AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_ecoli_reg_100.orf -o00190_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/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 ybaR 261 putative ATPase #2 kdpB 22 ATPase of high-affinity potassium transport system, B chain #3 kdpA 300 ATPase of high-affinity potassium transport system, A chain #4 sdhC 300 succinate dehydrogenase, cytochrome b556 #5 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #6 nuoN 186 NADH dehydrogenase I chain N #7 nuoM 89 NADH dehydrogenase I chain M #8 BIME110 38 BIME #9 nuoG 46 NADH dehydrogenase I chain G #10 nuoC 93 NADH dehydrogenase I chain C, D #11 nuoA 300 NADH dehydrogenase I chain A #12 ppk 171 polyphosphate kinase #13 atpD 26 membrane-bound ATP synthase, F1 sector, beta-subunit #14 atpG 50 membrane-bound ATP synthase, F1 sector, gamma-subunit #15 atpF 61 membrane-bound ATP synthase, F0 sector, subunit b #16 atpE 46 membrane-bound ATP synthase, F0 sector, subunit c #17 atpI 300 membrane-bound ATP synthase, dispensable protein, affects expression of atpB #18 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #19 ppa 300 inorganic pyrophosphatase Motif number 1 AAATTAATAAACCAGGCGGGTAAAAGTCCG 1 171 0 ACCAGGCGGG 0.947799 -91 TGTTCCGGAGACCTGGCGGCAGTATAGGCT 4 73 0 ACCTGGCGGC 0.992264 -228 CGCGCACCTCGTGGCTGATTATGGA 5 200 0 ACCTCGTGGC 0.849962 -15 TGGTTTGTTGGCCAGGCGGGCGCT 6 173 1 GCCAGGCGGG 0.979615 -14 TTTGCGCCTGTCGGCAAAGGGATTT 10 6 1 GCCTGTCGGC 0.992075 -88 GGTCCGTGGTGACTGTCGGCGCAGTAAGCT 10 67 0 GACTGTCGGC 0.973308 -27 CGTCTGGCGGCTTGCCTTAGG 14 2 1 GTCTGGCGGC 0.97513 -49 TCTCCTCAATGCCTTGCGGCCTGCCCTAAG 14 26 0 GCCTTGCGGC 0.988559 -25 ACATTTATTCACCTTTTGGCTACTTATTGT 17 174 1 ACCTTTTGGC 0.705639 -127 AGTTTTATACGACACGCGGCATACCTCGAA 17 271 1 GACACGCGGC 0.941122 -30 AACAAGCGAAGACATTCGGCGCGAGTTGGC 19 234 1 GACATTCGGC 0.875709 -67 ********** Masking position 3 Map Score: 15.0719 Number of sites scoring better than the average of aligned sites = 1483 Number in coding regions = 1415 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 CTTTTGTTAACTCCTTTTTATAGATGCGGGA 1 6 1 GTTCCCTTTT 0.904604 -256 GGATTAGACATTTATCTCTTTGTTTTCCTGTAGTTA 1 103 0 TTTCCTGTTT 0.723882 -159 TTTACGGACTTTTACCCGCCTGGTTTATTAATTTCT 1 167 1 TTTCGCGGTT 0.797972 -95 TTTGTTGCTATTTAGCGCCTTTGTCTTATTGACTTA 5 51 0 TTTCCCTGTT 0.97948 -164 GCGGCGCTGGTTTCGCTCTGGTTTGTTGGCCAGGCG 6 155 1 TTTCCTTTTT 0.900318 -32 TGATGTGGTTTTTTACTCCTTTCTATAACCTTTTGT 11 151 0 TTTCCCTCTT 0.931303 -150 TCCAGCAGTTTTTTTCCCCCTTTTCTGGCATAGTTG 12 76 1 TTTCCCTTTT 0.98485 -96 TACCACTTTTACTCCGTTTTATTCACGGGACA 12 150 0 TTTCCCTTTT 