AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -igalR_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #2 TP0076 39 sugar ABC transporter, permease protein (y4oR) #3 TP0077 40 capsular polysaccharide biosynthesis protein (cap5D) #4 TP0418 26 galactokinase #5 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #6 TP0547 143 penicillin tolerance protein (lytB) #7 TP0685 119 methylgalactoside ABC transporter, ATP binding protein (mglA) Motif number 1 AGATGCTGGATATGAGCGGAAACAGAATGACG 1 47 1 TATGGCGGAA 0.930454 -72 TGGAGCGCGTTACGTTGGGTAGCGTAAGAGGG 1 90 1 TACGTGGGAG 0.986074 -29 TTGGGTAGCGTAAGAGGGGGAGTGC 1 104 1 TAAGGGGGAG 0.984266 -15 GGGTTGCGTACGGGTTAGATAAGAGCAG 2 7 1 CGTAGGGTAG 0.838269 -33 ACGGGTTAGATAAGAGCAGGAGCAGATAGC 2 20 1 TAAGGCAGAG 0.892932 -20 ATAAACACTCTGCGCGGGTGAGTACGTGCAGC 3 15 1 TGCGGGGTAG 0.994668 -26 CGCGGGTGAGTACGTGCAGCAGAT 3 27 1 TACGGCAGAG 0.967275 -14 ATATTCCTCGCGCGGGTATCAGGGTGTGAGGG 5 16 1 CGCGGTATAG 0.806735 -69 GGTATCAGGGTGTGAGGGGAAAGAAGTGTCAA 5 30 1 TGTGGGGGAA 0.982546 -55 CAAATCAGAATGCGCTGGTGAACATGAGGAGG 5 59 1 TGCGTGGTAA 0.933628 -26 CGCTGGTGAACATGAGGAGGAAAT 5 71 1 CATGGGAGAA 0.858493 -14 AAGGGCGCGGCGTGGTGGTGAGTTCTTCTTCT 6 52 0 CGTGTGGTAG 0.966952 -92 GGTTTGGACGTGCGTTGGGTAGCTGCTGTTCC 7 18 1 TGCGTGGGAG 0.994092 -102 GAAAGCGGTGCGAGGTCGGTAGACCCTACCTA 7 73 0 CGAGTCGGAG 0.966761 -47 GCACCGCTTTCGCGCGCGAGAGGAGTGATAGT 7 94 1 CGCGGCGAAG 0.965715 -26 **** **** ** Masking position 11 Map Score: 24.3644 Number of sites scoring better than the average of aligned sites = 1816 Number in coding regions = 1649 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 TCTTTTCTGCCCTCTCTTCCCCCAAGAAGAAGAGAC 1 14 0 CCCTTCCCCG 0.932316 -105 ACGCTACCCAACGTAACGCGCTCCACAGATAGAACA 1 79 0 ACACGCGCCC 0.995236 -40 AGGGATAAACACTCTGCGCGGGTGAGTACGTGCA 3 9 1 ACCTGCGCGG 0.993804 -32 TTTCTATATTCCTCGCGCGGGTATCAGGGTG 5 6 1 ATCCTCGCCG 0.983463 -79 AAGTGTCAAATCAGAATGCGCTGGTGAACATGAGGA 5 53 1 TCATGCGCGG 0.915212 -32 GAACTCACCACCACGCCGCGCCCTTGCATGACCTGG 6 59 1 CCCCGCGCCG 0.996834 -85 CGCCGAGTGTACCAAAGGCACCCAGGTCATGCAAGG 6 80 0 ACAGGCACCG 0.96441 -64 TGCCTTTGGTACACTCGGCGCGCCAGTTTTCTTCCG 6 96 1 ACCGGCGCCG 0.998603 -48 TATTCAACGAACAGGACGTGCACCAGGAACAGCAGC 7 39 0 ACACGTGCCG 0.985713 -81 GGTAGGGTCTACCGACCTCGCACCGCTTTCGCGCGC 7 75 1 ACCCTCGCCC 0.994457 -45 CGCAACTATCACTCCTCTCGCGCGCGAAAGCGGTGC 7 94 0 ACTCTCGCCG 0.98989 -26 ** ****** * * Masking position 11 Map Score: 19.5771 Number of sites scoring better than the average of aligned sites = 818 Number in coding regions = 758 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 AAAGTCTCTTCTTCTTGGGGGAAGA 1 6 1 CTCTTCTTCT 0.762524 -113 TCTTTTCTGCCCTCTCTTCCCCCAAGAAGA 