AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jcspA.reg -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 = 140 Input sequences: #1 hns 300 bp hns 137 1-414 CDS #2 gyrA 146 bp gyrA 875 1-2628 CDS Motif number 1 ACTAATACAGAAGACTGAAAGGTCGTCAGCCT 1 33 1 AAGATAAAGG 0.9146 -268 TGATTCATGTCACATTTTATGGGGAGATTATC 1 67 0 CACATTATGG 0.922212 -234 TGCAATAGCCAGGAATGTAAGGAATTCAAAAT 1 213 0 AGGATTAAGG 0.98646 -88 TATTGCACAACTGAATTTAAGGCTCTATTATT 1 238 1 CTGATTAAGG 0.983881 -63 AACAAACCACCCCAATATAAGTTTGAGATTAC 1 275 1 CCCATTAAGT 0.927057 -26 TTGCCAATTACGGAGTAGAAGTGCCA 2 5 0 CGGATGAAGT 0.96382 -142 AACACAGCCGCGCAGTTTGAGGTAAACCTATA 2 76 0 CGCATTGAGG 0.981133 -71 TACTGTATCCCGGATTCAAAGGTCGCAAATTA 2 109 0 CGGATAAAGG 0.992835 -38 **** * ***** Masking position 4 Map Score: 6.15902 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 209 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 GGAATTCTCGTAAACACAACTAATACAGAA 1 15 1 TAAACACAAC 0.917595 -286 CAGCCTACGATAATCTCCCCATAAAATGTG 1 59 1 TAATCTCCCC 0.973459 -242 CAGGAAGTTTTAACCTCACGTGCTGCGAAA 1 97 1 TAACCTCACG 0.978638 -204 GGCTCTATTATTACCTCAACAAACCACCCC 1 258 1 TTACCTCAAC 0.983082 -43 TTACCTCAACAAACCACCCCAATATAAGTT 1 268 1 AAACCACCCC 0.907435 -33 TGTAGTAATCTCAAACTTATATTGG 1 286 0 TAATCTCAAA 0.938467 -15 GCGTATAGGTTTACCTCAAACTGCGCGGCT 2 73 1 TTACCTCAAA 0.951539 -74 ********** Masking position 3 Map Score: 4.34505 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 395 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 AGACGCGGCATATAGCCCTATTTACACCGATG 1 128 0 TATGCCTATT 0.973519 -173 CGGCACAAAATAAAGAACAATTTTGAATTCCT 1 194 1 TAAGACAATT 0.920675 -107 CATTCCTGGCTATTGCACAACTGAATTTAAGG 1 228 1 TATGCCAACT 0.988804 -73 CAACTGAATTTAAGGCTCTATTATTACCTCAA 1 245 1 TAAGCCTATT 0.988325 -56 CTAACCGCTATCCCTCTACTGTATCCCGGA 2 127 0 TATCCCTACT 0.974783 -20 *** ** ***** Masking position 10 Map Score: 2.06977 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 83 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TGTTTACGAGAATTCCCTAT 1 1 0 AATTCCCTAT 0.976235 -300 TGAGGTTAAAACTTCCTGATTCATGTCACA 1 85 0 ACTTCCTGAT 0.984507 -216 AACAATTTTGAATTCCTTACATTCCTGGCT 1 209 1 AATTCCTTAC 0.976236 -92 ATTCACATCCAATGCCTGATATACTCGTTT 2 40 0 AATGCCTGAT 0.984506 -107 ********** Masking position 3 Map Score: 1.25469 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 136 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TTAACCTCACGTGCTGCGAAATCATCGGTG 1 106 1 GTGCTGCGAA 0.994098 -195 TCTTTATTTTGTGCCGCCAATAAATATCTT 1 180 0 GTGCCGCCAA 0.988642 -121 ATACTCGTTTGTCTTGCCAATTACGGAGTA 2 20 0 GTCTTGCCAA 0.98449 -127 ********** Masking position 9 Map Score: 0.408445 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 42 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 6 ACAGAAGACTGAAAGGTCGTCAGCCTACGA 1 39 1 GAAAGGTCGT 0.991372 -262 AAATTAGCCAGAAAAGACGCGGCATATAGC 1 144 0 GAAAAGACGC 0.984887 -157 ATCCCGGATTCAAAGGTCGCAAATTATAAC 2 105 0 CAAAGGTCGC 0.994161 -42 ********** Masking position 4 Map Score: 0.408445 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 66 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ********** No masking Map Score: 5.92755e-14 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: 5.92755e-14 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: 5.92755e-14 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