AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -idnaA_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 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 ftsY 149 cell division membrane protein #5 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #6 HI0266 82 conserved hypothetical protein #7 HI0267 41 nitrate/nitrite sensor protein (narQ) #8 HI0269 125 RNA polymerase sigma-32 factor (rpoH) #9 HI0993 191 chromosomal replication initiator protein (dnaA) #10 HI0994 27 transferrin-binding protein 1 precursor (tbp1) #11 HI0995 97 transferrin-binding protein 2 precursor (tbp2) #12 HI1655 71 antigen #13 HI1658 56 hemolysin, putative #14 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #15 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) Motif number 1 TATTGAGATGCCGGATGCGGCGTAAACGCCTT 2 10 1 GCCGATGGCG 0.99842 -224 CGAGCCGTAGGCCGGATAAGGCGTTTACGCCGC 2 27 0 GCCGATAGCG 0.9987 -207 CGGTTTGTAGGCCTGATAAGACGCGCCAGCGTC 2 58 1 GCCGATAGCG 0.9987 -176 GGCACCCGGAGCCTGATGCGACGCTGGCGCGTC 2 77 0 GCCGATGGCG 0.99842 -157 GGCTCCGGGTGCCGGATGCAGCGTGAACGCCTT 2 97 1 GCCGATGACG 0.993653 -137 CGAGCCGTAGGCCGGATAAGGCGTTCACGCTGC 2 114 0 GCCGATAGCG 0.9987 -120 GGATTTGTAGGCCTGATAAGACGCGCCAGCGTC 2 146 1 GCCGATAGCG 0.9987 -88 CGCATCCTGTGCCTGATGCGACGCTGGCGCGTC 2 165 0 GCCGATGGCG 0.99842 -69 GGAGTTTAATGCCGGATAAGGCATTTTACGCCG 2 196 0 GCCGATAGCA 0.99598 -38 TAAAATCACGGTCTGATAAAACAGTGAATGATA 3 146 1 GTCGATAACA 0.814947 -99 TGCTCAATCCGCCAGATAACACATACTTGCAGG 4 18 1 GCCGATACCA 0.972975 -132 ATTAAAATGCGCCAGATAGATTAAATATGCTAT 9 11 1 GCCGATAATA 0.814947 -181 *** **** * ** Masking position 6 Map Score: 41.0204 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 117 Number in noncoding regions = 577 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 2 AAAAGTGGCTTTCGCGCACCTTAGGTCAGACA 1 106 0 TTGCGCACTT 0.986072 -195 TGATGCGACGCTGGCGCGTCTTATCAGGCCTA 2 65 0 CTGCGCGCTT 0.981016 -169 TGATGCGACGCTGGCGCGTCTTATCAGGCCTA 2 153 0 CTGCGCGCTT 0.981016 -81 CAGAAGATCTCTTGCGCAGTTTAGGCTATGAT 5 122 1 CTGCGCATTT 0.993103 -179 AAATTTTACCGCACTTTTCTAAATTTC 7 6 1 TTCCGCATTT 0.984489 -36 TTTAATCTATCTGGCGCATTTTAAT 9 4 0 CTGCGCATTT 0.993103 -188 CTATACAATACTGGCGCATTTTTTTCTGTTCT 9 46 1 CTGCGCATTT 0.993103 -146 CCGACAATTTTTACCGCACTTTTCTCTATTAC 9 149 1 TTCCGCATTT 0.984489 -43 GTTGAATTTTTCACCGCACTTTGAAGGA 14 7 0 TCCCGCATTT 0.922797 -173 CAACAAATTTTTACCGCACTTTTTCTTATTTT 14 35 1 TTCCGCATTT 0.984489 -145 CCCCTATTGTCTTCCCCAACTTATGGGGAAGA 15 14 1 CTCCCCACTT 