AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i044_Trehalose_Metabolism_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 otsB 166 trehalose-6-phosphate phophatase, biosynthetic #2 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #3 araG 69 ATP-binding component of high-affinity L-arabinose transport system #4 araF 300 L-arabinose-binding periplasmic protein Motif number 1 TGACGGGGGTCGCCATTTGCAACGAAGAACA 1 73 0 CGCCATTGCA 0.956441 -94 CAAATGGCGACCCCCGTCACACTGTCTATAC 1 85 1 CCCCCGCACA 0.968778 -82 TTGCGCAGAACGCGCTTTACAGACATGTAAG 1 115 0 CGCGCTTACA 0.982822 -52 AAGCGCGTTCTGCGCAACACAATAAGAAAAG 1 129 1 TGCGCACACA 0.700359 -38 CCGGAAAAATTCCCCTCTGCATGATGCAGAG 3 15 1 TCCCCTTGCA 0.995239 -55 GTCGTTCACACCCCCTCTGCATCATGCAGAG 3 29 0 CCCCCTTGCA 0.996416 -41 TATGGATTAATCTGCTGTGCATTCGACAATT 4 48 1 TCTGCTTGCA 0.906385 -253 GTGATATTGCTCTCCTATGGAGAATTAATTT 4 152 1 TCTCCTTGGA 0.860781 -149 CATTCGTTTTTGCCCTACACAAAACGACACT 4 264 1 TGCCCTCACA 0.982996 -37 ****** **** Masking position 11 Map Score: 10.1738 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 799 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 GCGGTTGGCTATGGTGGGAAAAAACGCTAAAT 1 28 0 ATGTGGAAAA 0.950094 -139 TTTGCCGGAAAAATTCCCCTCT 3 1 1 TTGCCGAAAA 0.781171 -69 ATCCATAAGATTAGCCTGGAAATCCTTGTTGT 4 23 0 TTGCCGGAAA 0.986433 -278 CATTCGACAATTTGTCTGACAAATTGGCTTTC 4 67 1 TTGTCGACAA 0.973612 -234 GTGCATAAATTTAGCGGGAAAAGACATAAGGG 4 98 0 TTGCGGAAAA 0.976912 -203 TGACATAGTTTTAGCGAGAAATTAATTCTCCA 4 169 0 TTGCGGAAAT 0.975338 -132 ATTCGTTAAATTAATCGGAAAACAAAGCATTA 4 230 0 TTATCGAAAA 0.940106 -71 ** *** ***** Masking position 11 Map Score: 8.60713 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 363 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 CTTTTTTCTGCAACAATTTAGCGTTTTTTCCC 1 13 1 CACATTTAGC 0.987221 -154 CAGATTAATCCATAAGATTAGCCTGGAAATCC 4 30 0 CAAAATTAGC 0.991658 -271 TGAGAACGTGCATAAATTTAGCGGGAAAAGAC 4 105 0 CAAATTTAGC 0.993599 -196 ACTGTGTTGACATAGTTTTAGCGAGAAATTAA 4 176 0 CAAGTTTAGC 0.994603 -125 AATCGGAAAACAAAGCATTACCTTTTAACTAA 4 218 0 CAAGATTACC 0.973473 -83 ** ** ****** Masking position 8 Map Score: 5.10958 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GTTATGGCGGTTGGCTATGGTGGGAAAAAACG 1 34 0 TTGGCTTGTG 0.95517 -133 GCCATAACGGTTGGCTGTTCTTCGTTGCAAAT 1 58 1 TTGGCTTCTT 0.991202 -109 CCCCGTCACACTGTCTATACTTACATGTCTGT 1 96 1 CTGTCTTCTT 0.975737 -71 GTTCTCCTCCTTCTCTTTTCTTATTGTGTTGC 1 142 0 TTCTCTTCTT 0.961728 -25 CGGAATTATTCTGGCTTCACGT 2 12 1 CTGGCTCCGT 0.929622 -12 GAAATCCTTGTTGTCTTTGGTACCCA 4 5 0 TTGTCTTGTA 0.900629 -296 GTCTGACAAATTGGCTTTCCCTTATGTCTTTT 4 80 1 TTGGCTTCCT 0.986981 -221 GGTTCTCTCCAGCTTTAGTGTCGT 4 287 0 TTCTCTCGCT 0.854766 -14 ****** * *** Masking position 6 Map Score: 3.74386 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 320 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 GTTCTTCGTTGCAAATGGCGACCCCCGTCA 1 74 1 GCAAATGGCG 0.950845 -93 TATAGACAGTGTGACGGGGGTCGCCATTTG 1 85 0 GTGACGGGGG 0.978853 -82 TTACATGTCTGTAAAGCGCGTTCTGCGCAA 1 116 1 GTAAAGCGCG 0.948006 -51 AATAAGAAAAGAGAAGGAGGAGAACCGG 1 149 1 GAGAAGGAGG 0.885355 -18 TCTGCATCATGCAGAGGGGAATTTTTCCGG 3 15 0 GCAGAGGGGA 0.977925 -55 TCTGCATGATGCAGAGGGGGTGTGAACGAC 3 30 1 GCAGAGGGGG 0.99388 -40 GTGTCGTTTTGTGTAGGGCAAAAACGAATG 4 264 0 GTGTAGGGCA 0.904728 -37 ********** Masking position 1 Map Score: 3.38928 Number of sites scoring better than the average of aligned sites = 1202 Number in coding regions = 1095 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 AGCCAACCGCCATAACGGTTGGCTGTTCTT 1 50 1 CATAACGGTT 0.827585 -117 CTGCATCATGCAGAGGGGAATTTTTCCGGC 3 14 0 CAGAGGGGAA 0.987288 -56 CTGCATGATGCAGAGGGGGTGTGAACGACC 3 31 1 CAGAGGGGGT 0.965984 -39 TTGTCGAATGCACAGCAGATTAATCCATAA 4 47 0 CACAGCAGAT 0.93959 -254 CGGGAAAAGACATAAGGGAAAGCCAATTTG 4 86 0 CATAAGGGAA 0.962343 -215 AGCAATATCACATCGCAGAATTACAGTGAG 4 133 0 CATCGCAGAA 0.913978 -168 ATTAATTCTCCATAGGAGAGCAATATCACA 4 151 0 CATAGGAGAG 0.963776 -150 ********** Masking position 2 Map Score: 2.24784 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 451 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 ACGTGAAGCCAGAATAATTCCGG 2 5 0 CAGAATAATT 0.968311 -19 TTTGCCGGAAAAATTCCCCTCTGCA 3 6 1 CGGAAAAATT 0.91358 -64 CAAGGATTTCCAGGCTAATCTTATGGATTA 4 27 1 CAGGCTAATC 0.920821 -274 GAATGCACAGCAGATTAATCCATAAGATTA 4 42 0 CAGATTAATC 0.967173 -259 GCCAATTTGTCAGACAAATTGTCGAATGCA 4 65 0 CAGACAAATT 0.97319 -236 ATGTCTTTTCCCGCTAAATTTATGCACGTT 4 103 1 CCGCTAAATT 0.91066 -198 GCTTTGTTTTCCGATTAATTTAACGAATGT 4 234 1 CCGATTAATT 0.97319 -67 ********** Masking position 7 Map Score: 5.37958 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 165 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 ********** No masking Map Score: -1.11312e-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: -1.11312e-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: -1.11312e-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