATTGCATTCC 10 63 0 TAACTAAAAT 0.893766 -237 AGCGAACAAAAAAACACAAAAAAATTACCGCAC 10 90 1 AAACAAAAAA 0.957839 -210 TTCACTATCTTTATCTCAAAAAATCTTCTAAAA 10 176 1 TTACAAAAAA 0.917485 -124 *** * ****** Masking position 9 Map Score: 8.8139 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 188 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 CCGCAGCGGCGTTAGCTTCACGCCCTCACCCCAG 3 227 0 GTTACTAGCC 0.948112 -74 TAACGCCGCTGCGGCCTGAAAGACGACGGGTATG 3 247 1 GCGGCTAGAC 0.987415 -54 GTTATCTTCAGCTATCTGGATGTCTAAACGTATA 4 107 1 GCTACTAGTC 0.911985 -50 AACAACCGTTGCTGACTGTAGGCCGGATAAGGCG 7 16 1 GCTGCTAGCC 0.995944 -167 ATTGCCGGATGCGGCGTGAACGCCTTATCCGGCC 7 36 0 GCGGGTAGCC 0.995349 -147 ATTGCCGGATGCGGCGTAAACGCCTTATCCAGCC 7 134 0 GCGGGTAGCC 0.995348 -49 TCATTAATCGGTGGGCTTAAAGCCCACCTACAGA 8 11 0 GTGGCTAGCC 0.992824 -103 **** ** * *** Masking position 10 Map Score: 7.00932 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 294 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 AGGTGAATACTTTGTTACTTTAGCGTCACAG 1 226 1 TTTGTTATTT 0.744379 -75 ACAACATCTTCTGGATAATTTTTACCAGAAA 2 16 0 CTGGATATTT 0.943647 -145 GCTTTTTTCTGGTAATCTCATGAATGTAT 3 9 1 CTGGTAACTC 0.805665 -292 GATTCTGGCGCTTGCTACCTTGCTGCACCCA 3 171 0 CTTGCTACTT 0.924704 -130 TAGTCTTTTCCTTGAAACTTTCTCACCTTCA 4 45 1 CTTGAAATTT 0.877636 -112 AGGCTCGACATTGGCAAATTTTCTGGTTATC 4 82 1 TTGGCAATTT 0.680964 -75 GGCAAATTTTCTGGTTATCTTCAGCTATCTG 4 94 1 CTGGTTACTT 0.966782 -63 ATTAAAAATACTTGATAACTTGTTGATAACA 5 122 0 CTTGATACTT 0.919201 -147 CAATATTTTACTGGTTATTTTAGCGAACAAA 10 69 1 CTGGTTATTT 0.964111 -231 TTTAACAAATCTTGTAAATTTTAGAAGATTT 10 196 0 CTTGTAATTT 0.920039 -104 ******* *** Masking position 7 Map Score: 5.28377 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 389 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 TGAGTAGTCTTAGTTGTGCTGAACGAAAAG 5 188 1 TAGTTGTGCT 0.952647 -81 GAACGAAGGATCGTTGTGCTCTTTTCGTTC 5 208 0 TCGTTGTGCT 0.968866 -61 TCTGTAGGTGGGCTTTAAGCCCAC 8 5 1 TAGGTGGGCT 0.990304 -109 ATTTCATTAATCGGTGGGCTTAAAGCCCAC 8 18 0 TCGGTGGGCT 0.99371 -96 AATGAAATCTTTGGTGGGCAGAAACCCATC 8 40 1 TTGGTGGGCA 0.946249 -74 ********** Masking position 5 Map Score: 3.57711 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 41 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ACCAATTGACTTCGGCAAGTGGCTTAAGAC 1 273 1 TTCGGCAAGT 0.823267 -28 TATTGAGCTTTCCGGCGAGAGTTCAATGGG 2 94 1 TCCGGCGAGA 0.979743 -67 GGTCGTTCTATCCGTCGGTATTTTACAAAA 3 99 0 TCCGTCGGTA 0.870913 -202 TATATTTATCTCCGGCGGTCATACCCGTCG 3 270 0 TCCGGCGGTC 0.982177 -31 TCACGCCGCATCCGGCAATCGGTGCACGAT 7 51 1 TCCGGCAATC 0.985749 -132 