0.98485 -22 TGAAGCACGCTTTATCACCAGTGTTTACGCGTTATT 17 70 1 TTTCCCTGTT 0.97948 -231 CACCGTATAATTTGACCGCTTTTTGATGCTTGACTC 17 221 1 TTTCGCTTTA 0.776659 -80 AAATAAAACGTTAATCACAAGTTTGTAATCGCTTTC 19 109 1 TTACCATTTT 0.470602 -192 CGGTTATGGATTTTCCTGCTCTGTATACCGTCTTAA 19 169 1 TTTCGCTGTT 0.931543 -132 TTCATTTTCCTTTTTCACCAGTTTTAAGACGGTATA 19 192 0 TTTCCCTTTA 0.924233 -109 TCGGCACTTGTTTGCCACATATTTTTAAAGGAAACA 19 272 1 TTTCCATTTT 0.900318 -29 *** * ** *** * Masking position 14 Map Score: 13.4106 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 268 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 TTTTTATAGATGCGGGAGGTAATTCCTCAC 1 25 1 TGCGGGAGGT 0.956981 -237 GTAGTTAAGTTGCGGGTGCTAAGTTAAATC 1 80 0 TGCGGGTGCT 0.966869 -182 CGCAAAAATCTGCGGGCGGGGTGTAAAAAA 3 131 0 TGCGGGCGGG 0.986058 -170 GCACTGTGAGTGCAGGCGTGATAACCGGCG 3 217 1 TGCAGGCGTG 0.900646 -84 ACCGGCGTATTGCTGGTGTTTTTATTACTG 3 240 1 TGCTGGTGTT 0.920334 -61 TCCTCCGGTCTGCTTGCGGGTCAGACAGCG 4 191 0 TGCTTGCGGG 0.777593 -110 AAGAACAGCATGTGGGCGTTATTC 4 287 1 TGTGGGCGTT 0.88055 -14 TTGTTGGCCAGGCGGGCGCT 6 177 1 GGCGGGCGCT 0.971698 -10 CCAGCGGCAGAGCTGGCGCTTTAATTACGG 12 16 0 AGCTGGCGCT 0.93482 -156 CCAGCTCTGCCGCTGGCGTTTTTCAATTCA 12 30 1 CGCTGGCGTT 0.931992 -142 GGAAAAAAACTGCTGGAGCTTGCGATTTAC 12 63 0 TGCTGGAGCT 0.948218 -109 ********** Masking position 6 Map Score: 9.52334 Number of sites scoring better than the average of aligned sites = 2458 Number in coding regions = 2371 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 ACAGGATGAATGTAAATAAACCATCAATAA 3 31 0 TGTAAATAAA 0.868433 -270 GCGGGCGGGGTGTAAAAAAAGTATAAAAAT 3 120 0 TGTAAAAAAA 0.886947 -181 CAGATAACCCAGTAATAAAAACACCAGCAA 3 249 0 AGTAATAAAA 0.830137 -52 TATAGAAAGGAGTAAAAAACCACATCAATT 11 160 1 AGTAAAAAAC 0.883171 -141 CATGGGGAGGAATAAAAAAAACCTTACAAT 11 216 0 AATAAAAAAA 0.658813 -85 TCATTTGCCAAGTAAATAAATATGCTGTGC 17 17 1 AGTAAATAAA 0.9431 -284 CATGAAAAACTGTAAATAACGCGTAAACAC 17 90 0 TGTAAATAAC 0.717023 -211 GTGGGCAGTGACTAAAAAAAGCACGATCTG 18 66 1 ACTAAAAAAA 0.84043 -229 CTGATGGTTTAGTAATTAAATTAATCATCT 18 93 1 AGTAATTAAA 0.804377 -202 CCTCTTGCGCACTAAAAAAATCGATCTCGT 18 139 1 ACTAAAAAAA 0.84043 -156 ACTTCAAAAAAGTAAATAAAACGTTAATCA 19 96 1 AGTAAATAAA 0.9431 -205 ********** Masking position 5 Map Score: 7.54592 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 109 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 GGTAATTCCTCACCCCGGTGCCGATTTTCAGGC 1 42 1 CACCGGTGCG 0.970864 -220 ATGCCCTGATCAATGCGGAGGCGTTCTG 3 283 1 CATGGGAGCG 0.971833 -18 TAACTTTCTGTTACCTGGAGACGTCGGGATTTC 4 223 0 TTCCGGAGCG 0.96093 -78 TACCAGAAATTATCCGGGAGACGAGA 5 4 0 TACCGGAGCG 