AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i245_bsub_mtub_300.orf -o245_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 0.957848 -114 ATACTATATGAAATAGAATGACAAAGACCC 2 7 1 TTGAAAGAAG 0.992552 -155 ATATGACATATCTCATAGAGAAGGAGGGAAGCCG 2 138 1 TTCAAAGAAG 0.939625 -24 GTGTCTTGCGTTAGAAATAGAAGGAATGCCGCGA 3 52 0 TAGAAAGAAG 0.944237 -109 AACCAAACCATTTGAGGTATAATGGATAAAGTGA 3 93 1 TTGAGATAAG 0.868016 -68 GATTGATATATATGAAAGAGAGTGGAACATC 3 140 1 TTGAAAGAGG 0.99444 -21 CTGTAACCTATGTGAAGGAGAGAGTAAAT 4 116 1 TTGAGAGAGG 0.991151 -19 CCTTAATAGGTATGAGGCAGGAGGCATGATTATG 6 74 0 TTGAGAGGAG 0.98123 -53 GGTCATTGTTTTTGAGAAAGGAGGAGCCGGA 6 106 1 TTGAAAGGAG 0.988161 -21 TAAAAGGGTGTATGAAAGAGAGGCCAATCTGCCT 7 12 0 TTGAAAGAGC 0.954307 -113 ATTTTCTCTGTATGTAAAAGGGTGTATGAAAGAG 7 26 0 TTGTAAGGGG 0.93435 -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 GACCATTTCCCTTCTTTTGTTCGC 1 5 1 ATTTCCCTTC 0.873957 -131 GGTCTTTGTCATTCTATTTCATATAGTAT 2 10 0 ATTCTATTTC 0.784948 -152 AAAAAACAATTTCTTCCTTCTATATTGTTT 2 87 1 TTCTTCCTTC 0.949663 -75 CGGCTTCCCTCCTTCTCTATGAGAT 2 147 0 TCCCTCCTTC 0.965358 -15 GGCTTTTTCTTGCTTTACGGAAG 3 4 1 TTTTTCTTGC 0.868758 -157 CGCGGCATTCCTTCTATTTCTAACGCAAGA 3 53 1 CTTCTATTTC 0.710661 -108 GATGTTCCACTCTCTTTCATATATATCA 3 143 0 ACTCTCTTTC 0.960736 -18 ATTTACTCTCTCCTTCACATAGGTTA 4 119 0 TCTCTCCTTC 0.968392 -16 CATCACCTCATTTTTATTTCTAGACTATTC 5 55 0 TTTTTATTTC 0.805239 -24 TCCGGCTCCTCCTTTCTCAAAAACAA 6 111 0 TCCTCCTTTC 0.920641 -16 GGCAGATTGGCCTCTCTTTCATACACCCTT 7 13 1 CCTCTCTTTC 0.942743 -112 ACCGGCAGGAATTTTCTTTCGAAAGGAGAA 8 49 1 ATTTTCTTTC 0.943071 -66 TAATATGTATTTCTCCTTTCGAAAGAAAAT 8 59 0 TTCTCCTTTC 0.905172 -56 CACCTTCCTGCTTTGGAAAAC 8 104 0 ACCTTCCTGC 0.828607 -11 ********** Masking position 8 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 CCTTTATGCAAGGGTCTTTGTCATTCTATTT 2 21 0 AGGGTCTTTT 0.965391 -141 GCAGGCTGTTATGGCCTGCTTTTTTTTGTCC 4 18 1 ATGGCCTGCT 0.951515 -117 GGAAGCGCCGAAGGTCTTTCTAGA 6 4 0 AAGGTCTTTT 0.984106 -123 GGCGCTTCCGAAGGTCTTCTTATTGAAAAAG 6 26 1 AAGGTCTTCT 0.983666 -101 CATACCTATTAAGGTCATTGTTTTTGAGAAA 6 94 1 AAGGTCATTT 0.917329 -33 TACAGAGAAAATGGTCTGTTTTTGCAGTTTG 7 48 1 ATGGTCTGTT 0.986913 -77 TTTTTGCAGTTTGGTCTGCATTATAATCAAG 7 66 1 TTGGTCTGCT 0.929818 -59 CATTATAATCAAGGTGTGTGTGCAAGCTTAC 7 84 1 AAGGTGTGTT 0.942047 -41 ********* * Masking position 11 Map Score: 7.7704 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 