AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i192_topoisomerase_ecoli_hinf_reg_300.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 b3020 132 putative transport periplasmic protein #3 b3022 204 orf, hypothetical protein #4 b3023 52 orf, hypothetical protein #5 ygiW 151 orf, hypothetical protein #6 parE 28 DNA topoisomerase IV subunit B #7 icc 24 regulator of lacZ #8 yqiE 198 orf, hypothetical protein #9 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #10 HI1528 73 topoisomerase IV, subunit B (parE) #11 HI1529 66 topoisomerase IV, subunit A (parC) Motif number 1 TCTGCCGCGTCGAGTCACAGGAGATCAACGTGA 1 49 0 CGATCCGGAG 0.916193 -89 ACTCGCTTTTTTCTTTACCGGAGTGTGAGCCAA 2 31 1 TTCTTCGGAG 0.948 -102 GGTATTCCTTACCGGAGAAATTATAAG 2 116 0 TTCTTCGGAG 0.946392 -17 TGCCTGACTCCAGCTTCCCTTAT 3 1 1 TGCTGCCCAG 0.775904 -204 ACCTAAAAGGTTAATTACAGCAATGAAAAAGCA 3 152 0 TTATTCGCAA 0.936644 -53 TTCCCGGGAACGCGTCCCGGGAGCGGTAACAA 4 10 0 CGCTCCGGAG 0.946073 -43 CCCTGCGAAATTATTCCCGGGAACGCGTCCCGG 4 23 0 TTATCCGGAA 0.968155 -30 TTTGCCTCCCTGCGAAATTATTCCC 4 38 0 TGCTCCGCGA 0.973059 -15 TTTTTCATCCCTGCGATAACCGTATT 5 4 1 TTCTCCGCGA 0.967446 -148 ACAACACGGTTTACTGGCAGCAAATACGGTTAT 5 26 0 TTATGCGCAA 0.930907 -126 CGCTAAATACTGCTTCACCACAAGGA 8 4 0 TGCTCCACAA 0.837911 -195 GAATTAAATGTGAATTTCAGCGACGTTTGACTG 8 152 0 TGATTCGCGA 0.892111 -47 TAATTCACTATTAGTGCCAGGACATTAACA 8 179 1 TTATGCGGAC 0.75796 -20 ACTAAATTAATCTCAGCAAATCCGAATTT 11 7 1 TTATCCGCAA 0.975749 -60 *** ** * **** Masking position 5 Map Score: 13.2149 Number of sites scoring better than the average of aligned sites = 1648 Number in coding regions = 1506 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 2 ACGTGCTCCGACGGCGATAAAGGCA 1 5 0 ACGGCGATAA 0.916665 -133 AGCACGTCCGGCGGCGCTATTCACGTTGATC 1 29 1 GCGGCGCTAT 0.982407 -109 GGCAATATTGCCGGAGATACTACATTATCTG 1 78 0 CCGGAGATAT 0.982384 -60 CCTTTGAAGGCTGGCGAATAAGTTGAGGAAT 1 109 1 CTGGCGAATA 0.589364 -29 GTATTCCTTACCGGAGAAATTATAAGCCCAA 2 111 0 CCGGAGAAAT 0.951986 -22 CTGCTTCAAACTGGCGCTACTAATGCGCCAC 3 40 1 CTGGCGCTAT 0.975959 -165 AGTTAGATGTACGGAGATAGTGACCACACAA 3 110 0 ACGGAGATAT 0.916537 -95 TTTGCCTCCCTGCGAAATTATTCCCGGGA 4 34 0 CCTGCGAAAT 0.917501 -19 TTTTTCATCCCTGCGATAACCGTATTTGCT 5 10 1 CCTGCGATAC 0.867084 -142 TGTTAATGTCCTGGCACTAATAGTGAATTAA 8 178 0 CTGGCACTAT 0.74443 -21 AACCAAAATTGTGGCGATTTTACCACAACTC 9 33 1 GTGGCGATTT 0.878324 -52 ATCAAAAAGTGCGGTGATATTCGACCGCACT 10 12 0 GCGGTGATAT 0.907342 -62 ********* * Masking position 4 Map Score: 9.64837 Number of sites scoring better than the average of aligned sites = 3810 Number in coding regions = 3595 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 3 GGCTGGCGAATAAGTTGAGGAATCAGAATT 1 117 1 TAAGTTGAGG 0.959239 -21 TCACTCGCGATAAGTTTGAGCGAACAATGC 2 65 1 TAAGTTTGAG 0.976207 -68 AGTCATGTGTTAAATTGAGGCACATTAACG 8 112 0 TAAATTGAGG 0.937367 -87 TAGTTTATCGTAAATTTGAGTTGTGGTAAA 9 51 0 TAAATTTGAG 0.96309 -34 GTAAGTTAGGGGCGTAGTTTA 9 74 0 TAAGTTAGGG 0.962312 -11 GTTAATTTTTTAAATTTGAGAAAATTCTAT 10 41 0 TAAATTTGAG 0.96309 -33 ********** Masking position 5 Map Score: 4.59151 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 21 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 GCAATATTGCCCCTTTGAAGGCTGGCGAATA 