TTACGCCGCATCCGGCAATTCTCTGCTCCT 7 149 1 TCCGGCAATT 0.978132 -34 TAAACACGAATACGGCAATATTTGCTTTTC 10 234 0 TACGGCAATA 0.908117 -66 ********** Masking position 1 Map Score: 3.79533 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 854 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 9 TGATTTTTAATTCAATTAAAACGAATTTAAA 1 18 0 TTCAATAAAA 0.95087 -283 GTTTCATGATTTCAATCAAAACCTGTATGGA 1 191 1 TTCAATAAAA 0.950945 -110 GATTTGTCTATTCGCTAATAACCTCAATACA 3 35 0 TTCGCTATAA 0.764454 -266 GTGAGAAAGTTTCAAGGAAAAGACTACGTTA 4 40 0 TTCAAGAAAA 0.837366 -117 ATCAAGTATTTTTAATTAAAATGGAAATTGT 5 137 1 TTTAATAAAA 0.862114 -132 CTGAGTCCTTTTTGAAAAAAATCTGAAAAAA 10 13 1 TTTGAAAAAA 0.594116 -287 TGTTTTTTTGTTCGCTAAAATAACCAGTAAA 10 75 0 TTCGCTAAAT 0.764454 -225 GATATGATGATTTGATGAAAATTCACTATCT 10 155 1 TTTGATAAAA 0.88945 -145 TAAACTAATATTCACTCAAAACAGATTAAGG 10 272 1 TTCACTAAAA 0.941142 -28 ****** **** Masking position 8 Map Score: 2.39969 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 104 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 AAAGTATTCACCTTATGTCCATACAGGTTTTGAT 1 205 0 CCTATGCTAC 0.865199 -96 ACCCTAACCACCACCGGGTCGTTCTATCCGTCGG 3 111 0 CCCCGGCTTC 0.989905 -190 GCGCCAGAATCCCCAGGAGCTTACATAAGTAAGT 3 191 1 CCCAGGCTAC 0.996285 -110 CACGCCCTCACCCCAGTCACTTACTTATGTAAGC 3 209 0 CCCAGTCTAC 0.980912 -92 GTCTTTCAGGCCGCAGCGGCGTTAGCTTCACGCC 3 237 0 CCCAGCCTTA 0.921771 -64 CAGCACCTTACCTCAGGCACCTTCGGGTGCCTTT 5 41 1 CCCAGGCTTC 0.996285 -228 ** **** * *** Masking position 12 Map Score: 0.925489 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 74 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: 5.23913e-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 AAATTGGTAAGTGAATCGGTTCAATTCGGATT 1 51 1 GTGAACGTTC 0.977605 -250 GTCTACATTTGTGCATAGTTACAACTTTGAAA 1 126 1 GTGCAAGTAC 0.940881 -175 TTGTTAAAATGTGCACAGTTTCATGATTTCAA 1 174 1 GTGCAAGTTC 0.987346 -127 ATAGTCGATCGTTAAGCGATTCAGCACCTTAC 5 20 1 GTTAACGTTC 0.850835 -249 CGTGCAGCTCCTCGTCATGGATC 5 256 0 GTGCACTCTC 0.958261 -13 GTGCAGATGCTCCATAGTTATG 6 18 0 GTGCAATCTC 0.776544 -12 ATCAGGCATCGTGCACCGATTGCCGGATGCGG 7 56 0 GTGCACGTTG 0.968741 -127 ***** ** *** Masking position 5 Map Score: 1.71299 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 295 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ********** No masking Map Score: 5.23913e-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 14 ********** No masking Map Score: 5.23913e-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 15 ********** No masking Map Score: 5.23913e-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