AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i302_bsub_mtub_300.orf -o302_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybfT 218 similar to glucosamine-6-phosphate isomerase #2 nagA 181 N-acetylglucosamine-6-phosphate deacetylase #3 Rv3329 59 hypothetical protein Rv3329 #4 Rv3330 68 hypothetical protein Rv3330 #5 sugI 95 sugI Motif number 1 GAATTTAGCACCGCCCTTATCAAACTGTCAAT 1 128 0 CCGCCTTACA 0.947601 -91 TCCTCCTGTTCCGGGCTGCCCCGAGCTTGCTC 2 18 1 CCGGGTGCCC 0.993421 -164 TTATCACTTTCGGGCTTGAACCTAAAACAGAT 2 64 1 CGGGCTGACC 0.991229 -118 GCGCTAGGCTCGGGCAATGACCTCG 3 4 0 CGGGCATGCC 0.986185 -56 CTTTCGTCCCGCCAGTCACAGCGCGGCTCC 4 9 1 CCGCCGTCCA 0.973411 -60 GGCGGCCCGACCGCGAGGAGCCGCGCTGTGAC 4 25 0 CCGCGGGACC 0.980115 -44 CGCGGTCGGGCCGCCGATCACCTACTCTGCAC 4 42 1 CCGCCATCCC 0.989473 -27 GCGTCGTTTGCGGGCGGGCATCCTAGCCGGCC 5 32 1 CGGGCGGCTC 0.975403 -64 GGCATCCTAGCCGGCCTTGGTCGGCACCGAAA 5 48 1 CCGGCTTGTC 0.976749 -48 GCACCGAAATCGGGGCTTGACCAGCGGTTGAC 5 71 1 CGGGGTTGCC 0.986482 -25 ***** *** ** Masking position 1 Map Score: 14.2608 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 909 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 TTACGAATTTAGCACCGCCCTTATCAAACT 1 134 0 AGCACCGCCC 0.963606 -85 GTGACACCCCCTCAAAGAGA 1 209 0 GTGACACCCC 0.920163 -10 GAGCAAGCTCGGGGCAGCCCGGAACAGGAG 2 20 0 GGGGCAGCCC 0.927288 -162 TCTGTTTTAGGTTCAAGCCCGAAAGTGATA 2 65 0 GTTCAAGCCC 0.949727 -117 CGTGTTGGCGAGCGCAGCGCTAGGCTCGGG 3 22 0 AGCGCAGCGC 0.945476 -38 CGTCCCGCCAGTCACAGCGCGGCTCCTCGC 4 15 1 GTCACAGCGC 0.934895 -54 AGGTGATCGGCGGCCCGACCGCGAGGAGCC 4 35 0 CGGCCCGACC 0.886252 -34 GCCGGCTAGGATGCCCGCCCGCAAACGACG 5 33 0 ATGCCCGCCC 0.97019 -63 CCCCGATTTCGGTGCCGACCAAGGCCGGCT 5 56 0 GGTGCCGACC 0.942382 -40 GTCAACCGCTGGTCAAGCCCCGATTTCGGT 5 73 0 GGTCAAGCCC 0.935901 -23 GCGGTCAACCGCTGGTCAAGCC 5 84 0 GGTCAACCGC 0.829465 -12 ********** Masking position 10 Map Score: 12.3864 Number of sites scoring better than the average of aligned sites = 1713 Number in coding regions = 1539 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 AATTCGTAATGACAAGTATCATAAATTGGT 1 155 1 GACAAGTATC 0.736023 -64 CAAAGAGATAGACAAGCACCATATTTGTTA 1 187 0 GACAAGCACC 0.986001 -32 TTCCAGAAAGGCGGATCATCT 2 171 1 GCGGATCATC 0.835055 -11 GCTAGGCTCGGGCAATGACCTCG 3 4 0 GGCAATGACC 0.932138 -56 TCGTCGTGTTGGCGAGCGCAGCGCTAGGCT 3 26 0 GGCGAGCGCA 0.897582 -34 CTTTCGTCCCGCCAGTCACAGCGCGGCTCC 4 11 1 GCCAGTCACA 0.893852 -58 CGGTCGGGCCGCCGATCACCTACTCTGCAC 4 44 1 GCCGATCACC 0.97095 -25 GTCGTTTGCGGGCGGGCATCCTAGCCGGCC 5 34 1 GGCGGGCATC 0.971655 -62 TCAACCGCTGGTCAAGCCCCGATTTCGGTG 5 72 0 GTCAAGCCCC 0.919364 -24 ********** Masking position 1 Map Score: 3.84029 Number of sites scoring better than the