AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ioxyR_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 dps 298 global regulator, starvation conditions #2 ybiF 300 putative transmembrane subunit #3 yhiR 202 orf, hypothetical protein #4 gor 71 glutathione oxidoreductase #5 katG 300 catalase; hydroperoxidase HPI(I) #6 argC 153 N-acetyl-gamma-glutamylphosphate reductase #7 argH 60 argininosuccinate lyase #8 oxyR 266 activator, hydrogen peroxide-inducible genes #9 HI0161 215 glutathione reductase (gor) #10 HI0162 93 lipoprotein, putative #11 HI0571 122 hydrogen peroxide-inducible genes activator (oxyR) #12 HI1349 273 conserved hypothetical protein Motif number 1 AGACGGTGTAGAGGAAAAGTAGCGAGAAAT 1 48 0 GAGGAAAAGT 0.772961 -251 GTCTGGTGATTAGGAATAATCTGGATGAAT 2 149 0 TAGGAATAAT 0.824581 -152 TAGTCAAAACGGGGGAAAATTTTTTCAACA 2 207 1 GGGGGAAAAT 0.926568 -94 CGAAATGAGGGCGGGAAAATAAGGTTATCA 5 49 1 GCGGGAAAAT 0.872715 -252 TTCAAGTAATGAGGGAGAAAACAAGGCTGA 5 76 0 GAGGGAGAAA 0.819936 -225 GAATGCTTGATAGGGATAATCGTTCATTGC 8 201 1 TAGGGATAAT 0.912164 -66 TTCATGGCGATAGGTAGAATAGCAATGAAC 8 222 0 TAGGTAGAAT 0.809562 -45 TATCTACAGTGAGGAAGATTGAACAATCTT 9 16 1 GAGGAAGATT 0.870523 -200 GATAGAAAAAGAGGAAGATTGTTCAATCTT 9 30 0 GAGGAAGATT 0.870523 -186 TTATAAAAATTAGGCAGAATACAAAAAAAT 9 172 1 TAGGCAGAAT 0.863025 -44 AATTGATTTATGGGGAAATT 10 84 1 TGGGGAAATT 0.769225 -10 TGCTGTATTATAGGGAAAATTATGATATAG 11 49 1 TAGGGAAAAT 0.970469 -74 AATTTTTCTATAGGGAAAATCTC 11 110 1 TAGGGAAAAT 0.970469 -13 AACATATCCTTAGGAAAAATATTAAAAATT 12 11 1 TAGGAAAAAT 0.937009 -263 ********** Masking position 6 Map Score: 12.4954 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 134 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 GCAGATAAATAAGAATTGTTCTTATCAATATATCT 1 128 1 AAATGCTTAT 0.94664 -171 CAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGA 2 86 0 AAATGTTAAA 0.527246 -215 GACAAAGTGTCCTTATCGTTGATTAC 4 56 0 AAATGCTTAT 0.946639 -16 GAGATGTAGATCAAATTGATCTTAATTAAGCTTTT 5 164 0 TAATGCTTAA 0.884541 -137 AGAGAGAAGTTATAATTGAATTAATCCACGGATGC 5 231 0 TAATGTTAAT 0.911796 -70 GATGATTAGTTTGAAATGATTTTATGTGAAGCCTA 9 81 0 TAATGTTTAT 0.938218 -135 TATAAATTGATGTAATTGGTTTTATGAATATTTTT 9 130 0 TAATGTTTAT 0.939317 -86 ATAAATCAATTAGAATTGTGCTATTCTTACAAACT 10 60 0 TAATGCTATT 0.898313 -34 ATTCTATTCTTTTAATTGAATTTTTCTATAGGGAA 11 92 1 TAATGTTTTT 0.829762 -31 TATTAAAAATTATAACTGTACTTATTAAATCAAAA 12 30 1 TAATGCTTAT 0.971592 -244 TAATTTGAAGTGAAATTGTTCTATTCAATATAATT 12 178 0 TAATGCTATT 0.898312 -96 TTTCTAGTTGAATAATTGAGCTAATGCCCTCCCTT 12 237 0 AAATGCTAAT 0.927237 -37 * ** ** ***** Masking position 5 Map Score: 9.82533 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 44 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TTATCTGCTCGCCAGGAATTTTCGGAATAA 1 106 0 GCCAGGAATT 0.75597 -193 GATAGGAACAGCCAGAATAGCGGAACACAT 1 218 1 GCCAGAATAG 0.851121 -81 ACTAAAATGCGCCAGGATTGATGGAATCAT 2 181 0 GCCAGGATTG 0.988614 -120 CAAATGCTCAACCAGCATTGGGTATATCCA 2 235 1 ACCAGCATTG 0.915751 -66 AACCTCTTTAACCAGGACTGCGCGA 3 6 0 ACCAGGACTG 0.866794 -197 AGAGGCCGCCGCCGCGAAAGCGTAACGTTT 3 106 0 GCCGCGAAAG 0.926651 -97 CGTAATAGGTGCCAGCAATGGCTGCAA 4 8 0 GCCAGCAATG 0.945781 -64 ATCGTTGATTACCGCGATTGTAGCGCGAGA 4 38 0 ACCGCGATTG 0.930323 -34 GGCGCAGCTTTCCGGCATTGAATTTCAAAA 7 26 1 TCCGGCATTG 0.800921 -35 ATCCTCCATCGCCACGATAGTTCATGGCGA 8 242 0 GCCACGATAG 0.967568 -25 TTTATTGTTAGCCGCGATAGTTTGATTAAA 12 65 1 GCCGCGATAG 0.965399 -209 ********** Masking position 7 Map Score: 9.75112 Number of sites scoring better than the average of aligned sites = 1134 Number in coding regions = 1059 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 ATTAACGAGATTAAGTATAGCACCGGCTATGT 1 244 0 TTAGTTAGCA 0.918443 -55 TCGCGATTTGTGATGTCTAACGGGCCATTTCA 2 26 1 TGAGTTAACG 0.82239 -275 ATATCTAGACTTAAGTAAAGCGTGGAGTGTAC 2 265 0 TTAGTAAGCG 0.981447 -36 GCTACACACATTATGTAAAGCGCCTGTTGAGC 3 44 0 TTAGTAAGCG 0.981447 -159 TAGCATGGGGTTAAGTGTAGTGAATTTCAATG 3 72 1 TTAGTTAGTG 0.898069 -131 CTGGCACCTATTACGTCTCGCGCTACAATCGC 4 23 1 TTAGTTCGCG 0.954609 -49 AAAAATACACTAACGTTGAGCGTAATAAAACC 6 65 1 TAAGTGAGCG 0.907455 -89 GGTGAATGTTTTACGTTTAACCTGGCAACCAG 6 109 1 TTAGTTAACC 0.84152 -45 TGAAATGATTTTATGTGAAGCCTAGTATGTAG 9 73 0 TTAGTAAGCC 0.941564 -143 ACTTCCTTATTAATGTATAGCGTTTCATTTTA 10 31 0 TAAGTTAGCG 0.969575 -63 *** ** ***** Masking position 6 Map Score: 7.19811 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 121 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTTGTTTTTCACGCTTGTTACCACTATTAG 1 185 1 ACGCTTGTTA 0.509153 -114 GCGCTTCCTTAACCTCTTTAACCAGGACTG 3 16 0 AACCTCTTTA 0.67446 -187 TCGCGGCGGCGGCCTCTTTTCGGTATACTG 3 119 1 GGCCTCTTTT 0.891062 -84 TTATTTTCCCGCCCTCATTTCGAGGCAGCA 5 41 0 GCCCTCATTT 0.694538 -260 CAAGGCTGATAACCTTATTTTCCCGCCCTC 5 55 0 AACCTTATTT 0.793392 -246 TAAGGTTATCAGCCTTGTTTTCTCCCTCAT 5 68 1 AGCCTTGTTT 0.917622 -233 TGAAGCTAAAACCCTTTTTTATAAAGCATT 5 111 1 ACCCTTTTTT 0.946766 -190 GATCTTAATTAAGCTTTTTTGATTATGTCC 5 152 0 AAGCTTTTTT 0.862983 -149 GCTTATCGCCGGGCTTTTTTATGGCAAAAA 8 40 1 GGGCTTTTTT 0.835491 -227 TCTCCAGGATCCGCTTTTTTTTGCCATAAA 8 57 0 CCGCTTTTTT 0.777116 -210 AACGGAGCGGCACCTCTTTTAACCCTTGAA 8 150 0 CACCTCTTTT 0.813491 -117 