AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i046_bsub_mtub_300.orf -o046_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 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #2 yqiS 124 similar to phosphate butyryltransferase #3 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) Motif number 1 TCAAGCCCCTCCTTTATGCTTTTAAAAATGAA 1 52 0 CCTTTATGTT 0.98274 -22 CAGATGTTTGCGTTTATTCTGCAAA 2 4 0 CGTTTATTTC 0.981619 -121 TCGACTCCGCCTTTTATTATGCAAGTTCCATG 2 83 0 CTTTTATTTC 0.984496 -42 CTGTTACCACCTTTCTTGTTTCGACTCCGCC 2 104 0 CCTTTCTTTT 0.990547 -21 TCAGAAAACCCCTTTATCTTTTCATTTCCTTT 3 13 1 CCTTTATCTT 0.98274 -140 CTTTTCATTTCCTTTATTGTCCAGCGGAAAAA 3 30 1 CCTTTATTTC 0.99471 -123 ATGTTACCACGTTTTCTTCTCTTGACAAAATA 3 63 0 GTTTTCTTTT 0.871903 -90 ******** * * Masking position 7 Map Score: 8.29772 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 330 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 GCCAGCTCTTAAGGGTGCTGTCATACCAGGTA 2 52 0 AAGGGGCTTC 0.98535 -73 TTGCATAATAAAAGGCGGAGTCGAAACAAGAA 2 91 1 AAAGGGGATC 0.993782 -34 TCGAAACAAGAAAGGTGGTAACAG 2 111 1 AAAGGGGTAC 0.997129 -14 ATGAAAAGATAAAGGGGTTTTCTGAAG 3 6 0 AAAGGGTTTC 0.992007 -147 CAAGAGAAGAAAACGTGGTAACATAGGGTTGT 3 71 1 AAACGGGTAC 0.989963 -82 TTTTTTCATACAAAGGGGTATCGGG 3 138 1 CAAAGGGTTC 0.978446 -15 ***** *** ** Masking position 2 Map Score: 7.47179 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 143 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 TTAAAAATGAATGGCTTTGCCATCTGCGGC 1 33 0 ATGGCTTTGC 0.950275 -41 ACATTCGTGCAGATGTTTGCGTTTATTCTG 2 15 0 AGATGTTTGC 0.981065 -110 GAAAAGATAAAGGGGTTTTCTGAAG 3 6 0 AGGGGTTTTC 0.969219 -147 TCTTGACAAAATATTTTTTCCGCTGGACAA 3 46 0 ATATTTTTTC 0.914281 -107 GTGGTAACATAGGGTTGTGCAAATTATTGC 3 85 1 AGGGTTGTGC 0.974209 -68 AGGGTTGTGCAAATTATTGCAACGGAATAA 3 95 1 AAATTATTGC 0.773376 -58 AACGGAATAAATAGGTGTGCAAATTTTTTC 3 115 1 ATAGGTGTGC 0.967316 -38 ATAGGTGTGCAAATTTTTTCATACAAAGGG 3 125 1 AAATTTTTTC 0.881567 -28 ********** Masking position 1 Map Score: 6.81093 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 798 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 AGGGTGCTGTCATACCAGGTATACCGAAAC 2 43 0 CATACCAGGT 0.986863 -82 ATGCAAGTTCCATGCCAGCTCTTAAGGGTG 2 67 0 CATGCCAGCT 0.971297 -58 CTGTTACCACCTTTCTTGTTTC 2 113 0 GTTACCACCT 0.99109 -12 ACAACCCTATGTTACCACGTTTTCTTCTCT 3 73 0 GTTACCACGT 0.99109 -80 CCCGATACCCCTTTGTATGAAAA 3 140 0 GATACCCCTT 0.963402 -13 ********** Masking position 3 Map Score: 3.73656 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 35 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TTGCAGAATAAACGCAAACATCTGCACGAA 2 12 1 AACGCAAACA 0.942267 -113 ATACCAGGTATACCGAAACATTCGTGCAGA 2 32 0 TACCGAAACA 0.941515 -93 TAAAAGGCGGAGTCGAAACAAGAAAGGTGG 2 99 1 AGTCGAAACA 0.967777 -26 AAACAAGAAAGGTGGTAACAG 2 114 1 GGTGGTAACA 0.933326 -11 TTTATTGTCCAGCGGAAAAAATATTTTGTC 3 42 1 AGCGGAAAAA 0.981356 -111 GAGAAGAAAACGTGGTAACATAGGGTTGTG 3 74 1 CGTGGTAACA 0.933326 -79 AAATTATTGCAACGGAATAAATAGGTGTGC 3 105 1 AACGGAATAA 0.856054 -48 TACCCCTTTGTATGAAAAAATTTGCACACC 3 128 0 TATGAAAAAA 0.592582 -25 ********** Masking position 7 Map Score: 2.81637 Number of sites scoring better than the average of aligned sites = 3043 Number in coding regions = 2745 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 6 ********** No masking Map Score: -3.59945e-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: -3.59945e-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: -3.59945e-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