AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -idnaA_ecoli_hinf_100.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 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #2 nrdB 233 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #3 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #4 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #5 HI0269 125 RNA polymerase sigma-32 factor (rpoH) #6 HI0993 191 chromosomal replication initiator protein (dnaA) #7 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #8 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) Motif number 1 AAGGCGTTTACGCCGCATCCGGCATCTCAATA 2 10 0 CGCATCCGGC 0.999539 -224 GCGGCGTAAACGCCTTATCCGGCCTACGGCTCG 2 27 1 CGCATCCGGC 0.999539 -207 GACGCTGGCGCGTCTTATCAGGCCTACAAACCG 2 58 0 CGCATCAGGC 0.998921 -176 GACGCGCCAGCGTCGCATCAGGCTCCGGGTGCC 2 77 1 CGCATCAGGC 0.998921 -157 AAGGCGTTCACGCTGCATCCGGCACCCGGAGCC 2 97 0 CGTATCCGGC 0.994752 -137 GCAGCGTGAACGCCTTATCCGGCCTACGGCTCG 2 114 1 CGCATCCGGC 0.999539 -120 GACGCTGGCGCGTCTTATCAGGCCTACAAATCC 2 146 0 CGCATCAGGC 0.998921 -88 GACGCGCCAGCGTCGCATCAGGCACAGGATGCG 2 165 1 CGCATCAGGC 0.998921 -69 AGGCATTTTACGCCGCATCCTGTGCCTGATGCG 2 178 0 CGCATCCTGT 0.943055 -56 CGGCGTAAAATGCCTTATCCGGCATTAAACTCC 2 196 1 TGCATCCGGC 0.994752 -38 ** * ******* Masking position 7 Map Score: 41.8005 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 74 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GCCGAACAGTTATTTTTAACAAATTTTTCTCTTCC 1 50 1 TTTTAACATT 0.933233 -251 GGAAAAAGTGGCTTTCGCGCACCTTAGGTCAGACA 1 106 0 GTTTCGCATT 0.940592 -195 CTATATATAGTGTTCTAAGCAGCTTCCCGTACTAC 1 221 1 TTTCAGCATT 0.947177 -80 GTATTTCATCTCTATGTCACATTTTGTGCGTAATT 3 82 1 TTATCACATT 0.862492 -163 CAGACCGTGATTTTATCCACAAGTTCAATGCAAGC 3 126 0 TTTACACATT 0.842017 -119 GCGGGCACGATTTACGCCGCATATTGGAAAATTTA 4 14 0 TTACCGCATT 0.889457 -287 TTTCCCGATTTATCCACAGGACTTTCCAGAACTCG 4 75 0 TTCCAGGATT 0.75932 -226 AGAGATCTTCTGTTTCTCACAGATTTTCCCGATTT 4 99 0 TTTTCACATT 0.968464 -202 AAACAGAAGATCTCTTGCGCAGTTTAGGCTATGAT 4 119 1 TTCTCGCATT 0.98561 -182 GGTCCCGATCGTTTTGCAGGATCTTGACTCGGGCA 4 158 1 GTTTAGGATT 0.586761 -143 ATAAAATCTGTCTTATTAACAAATTGGTTCAATAA 5 37 1 TTTAAACATT 0.708106 -89 ATATTTAATCTATCTGGCGCATTTTAAT 6 4 0 TTCTCGCATT 0.985609 -188 GTTTGACCTTTCACTTAAGCAGATTATAGAACAGA 6 70 0 TACTAGCATT 0.69044 -122 AAACTTGGATTTTTTAGAAGATCTTTTCACGCATT 6 101 1 TTTTAAGATT 0.733627 -91 TCTCCGACAATTTTTACCGCACTTTTCTCTATTAC 6 146 1 TTTTCGCATT 0.98713 -46 TTTGTTGAATTTTTCACCGCACTTTGAAGGA 7 7 0 TTTCCGCATT 0.975245 -173 ATTCAACAAATTTTTACCGCACTTTTTCTTATTTT 7 32 1 TTTTCGCATT 0.98713 -148 CTTGCGATCTTTTCTCAAACACATTATCTT 7 160 1 TTCTAACATT 0.925826 -20 ACGCCCCTATTGTCTTCCCCAACTTATGGGGAAGA 8 11 1 TTCTCCCATT 0.879281 -131 * *** **** ** Masking position 14 Map Score: 24.7683 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 461 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 