AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i324_bsub_mtub_300.orf -o324_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 yvdH 39 similar to maltodextrin transport system permease #2 yvdG 95 similar to maltose/maltodextrin-binding protein #3 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #4 yvdE 205 similar to transcriptional regulator (LacI family) #5 yvdD 116 similar to hypothetical proteins #6 Rv3399 22 hypothetical protein Rv3399 #7 Rv3400 63 hypothetical protein Rv3400 Motif number 1 CGCCCTCTATTCTTCCGGACGCTATCCCGCCGTT 1 10 0 TCTCCGCTAT 0.975007 -30 TTTTCCGCCCTCTATTCTTCCGGAC 1 25 0 TTTCCGCTAT 0.960728 -15 CTCTTTTCCTCCTTCTATTTACGAAACTAT 2 76 0 TTCTCCCTTT 0.970133 -20 GTGAAAAGGATTGTTCCCACAATTTCATCATGATA 3 38 1 TTTTCCCTTT 0.944684 -75 GTTTCCCCCTTTGATTTCCGTTTTATT 3 96 0 TTCCCCTTTT 0.931603 -17 GCAGACTCATTCTCTCCACTTCCATCAGAAAATCT 4 16 0 TCCTCCTCAT 0.871201 -190 TTTCATCCCCTCCTTATCTGTGCTTAT 4 189 0 TCTCCCCTAT 0.993929 -17 CCTCATCACTCCTGCATTCTTTATGTATTT 5 6 1 TCCTCCCTCT 0.968137 -111 ACACTATATATTGTCCCATCTTCATGTGATAATAT 5 48 0 TTTCCCCCAT 0.975247 -69 CTTGTCATCTCCGCATCTATATATCGTGTTAA 5 95 0 TCCCGCCTAT 0.973235 -22 GTGGCCCCGGCACTATAGCCGGGCCT 7 2 1 TGCCCCCTAT 0.986186 -62 ** **** * *** Masking position 1 Map Score: 12.0116 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 629 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 2 AACGGCGGGATAGCGTCCGGAAGAATAGAG 1 10 1 AAGCGTCCGG 0.910003 -30 GTCCGGAAGAATAGAGGGCGGAAAA 1 25 1 AAGAGGGCGG 0.995144 -15 GTATTGTCCTATAGAAAGCGGTTACAACAAC 2 38 0 AAGAAAGCGG 0.982193 -58 AGTTTCGTAAATAGAAGGAGGAAAAGAG 2 78 1 AAGAAGGAGG 0.99449 -18 GTTACCGATAACAGAATAAGGCGC 3 4 0 AAGAATAAGG 0.939957 -109 TTTCCGTTTTATTGAAGCCGGCTCATAGTTT 3 78 0 ATGAAGCCGG 0.925014 -35 ATGGAAGTGGAGAGAATGAGTCTGCCACCTA 4 26 1 AAGAATGAGT 0.92452 -180 AGTGTTTTTAACAAAGTGAGGTTTCCTTAAG 4 80 1 AAAAGTGAGG 0.907286 -126 TAATAAGCACAGATAAGGAGGGGATGAAA 4 187 1 AATAAGGAGG 0.946509 -19 TGAAATACATAAAGAATGCAGGAGTGATGAG 5 12 0 AAGAATGCAG 0.951298 -105 * ********* Masking position 1 Map Score: 11.73 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 842 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 CTCTATTCTTCCGGACGCTATCCCGCCGTT 1 11 0 CCGGACGCTA 0.957022 -29 TTTTCCGCCCTCTATTCTTCCGGA 1 26 0 CCGCCCTCTA 0.996517 -14 GTTGTTGTAACCGCTTTCTATAGGACAATA 2 38 1 CCGCTTTCTA 0.98523 -58 CTCTTTTCCTCCTTCTATTTACGAAAC 2 79 0 CCTCCTTCTA 0.98069 -17 AAACTATGAGCCGGCTTCAATAAAACGGAA 3 78 1 CCGGCTTCAA 0.982239 -35 ********** Masking position 10 Map Score: 4.38847 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 179 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 4 CATTCTGTTATCGGTAACAAATCGAAAGT 2 10 1 ATCGGTAACA 0.994246 -86 TCCTATAGAAAGCGGTTACAACAACTTTCG 2 33 0 AGCGGTTACA 0.990635 -63 TTATTCTGTTATCGGTAACAGGGTGAAAAG 3 16 1 ATCGGTAACA 0.994246 -97 TCGTATATTTAGCAGTAATAGAGGACTTTA 4 144 1 AGCAGTAATA 0.944238 -62 ********** Masking position 6 Map Score: 3.98287 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 40 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 5 