0.929501 -128 ** ***** *** Masking position 11 Map Score: 23.2254 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 197 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 ATGAAACTATTGCGGAAAGAATTCCAAAAAC 1 267 1 TGCGGAAGAA 0.955365 -34 AGATGCCGGATGCGGCGTAAACGCCTTATCC 2 16 1 TGCGGGTAAA 0.987728 -218 GGGTGCCGGATGCAGCGTGAACGCCTTATCC 2 103 1 TGCAGGTGAA 0.848784 -131 AGGCACAGGATGCGGCGTAAAATGCCTTATC 2 184 1 TGCGGGTAAA 0.987728 -50 GGGAGTTTAATGCCGGATAAGGCATTTTACG 2 199 0 TGCCGATAAG 0.821798 -35 CGGAACCCATTGCAGGGAAAGAGTATAACAC 3 18 0 TGCAGGAAAG 0.958113 -227 TGGGTTCCGTAGCAGGGAAAGAGACCCCGTT 3 40 1 AGCAGGAAAG 0.70881 -205 TTTTCCAATATGCGGCGTAAATCGTGCCCGC 5 18 1 TGCGGGTAAA 0.987728 -283 TTTAGAAAAGTGCGGTAAAATTT 7 3 0 TGCGGAAAAT 0.914384 -39 TTACAATAAATGCGTGAAAAGATCTTCTAAA 9 113 0 TGCGTAAAAG 0.785914 -79 TAGAGAAAAGTGCGGTAAAAATTGTCGGAGA 9 146 0 TGCGGAAAAA 0.985454 -46 TCCTTCAAAGTGCGGTGAAAAATTCAACAAA 14 11 1 TGCGGGAAAA 0.992123 -169 TAAGAAAAAGTGCGGTAAAAATTTGTTGAAT 14 32 0 TGCGGAAAAA 0.985454 -148 ***** ***** Masking position 10 Map Score: 21.3395 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 483 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 GGCCTGATAAGACGCGCCAGCGTCGCATCA 2 67 1 GACGCGCCAG 0.993292 -167 GGCCTGATAAGACGCGCCAGCGTCGCATCA 2 155 1 GACGCGCCAG 0.993292 -79 GGTAGCAACAACTGTGCCAGAGCTTAAGAG 3 188 0 ACTGTGCCAG 0.970582 -57 TGCTACCACTGAAGCGCCAGAAGATATCGA 3 211 1 GAAGCGCCAG 0.981914 -34 TAAATTGCTCAATCCGCCAGATAACACATA 4 13 1 AATCCGCCAG 0.967229 -137 TAGCGTTAACGCTGTGCCATGAAGCAACAG 4 112 1 GCTGTGCCAT 0.806356 -38 CATAGCCTAAACTGCGCAAGAGATCTTCTG 5 122 0 ACTGCGCAAG 0.942438 -179 ATTAAAATGCGCCAGATAGATTAAA 9 6 1 AATGCGCCAG 0.995092 -186 AACAGAAAAAAATGCGCCAGTATTGTATAG 9 46 0 AATGCGCCAG 0.995092 -146 ********** Masking position 9 Map Score: 16.7678 Number of sites scoring better than the average of aligned sites = 1317 Number in coding regions = 1246 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TCCCATTGACTTTCCCGGACACCTTGTCTG 1 82 1 TTTCCCGGAC 0.958452 -219 AAAAAGTGGCTTTCGCGCACCTTAGGTCAG 1 109 0 TTTCGCGCAC 0.95831 -192 ATGTTTGGGATTCACTGCAAGATAGTGTGA 1 186 0 TTCACTGCAA 0.879793 -115 GTTATACTCTTTCCCTGCAATGGGTTCCGT 3 20 1 TTCCCTGCAA 0.877444 -225 AAATTTTACCGCACTTTTCTAAAT 7 5 1 TTTACCGCAC 0.993043 -37 TCCGACAATTTTTACCGCACTTTTCTCTAT 9 148 1 TTTACCGCAC 0.993043 -44 TGTTGAATTTTTCACCGCACTTTGAAGGA 14 10 0 TTCACCGCAC 0.992902 -170 TCAACAAATTTTTACCGCACTTTTTCTTAT 14 34 1 TTTACCGCAC 0.993043 -146 ********** Masking