0.990013 -211 CGTCCATAATCAGCCACGAGGTGCGCG 5 198 1 CACCCGAGTG 0.88501 -17 TCACAACCACCACCGTCAAGCCGACGATCAGCA 6 57 0 CACGCAAGCG 0.888104 -130 ATGCTCTCCATTGCGTGGCGACGCAATCATTTC 6 89 1 TTCGGGCGCG 0.953999 -98 TTATTGGGCTTAACGCGGCGCTGGTTTCGCTCT 6 141 1 TACGGGCGTG 0.850621 -46 AACATCTAATTATCCTGGAGTCGTCAAGGATCT 11 44 1 TACCGGAGCG 0.990012 -257 GGCCGCAAGGCATTGAGGAGAAGCTC 14 35 1 CATGGGAGAG 0.772517 -16 AGTCTACTCGCAACGCGACGGCGAGACAAATTT 18 13 1 CACGGACGCG 0.815291 -282 ** ** **** ** Masking position 10 Map Score: 7.29932 Number of sites scoring better than the average of aligned sites = 1293 Number in coding regions = 1229 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 GGCTCGATTTGCATCAGGATTAGACATTTATCTCTTTG 1 117 0 GCTCGGACTT 0.826177 -145 AGAATTCTACCCTTCCGGTATCACTTTTAGGCCACTGG 3 175 1 CCTCGACTTT 0.975382 -126 CGGAGACCTGGCGGCAGTATAGGCTGTTCACAAAATCA 4 60 0 GCGCGGCTTT 0.967479 -241 TGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATGACG 4 136 1 GCTCGAGTTT 0.832109 -165 ACTACCCCCAGTCCGAAGAGAATTTTCTGTCGTGAG 7 9 1 CATCGAATTT 0.663164 -81 TGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTC 7 46 0 CCTCGGATTT 0.969843 -44 GAAGAGCAGTGAATCTGGCGCTACTTTTGATGAGTAAG 11 271 1 GATCGACTTT 0.84013 -30 AAAAACGCCAGCGGCAGAGCTGGCGCTTTAATTACGGG 12 15 0 GCGCGGCGTT 0.836256 -157 ATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAG 15 20 0 CGTCGGCTTT 0.959613 -42 AATTACTAAACCATCAGATCGTGCTTTTTTTAGTCACT 18 72 0 CCTCGGCTTT 0.99007 -223 TCAGACTTATCCATCAGACTATACTGTTGTACCTATAA 18 175 1 CCTCGACTTT 0.975382 -120 CTGAAAGTTACGGTCTGCGAACGCTATTCCACTGCTCC 18 214 0 CGTCGGCTTT 0.959613 -81 GAAAAATGCGGCTACGGTTATGGATTTTCCTGCTCTGT 19 155 1 GCACGGATTT 0.778659 -146 ** ** * *** ** Masking position 17 Map Score: 8.93398 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 562 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 ATTCAGTGCTCACTCAATATCA 2 10 0 CAGTGCTCAC 0.964709 -13 CCTGCACTCACAGTGCACCTCCAGTGGCCT 3 203 0 CAGTGCACCT 0.905543 -98 TCATGCAAAACACTGCTTCCAGATGCGAAA 4 142 0 CACTGCTTCC 0.961629 -159 AACCTGATCGCACTGCTACCGTTGCTGATC 6 35 1 CACTGCTACC 0.934264 -152 GCGCCAGATTCACTGCTCTTCACGGCAGAT 11 262 0 CACTGCTCTT 0.873112 -39 AATATTTTTCCAGTGCATACAATTGCGACT 17 141 0 CAGTGCATAC 0.764395 -160 TTTTTTTAGTCACTGCCCACCGCTGTTTGA 18 56 0 CACTGCCCAC 0.942077 -239 AACGCTATTCCACTGCTCCTTTATAGGTAC 18 203 0 CACTGCTCCT 0.972907 -92 ********** Masking position 2 Map Score: 4.39714 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 260 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 TATGCCCTGATCAATGCGGAGGCGTTCTG 3 282 1 TCAATGCGGA 0.63719 -19 CTGTTCAGGATAAAACCCGACAAACTATAT 4 15 1 