AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_bsub_mtub_100.orf -o127_bsub_mtub_100.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 yurN 57 similar to sugar permease #2 yurO 80 similar to multiple sugar-binding protein #3 yurP 215 similar to opine catabolism #4 msmX 120 multiple sugar-binding transport ATP-binding protein #5 Rv1234 149 hypothetical protein Rv1234 Motif number 1 ATAATGTTATATAACATTATAGTCTAATGC 2 33 0 ATAACATTAT 0.572576 -48 ATAATGTTATATAACATTATAGTCTAATGT 2 43 1 ATAACATTAT 0.572576 -38 GGACTTTAATATAACAATATATAATGTTAT 3 161 1 ATAACAATAT 0.85937 -55 ATAACGTTATATAACATTATATATTGTTAT 3 171 0 ATAACATTAT 0.572576 -45 ATAATGTTATATAACGTTATATAATAAAAA 3 181 1 ATAACGTTAT 0.499919 -35 ********** Masking position 4 Map Score: 12.0364 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 6 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 GTGCGAAGCTTCACCTTTTCTTTGAT 1 7 0 TCACCTTTTC 0.967712 -51 GTGAAGCTTCGCACCTTTTCTTTTTATAAA 1 23 1 GCACCTTTTC 0.990465 -35 TTTGATTTGGGCATTTTTTCGCATATAGAC 3 65 1 GCATTTTTTC 0.906267 -151 TTCGCATATAGACCCTTTGTCTGTCATCCG 3 82 1 GACCCTTTGT 0.823109 -134 ATCCTTCACTCCTCGTTTTTATTATATAA 3 197 0 TCCTCGTTTT 0.880887 -19 AAATCACCCAGCCATTTTTCGTGCATATTT 4 16 0 GCCATTTTTC 0.824164 -105 CTAACATCCCCCTTTGTTATTGTAAAC 4 104 0 CCCCCTTTGT 0.97036 -17 CGAACGGCGAGCATCGTTGCCGGGATAGGT 5 19 0 GCATCGTTGC 0.802034 -131 TTTTTCAGCGCCATCGTTTCATGTCCAGTC 5 105 0 CCATCGTTTC 0.960094 -45 TCTCCTCCGCCCCCCTTTTTCAGCGCCATC 5 120 0 CCCCCTTTTT 0.978714 -30 ********** Masking position 7 Map Score: 9.19931 Number of sites scoring better than the average of aligned sites = 2090 Number in coding regions = 1678 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 411 Fraction of orfs with sites within 600 bp upstream = 0.0660135 Motif number 3 TCTGAAAATGAAGAACCATTA 2 2 1 CTGAAAATGA 0.97928 -79 TTGGCCTCCTCTGGACATTAGACTATAATG 2 57 0 CTGGACATTA 0.976822 -24 AATCAAAAGCCAGAACTTGACTTAAGCTCT 3 42 0 CAGAACTTGA 0.957957 -174 TGAGAAATTTCAGAAAATAATATTGACAAT 3 122 1 CAGAAAATAA 0.829176 -94 CCGGGAGTAGCTGGACCTGACTGGACATGA 5 87 1 CTGGACCTGA 0.990008 -63 CTGGACCTGACTGGACATGAAACGATGGCG 5 97 1 CTGGACATGA 0.995474 -53 ********** Masking position 5 Map Score: 6.3187 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 171 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GACGTCAGTCTGCGGATTGAACAGCGAAG 3 8 1 GTTGCGGATG 0.986033 -208 TTATATTAAAGTCCGCGGGTAGGATTGTCAAT 3 143 0 GTCGCGGGTG 0.997911 -73 CGGCAACGATGCTCGCCGTTCGGTGGGCCTCG 5 27 1 GCCGCCGTTG 0.991592 -123 GGCCTCGGTCGCTCGCGGGTTGAGTGGATAGT 5 52 1 GCCGCGGGTG 0.998529 -98 TGAGTGGATAGTGTGCCGGGAGTAGCTGGACC 5 72 1 GTTGCCGGGG 0.988607 -78 ** ******* * Masking position 6 Map Score: 5.52378 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 27 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 ACTTAAGCTCTGGCTTCGCTGTTCAATCCGC 3 22 0 TGGCTCGCTG 0.985103 -194 TCGCTAAAATGGGCAGCGTTCATAAAATCAC 4 39 0 GGGCGCGTTC 0.984347 -82 TTTAGCGAGAGGGAATTGCTGTTACACTCAA 4 62 1 GGGATTGCTG 0.963992 -59 ACCGAACGGCGAGCATCGTTGCCGGGATAGG 5 20 0 GAGCTCGTTG 0.96696 -130 GCCGTTCGGTGGGCCTCGGTCGCTCGCGGGT 5 41 1 GGGCTCGGTC 0.993211 -109 ATAGTGTGCCGGGAGTAGCTGGACCTGACTG 5 79 1 GGGATAGCTG 0.9792 -71 TGAAAAAGGGGGGCGGAGGAGAATGAGAACC 5 128 1 GGGCGAGGAG 0.943176 -22 **** ****** Masking position 8 Map Score: 5.58874 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 334 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 TTATGCATTAGACTATAATGTTATATAACA 2 29 1 GACTATAATG 0.987534 -52 CTGGACATTAGACTATAATGTTATATAACA 2 47 0 GACTATAATG 0.987534 -34 AGAAATTTCAGAAAATAATATTGACAATCC 3 124 1 GAAAATAATA 0.853011 -92 CCTACCCGCGGACTTTAATATAACAATATA 3 152 1 GACTTTAATA 0.958356 -64 ********** Masking position 6 Map Score: 1.96149 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 32 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ATGTCCAGAGGAGGCCAACCCT 2 69 1 GAGGCCAACC 0.996548 -12 GGTGATCAACCTATCCCGGCA 5 2 1 GTGATCAACC 0.948989 -148 GCGAGCGACCGAGGCCCACCGAACGGCGAG 5 38 0 GAGGCCCACC 0.997735 -112 CATGTCCAGTCAGGTCCAGCTACTCCCGGC 5 86 0 CAGGTCCAGC 0.975727 -64 ********** Masking position 8 Map Score: 1.27543 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AACCATTATGCATTAGACTATAATGTTATA 2 24 1 CATTAGACTA 0.991365 -57 CTCCTCTGGACATTAGACTATAATGTTATA 2 52 0 CATTAGACTA 0.991365 -29 ********** Masking position 5 Map Score: 0.161442 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 Motif number 11 ********** 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