position 9 Map Score: 12.4054 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 180 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TGGCTTTCGCGCACCTTAGGTCAGACAAGGTGTC 1 99 0 GCCTAGGTCG 0.913167 -202 CCTACAAACCGAGCCGTAGGCCGGATAAGGCGTT 2 35 0 GCCGAGGCCG 0.997871 -199 CCTACGGCTCGGTTTGTAGGCCTGATAAGACGCG 2 49 1 GTTGAGGCCG 0.987379 -185 GTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTG 2 88 1 GCCGGTGCCG 0.992174 -146 CTACAAATCCGAGCCGTAGGCCGGATAAGGCGTT 2 122 0 GCCGAGGCCG 0.997871 -112 CTACGGCTCGGATTTGTAGGCCTGATAAGACGCG 2 137 1 GTTGAGGCCG 0.987379 -97 ATTTTACGCCGCATCCTGTGCCTGATGCGACGCT 2 173 0 GTCCGTGCCG 0.925406 -61 GTCCTGTTGGGAGTTTAATGCCGGATAAGGCATT 2 204 0 GTTTATGCCG 0.854328 -30 TTTAGGCTATGATCCGCGGTCCCGATCGTTTTGC 5 141 1 GCCGGGTCCG 0.974309 -160 * *** ***** * Masking position 12 Map Score: 11.5893 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 292 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ATTTGTTAAAAATAACTGTTCGGCGATTTCTT 1 42 0 AATAATGTTG 0.739862 -259 TGGGAAGAGAAAAATTTGTTAAAAATAACTGT 1 55 0 AAAATTGTTA 0.810938 -246 ATAGCAGCTAAAAAAATGATGAAATAGTCTAT 4 75 0 AAAAATGATA 0.958084 -75 TTATTCTACCCAAAATTGATAGCATACGCCTA 6 33 0 CAAAATGATG 0.814792 -50 CTCCAGCAAGAAAAACTGTTCGTTATTCTACC 6 55 0 AAAAATGTTG 0.938104 -28 AAAGTGCGGTAAAAATTGTCGGAGATTTTACA 9 139 0 AAAAATGTCG 0.688561 -53 CCATGAACTTAAAAAATTATAAGTTGACATTA 11 18 1 AAAAATTATA 0.805597 -80 TATTACAAAAAAAAAATGATAATGCGAACAAT 11 48 1 AAAAATGATA 0.958084 -50 TATTCTTATACAAAATTGATAATTGTTCGCAT 11 69 0 CAAAATGATA 0.86902 -29 AAGTGCGGTAAAAATTTGTTGAATTTTTCACC 14 24 0 AAAATTGTTA 0.810938 -156 TTTTCTAAATAAAAAATTTTAATTTTTATTCT 14 64 1 AAAAATTTTA 0.805544 -116 TTATTCTCACAAAAACCGTTTATTTTTAAATA 14 89 1 AAAAACGTTA 0.769281 -91 AATCAAATCAAAAAATTTATTACTTGCGATCT 14 138 1 AAAAATTATA 0.805597 -42 GGGAAAGCTAAATAAATGATAAGTTCTATTTA 15 107 1 AATAATGATA 0.810938 -35 ***** **** * Masking position 4 Map Score: 9.92575 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 186 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 CCACTTTTTCCTTCCTGAGTTATCCACAAAGTTATGCA 1 130 1 CTTCTTCACA 0.952815 -171 CTTCCCGGTATTTCATCTCTATGTCACATTTTGTGCGT 3 75 1 TTTCTTCACA 0.960039 -170 GTCACATTTTGTGCGTAATTTATTCACAAGCTTGCATT 3 97 1 GTGCTTCACA 0.966109 -148 TCTCACAGATTTTCCCGATTTATCCACAGGACTTTCCA 5 82 0 TTTCCTCACA 0.833618 -219 CTGCGCAAGAGATCTTCTGTTTCTCACAGATTTTCCCG 5 103 0 GATCTTCACA 0.988143 -198 CGTTTTGCAGGATCTTGACTCGGGCATATAACCGCAGA 5 167 1 GATCTTCATA 0.935091 -134 