1 20 0 CCTCTCTTCC 0.975117 -99 TCATATCCAGCATCTTTTCTGCCCTCTCTT 1 32 0 CATCTTTTCT 0.715667 -87 CATTCTGTTTCCGCTCATATCCAGCATCTT 1 46 0 CCGCTCATAT 0.79778 -73 GCACTCCCCCTCTTACGCTACCCAAC 1 103 0 CCCCTCTTAC 0.958049 -16 CTATCTGCTCCTGCTCTTATCTAACCCGTA 2 19 0 CTGCTCTTAT 0.966251 -21 AAATGCTTTTCTGGCAGGGGAA 4 15 0 ATGCTTTTCT 0.734103 -12 TGATTTGACACTTCTTTCCCCTCACACCCT 5 36 0 CTTCTTTCCC 0.929629 -49 ATTTCCTCCTCATGTTCACCAGCGC 5 70 0 CTCCTCATGT 0.814529 -15 AAAAGACACGTTGCTTTTCCTGCGCGA 6 8 0 TTGCTTTTCC 0.815858 -136 GTGAGTTCTTCTTCTTTTATTTATTTTGAA 6 37 0 CTTCTTTTAT 0.867936 -107 CGTTGGGTAGCTGCTGTTCCTGGTGCACGT 7 30 1 CTGCTGTTCC 0.953913 -90 CGACCTCGCACCGCTTTCGCGCGCGAGAGG 7 87 1 CCGCTTTCGC 0.909788 -33 GCAACTATCACTCCTCTCGCGCGCGAAAGC 7 99 0 CTCCTCTCGC 0.945306 -21 ********** Masking position 5 Map Score: 13.3991 Number of sites scoring better than the average of aligned sites = 1273 Number in coding regions = 1133 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 CTCTTACGCTACCCAACGTAACGCGCTCCA 1 90 0 ACCCAACGTA 0.99187 -29 TCTTATCTAACCCGTACGCAACCC 2 5 0 CCCGTACGCA 0.978255 -35 TCCTCATGTTCACCAGCGCATTCTGATTTG 5 59 0 CACCAGCGCA 0.944347 -26 CGCCGAGTGTACCAAAGGCACCCAGGTCAT 6 86 0 ACCAAAGGCA 0.940824 -58 AACAGCAGCTACCCAACGCACGTCCAAACC 7 18 0 ACCCAACGCA 0.99724 -102 AGGTCGGTAGACCCTACCTATTCAACGAAC 7 63 0 ACCCTACCTA 0.937594 -57 ********** Masking position 10 Map Score: 4.16269 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 249 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 GGGTTGCGTACGGGTTAGATAAGAG 2 6 1 GCGTACGGGT 0.977438 -34 ACTCACCCGCGCAGAGTGTTTATCCCT 3 8 0 GCAGAGTGTT 0.910364 -33 ATGCAAGGGCGCGGCGTGGTGGTGAGTTCT 6 58 0 GCGGCGTGGT 0.992891 -86 TGTACCAAAGGCACCCAGGTCATGCAAGGG 6 79 0 GCACCCAGGT 0.961683 -65 GCAGCCGGGTTTGGACGTGC 7 1 1 GCAGCCGGGT 0.994583 -119 TTCCTGGTGCACGTCCTGTTCGTTGAATAG 7 46 1 ACGTCCTGTT 0.861276 -74 ********** Masking position 10 Map Score: 3.0251 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 259 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TACTCACCCGCGCAGAGTGTTTATCCCT 3 9 0 CGCAGAGTGT 0.995946 -32 GCGCAGGAAAAGCAACGTGTCTTTTTCAAA 6 13 1 AGCAACGTGT 0.960125 -131 CATGCAAGGGCGCGGCGTGGTGGTGAGTTC 6 59 0 CGCGGCGTGG 0.994636 -85 AAAACTGGCGCGCCGAGTGTACCAAAGGCA 6 96 0 CGCCGAGTGT 0.995163 -48 ********** Masking position 8 Map Score: 2.78808 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 102 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 1.74326e-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 8 ********** No masking Map Score: 1.74326e-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: 1.74326e-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