AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i335_2_7_7_40_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 b2748 193 orf, hypothetical protein #2 HI0673 122 conserved hypothetical protein Motif number 1 TTATTAGTTACGGTTTGAATTATGAACAGA 1 30 0 CGGTTTGAAT 0.907382 -164 CCTGCCCCCTGAAAAACGGCATCATC 1 178 0 CCCTGAAAAA 0.920636 -16 CAAAAAAGTGCGGTTAAAATAAAAGAATTT 2 19 1 CGGTTAAAAT 0.993514 -104 AAAGAAAGTGCGGTTAAAAATTCTTTTATT 2 36 0 CGGTTAAAAA 0.99158 -87 ATTAGGAAAAACGATAAAATGAAAGAAAGT 2 57 0 ACGATAAAAT 0.868637 -66 AACCTGTTTACCGTGAAAAATTAGGAAAAA 2 76 0 CCGTGAAAAA 0.983698 -47 CACGGTAAACAGGTTAAAATTTTACTCACA 2 91 1 AGGTTAAAAT 0.976554 -32 ********** Masking position 8 Map Score: 8.70459 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 565 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 TTGTACTTTCCCGTCTCCTCTGTTCATAAT 1 12 1 CCGTCTCCTC 0.981295 -182 AGATTATGTTCTGCACGCCCTGGGTATACG 1 62 1 CTGCACGCCC 0.977708 -132 CGCGTTGTCGCGGTATCCCCAACAGAGGAT 1 121 1 CGGTATCCCC 0.986467 -73 GAAGACGACTCTACATCCTCTGTTGGGGAT 1 135 0 CTACATCCTC 0.980151 -59 CCCTGAAAAACGGCATCATCATCCCATGCA 1 168 0 CGGCATCATC 0.981526 -26 CCTGCCCCCTGAAAAACGGCA 1 183 0 CTGCCCCCTG 0.980487 -11 ********** Masking position 1 Map Score: 4.11697 Number of sites scoring better than the average of aligned sites = 864 Number in coding regions = 775 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 TACGGTTTGAATTATGAACAGAGGAGACGGGAAA 1 18 0 ATAAACAGGG 0.994607 -176 CGCCCTGGGTATACGTAACAATGGACAAATGTGG 1 77 1 ATCAACAAGG 0.989899 -117 TTGTCGCGGTATCCCCAACAGAGGATGTAGAGTC 1 125 1 ATCAACAGGG 0.996564 -69 TTTTTATACAAAAAAGTGCGGTTAAAATA 2 6 1 ATCAAAAGGC 0.992164 -117 AAACGATAAAATGAAAGAAAGTGCGGTTAAAAAT 2 45 0 ATAGAAAGGC 0.967152 -78 ACCGTGAAAAATTAGGAAAAACGATAAAATGAAA 2 63 0 ATAAAAAAGA 0.908889 -60 ** * ***** ** Masking position 8 Map Score: 4.25004 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 175 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 ACGTATACCCAGGGCGTGCAGAACATAATC 1 63 0 AGGGCGTGCA 0.989179 -131 ATACCGCGACAACGCGGGCAAATGTACCAC 1 107 0 AACGCGGGCA 0.986266 -87 TATACAAAAAAGTGCGGTTAAAATAAAAGA 2 15 1 AGTGCGGTTA 0.994708 -108 AATGAAAGAAAGTGCGGTTAAAAATTCTTT 2 40 0 AGTGCGGTTA 0.994708 -83 ********** Masking position 1 Map Score: 3.51164 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 180 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ATACAAAAAAGTGCGGTTAAAATAAAAGAA 2 16 1 GTGCGGTTAA 0.998377 -107 ATGAAAGAAAGTGCGGTTAAAAATTCTTTT 2 39 0 GTGCGGTTAA 0.998377 -84 ********** Masking position 7 Map Score: 2.3008 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 GTCCATTGTTACGTATACCCAGGGCGTGCA 1 73 0 ACGTATACCC 0.974557 -121 CAAATGTACCACATTTGTCCATTGTTACGT 1 89 0 ACATTTGTCC 0.991135 -105 CAAATGTGGTACATTTGCCCGCGTTGTCGC 1 102 1 ACATTTGCCC 0.994251 -92 TTTCATTTTATCGTTTTTCCTAATTTTTCA 2 63 1 TCGTTTTTCC 0.96168 -60 ********** Masking position 6 Map Score: 2.24576 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 175 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 ********** No masking Map Score: -3.24418e-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 8 ********** No masking Map Score: -3.24418e-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 9 ********** No masking Map Score: -3.24418e-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