GCAGACAGCGGTTCGTGCGTCACCCTCAAGCAGGGTCT 5 200 1 GTTCTTCTCA 0.944956 -101 GCCAATCAATGTACCTAGTTATAGCACAATAAGCTATC 8 72 0 GTACTTCACA 0.950576 -54 AGTCGTAGCAGATCTTACTTATCTCATAACTTAAAAGC 12 19 0 GATCTTCATA 0.935091 -53 TATTACTTGCGATCTTTTCTCAAACACATTATCTT 14 155 1 GATCTTCACA 0.988143 -25 **** * * **** Masking position 10 Map Score: 6.86111 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 34 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AAGGTGTCCGGGAAAGTCAATGGGAAGAGAAAAAT 1 72 0 GGAAATCGGA 0.994637 -229 GTAGTCTGCATGAAACTATTGCGGAAAGAATTCCA 1 258 1 TGAAATAGGA 0.9065 -43 AGCGAGTTCTGGAAAGTCCTGTGGATAAATCGGGA 5 73 1 GGAAATCGGA 0.994637 -228 GGATAAATCGGGAAAATCTGTGAGAAACAGAAGAT 5 95 1 GGAAATCAGA 0.984294 -206 AGGAAACTCCAGTGGAAATTTAGAAA 7 26 0 GGAAATCGGA 0.994637 -16 GTTTATCAGGGGAAACTATCAAAGACTGAGGAAAG 15 71 0 GGAAATAAGA 0.954907 -71 ***** ** *** Masking position 7 Map Score: 4.9572 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 10 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ATATCAATTTATCTAACCTATTATG 1 6 1 AATTTATCTA 0.923513 -295 TTTCCTTCCTGAGTTATCCACAAAGTTATG 1 136 1 GAGTTATCCA 0.814329 -165 TTTTGTGCGTAATTTATTCACAAGCTTGCA 3 103 1 AATTTATTCA 0.674537 -142 TCAGACCGTGATTTTATCCACAAGTTCAAT 3 132 0 ATTTTATCCA 0.959551 -113 AGATTTTCCCGATTTATCCACAGGACTTTC 5 84 0 GATTTATCCA 0.910716 -217 AATAAGACAGATTTTATCAATTGAAAGTTC 8 24 0 ATTTTATCAA 0.785862 -102 GATATAGCATATTTAATCTATCTGGCGCAT 9 17 0 ATTTAATCTA 0.77045 -175 ATTTTATCCATGAACTTAAA 11 1 1 ATTTTATCCA 0.959551 -97 ACTAATAGTAATTTAATCTAAAAAGGAGTT 13 33 1 ATTTAATCTA 0.77045 -24 ATTTTTAAATAAGTTATCTATTGTCAAGAA 14 110 1 AAGTTATCTA 0.838489 -70 ********** Masking position 6 Map Score: 5.75508 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 194 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 11 CCTACAAACCGAGCCGTAGGCCGGATAAGGC 2 38 0 GACCGTAGGC 0.972511 -196 CCTACGGCTCGGTTTGTAGGCCTGATAAGAC 2 49 1 GGTTGTAGGC 0.972372 -185 CTACAAATCCGAGCCGTAGGCCGGATAAGGC 2 125 0 GACCGTAGGC 0.972511 -109 CTACGGCTCGGATTTGTAGGCCTGATAAGAC 2 137 1 GATTGTAGGC 0.987362 -97 AGATAACACATACTTGCAGGCGGTGATGTGA 4 31 1 TATTGCAGGC 0.934818 -119 GGTCCCGATCGTTTTGCAGGATCTTGACTCG 5 158 1 GTTTGCAGGA 0.785174 -143 TCCTCTAAAATTATTGTAGGCGTATGCTATC 6 17 1 TTTTGTAGGC 0.919505 -66 ** ******** Masking position 8 Map Score: 2.64075 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 158 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 GGAAAGTCAATGGGAAGAGAAAAATTTGTT 1 67 0 TGGGAAGAGA 0.877085 -234 