AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i138_bsub_mtub_300.orf -o138_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 rapJ 122 response regulator aspartate phosphatase #2 ycdF 106 similar to glucose 1-dehydrogenase #3 ycdG 24 similar to oligo-1,6-glucosidase #4 ycdH 187 similar to adhesion protein #5 ycdI 55 similar to ABC transporter (ATP-binding protein) Motif number 1 ATCGGTCTCACTTTCTCAAGATGTGCT 1 7 1 CTCCTTTCTC 0.98834 -116 CGGTCTGCCTCCTTCCTCCTGCTACTAT 1 105 0 CCTCTTCCTC 0.866067 -18 ACTACAGGTTCTCTGCTTTTTTTGTGCTGTT 2 24 1 CTCGCTTTTT 0.914648 -83 GTGGAAAATACCCTGTTTTTCCGAGTTGAAA 2 54 0 CCCGTTTTTC 0.994416 -53 TGATATCCTCCTCTGTTTCTCACTATGCAGT 2 83 0 CTCGTTTCTC 0.986125 -24 CCCGCAATCCCCCTGTTTTGTCTT 3 6 0 CCCCTGTTTT 0.948004 -19 ATTGAAGTAGCCCGGCATTTTTAGCCGGGTT 4 13 1 CCCGCATTTT 0.874691 -175 GCATTTTTAGCCGGGTTTTTTTAGTACATAT 4 27 1 CCGGTTTTTT 0.904821 -161 ATCGTATATCCCCTCTTTTTCAGTAACTTTA 4 167 0 CCCCTTTTTC 0.995314 -21 CGGAGGGGTGCACACTATTTCTTTGTGAGAA 5 23 1 CACCTATTTC 0.884503 -33 GTTAATCTTCCTTTCTCACAAAGAAAT 5 39 0 CTTCTTTCTC 0.936117 -17 *** ******* Masking position 10 Map Score: 14.9281 Number of sites scoring better than the average of aligned sites = 1548 Number in coding regions = 1252 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 2 ATCGGTCTCACTTTCTCAAGATGTG 1 6 1 TCTCACTTTC 0.856646 -117 CGGTCTGCCTCCTTCCTCCTGCTAC 1 108 0 TGCCTCCTTC 0.950082 -15 AACTACAGGTTCTCTGCTTTTTTTGTGCTG 2 23 1 TCTCTGCTTT 0.946354 -84 AGTGGAAAATACCCTGTTTTTCCGAGTTGA 2 56 0 ACCCTGTTTT 0.927046 -51 TTGATATCCTCCTCTGTTTCTCACTATGCA 2 85 0 CCTCTGTTTC 0.977117 -22 CCCGCAATCCCCCTGTTTTGTCTT 3 6 0 CCCCTGTTTT 0.985144 -19 CATTTATTTTTCCCGCCTGCAGAGCGAATA 4 57 0 TCCCGCCTGC 0.944464 -131 ATCGTATATCCCCTCTTTTTCAGTAACTT 4 169 0 CCCCTCTTTT 0.987972 -19 ATAGTGTGCACCCCTCCGGCGCACACTATC 5 11 0 CCCCTCCGGC 0.959561 -45 ********** Masking position 4 Map Score: 8.38806 Number of sites scoring better than the average of aligned sites = 1519 Number in coding regions = 1127 Number in noncoding regions = 392 Number of orfs with sites within 600 bp upstream = 382 Fraction of orfs with sites within 600 bp upstream = 0.0613556 Motif number 3 ATGTGCTGAATGTTAACGCTTTTAAGTGATTG 1 31 1 TTTAACGTTT 0.973298 -92 CTCCTGCTACTATTTATGTTATATTTTATCAT 1 86 0 TTTTATGTAT 0.941783 -37 TAAACCGAAGTCATTACGTTTTGCAAGAATAA 4 97 0 TATTACGTTT 0.986814 -91 TGACTTCGGTTTATTATGATATAGGATTACAA 4 116 1 TATTATGTAT 0.958385 -72 TAAATCAAAATGATAACGATTTTGTAATCCTA 4 137 0 TATAACGTTT 0.981211 -51 * ****** *** Masking position 6 Map Score: 1.46921 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 123 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 ATCCTCCTCTGTTTCTCACTATGCAGTGGA 2 80 0 GTTTCTCACT 0.955974 -27 GCACCCCTCCGGCGCACACTATC 5 4 0 GGCGCACACT 0.994662 -52 GCGCCGGAGGGGTGCACACTATTTCTTTGT 5 19 1 GGTGCACACT 0.98415 -37 ********** Masking position 8 Map Score: 0.69814 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 TGTTTTTCCGAGTTGAAAACAGCACAAAAA 2 42 0 AGTTGAAAAC 0.892223 -65 CTCACTATGCAGTGGAAAATACCCTGTTTT 2 66 0 AGTGGAAAAT 0.972673 -41 AGTGAGAAACAGAGGAGGATATCAAGT 2 90 1 AGAGGAGGAT 0.952688 -17 CGGGAAAAATAAATGAAAATGAAATTTATT 4 72 1 AAATGAAAAT 0.964106 -116 CAGTAACTTTAAATCAAAATGATAACGATT 4 148 0 AAATCAAAAT 0.860329 -40 TCTTTGTGAGAAAGGAAGATTAAC 5 42 1 AAAGGAAGAT 0.97224 -14 ********** Masking position 6 Map Score: 1.85294 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 662 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 6 ********** No masking Map Score: 5.06917e-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: 5.06917e-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: 5.06917e-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