AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i123_bsub_mtub_100.orf -o123_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 yfiL 143 similar to ABC transporter (ATP-binding protein) #2 fadD26 286 fadD26 Motif number 1 CGTGCGGCATGTAGCGGCAGATAGAACATAG 1 73 0 GTGCGGCAGA 0.825682 -71 CTGCCGCTACATGCCGCACGCCTTTCTTTCT 1 84 1 ATCCGCACGC 0.968809 -60 TTCGTCACCGGCATCGCACACGTCACACCAA 2 18 1 GCTCGCACAC 0.961718 -269 CACACCAACCACAGCGGACGCGGCACGGCAC 2 41 1 ACGCGGACGC 0.985583 -246 AGCGGACGCGGCACGGCACGCGGAAGGGACG 2 53 1 GCCGGCACGC 0.993475 -234 GGGACGTTAGACTCGGCTAGCACCACCACCG 2 78 1 ACCGGCTAGC 0.870855 -209 CCACCACCGTGCCCAGGCAACGACGCCGGCC 2 100 1 GCCAGGCAAC 0.912749 -187 CCAGGCAACGACGCCGGCCGTCGCTAAGAAA 2 112 1 ACCCGGCCGT 0.949755 -175 CATGAATAAGGCCGCGCCCGCCCCGACAAAT 2 155 1 GCGCGCCCGC 0.911828 -132 GCTCCGCTATGCCTAGCCCGCAAATGTAAGG 2 191 0 GCTAGCCCGC 0.982351 -96 GCATGTCTGCGCAGCGCCAGCCGATCTCCCC 2 238 0 GCGCGCCAGC 0.91101 -49 GCGCAGACATGCTGCGGAAGCAGAACTGCGT 2 257 1 GCGCGGAAGC 0.604276 -30 ** ******** Masking position 6 Map Score: 23.2107 Number of sites scoring better than the average of aligned sites = 2150 Number in coding regions = 2036 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 CGCTTCTCTGAAAAGGCCTTTTACAGGCCT 1 31 1 AAAAGGCCTT 0.988758 -113 GGGCATGAAAAAAAGGCCTGTAAAAGGCCT 1 44 0 AAAAGGCCTG 0.997834 -100 GTAGAAGAAAGAAAGGCGTGCGGCATGTAG 1 90 0 GAAAGGCGTG 0.993044 -54 ATGGATCAAAAAAAGGAGTGAGACGAC 1 127 1 AAAAGGAGTG 0.983797 -17 CCCCTAGACTAAAACCCCTGCTCCGCTATG 2 211 0 AAAACCCCTG 0.973791 -76 ********** Masking position 4 Map Score: 6.90779 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 348 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TCTGCCGCTACATGCCGCACGCCTTTCTTT 1 83 1 CATGCCGCAC 0.964661 -61 TTCCGCGTGCCGTGCCGCGTCCGCTGTGGT 2 48 0 CGTGCCGCGT 0.995305 -239 GTCTAACGTCCCTTCCGCGTGCCGTGCCGC 2 60 0 CCTTCCGCGT 0.968841 -227 GCACCACCACCGTGCCCAGGCAACGACGCC 2 97 1 CGTGCCCAGG 0.959526 -190 TAAGGCCGCGCCCGCCCCGACAAATGATTA 2 161 1 CCCGCCCCGA 0.984171 -126 CTCCGCTATGCCTAGCCCGCAAATGTAAGG 2 191 0 CCTAGCCCGC 0.913949 -96 GACTAAAACCCCTGCTCCGCTATGCCTAGC 2 205 0 CCTGCTCCGC 0.995286 -82 GAGATCGGCTGGCGCTGCGCAGACATGCTG 2 241 1 GGCGCTGCGC 0.935911 -46 GCTGCGCAGACATGCTGCGGAAGCAGAACT 2 254 1 CATGCTGCGG 0.979464 -33 ********** Masking position 8 Map Score: 10.6071 Number of sites scoring better than the average of aligned sites = 1263 Number in coding regions = 1178 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 TTTTCAGAGAAGCGTATATGCAAAACGTCAT 1 14 0 AGCTATATGC 0.986368 -130 GCGCAGCGCCAGCCGATCTCCCCCTAGACTA 2 230 0 AGCGATCTCC 0.994008 -57 CTGCTTCCGCAGCATGTCTGCGCAGCGCCAG 2 249 0 AGCTGTCTGC 0.994105 -38 ATGCTGCGGAAGCAGAACTGCGTAATCGTCA 2 265 1 AGCGAACTGC 0.99435 -22 *** ******* Masking position 9 Map Score: 2.18451 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 156 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 AAGCGTATATGCAAAACGTCATATG 1 6 0 GCAAAACGTC 0.972884 -138 AAAAAGGCCTGTAAAAGGCCTTTTCAGAGA 1 35 0 GTAAAAGGCC 0.992913 -109 TAGGGCATGAAAAAAAGGCCTGTAAAAGGC 1 46 0 AAAAAAGGCC 0.964091 -98 TGCTAGCCGAGTCTAACGTCCCTTCCGCGT 2 70 0 GTCTAACGTC 0.930592 -217 TTGACTTCATGAATAAGGCCGCGCCCGCCC 2 148 1 GAATAAGGCC 0.989874 -139 ********** Masking position 5 Map Score: 2.5886 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 313 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ********** No masking Map Score: -5.51791e-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 7 ********** No masking Map Score: -5.51791e-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 8 ********** No masking Map Score: -5.51791e-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