average of aligned sites = 1838 Number in coding regions = 1672 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 TCCTGTTCCGGGCTGCCCCGAGCTTGCTCA 2 21 1 GGCTGCCCCG 0.986858 -161 CAGCTGAGGTGTTTTCCCCCCTTTTATAAA 2 96 0 GTTTTCCCCC 0.92266 -86 CTTTCGTCCCGCCAGTCACAGC 4 3 1 TTCGTCCCGC 0.902177 -66 GTCACAGCGCGGCTCCTCGCGGTCGGGCCG 4 25 1 GGCTCCTCGC 0.953258 -44 GTAGGTGATCGGCGGCCCGACCGCGAGGAG 4 37 0 GGCGGCCCGA 0.977964 -32 CTGCTTACCCCGATACCTTCG 5 2 1 TGCTTACCCC 0.90912 -94 AGGCCGGCTAGGATGCCCGCCCGCAAACGA 5 35 0 GGATGCCCGC 0.989895 -61 CTTGACCAGCGGTTGACCGC 5 86 1 GGTTGACCGC 0.97561 -10 ********** Masking position 8 Map Score: 6.23792 Number of sites scoring better than the average of aligned sites = 1200 Number in coding regions = 1066 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 AATTTGTTATAAAAGAAGGATACAAATCTTTCATATT 1 78 0 AAAAAAAAAT 0.853328 -141 CGCCCTTATCAAACTGTCAATATTAATTTCTGAAAAT 1 112 0 AAAGTAAAAT 0.917119 -107 CAAGTATCATAAATTGGTCATAACAAATATGGTGCTT 1 167 1 AAAGGAAAAA 0.97416 -52 TTCAAGCCCGAAAGTGATAAAATGAAAGTATTGTGAG 2 47 0 AAAGAAAAAA 0.990394 -135 CTTGAACCTAAAACAGATTTTATAAAAGGGGGGAAAA 2 78 1 AAAGATAAAA 0.955368 -104 CACTAGTCTGAAAAAGAGTAAAATAAAGGTATTCAAA 2 134 1 AAAGAAAAAA 0.990394 -48 TGCGCTCGCCAACACGACGACACGAAACCTTTGG 3 36 1 AACGAAAAAA 0.969443 -24 *** ** * * *** Masking position 12 Map Score: 3.03772 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 328 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 ATTCTGTATGCAATCCGTTCTTTTTCATTG 1 23 1 CAATCCGTTC 0.94683 -196 AAGAAGGATACAAATCTTTCATATTGGGAG 1 73 0 CAAATCTTTC 0.884056 -146 AGCTTGCTCACAATACTTTCATTTTATCAC 2 41 1 CAATACTTTC 0.979108 -141 TCTGGAATTTGAATACCTTTATTTTACTCT 2 148 0 GAATACCTTT 0.891409 -34 CACGACGACACGAAACCTTTGG 3 48 1 CGAAACCTTT 0.940874 -12 CTGCTTACCCCGATACCTTCGGCGTCGTTT 5 11 1 CGATACCTTC 0.988747 -85 ********** Masking position 3 Map Score: 1.55519 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 453 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 TATGGTCTCAATGAAAAAGAACGGATTGCA 1 31 0 ATGAAAAAGA 0.941429 -188 GTGACACCCCCTCAAAGAGATAGACAAGCA 1 199 0 CTCAAAGAGA 0.979757 -20 AGGTTCAAGCCCGAAAGTGATAAAATGAAA 2 57 0 CCGAAAGTGA 0.94671 -125 GGGCTTGAACCTAAAACAGATTTTATAAAA 2 75 1 CTAAAACAGA 0.946652 -107 GATCACTAGTCTGAAAAAGAGTAAAATAAA 2 131 1 CTGAAAAAGA 0.988219 -51 ********** Masking position 5 Map Score: 1.34198 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 403 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 ********** No masking Map Score: 1.18904e-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: 1.18904e-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: 1.18904e-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