GCATAACTTTGTGGATAACTCAGGAAGGAAAAAGT 1 132 0 GGTCTCAGGA 0.670837 -169 CCTACAAACCGAGCCGTAGGCCGGATAAGGCGTTT 2 34 0 GGGGGCCGGA 0.99774 -200 CCTACGGCTCGGTTTGTAGGCCTGATAAGACGCGC 2 49 1 GTGGGCCTGA 0.963197 -185 GGAGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 2 68 0 GGGGGCGCGT 0.973509 -166 GTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGA 2 88 1 GTGTGCCGGA 0.951878 -146 CTACAAATCCGAGCCGTAGGCCGGATAAGGCGTTC 2 121 0 GGGGGCCGGA 0.99774 -113 CTACGGCTCGGATTTGTAGGCCTGATAAGACGCGC 2 137 1 GTGGGCCTGA 0.963197 -97 TGTGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 2 156 0 GGGGGCGCGT 0.973509 -78 GTCCTGTTGGGAGTTTAATGCCGGATAAGGCATTT 2 203 0 GGTTGCCGGA 0.951878 -31 CGATCCTGCCGCGAGGCGGGCACGATTTACGCCGC 4 29 0 GGGGGCACGA 0.99387 -272 GGAAAGTCCTGTGGATAAATCGGGAAAATCTGTGA 4 83 1 GGTATCGGGA 0.614058 -218 TTTAGGCTATGATCCGCGGTCCCGATCGTTTTGCA 4 141 1 GTGGTCCCGA 0.954012 -160 GACCCTGCTTGAGGGTGACGCACGAACCGCTGTCT 4 202 0 GGTCGCACGA 0.918309 -99 CCAACTTATGGGGAAGATAGCACGACATAACGAAT 8 29 1 GGGAGCACGA 0.965557 -113 * * * ******* Masking position 11 Map Score: 20.4475 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 1023 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 AAGTCAATGGGAAGAGAAAAATTTGTTAAAAA 1 62 0 GAAGGAAAAT 0.852867 -239 GATAACTCAGGAAGGAAAAAGTGGCTTTCGCG 1 122 0 GAAGAAAAAT 0.709249 -179 TGAAACTATTGCGGAAAGAATTCCAAAAACAG 1 268 1 GCGGAAGAAT 0.917712 -33 GATGCCGGATGCGGCGTAAACGCCTTATCCGG 2 17 1 GCGGGTAAAG 0.961455 -217 GGTGCCGGATGCAGCGTGAACGCCTTATCCGG 2 104 1 GCAGGTGAAG 0.785557 -130 GGCACAGGATGCGGCGTAAAATGCCTTATCCG 2 185 1 GCGGGTAAAT 0.974106 -49 GGAACCCATTGCAGGGAAAGAGTATAACACGC 3 16 0 GCAGGAAAGG 0.955838 -229 GGGTTCCGTAGCAGGGAAAGAGACCCCGTTGT 3 41 1 GCAGGAAAGG 0.955838 -204 TTTCCAATATGCGGCGTAAATCGTGCCCGCCT 4 19 1 GCGGGTAAAC 0.876304 -282 AGATTATAGAACAGAAAAAAATGCGCCAGTAT 6 53 0 ACAGAAAAAT 0.709249 -139 TACAATAAATGCGTGAAAAGATCTTCTAAAAA 6 111 0 GCGTAAAAGT 0.586914 -81 AGAGAAAAGTGCGGTAAAAATTGTCGGAGATT 6 144 0 GCGGAAAAAT 0.976494 -48 CCTTCAAAGTGCGGTGAAAAATTCAACAAATT 7 12 1 GCGGGAAAAT 0.989972 -168 AAGAAAAAGTGCGGTAAAAATTTGTTGAATTT 7 30 0 GCGGAAAAAT 0.976494 -150 CCCCTGATAAACAGGGAAAGCTAAATAAATGA 8 94 1 ACAGGAAAGT 0.777962 -48 **** ***** * Masking position 9 Map Score: 17.8889 Number of sites scoring better than the average of aligned sites = 2019 Number in coding regions = 1768 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 5 TCCCATTGACTTTCCCGGACACCTTGTCTG 1 82 1 TTTCCCGGAC 0.886813 -219 AAAAAGTGGCTTTCGCGCACCTTAGGTCAG 1 109 0 TTTCGCGCAC 0.899216 -192 ATGTTTGGGATTCACTGCAAGATAGTGTGA 1 186 0 TTCACTGCAA 0.955266 -115 GTTATACTCTTTCCCTGCAATGGGTTCCGT 3 20 1 TTCCCTGCAA 0.96379 -225 CGGGGTCTCTTTCCCTGCTACGGAACCCAT 3 39 0 TTCCCTGCTA 0.812571 -206 TATCCACAAGTTCAATGCAAGCTTGTGAAT 3 118 0 TTCAATGCAA 0.70442 -127 TCCGACAATTTTTACCGCACTTTTCTCTAT 6 148 1 TTTACCGCAC 0.976732 -44 TGTTGAATTTTTCACCGCACTTTGAAGGA 