CAAGGTGTCCGGGAAAGTCAATGGGAAGAG 1 78 0 GGGAAAGTCA 0.858133 -223 CCTAAGGTGCGCGAAAGCCACTTTTTCCTT 1 113 1 GCGAAAGCCA 0.786614 -188 ACCTGTAGTACGGGAAGCTGCTTAGAACAC 1 230 0 CGGGAAGCTG 0.734923 -71 ACCCATTGCAGGGAAAGAGTATAACACGCT 3 15 0 GGGAAAGAGT 0.84338 -230 TTCCGTAGCAGGGAAAGAGACCCCGTTGTC 3 44 1 GGGAAAGAGA 0.974535 -201 GATGAAATACCGGGAAGAGACAACGGGGTC 3 62 0 CGGGAAGAGA 0.951132 -183 CCCATAAGTTGGGGAAGACAATAGGGGCGT 15 11 0 GGGGAAGACA 0.982274 -131 CCCAACTTATGGGGAAGATAGCACGACATA 15 28 1 GGGGAAGATA 0.978673 -114 CTGTTTATCAGGGGAAACTATCAAAGACTG 15 78 0 GGGGAAACTA 0.796639 -64 CTGATAAACAGGGAAAGCTAAATAAATGAT 15 97 1 GGGAAAGCTA 0.963154 -45 ********** Masking position 5 Map Score: 9.84311 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 303 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 CGAACAGTTATTTTTAACAAATTTTTCTCTT 1 52 1 TTTTTACAAA 0.65061 -249 TTTACGCCGCATATTGGAAAATTTAATG 5 8 0 ATATTGAAAA 0.726591 -293 GAAAGTTCAATTATTATAAAA 8 1 0 TTATTAAAAA 0.937391 -125 AAAATCTGTCTTATTAACAAATTGGTTCAAT 8 39 1 TTATTACAAA 0.92521 -87 CTAGGTACATTGATTGGCAAAAGCCAAAATA 8 92 1 TGATTGCAAA 0.740795 -34 TTTCACGCATTTATTGTAAAATCTCCGACAA 9 125 1 TTATTGAAAA 0.936683 -67 GCACTTTTCTCTATTACAAAAACAATAAGGA 9 164 1 CTATTAAAAA 0.80072 -28 TAAGTTGACATTATTACAAAAAAAAAATGAT 11 37 1 TTATTAAAAA 0.937391 -61 AATAGATAACTTATTTAAAAATAAACGGTTT 14 101 0 TTATTTAAAA 0.735621 -79 ****** **** Masking position 5 Map Score: 1.89089 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 64 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 CACTTGCAAGAGGGTCATTTTCACACTATC 1 166 1 AGGGTCATTT 0.939668 -135 GCCTCGCGGCAGGATCGTTTACACTTAGCG 5 47 1 AGGATCGTTT 0.965331 -254 ACCCTCAAGCAGGGTCTTTTCGACGTACGT 5 221 1 AGGGTCTTTT 0.964864 -80 GATTTTTTAGAAGATCTTTTCACGCATTTA 9 108 1 AAGATCTTTT 0.836684 -84 AAAAACAATAAGGATCCTTTT 9 181 1 AGGATCCTTT 0.980856 -11 ATAACGAATTAGGATACTTTCCTCAGTCTT 15 55 1 AGGATACTTT 0.887942 -87 ********** Masking position 5 Map Score: 2.43658 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 15 AGTTATGCACTTGCAAGAGGGTCATTTTCAC 1 159 1 TTGCAGAGGG 0.961578 -142 CGAAAAGACCCTGCTTGAGGGTGACGCACGA 5 212 0 CTGCTGAGGG 0.988875 -89 TTATCGACTTTTGTTCGAGTGGAGTCCGCC 5 281 1 TTGTTGAGTG 0.935965 -20 ACAGTTTTTCTTGCTGGAGTGCAAA 6 68 1 TTGCTGAGTG 0.987059 -15 GTTCTATAATCTGCTTAAGTGAAAGGTCAAA 9 73 1 CTGCTAAGTG 0.940399 -119 ***** ***** Masking position 8 Map Score: 0.438668 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 19 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701