158 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 AGTCATTTGGCATGTGTCTTTATTCGTGGA 1 101 1 CATGTGTCTT 0.946585 -35 ACCCTTTATGCAAGGGTCTTTGTCATTCTA 2 24 0 CAAGGGTCTT 0.992445 -138 TTGGTTGTTTCGAGTGTCTTGCGTTAGAAA 3 69 0 CGAGTGTCTT 0.992445 -92 TCGGAAGCGCCGAAGGTCTTTCTAGA 6 7 0 CGAAGGTCTT 0.992445 -120 TCGGCGCTTCCGAAGGTCTTCTTATTGAAA 6 24 1 CGAAGGTCTT 0.992445 -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 0.975944 -67 TTTTATGAAAAAAACAAATTGACAGGATGA 2 58 1 AAAACAAATT 0.924991 -104 ACAGGATGAAAAAACAATTTCTTCCTTCTA 2 79 1 AAAACAATTT 0.974978 -83 CCAAATTTTGAAAACAATATAGAAGGAAGA 2 98 0 AAAACAATAT 0.94637 -64 ACATACAGCTAAAACAATTTCCGGGACAAA 4 42 0 AAAACAATTT 0.974978 -93 GATTATGACTAAAACACGACTTAGCTTTTT 6 51 0 AAAACACGAC 0.844726 -76 CCTGCTTTGGAAAACGCTTTCATTTTAAAG 8 89 0 AAAACGCTTT 0.904703 -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 0.915965 -11 GGAGTGAGCAGGCTGTTATGGCC 4 4 1 GTGAGCAGGC 0.964722 -131 GCTGTATGTAGGCGGCCGCCTATACGATCT 4 63 1 GGCGGCCGCC 0.499929 -72 ATAGGTATGAGGCAGGAGGCATGATTATGA 6 73 0 GGCAGGAGGC 0.988339 -54 TTTTTGAGAAAGGAGGAGCCGGA 6 114 1 AGGAGGAGCC 0.966699 -13 GTTGAGAGACGGCAGCAGCC 8 1 0 GGCAGCAGCC 0.649688 -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 0.93482 -40 ACAAAAAAAAGCAGGCCATAACAGCCTGCT 4 17 0 GCAGGCCATA 0.980007 -118 CACATAGGTTACAGTCCAGAGTATGAGAAT 4 100 0 ACAGTCCAGA 0.95643 -35 TCTAGACTATTCAGTCCAAAAAGTACATAC 5 37 0 TCAGTCCAAA 0.937158 -42 TGTATGAAAGAGAGGCCAATCTGCCTA 7 8 0 AGAGGCCAAT 0.902255 -117 AACTGCAAAAACAGACCATTTTCTCTGTAT 7 47 0 ACAGACCATT 0.91961 -78 TGATTATAATGCAGACCAAACTGCAAAAAC 7 65 0 GCAGACCAAA 0.976013 -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 ATCCCGACCCGTGGTAAAATTTTGATATTG 1 36 0 GTGGTAAAAT 0.879438 -100 ACGTGTTTTGGTGGAAAAATGAGTCATTTG 1 80 1 GTGGAAAAAT 0.952213 -56 ATGCCGCGATGTGGAAAATGGAACCGTCTT 3 31 0 GTGGAAAATG 0.96361 -130 TTGAGGTATAATGGATAAAGTGAATAACAG 3 104 1 ATGGATAAAG 0.883167 -57 CATGTGGTAAAGGATTCTTTGCC 5 4 1 GTGGTAAAGG 0.963559 -75 AGGTCTTCTTATTGAAAAAGCTAAGTCGTG 6 37 1 ATTGAAAAAG 0.824862 -90 TTTTCTCTGTATGTAAAAGGGTGTATGAAA 7 29 0 ATGTAAAAGG 0.796134 -96 CCTTCCTGCTTTGGAAAACGCTTTCATTTT 8 93 0 TTGGAAAACG 0.882638 -22 ********** Masking position 7 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 ********** 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 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