AGTTTGAACCTTTTTTAAACTAAAAT 9 200 0 AACCTTTTTT 0.932498 -16 TGATAGTCTTAGCCTTGTTTGTTAAGAAAT 12 149 0 AGCCTTGTTT 0.917622 -125 ********** Masking position 5 Map Score: 6.16847 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 406 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 6 ATGGTTATGCATAACCATGCAGAAATGTAAA 1 12 0 ATAACATGCA 0.902266 -287 ATGGTTATGCATAACCATGCAGAATTTCTCG 1 25 1 ATAACATGCA 0.902266 -274 AATTTTCGGAATAAATATGCTTTTGCATAAT 1 89 0 ATAAAATGCT 0.785277 -210 TATATTGATAAGAACAATTCTTATTTATCTG 1 129 0 AGAACATTCT 0.609727 -170 AACAAAACTAATAAAGATTCAATGAGTTAGA 1 160 0 ATAAAATTCA 0.953912 -139 TCATGATAGTATCAATATTCATGCAGTATTT 6 28 1 ATCAAATTCA 0.795856 -126 GTATTTATGAATAAAAATACACTAACGTTGA 6 53 1 ATAAAATACA 0.787685 -101 AGGTTAAACGTAAAACATTCACCTTACGGCT 6 101 0 TAAAAATTCA 0.618761 -53 CAAAAGAGTAAAAAATATTCATAAAACCAAT 9 120 1 AAAAAATTCA 0.8674 -96 TTTTCCCTATAGAAAAATTCAATTAAAAGAA 11 98 0 AGAAAATTCA 0.909488 -25 GATAGTTTGATTAAATATTCATTAAAACTGT 12 80 1 TTAAAATTCA 0.837008 -194 ***** ***** Masking position 7 Map Score: 3.81752 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 105 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 TCCGAAAATTCCTGGCGAGCAGATAAATAAGA 1 110 1 CCTGGCGACG 0.997755 -189 TTACGTTTAACCTGGCAACCAGACATAAGAAG 6 119 1 CCTGGCAACG 0.988592 -35 CATAAAAAAGCCCGGCGATAAGCCAGGCTCAA 8 31 0 CCCGGCGAAG 0.989026 -236 AAAAGCGGATCCTGGAGATCCGCAAAAGTTCA 8 69 1 CCTGGAGACG 0.988653 -198 CACGATAGTTCATGGCGATAGGTAGAATAGCA 8 228 0 CATGGCGAAG 0.959879 -39 ******** * * Masking position 8 Map Score: 2.50998 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 173 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TGGTTGAGCATTTGTTGAAAAAATTTTCCCC 2 218 0 TTTGTTAAAA 0.962491 -83 CATTTTGTGCTCTGTTTAAAATTTGTGATCA 5 12 0 TCTGTTAAAA 0.94535 -289 GAACAGATGATTAGTTTGAAATGATTTTATG 9 90 0 TTAGTTGAAA 0.774833 -126 AAACTAATCATCTGTTCAAAAGAGTAAAAAA 9 104 1 TCTGTTAAAA 0.94535 -112 CAAAAAAATTTTAGTTTAAAAAAGGTTCAAA 9 193 1 TTAGTTAAAA 0.917919 -23 CATTTTAGTTTTTGTGGAGAACTTATA 10 7 0 TTTGTGAGAA 0.841842 -87 CTTAGCCTTGTTTGTTAAGAAATTGTAATAA 12 141 0 TTTGTTAGAA 0.945262 -133 ****** **** Masking position 10 Map Score: 0.898013 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 35 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 ********** No masking Map Score: -4.71557e-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 10 ********** No masking Map Score: -4.71557e-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 11 ********** No masking Map Score: -4.71557e-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