TAAAACCCGA 0.63524 -286 GGAACACCCTGCAATCCCGAGCCACCCAGC 4 97 1 GCAATCCCGA 0.95906 -204 TGACCCGCAAGCAGACCGGAGGAAGGAAAT 4 198 1 GCAGACCGGA 0.956798 -103 CCGGAGGAAGGAAATCCCGACGTCTCCAGG 4 213 1 GAAATCCCGA 0.82344 -88 ATTTCTGGTAGCAAAGCCTACCAGTAAGTC 5 27 1 GCAAAGCCTA 0.66714 -188 TCCCGGGTCAGCAAACTCGAAAAATTGACG 5 138 0 GCAAACTCGA 0.952624 -77 GGCGTTATTGGCAAAGTGGAACAAGACTCA 5 169 0 GCAAAGTGGA 0.897126 -46 CGCCTGGCCAACAAACCAGAGCGAAACCAG 6 161 0 ACAAACCAGA 0.659758 -26 CTCTGACTGAGAAAACTGGAAGC 9 34 1 GAAAACTGGA 0.847234 -13 TTTAACTGAAACAAACTGGAGACTGTC 16 30 1 ACAAACTGGA 0.873422 -17 AATAGCGTTCGCAGACCGTAACTTTCAGGT 18 224 1 GCAGACCGTA 0.736991 -71 TGGGATAAAAACAATCTGGAGGAATGTC 18 277 1 ACAATCTGGA 0.761588 -18 ********** Masking position 3 Map Score: 5.19873 Number of sites scoring better than the average of aligned sites = 1539 Number in coding regions = 1425 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 9 AGGTAATTCCTCACCCCGGTGCCGATTTTC 1 41 1 TCACCCCGGT 0.950978 -221 CAACGAATTCTCACGACAGAAAATTCTCTT 7 26 0 TCACGACAGA 0.969504 -64 GCGCCGACAGTCACCACGGACCATTTGCA 10 75 1 TCACCACGGA 0.986452 -19 TTCCATTGCTTCACAACGGACACGATTCAA 11 13 1 TCACAACGGA 0.94828 -288 TAATGCCCTTTCACCCCAGATCCTTGACGA 11 64 0 TCACCCCAGA 0.980317 -237 TCACTGCTCTTCACGGCAGATGGACGCCAC 11 253 0 TCACGGCAGA 0.94892 -48 ********** Masking position 3 Map Score: 3.33493 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 91 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 GCAAAGATTTCGCAAAAATCTGCGGGCGGGGTGTA 3 136 0 CGAAACGCGG 0.922005 -165 TGAGTGCAGGCGTGATAACCGGCGTATTGCTGGTG 3 223 1 CGGTACGCGT 0.986923 -78 CCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGT 4 104 1 CGGCACGCGT 0.994847 -197 GGTCTGCTTGCGGGTCAGACAGCGTCCTTTCTATA 4 180 0 CGGCACGCGT 0.994847 -121 AACAAAAAAACGGGTTTATTGGCGGATAGAAAAAA 5 81 1 CGGTTTGCGG 0.73845 -134 ATCTATTTCGCGAAGCTTACTGCGCCGACAGTCAC 10 54 1 CGACTCGCGC 0.943109 -40 CTGCTCCCTTCGAGGTATGCCGCGTGTCGTATAAA 17 274 0 CGGTACGCGT 0.986923 -27 ATTTTACGCAGGAATCAAACAGCGGTGGGCAGTGA 18 42 1 GGACACGCGG 0.958805 -253 GAAAACAAGCGAAGACATTCGGCGCGAGTTGGCTA 19 231 1 GAGCACGCGC 0.826977 -70 ** * ** * **** Masking position 13 Map Score: 4.34331 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 842 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 GATAAAGGTTAAACCTTCCAGCAAGGGGAAGGTCA 1 203 0 ACCTTCAGAG 0.991701 -59 AAAACACTCCTTTAAGACAGTTTTGACTGG 1 242 0 ACCTTAAGAG 0.982969 -20 ATTTTTGCGAAATCTTTGCAGCCAGAATTCTACCC 3 152 1 ACTTTCAGAG 0.939536 -149 TCTGGTAGCAAAGCCTACCAGTAAGTCAATAAGAC 5 30 1 ACCTACAGAG 0.96727 -185 CTTCTCCTCAATGCCTTGCGGCCTGCCCTAAGGCA 14 23 0 ACCTTCGGTG 0.884425 -28 GCTTGACTCTAAGCCTTAAAGAAAGTTTTATACGA 17 248 1 ACCTTAAGAG 0.982701 -53 GACACGCGGCATACCTCGAAGGGAGCAGGA 17 281 1 ACCTCAAGAG 0.94923 -20 * **** *** ** Masking position 1 Map Score: 1.66994 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 87 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 TTGACTGGCTGTGATAAAGGTTAAACCTTC 1 220 0 GTGATAAAGG 0.979326 -42 TGGCCTAAAAGTGATACCGGAAGGGTAGAA 3 179 0 GTGATACCGG 0.934892 -122 GAGTGCAGGCGTGATAACCGGCGTATTGCT 3 224 1 GTGATAACCG 0.953543 -77 GTAAACACTGGTGATAAAGCGTGCTTCAGA 17 68 0 GTGATAAAGC 0.915691 -233 TTACAAACTTGTGATTAACGTTTTATTTAC 19 107 0 GTGATTAACG 0.859317 -194 CTTAAAACTGGTGAAAAAGGAAAATGAAGA 19 200 1 GTGAAAAAGG 0.921176 -101 ********** Masking position 4 Map Score: 0.886208 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 141 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 AAAGGTTAAACCTTCCAGCAAGGGGAAGGT 1 205 0 CCTTCCAGCA 0.954798 -57 AGAATTCTACCCTTCCGGTATCACTTTTAG 3 175 1 CCTTCCGGTA 0.929414 -126 GCAAAACACTGCTTCCAGATGCGAAAACGA 4 138 0 GCTTCCAGAT 0.930889 -163 GGTAGGCTTTGCTACCAGAAATTATCCGGG 5 19 0 GCTACCAGAA 0.930889 -196 GGTAGCAAAGCCTACCAGTAAGTCAATAAG 5 33 1 CCTACCAGTA 0.95074 -182 GCTTCCAGTTTTCTCAGTCA 9 37 0 GCTTCCAGTT 0.95074 -10 ********** Masking position 3 Map Score: 0.884425 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 334 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 CTTTTGTTAACTCCTTTTTA 1 1 1 CTTTTGTTAA 0.885567 -261 TAAATCATGGCTTTTGCCATTTTTATACTT 3 102 1 CTTTTGCCAT 0.89883 -199 TGTGAAGAAACTTTTGTTAAAGTTGACAAA 11 126 1 CTTTTGTTAA 0.885567 -175 TTTCTATAACCTTTTGTCAACTTTAACAAA 11 138 0 CTTTTGTCAA 0.958163 -163 CATAGTTGGACATCTGCCAATATTGCTCGC 12 104 1 CATCTGCCAA 0.875891 -68 AAGGCATCATTTGCCAAGTAAATAAAT 17 8 1 CATTTGCCAA 0.950742 -293 ********** Masking position 5 Map Score: 0.475491 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 86 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 CCAGTCAAAACTGTCTTAAAGGAGTGTTTT 1 242 1 CTGTTAAAGG 0.840665 -20 GGAGACCTGGCGGCAGTATAGGCTGTTCACAA 4 65 0 CGGGTATAGG 0.925392 -236 TTGCATGACGCGCAGTTATAGAAAGGACGCTG 4 164 1 CGCTTATAGA 0.762201 -137 AACAAAAAAACGGGTTTATTGGCGGATAGAAA 5 81 1 CGGTTATTGG 0.979035 -134 TGATTATGGACGGCGTTATTGGCAAAGTGGAA 5 178 0 CGGTTATTGG 0.979035 -37 ACGCTACGCTCTCGGTTATTGGGCTTAACGCG 6 126 1 CTCTTATTGG 0.947633 -61 TGGTTTCGCTCTGGTTTGTTGGCCAGGCGGGC 6 162 1 CTGTTGTTGG 0.886619 -25 TATTCCACTGCTCCTTTATAGGTACAACAGTA 18 196 0 CTCTTATAGG 0.947633 -99 *** ******* Masking position 7 Map Score: 1.34422 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 165 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357