AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i213_transposase_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 yi5A 300 IS150 hypothetical protein #2 HI1720 61 conserved hypothetical protein #3 HI1721 167 transposase, putative Motif number 1 TACGGCGTTGCGCATTCTCATTGCACCCAAATT 1 13 0 CGCTTCTATG 0.977989 -288 AAGACTCTTACTCTTTCAATTTGCAGGCTAAAA 1 72 1 CTCTTCATTG 0.934014 -229 ATTTGTTTCACGCTTTTATTTTTCACCTGGATG 1 163 0 CGCTTTATTT 0.98049 -138 ATGTACTGCACCCATTTTGTTGGACGATGAAAT 1 263 1 CCCTTTTTTG 0.991429 -38 ATGAATTGCCTTTTGTTAGATCGAAGTCG 2 7 1 TGCTTTTTTG 0.974879 -55 ATACGCCCTTTTTGTTTTTCTTTATAAT 2 44 0 CCCTTTTTTT 0.974304 -18 AGGCATTACGCGTTCATTTTCCGCTGCCCAT 3 9 1 CGCTTCATTC 0.954522 -159 TTTTCCGCTGCCCATTTTATTAGATTTAATCGG 3 27 1 CCCTTTTTTG 0.991415 -141 GTGAGAGTGCTGCATTTTTATCGTTTTTCGTCT 3 92 0 TGCTTTTATG 0.915166 -76 CACAAGAAATCGCCTCTATTTATCACGATAATC 3 122 1 CGCTCTATTT 0.912896 -46 *** **** ** * Masking position 5 Map Score: 12.6032 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 594 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 AGAGTAAGAGTCTTCGGCGGGAAATTATTCC 1 55 0 TCTTCGCGGG 0.954612 -246 CTGGCGGCGTTTTTAGCCTGCAAATTGAAAG 1 84 0 TTTTACCTGC 0.956817 -217 ACGCTTTTATTTTTCACCTGGATGATAAGAG 1 156 0 TTTTCCCTGG 0.97165 -145 AGTAATCTATATTTCTGCGGCATTCCCAGCC 1 209 1 ATTTCGCGGC 0.992883 -92 GGGCTATTCCATTTCATCGTCCAACAAAATG 1 275 0 ATTTCTCGTC 0.953039 -26 TACGCGTTCATTTTCCGCTGCCCATTTTATT 3 17 1 TTTTCGCTGC 0.992963 -151 ATTTTATTAGATTTAATCGGCTTGGCACGCA 3 40 1 ATTTATCGGC 0.953039 -128 TTTTTATCGTTTTTCGTCTTCAAGTGATAGA 3 80 0 TTTTCTCTTC 0.953544 -88 ***** ***** Masking position 4 Map Score: 8.96356 Number of sites scoring better than the average of aligned sites = 1753 Number in coding regions = 1672 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 CCGTAAGTAAGGCGGGAATAATTTCCCGCC 1 41 1 GGCGGGAATA 0.954709 -260 AAGAGTCTTCGGCGGGAAATTATTCCCGCC 1 51 0 GGCGGGAAAT 0.99157 -250 GGCGTTTTTAGCCTGCAAATTGAAAGAGTA 1 80 0 GCCTGCAAAT 0.90905 -221 GTTATGAGCTGGCGGCGTTTTTAGCCTGCA 1 93 0 GGCGGCGTTT 0.982282 -208 CAACACAGGAGGCTGGGAATGCCGCAGAAA 1 220 0 GGCTGGGAAT 0.978292 -81 TAAAATGGGCAGCGGAAAATGAACGCGTAA 3 16 0 AGCGGAAAAT 0.889822 -152 CTTGTGAGAGTGCTGCATTTTTATCGTTTT 3 98 0 TGCTGCATTT 0.773744 -70 CGTGATAAATAGAGGCGATTTCTTGTGAGA 3 119 0 AGAGGCGATT 0.821846 -49 ********** Masking position 5 Map Score: 4.30516 Number of sites scoring better than the average of aligned sites = 3749 Number in coding regions = 3462 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 4 CCTTACTTACGGCGTTGCGCATTCTCATTG 1 23 0 GGCGTTGCGC 0.993563 -278 CAGGAGGCTGGGAATGCCGCAGAAATATAG 1 215 0 GGAATGCCGC 0.98539 -86 ACGATGAAATGGAATAGCCCCTAAT 1 286 1 GGAATAGCCC 0.960503 -15 AGGCATTACGCGTTCATTTTC 3 2 1 GGCATTACGC 0.985141 -166 AGATTTAATCGGCTTGGCACGCAGTGTTTT 3 48 1 GGCTTGGCAC 0.975958 -120 ********** Masking position 5 Map Score: 1.99554 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 818 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 GCGCATTCTCATTGCACCCAAATTTA 1 7 0 ATTGCACCCA 0.988293 -294 TTTAATATGCAATTCACACAGTGAATCTCT 1 130 1 AATTCACACA 0.97244 -171 ACTCGTTGGAAATCAACACAGGAGGCTGGG 1 233 0 AATCAACACA 0.929392 -68 ACGAGTATGTACTGCACCCATTTTGTTGGA 1 257 1 ACTGCACCCA 0.992071 -44 ********** Masking position 6 Map Score: 0.187386 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 99 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AAATAAAAGCGTGAAACAAATCACTATTAA 1 175 1 GTGAAACAAA 0.94586 -126 CCATTTCATCGTCCAACAAAATGGGTGCAG 1 268 0 GTCCAACAAA 0.985798 -33 AACGACTTCGATCTAACAAAAGGCAATTCA 2 12 0 ATCTAACAAA 0.981614 -50 AGCCGATTAAATCTAATAAAATGGGCAGCG 3 32 0 ATCTAATAAA 0.930737 -136 ********** Masking position 5 Map Score: 0.0674239 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 46 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 ********** No masking Map Score: -3.74156e-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: -3.74156e-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: -3.74156e-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