AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i310_bsub_mtub_100.orf -o310_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 ydiA 300 alternate gene name: ydxA; similar to thiamin-monophosphate kinase #2 Rv2979c 211 hypothetical protein Rv2979c Motif number 1 CTATACAAATATGGTCCGGTAGTTCAGTTGGT 1 42 1 ATGTCCGGAG 0.850898 -259 CTGTCACGCAGGAGGTCGCGGGTTCGAGTCCC 1 86 1 GGGGTCGCGG 0.993694 -215 TACATTAATGGCGGTCCGGACGGGACTCGAAC 1 107 0 GCGTCCGGCG 0.996963 -194 AGAGCAAAGAGGTGGCCGCGCAG 2 2 0 GGGGCCGCCA 0.973092 -210 ATACACTGGCGCGGTCCGCTCGCGCCGGCAGT 2 35 1 GCGTCCGCCG 0.995517 -177 TCAACTTACCGCAGGTCGGGCGAGGTGTTCGA 2 70 1 GCGGTCGGCG 0.996863 -142 GGTCGGGCGAGGTGTTCGAAGGTCCACAGGGC 2 83 1 GGGTTCGAGG 0.96554 -129 CAGGGCCAGAACGGGCCGAAGGAGGCGGCGTG 2 109 1 ACGGCCGAGG 0.95093 -103 GCCGAAGGAGGCGGCGTGGGCGACGACGCATC 2 123 1 GCGCGTGGCG 0.911115 -89 ACGACGCATCGGGGGGTGCCAGCTGTTGCGGG 2 145 1 GGGGGTGCAG 0.956354 -67 TTGCGGGTTGAGTGGTCGGTAGTTGTCAGTGG 2 170 1 AGGGTCGGAG 0.97706 -42 AGTTGTCAGTGGCGTGCGGTAGGAACAGAGAT 2 190 1 GGGTGCGGAG 0.991902 -22 ** ****** ** Masking position 8 Map Score: 19.3893 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 976 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 GTATAGGATTATTTTGGTTGCACCCTTAGG 1 18 0 ATTTTGGTTG 0.544808 -283 AACCCGCGACCTCCTGCGTGACAGGCAGGC 1 80 0 CTCCTGCGTG 0.981094 -221 TTTACTGTATCTTCTGCTTGGTGTCATAGC 1 177 1 CTTCTGCTTG 0.961974 -124 AGTTTATCGAATTTTGCTGGAATATCCAAG 1 232 0 ATTTTGCTGG 0.814376 -69 TGCTCTCATACACTGGCGCGGTCCGCTCGC 2 28 1 CACTGGCGCG 0.948264 -184 ACGCCGCCTCCTTCGGCCCGTTCTGGCCCT 2 110 0 CTTCGGCCCG 0.940911 -102 GGGCCGAAGGAGGCGGCGTGGGCGACGACG 2 121 1 AGGCGGCGTG 0.912853 -91 GGCGACGACGCATCGGGGGGTGCCAGCTGT 2 141 1 CATCGGGGGG 0.944186 -71 GGGGTGCCAGCTGTTGCGGGTTGAGTGGTC 2 157 1 CTGTTGCGGG 0.978948 -55 CGGTAGTTGTCAGTGGCGTGCGGTAGGAAC 2 186 1 CAGTGGCGTG 0.975418 -26 ********** Masking position 6 Map Score: 6.4903 Number of sites scoring better than the average of aligned sites = 2315 Number in coding regions = 2129 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 AAACATGATCGTTTCGTTTACATTAATGGC 1 127 0 GTTTCGTTTA 0.935964 -174 AAACGATCATGTTTTCGTTTTTTTTGTGTT 1 143 1 GTTTTCGTTT 0.980776 -158 TTTTTTTTGTGTTTTCTTTTACTGTATCTT 1 160 1 GTTTTCTTTT 0.979279 -141 TCATAGCCAAGCTTTCTTTATATCGGGAAC 1 200 1 GCTTTCTTTA 0.955137 -101 TTGAAAGGAGGTTTTGGTTC 1 291 1 GTTTTGGTTC 0.967147 -10 ********** Masking position 4 Map Score: 1.75821 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 248 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TGACAGGCAGGCATTCTAACCAACTGAACTA 1 61 0 GCATTCAACC 0.989889 -240 GGTCCGGACGGGACTCGAACCCGCGACCTCC 1 96 0 GGACTCAACC 0.982646 -205 ACCAAAACCTCCTTTCAACCCTGCTTATGCC 1 278 0 CCTTTCACCC 0.983738 -23 CAACTACCGACCACTCAACCCGCAACAGCTG 2 164 0 CCACTCACCC 0.99587 -48 ****** **** Masking position 5 Map Score: 0.655751 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 GTGCCCTAAGGGTGCAACCAAAATAATCCTAT 1 14 1 GGGCACCAAA 0.931215 -287 GACCTCCTGCGTGACAGGCAGGCATTCTAACC 1 71 0 GTACAGCAGG 0.980987 -230 TCTGCTTGGTGTCATAGCCAAGCTTTCTTTAT 1 189 1 GTATACCAAG 0.984732 -112 GAATTTTGCTGGAATATCCAAGATGTTCCCGA 1 222 0 GGATACCAAG 0.993165 -79 AGCACAAATAGGCATAAGCAGGGTTGAAAGGA 1 268 1 GGATAGCAGG 0.9908 -33 ** *** ***** Masking position 6 Map Score: 0.691455 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 106 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ********** No masking Map Score: -9.78117e-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: -9.78117e-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: -9.78117e-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