AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i246_bsub_mtub_300.orf -o246_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 yeeG 135 yeeG #2 rapH 161 response regulator aspartate phosphatase #3 yeeI 160 similar to hypothetical proteins #4 yeeK 134 similar to hypothetical proteins #5 yesE 78 alternate gene name: yeeL #6 cotJA 126 cotJA #7 yesJ 124 alternate gene name: yeeN, yfxC, yfxD; similar to hypothetical proteins #8 yesL 114 similar to hypothetical proteins from B. subtilis Motif number 1 GTGGTAAAATTTTGATATTGAGCGAACAAAAGAA 1 22 0 TTGAATGAGG 0.960428 -114 ATACTATATGAAATAGAATGACAAAGACCC 2 7 1 TTGAAAGAAG 0.993023 -155 ATATGACATATCTCATAGAGAAGGAGGGAAGCCG 2 138 1 TTCAAAGAAG 0.943253 -24 GTGTCTTGCGTTAGAAATAGAAGGAATGCCGCGA 3 52 0 TAGAAAGAAG 0.947604 -109 AACCAAACCATTTGAGGTATAATGGATAAAGTGA 3 93 1 TTGAGATAAG 0.875378 -68 GATTGATATATATGAAAGAGAGTGGAACATC 3 140 1 TTGAAAGAGG 0.994792 -21 CTGTAACCTATGTGAAGGAGAGAGTAAAT 4 116 1 TTGAGAGAGG 0.991711 -19 CCTTAATAGGTATGAGGCAGGAGGCATGATTATG 6 74 0 TTGAGAGGAG 0.982405 -53 GGTCATTGTTTTTGAGAAAGGAGGAGCCGGA 6 106 1 TTGAAAGGAG 0.988907 -21 TAAAAGGGTGTATGAAAGAGAGGCCAATCTGCCT 7 12 0 TTGAAAGAGC 0.957094 -113 ATTTTCTCTGTATGTAAAAGGGTGTATGAAAGAG 7 26 0 TTGTAAGGGG 0.938275 -99 * *** * **** * Masking position 1 Map Score: 17.7397 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 259 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 GCGAACAAAAGAAGGGAAATGGTC 1 5 0 GAAGGGAAAT 0.864919 -131 ATACTATATGAAATAGAATGACAAAGACC 2 10 1 GAAATAGAAT 0.771198 -152 AAACAATATAGAAGGAAGAAATTGTTTTTT 2 87 0 GAAGGAAGAA 0.945717 -75 ATCTCATAGAGAAGGAGGGAAGCCG 2 147 1 GAAGGAGGGA 0.962593 -15 CTTCCGTAAAGCAAGAAAAAGCC 3 4 0 GCAAGAAAAA 0.859407 -157 TCTTGCGTTAGAAATAGAAGGAATGCCGCG 3 53 0 GAAATAGAAG 0.694013 -108 TGATATATATGAAAGAGAGTGGAACATC 3 143 1 GAAAGAGAGT 0.957618 -18 TAACCTATGTGAAGGAGAGAGTAAAT 4 119 1 GAAGGAGAGA 0.965861 -16 GAATAGTCTAGAAATAAAAATGAGGTGATG 5 55 1 GAAATAAAAA 0.792443 -24 TTGTTTTTGAGAAAGGAGGAGCCGGA 6 111 1 GAAAGGAGGA 0.914623 -16 AAGGGTGTATGAAAGAGAGGCCAATCTGCC 7 13 0 GAAAGAGAGG 0.938289 -112 TTCTCCTTTCGAAAGAAAATTCCTGCCGGT 8 49 0 GAAAGAAAAT 0.938641 -66 ATTTTCTTTCGAAAGGAGAAATACATATTA 8 59 1 GAAAGGAGAA 0.898111 -56 GTTTTCCAAAGCAGGAAGGTG 8 104 1 GCAGGAAGGT 0.816997 -11 ********** Masking position 3 Map Score: 15.8098 Number of sites scoring better than the average of aligned sites = 2030 Number in coding regions = 1594 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 449 Fraction of orfs with sites within 600 bp upstream = 0.0721169 Motif number 3 AAATAGAATGACAAAGACCCTTGCATAAAGG 2 21 1 AAAAGACCCT 0.970947 -141 GGACAAAAAAAAGCAGGCCATAACAGCCTGC 4 18 0 AGCAGGCCAT 0.959195 -117 TCTAGAAAGACCTTCGGCGCTTCC 6 4 1 AAAAGACCTT 0.986699 -123 CTTTTTCAATAAGAAGACCTTCGGAAGCGCC 6 26 0 AGAAGACCTT 0.986284 -101 TTTCTCAAAAACAATGACCTTAATAGGTATG 6 94 0 AAATGACCTT 0.93004 -33 CAAACTGCAAAAACAGACCATTTTCTCTGTA 7 48 0 AACAGACCAT 0.989052 -77 CTTGATTATAATGCAGACCAAACTGCAAAAA 7 66 0 AGCAGACCAA 0.940734 -59 GTAAGCTTGCACACACACCTTGATTATAATG 7 84 0 AACACACCTT 0.951161 -41 * ********* Masking position 1 Map Score: 7.7704 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 175 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 AGTCATTTGGCATGTGTCTTTATTCGTGGA 1 101 1 CATGTGTCTT 0.9367 -35 ACCCTTTATGCAAGGGTCTTTGTCATTCTA 2 24 0 CAAGGGTCTT 0.990966 -138 TTGGTTGTTTCGAGTGTCTTGCGTTAGAAA 3 69 0 CGAGTGTCTT 0.990966 -92 TCGGAAGCGCCGAAGGTCTTTCTAGA 