CTCATAGTTTGAAAGTATCATGATGAAATT 3 58 0 GAAAGTATCA 0.940718 -55 ACTTCCATCAGAAAATCTCTTTT 4 4 0 GAAAATCTCT 0.982235 -202 TTTCCCTTAAGGAAACCTCACTTTGTTAAA 4 86 0 GGAAACCTCA 0.974304 -120 TTTCCTTAAGGGAAATCTCTTTTTTATTTC 4 101 1 GGAAATCTCT 0.982553 -105 ATCTTCATGTGATAATATCAATATGAAATA 5 36 0 GATAATATCA 0.914599 -81 ********** Masking position 4 Map Score: 1.58062 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 213 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 GCGTCCGGAAGAATAGAGGGCGGAAAA 1 23 1 GAATAGAGGG 0.950911 -17 TATCGGTAACAAATCGAAAGTTGTTGTAAC 2 19 1 AAATCGAAAG 0.959784 -77 ATAGTTTCGTAAATAGAAGGAGGAAAAGAG 2 76 1 AAATAGAAGG 0.981179 -20 TATCATGATGAAATTGTGGGAACAATCCTT 3 43 0 AAATTGTGGG 0.939509 -70 AATAAAACGGAAATCAAAGGGGGAAAC 3 96 1 AAATCAAAGG 0.952408 -17 AATCCATGAAAAATCGAGTGTTTTTAACAA 4 64 1 AAATCGAGTG 0.965807 -142 AGCCGGGCCTAACTCGTAGGCTTGGTACGC 7 27 1 AACTCGTAGG 0.953812 -37 ********** Masking position 2 Map Score: 5.65741 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 330 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 GTTTTATTGAAGCCGGCTCATAGTTTGAAA 3 74 0 AGCCGGCTCA 0.981415 -39 AAATATACGATGCAGGCCAAAGAGAAATAA 4 124 0 TGCAGGCCAA 0.904238 -82 AGCACAGATAAGGAGGGGATGAAA 4 192 1 AGGAGGGGAT 0.875938 -14 CCGGCTATAGTGCCGGGGCCAC 7 3 0 TGCCGGGGCC 0.978728 -61 CCGGCACTATAGCCGGGCCTAACTCGTAGG 7 17 1 AGCCGGGCCT 0.939834 -47 GCCTGGCGGCTCTGCCCGCGTAC 7 51 0 TGGCGGCTCT 0.975479 -13 ********** Masking position 5 Map Score: 0.841321 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 964 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 ACTTTGTTAAAAACACTCGATTTTTCATGG 4 67 0 AAACACTCGA 0.982248 -139 TATTACTGCTAAATATACGATGCAGGCCAA 4 134 0 AAATATACGA 0.922407 -72 ACTAGTGATAAAGTCCTCTATTACTGCTAA 4 152 0 AAGTCCTCTA 0.850811 -54 AAACATTCAAAAACACACTATATATTGTCC 5 67 0 AAACACACTA 0.96087 -50 ATATCGTGTTAAACATTCAAAAACACACTA 5 77 0 AAACATTCAA 0.898546 -40 CCCGCGTACCAAGCCTACGAGTTAGGCCCG 7 30 0 AAGCCTACGA 0.96029 -34 ********** Masking position 2 Map Score: 0.429691 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 244 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 ACGGCGGGATAGCGTCCGGAAGAATAGAGG 1 12 1 AGCGTCCGGA 0.915188 -28 CCGGAAGAATAGAGGGCGGAAAA 1 27 1 AGAGGGCGGA 0.995036 -13 ATTGTCCTATAGAAAGCGGTTACAACAACT 2 37 0 AGAAAGCGGT 0.857694 -59 TTTCGTAAATAGAAGGAGGAAAAGAG 2 80 1 AGAAGGAGGA 0.942978 -16 TTCATACGCTAGGTGGCAGACTCATTCTCT 4 36 0 AGGTGGCAGA 0.916705 -170 AAATACATAAAGAATGCAGGAGTGATGAGG 5 11 0 AGAATGCAGG 0.884081 -106 AGGCTTGGTACGCGGGCAGAGCCGCCAGGC 7 44 1 CGCGGGCAGA 0.961179 -20 ********** Masking position 2 Map Score: 0.443689 Number of sites scoring better than the average of aligned sites = 1532 Number in coding regions = 1410 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 10 ********** No masking Map Score: 5.14023e-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 11 ********** No masking Map Score: 5.14023e-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 12 ********** No masking Map Score: 5.14023e-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