AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i310_bsub_mtub_300.orf -o310_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 ydiA 300 alternate gene name: ydxA; similar to thiamin-monophosphate kinase #2 Rv2979c 211 hypothetical protein Rv2979c Motif number 1 CTATACAAATATGGTCCGGTAGTTCAGTTGGT 1 42 1 ATGGTCGGAG 0.88748 -259 CTGTCACGCAGGAGGTCGCGGGTTCGAGTCCC 1 86 1 GGAGGCGCGG 0.98352 -215 TACATTAATGGCGGTCCGGACGGGACTCGAAC 1 107 0 GCGGTCGGCG 0.996477 -194 AGAGCAAAGAGGTGGCCGCGCAG 2 2 0 GGTGGCGCCA 0.922677 -210 GGACCGCGCCAGTGTATGAGAGCAAAGAGGTG 2 20 0 AGTGTTGAAG 0.662929 -192 ATACACTGGCGCGGTCCGCTCGCGCCGGCAGT 2 35 1 GCGGTCGCCG 0.994803 -177 TCAACTTACCGCAGGTCGGGCGAGGTGTTCGA 2 70 1 GCAGGCGGCG 0.990435 -142 GGTCGGGCGAGGTGTTCGAAGGTCCACAGGGC 2 83 1 GGTGTCGAGG 0.97117 -129 CAGGGCCAGAACGGGCCGAAGGAGGCGGCGTG 2 109 1 ACGGGCGAGG 0.963254 -103 GCCGAAGGAGGCGGCGTGGGCGACGACGCATC 2 123 1 GCGGCTGGCG 0.945394 -89 ACGACGCATCGGGGGGTGCCAGCTGTTGCGGG 2 145 1 GGGGGTGCAG 0.98144 -67 TTGCGGGTTGAGTGGTCGGTAGTTGTCAGTGG 2 170 1 AGTGGCGGAG 0.979693 -42 AGTTGTCAGTGGCGTGCGGTAGGAACAGAGAT 2 190 1 GGCGTCGGAG 0.979269 -22 ***** *** ** Masking position 8 Map Score: 18.1205 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 1064 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 TGGTTAGAATGCCTGCCTGTCACGCAGGAG 1 70 1 GCCTGCCTGT 0.975954 -231 TCGAACCCGCGACCTCCTGCGTGACAGGCA 1 83 0 GACCTCCTGC 0.894449 -218 GTCCCGTCCGGACCGCCATTAATGTAAACG 1 113 1 GACCGCCATT 0.900855 -188 CTGCGCGGCCACCTCTTTGCTCTCAT 2 7 1 GGCCACCTCT 0.954622 -205 CGCGAGCGGACCGCGCCAGTGTATGAGAGC 2 29 0 CCGCGCCAGT 0.977138 -183 GGTCCGCTCGCGCCGGCAGTGACTCAACTT 2 47 1 CGCCGGCAGT 0.947838 -165 GAACACCTCGCCCGACCTGCGGTAAGTTGA 2 70 0 CCCGACCTGC 0.831883 -142 TCGTCGCCCACGCCGCCTCCTTCGGCCCGT 2 119 0 CGCCGCCTCC 0.987294 -93 ACGCATCGGGGGGTGCCAGCTGTTGCGGGT 2 148 1 GGGTGCCAGC 0.930386 -64 TGTTCCTACCGCACGCCACTGACAACTACC 2 187 0 GCACGCCACT 0.922146 -25 ********** Masking position 7 Map Score: 6.60314 Number of sites scoring better than the average of aligned sites = 3100 Number in coding regions = 2830 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 3 CTAAGGGTGCAACCAAAATAATCCTATACA 1 19 1 AACCAAAATA 0.959727 -282 CATTAATGTAAACGAAACGATCATGTTTTC 1 129 1 AACGAAACGA 0.958637 -172 ACACAAAAAAAACGAAAACATGATCGTTTC 1 142 0 AACGAAAACA 0.992801 -159 AGATACAGTAAAAGAAAACACAAAAAAAAC 1 159 0 AAAGAAAACA 0.96354 -142 GAACCAAAACCTCCTTTCAAC 1 290 0 AACCAAAACC 0.977091 -11 ********** Masking position 5 Map Score: 3.22725 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 210 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 4 TGACAGGCAGGCATTCTAACCAACTGAACTA 1 61 0 GCATTCAACC 0.989733 -240 GGTCCGGACGGGACTCGAACCCGCGACCTCC 1 96 0 GGACTCAACC 0.982379 -205 ACCAAAACCTCCTTTCAACCCTGCTTATGCC 1 278 0 CCTTTCACCC 0.983484 -23 CAACTACCGACCACTCAACCCGCAACAGCTG 2 164 0 CCACTCACCC 0.995802 -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 ********** 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 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