6 7 0 CGAAGGTCTT 0.990966 -120 TCGGCGCTTCCGAAGGTCTTCTTATTGAAA 6 24 1 CGAAGGTCTT 0.990966 -103 ********** Masking position 7 Map Score: 7.38327 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TTTTTCCACCAAAACACGTTCTCACCCCAC 1 69 0 AAAACACGTT 0.974415 -67 TTTTATGAAAAAAACAAATTGACAGGATGA 2 58 1 AAAACAAATT 0.920477 -104 ACAGGATGAAAAAACAATTTCTTCCTTCTA 2 79 1 AAAACAATTT 0.973506 -83 CCAAATTTTGAAAACAATATAGAAGGAAGA 2 98 0 AAAACAATAT 0.943064 -64 ACATACAGCTAAAACAATTTCCGGGACAAA 4 42 0 AAAACAATTT 0.973506 -93 GATTATGACTAAAACACGACTTAGCTTTTT 6 51 0 AAAACACGAC 0.836227 -76 CCTGCTTTGGAAAACGCTTTCATTTTAAAG 8 89 0 AAAACGCTTT 0.902928 -26 ********** Masking position 4 Map Score: 6.22163 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 135 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 CATAGAGAAGGAGGGAAGCCG 2 151 1 GAGGGAAGCC 0.91904 -11 GGAGTGAGCAGGCTGTTATGGCC 4 4 1 GTGAGCAGGC 0.966083 -131 AGATCGTATAGGCGGCCGCCTACATACAGC 4 63 0 GGCGGCCGCC 0.499935 -72 ATAGGTATGAGGCAGGAGGCATGATTATGA 6 73 0 GGCAGGAGGC 0.988673 -54 TTTTTGAGAAAGGAGGAGCCGGA 6 114 1 AGGAGGAGCC 0.967989 -13 GTTGAGAGACGGCAGCAGCC 8 1 0 GGCAGCAGCC 0.645503 -114 ********** Masking position 5 Map Score: 3.40227 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 450 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 GAATAAAGACACATGCCAAATGACTCATTT 1 96 0 ACATGCCAAA 0.928749 -40 ACAAAAAAAAGCAGGCCATAACAGCCTGCT 4 17 0 GCAGGCCATA 0.978054 -118 CACATAGGTTACAGTCCAGAGTATGAGAAT 4 100 0 ACAGTCCAGA 0.952323 -35 TCTAGACTATTCAGTCCAAAAAGTACATAC 5 37 0 TCAGTCCAAA 0.93129 -42 TGTATGAAAGAGAGGCCAATCTGCCTA 7 8 0 AGAGGCCAAT 0.893523 -117 AACTGCAAAAACAGACCATTTTCTCTGTAT 7 47 0 ACAGACCATT 0.912258 -78 TGATTATAATGCAGACCAAACTGCAAAAAC 7 65 0 GCAGACCAAA 0.97367 -60 ********** Masking position 3 Map Score: 3.34251 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 344 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 CAATATCAAAATTTTACCACGGGTCGGGAT 1 36 1 ATTTTACCAC 0.868939 -100 CAAATGACTCATTTTTCCACCAAAACACGT 1 80 0 ATTTTTCCAC 0.947675 -56 AAGACGGTTCCATTTTCCACATCGCGGCAT 3 31 1 CATTTTCCAC 0.960108 -130 CTGTTATTCACTTTATCCATTATACCTCAA 3 104 0 CTTTATCCAT 0.872945 -57 GGCAAAGAATCCTTTACCACATG 5 4 0 CCTTTACCAC 0.960052 -75 CACGACTTAGCTTTTTCAATAAGAAGACCT 6 37 0 CTTTTTCAAT 0.810636 -90 TTTCATACACCCTTTTACATACAGAGAAAA 7 29 1 CCTTTTACAT 0.780192 -96 AAAATGAAAGCGTTTTCCAAAGCAGGAAGG 8 93 1 CGTTTTCCAA 0.872376 -22 ********** Masking position 9 Map Score: 2.93119 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 953 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 9 AACAAAAGAAGGGAAATGGTC 1 2 0 GGGAAATGGT 0.9817 -134 ACCACGGGTCGGGATAAGGTGGGGTGAGAA 1 51 1 GGGATAAGGT 0.902305 -85 GTGTTTTGGTGGAAAAATGAGTCATTTGGC 1 82 1 GGAAAAATGA 0.758414 -54 CTTGCTTTACGGAAGACGGTTCCATTTTCC 3 19 1 GGAAGACGGT 0.969199 -142 GCCGCGATGTGGAAAATGGAACCGTCTTCC 3 29 0 GGAAAATGGA 0.971973 -132 TTACATACAGAGAAAATGGTCTGTTTTTGC 7 43 1 AGAAAATGGT 0.911815 -82 TTCCTGCTTTGGAAAACGCTTTCATTTTAA 8 91 0 GGAAAACGCT 0.943 -24 ********** Masking position 6 Map Score: 3.24568 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 654 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 ********** No masking Map Score: 3.02224e-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: 3.02224e-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 12 ********** No masking Map Score: 3.02224e-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