7 10 0 TTCACCGCAC 0.988019 -170 TCAACAAATTTTTACCGCACTTTTTCTTAT 7 34 1 TTTACCGCAC 0.976732 -146 ********** Masking position 2 Map Score: 9.49959 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 701 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 6 GCCTGATAAGACGCGCCAGCGTCGCATCAG 2 68 1 ACGCGCCAGC 0.989683 -166 GCCTGATAAGACGCGCCAGCGTCGCATCAG 2 156 1 ACGCGCCAGC 0.989683 -78 ACGCCGCATCCTGTGCCTGATGCGACGCTG 2 172 0 CTGTGCCTGA 0.894878 -62 GTAGCAACAACTGTGCCAGAGCTTAAGAGC 3 187 0 CTGTGCCAGA 0.979383 -58 GCTACCACTGAAGCGCCAGAAGATATCGAT 3 212 1 AAGCGCCAGA 0.981229 -33 ATAGCCTAAACTGCGCAAGAGATCTTCTGT 4 121 0 CTGCGCAAGA 0.958664 -180 ATTAAAATGCGCCAGATAGATTAAAT 6 7 1 ATGCGCCAGA 0.995303 -185 ACAGAAAAAAATGCGCCAGTATTGTATAGA 6 45 0 ATGCGCCAGT 0.981228 -147 ********** Masking position 5 Map Score: 14.0698 Number of sites scoring better than the average of aligned sites = 1555 Number in coding regions = 1471 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 AGAGAAAAATTTGTTAAAAATAACTGTTCG 1 52 0 TTGTTAAAAA 0.746755 -249 GTGCATAACTTTGTGGATAACTCAGGAAGG 1 139 0 TTGTGGATAA 0.965977 -162 ATGTCACATTTTGTGCGTAATTTATTCACA 3 95 1 TTGTGCGTAA 0.838952 -150 CAATGCAAGCTTGTGAATAAATTACGCACA 3 106 0 TTGTGAATAA 0.964844 -139 TGCATTGAACTTGTGGATAAAATCACGGTC 3 129 1 TTGTGGATAA 0.965977 -116 CTGGAAAGTCCTGTGGATAAATCGGGAAAA 4 81 1 CTGTGGATAA 0.95937 -220 TCGGGAAAATCTGTGAGAAACAGAAGATCT 4 102 1 CTGTGAGAAA 0.860688 -199 TTGAACCAATTTGTTAATAAGACAGATTTT 5 39 0 TTGTTAATAA 0.846986 -87 CTTCAAAGTGCGGTGAAAAATTCAACAAAT 7 13 1 CGGTGAAAAA 0.747035 -167 ********** Masking position 4 Map Score: 6.67019 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 96 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 TATTGAGATGCCGGATGCGGCGTA 2 5 1 GAGATGCCGG 0.917346 -229 CCTACAAACCGAGCCGTAGGCCGGATAAGG 2 39 0 GAGCCGTAGG 0.957357 -195 GGAGCCTGATGCGACGCTGGCGCGTCTTAT 2 73 0 GCGACGCTGG 0.992572 -161 CTACAAATCCGAGCCGTAGGCCGGATAAGG 2 126 0 GAGCCGTAGG 0.957357 -108 TGTGCCTGATGCGACGCTGGCGCGTCTTAT 2 161 0 GCGACGCTGG 0.992572 -73 CGATCCTGCCGCGAGGCGGGCACGATTTAC 4 34 0 GCGAGGCGGG 0.962778 -267 CTGCTTGAGGGTGACGCACGAACCGCTGTC 4 203 0 GTGACGCACG 0.902967 -98 ********** Masking position 6 Map Score: 4.19144 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 1013 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 ATATCAATTTATCTAACCTATTATGCCG 1 9 1 TTATCTAACC 0.776978 -292 TAACAAATTTTTCTCTTCCCATTGACTTTC 1 66 1 TTCTCTTCCC 0.967531 -235 CCCGGACACCTTGTCTGACCTAAGGTGCGC 1 95 1 TTGTCTGACC 0.927285 -206 CTGGCGCGTCTTATCAGGCCTACAAACCGA 2 57 0 TTATCAGGCC 0.906395 -177 CTGGCGCGTCTTATCAGGCCTACAAATCCG 2 145 0 TTATCAGGCC 0.906395 -89 AGACAACGGGGTCTCTTTCCCTGCTACGGA 3 45 0 GTCTCTTTCC 0.664678 -200 AGACCCCGTTGTCTCTTCCCGGTATTTCAT 3 61 1 GTCTCTTCCC 0.927605 -184 ATTCACTGTTTTATCAGACCGTGATTTTAT 3 145 0 TTATCAGACC 0.899699 -100 CTGTCTGCGGTTATATGCCCGAGTCAAGAT 4 178 0 TTATATGCCC 0.819476 -123 ACGCCCCTATTGTCTTCCCCAACTTATGG 8 10 1 TTGTCTTCCC 0.953397 -132 TTATGTCGTGCTATCTTCCCCATAAGTTGG 8 29 0 CTATCTTCCC 0.894077 -113 ********** Masking position 4 Map Score: 7.55149 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 386 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 GATAGTGTGAAAATGACCCTCTTGCAAGTG 1 166 0 AAATGACCCT 0.95361 -135 CGCTAAGTGTAAACGATCCTGCCGCGAGGC 4 47 0 AAACGATCCT 0.97351 -254 ACGTACGTCGAAAAGACCCTGCTTGAGGGT 4 221 0 AAAAGACCCT 0.973148 -80 TAAATGCGTGAAAAGATCTTCTAAAAAATC 6 108 0 AAAAGATCTT 0.871135 -84 AAAAGGATCCTTATTGTTTTT 6 181 0 AAAGGATCCT 0.985427 -11 AAGACTGAGGAAAGTATCCTAATTCGTTAT 8 55 0 AAAGTATCCT 0.912704 -87 ********** Masking position 6 Map Score: 3.92622 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 41 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ********** No masking Map Score: -3.52839e-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 12 TGAAAATGACCCTCTTGCAAGTGCATAACTT 1 158 0 CCTTTGCAAG 0.828734 -143 ATGTTTGGGATTCACTGCAAGATAGTGTGAA 1 185 0 TTCCTGCAAG 0.704306 -116 AGCAGCTTCCCGTACTACAGGTAGTCTGCAT 1 238 1 CGTCTACAGG 0.857531 -63 CGGCATTAAACTCCCAACAGGACACACTC 2 215 1 CTCCAACAGG 0.878108 -19 TGCTACGGAACCCATTGCAGGGAAAGAGTAT 3 23 0 CCCTTGCAGG 0.982323 -222 TGCAATGGGTTCCGTAGCAGGGAAAGAGACC 3 35 1 TCCTAGCAGG 0.899775 -210 TCGTGCCCGCCTCGCGGCAGGATCGTTTACA 4 39 1 CTCCGGCAGG 0.934853 -262 CGGTCCCGATCGTTTTGCAGGATCTTGACTC 4 157 1 CGTTTGCAGG 0.951022 -144 CGTGCGTCACCCTCAAGCAGGGTCTTTTCGA 4 213 1 CCTAAGCAGG 0.856199 -88 *** ******* Masking position 9 Map Score: 0.814921 Number of sites scoring better than the average of aligned sites = 1979 Number in coding regions = 1855 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 13 ********** No masking Map Score: -3.52839e-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 14 ********** No masking Map Score: -3.52839e-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 15 TTCAATGCAAGCTTGTGAATAAATTACGCACAA 3 105 0 GCTTAATAAA 0.754175 -140 TCAAATCCTCTCAATCGATATCTTCTGG 3 227 0 TCCTAATCGA 0.715118 -18 ATAAGACAGATTTTATCAATTGAAAGTTCAATT 5 20 0 TTTTAATTGA 0.674264 -106 ATAAAATCTGTCTTATTAACAAATTGGTTCAAT 5 37 1 TCTTAACAAA 0.716168 -89 TTATTTTGGCTTTTGCCAATCAATGTACCTAGT 5 91 0 TTTTAATCAA 0.829761 -35 ATTGTCGGAGATTTTACAATAAATGCGTGAAAA 6 124 0 ATTTAATAAA 0.759094 -68 ATCCTTATTGTTTTTGTAATAGAGAAAAGTGCG 6 163 0 TTTTAATAGA 0.936113 -29 TTTTTCTTATTTTTCTAAATAAAAAATTTTAAT 7 54 1 TTTTAATAAA 0.926801 -126 TAAACGGTTTTTGTGAGAATAAAAATTAAAATT 7 78 0 TTGTAATAAA 0.725913 -102 TAGATAACTTATTTAAAAATAAACGGTTTTTGT 7 97 0 ATTTAATAAA 0.759098 -83 TTGATTTGATTCTTGACAATAGATAACTTATTT 7 116 0 TCTTAATAGA 0.944566 -64 TTTATTTATCCTTTAAATAGAACTTATCATT 8 121 0 TCCTAATAGA 0.867044 -21 **** ****** Masking position 8 Map Score: 1.94609 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 81 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899