AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i192_topoisomerase_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 parC 137 DNA topoisomerase IV subunit A #2 parE 28 DNA topoisomerase IV subunit B #3 icc 24 regulator of lacZ #4 yqiE 198 orf, hypothetical protein #5 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #6 HI1528 73 topoisomerase IV, subunit B (parE) #7 HI1529 66 topoisomerase IV, subunit A (parC) Motif number 1 AGCGGCTTCTGCTAGAATCCGCAATAATTTTACAGTTTGA 4 40 0 GAAATCATTT 0.986498 -159 AACGCCCTATGGCACGTAACGCCAACCTTTTGCGGTAGCG 4 76 0 GAGTACCTTT 0.947093 -123 GTGCCATAGGGCGTTAATGTGCCTCAATTTAACACATGAC 4 101 1 GTAATCATTT 0.96396 -98 GTGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGTCAT 4 136 0 GAGTTCCTTT 0.982653 -63 TTTGAGTTGTGGTAAAATCGCCACAATTTTGGTTATTCAA 5 27 0 GAAATCATTT 0.986498 -58 TAAGTTAGGGGCGTAGTTTATCGTAAATTTGAGTTGTGGT 5 54 0 GTGTTCATTT 0.976972 -31 AAGTGCGGTCGAATATCACCGCACTTTTTGATAGAAT 6 8 1 GGATACATTT 0.897464 -66 CGCACTTTTTGATAGAATTTTCTCAAATTTAAAAAATTAA 6 30 1 GAAATCATTT 0.986498 -44 GGTGAGGTTATTCGTTAATTTTTTAAATTTG 6 53 0 GAGTTCATTT 0.991445 -21 * * *** * * *** Masking position 18 Map Score: 10.9722 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 101 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TGCCTTTATCGCCGTCGGAGCACG 1 5 1 TTTATCGCCG 0.984517 -133 GATCAACGTGAATAGCGCCGCCGGACGTGC 1 30 0 AATAGCGCCG 0.993792 -108 TCAAAGGGGCAATATTGCCGGAGATACTAC 1 86 0 AATATTGCCG 0.981661 -52 TGAAGCAGTATTTAGCGCGATCAAACTGTA 4 20 1 TTTAGCGCGA 0.881242 -179 AAACTGTAAAATTATTGCGGATTCTAGCAG 4 42 1 ATTATTGCGG 0.952577 -157 ATTGAGGCACATTAACGCCCTATGGCACGT 4 99 0 ATTAACGCCC 0.919238 -100 TTAATTCACTATTAGTGCCAGGACATTAAC 4 178 1 ATTAGTGCCA 0.961929 -21 GAGTTGTGGTAAAATCGCCACAATTTTGGT 5 34 0 AAAATCGCCA 0.909617 -51 AGTGCGGTCGAATATCACCGCACTTTTTGA 6 12 1 AATATCACCG 0.941216 -62 ********** Masking position 4 Map Score: 10.3206 Number of sites scoring better than the average of aligned sites = 2557 Number in coding regions = 2402 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 CGGACGTGCTCCGACGGCGATAAAGGCA 1 9 0 CCGACGGCGA 0.936544 -129 CGGAGCACGTCCGGCGGCGCTATTCACGTT 1 26 1 CCGGCGGCGC 0.966891 -112 TACTACATTATCTGCCGCGTCGAGTCACAG 1 62 0 TCTGCCGCGT 0.926231 -76 TAATGTAGTATCTCCGGCAATATTGCCCCT 1 82 1 TCTCCGGCAA 0.859256 -56 ATTTTACAGTTTGATCGCGCTAAATACTGC 4 24 0 TTGATCGCGC 0.797641 -175 AGCAGAAGCCGCTACCGCAAAAGGTTGGCG 4 67 1 GCTACCGCAA 0.930438 -132 ACATTAACGCCCTATGGCACGTAACGCCAA 4 91 0 CCTATGGCAC 0.944329 -108 GCGGTGATATTCGACCGCACTT 6 3 0 TCGACCGCAC 0.988871 -71 ********** Masking position 7 Map Score: 5.07519 Number of sites scoring better than the average of aligned sites = 3823 Number in coding regions = 3691 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 4 CCTTTATCGCCGTCGGAGCACGTCCGGCGGCGCTAT 1 13 1 CGTCGACTCG 0.986196 -125 TTATCTGCCGCGTCGAGTCACAGGAGATCAACGTGA 1 49 0 CGTCGACGAG 0.997714 -89 CGTCGTGAAACCTAAGGACACCAT 3 1 1 CGTCGACTAG 0.991418 -24 TGAATTTCAGCGACGTTTGACTGCCGTTTGAGCAGT 4 139 0 CGACGACGCG 0.869394 -60 ***** ** * ** Masking position 10 Map Score: 2.26495 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 33 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 GACGCGGCAGATAATGTAGTATCTCCGGCA 1 71 1 ATAATGTAGT 0.875878 -67 GGTTTAAGTTAGTAATTCGAGTT 2 16 0 TTAAGTTAGT 0.93955 -13 AAATTCACATTTAATTCACTATTAGTGCCA 4 168 1 TTAATTCACT 0.914313 -31 TGTTAATGTCCTGGCACTAATA 4 187 0 TTAATGTCCT 0.895094 -12 AGGTTATTCGTTAATTTTTTAAATTTGAGA 6 50 0 TTAATTTTTT 0.846879 -24 TTTGCTGAGATTAATTTAGT 7 1 0 TTAATTTAGT 0.980587 -66 TGATATATTCTTAATTTATTAAAATTCGGA 7 31 0 TTAATTTATT 0.957299 -36 ********** Masking position 4 Map Score: 3.16315 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 93 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 TCACAGGAGATCAACGTGAATAGCGCCGCCG 1 37 0 TCAACGGAAT 0.985098 -101 CGATCAACTCGAATTACTAACTTA 2 4 1 TCAACTGAAT 0.987614 -25 GGTAGCGGCTTCTGCTAGAATCCGCAATAAT 4 52 0 TCTGCTGAAT 0.939856 -147 AATAGTGAATTAAATGTGAATTTCAGCGACG 4 160 0 TAAATGGAAT 0.934236 -39 TTAAAATCTCTCTATTTGAATAACCAAAATT 5 12 1 TCTATTGAAT 0.964513 -73 TAGTTTATCGTAAATTTGAGTTGTGGTAAAA 5 50 0 TAAATTGAGT 0.862362 -35 ****** **** Masking position 9 Map Score: 2.64828 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 105 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ********** No masking Map Score: -1.28365e-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 8 ********** No masking Map Score: -1.28365e-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 9 ********** No masking Map Score: -1.28365e-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