1 98 1 CCCTTTGAGG 0.959906 -40 CTTAAAGAATACGTTTTGTGTGGTCACTATC 3 95 1 ACGTTTTGGT 0.938404 -110 CATCTAACTAACCTTTTAGGTGCTTTTTCAT 3 132 1 ACCTTTTAGT 0.93569 -73 GCTGTAATTAACCTTTTAGGTTATAACTAAA 3 164 1 ACCTTTTAGT 0.93569 -41 GTTTATTACTCCCTTTAATGTCTGTTTCCGA 5 131 0 CCCTTTAAGT 0.920632 -21 CGTAACGCCAACCTTTTGCGGTAGCGGCTTC 8 71 0 ACCTTTTGGG 0.981661 -128 ******** ** Masking position 6 Map Score: 3.06275 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 41 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TTAGGTTATAACTAAAGTAACAGGGAGGCG 3 179 1 ACTAAAGTAA 0.929769 -26 TTCTTAAGGGAAAAAAATAAAATTTAGTGC 5 74 0 AAAAAAATAA 0.752756 -78 AACTCGAATTACTAACTTAAACC 6 16 1 ACTAACTTAA 0.914862 -13 TCTCAAATTTAAAAAATTAACGAATAACCT 10 50 1 AAAAAATTAA 0.90923 -24 ACTAAATTAATCTCAGCAAA 11 1 1 ACTAAATTAA 0.967092 -66 TCCGAATTTTAATAAATTAAGAATATATCA 11 31 1 AATAAATTAA 0.949212 -36 ********** Masking position 5 Map Score: 2.35329 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 50 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 ACTACATTATCTGCCGCGTCGAGTCACAGG 1 61 0 CTGCCGCGTC 0.958628 -77 TCAACTTATTCGCCAGCCTTCAAAGGGGCA 1 105 0 CGCCAGCCTT 0.942399 -33 AAGCGAGTTGCCCCCGCTTTTCCATTAA 2 9 0 CCCCCGCTTT 0.984337 -124 TGCCTGACTCCAGCTTCCCTTATAAAT 3 8 1 CTCCAGCTTC 0.987091 -197 CCCTTATAAATTCCTGCTTCAAACTGGCGC 3 27 1 TTCCTGCTTC 0.87027 -178 AACCCCCGCCTCCCTGTTACTT 3 193 0 CCCCCGCCTC 0.995044 -12 ********** Masking position 9 Map Score: 2.36471 Number of sites scoring better than the average of aligned sites = 660 Number in coding regions = 594 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 AAAGCGGGGGCAACTCGCTTTTTTCTTTAC 2 19 1 CAACTCGCTT 0.97177 -114 AGCCCAACAACAATACGCCTGTGGCATTGT 2 88 0 CAATACGCCT 0.882478 -45 TACTGGCAGCAAATACGGTTATCGCAGGGA 5 18 0 AAATACGGTT 0.835702 -134 GAGCGCGTTACAACACGGTTTACTGGCAGC 5 38 0 CAACACGGTT 0.974689 -114 CGATCAACTCGAATTACTAACTTA 6 5 1 CAACTCGAAT 0.957002 -24 GATTTTACCACAACTCAAATTTACGATAAA 9 48 1 CAACTCAAAT 0.742726 -37 TAATTTATTAAAATTCGGATTTGCTGAGAT 11 20 0 AAATTCGGAT 0.868827 -47 ********** Masking position 3 Map Score: 0.470116 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 394 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 GACGTGCTCCGACGGCGATAAAGGCA 1 6 0 GAGGCGATAA 0.950502 -132 GAGCACGTCCGGCGGCGCTATTCACGTTGAT 1 28 1 GGGGCGCTAT 0.96388 -110 CCTGCTTCAAACTGGCGCTACTAATGCGCCA 3 39 1 ACGGCGCTAC 0.912799 -166 ACCGCTCCCGGGACGCGTTCCCGGGAATAAT 4 16 1 GGCGCGTTCC 0.929053 -37 GTGCTGTACAGAGCGCGTTACAACACGGTTT 5 47 0 GACGCGTTAC 0.988137 -105 TTTACAGTTTGATCGCGCTAAATACTGCTTC 8 21 0 GACGCGCTAA 0.981004 -178 GATTCTAGCAGAAGCCGCTACCGCAAAAGGT 8 61 1 GAGCCGCTAC 0.967052 -138 ACCGCAAAAGGTTGGCGTTACGTGCCATAGG 8 80 1 GTGGCGTTAC 0.975531 -119 TTACGTGCCATAGGGCGTTAATGTGCCTCAA 8 97 1 TAGGCGTTAA 0.875855 -102 ** ******** Masking position 9 Map Score: 6.1153 Number of sites scoring better than the average of aligned sites = 1151 Number in coding regions = 1092 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 ********** No masking Map Score: -3.5787e-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: -3.5787e-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: -3.5787e-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