AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_bsub_mtub_300.orf -o064_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 hisZ 250 histidyl-tRNA synthetase #2 hisD 99 hisD #3 hisI 126 hisI Motif number 1 TAAGATAACAGCGGAGGTGCTCGGGTTG 1 233 1 GCGGAGGTGC 0.944955 -18 GACCGGCAAAGAGGAGCCGCC 2 2 0 GAGGAGCCGC 0.621242 -98 GTGCAGTAGAAAGGACCGGCAAAGAGGAGC 2 15 0 AAGGACCGGC 0.953892 -85 GGGCGGCGGCGCGGTCACGTAG 2 88 0 GCGGCGGCGC 0.506836 -12 GCCCTAATGCGCGGCGCGGCGGTGGCGAAC 3 69 1 GCGGCGCGGC 0.506966 -58 ********** Masking position 4 Map Score: 8.09872 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 209 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 CTTTATGTTTGGCATGCTATAATACAAATC 1 34 0 GGCATGCTAT 0.97397 -217 GGTCGAAGGAGGCAGCCGAAC 3 2 0 GGCAGCCGAA 0.994532 -125 GAATAACTAGGGTAGCCTAACCTATATTAG 3 36 1 GGTAGCCTAA 0.987248 -91 CGCGCATTAGGGCATCCTAATATAGGTTAG 3 52 0 GGCATCCTAA 0.994454 -75 ACCGTGACTTGGCTGGCTGACAC 3 114 1 GGCTGGCTGA 0.974345 -13 ********** Masking position 7 Map Score: 5.12254 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 173 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 TTTTAGTTCAAATATCCTTCTCCTCATTAT 1 110 0 AATATCCTTC 0.98999 -141 TTGAACTAAAAATATCCTTACTGAAGTTAA 1 129 1 AATATCCTTA 0.961377 -122 TTAAGCGTTGATTTTCATTCTTTCATCTGC 1 155 1 ATTTTCATTC 0.961377 -96 AGGATTCGGAATTTTCCTTCATAAGATAAC 1 212 1 ATTTTCCTTC 0.98999 -39 ********** Masking position 5 Map Score: 2.85288 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 93 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 CAAATAGAGAACAAGGAGATAAAG 1 1 0 ACAGAGTAAG 0.973673 -250 CATGCCAAACATAAAGAATTTGAGATATTACGTA 1 48 1 ATAGAATGAG 0.978075 -203 AAAATCATGAATAATGTATTAAAGGTACGTAATA 1 73 0 ATAGTATAAG 0.967843 -178 TGATTTTTTCATAATGAGGAGAAGGATATTTGAA 1 100 1 ATAGAGAAAG 0.961469 -151 AAAAATATCCTTACTGAAGTTAAGCGTTGATTTT 1 136 1 TTAGAATAAG 0.984937 -115 TATTATCATATTAGCGAACTAAAGGATTCGGAAT 1 190 1 TTAGAATAAG 0.984937 -61 *** *** * *** Masking position 3 Map Score: 2.78784 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 47 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GGCGGCTCCTCTTTGCCGGTCCTTTCTA 2 6 1 CCCTCTTGCG 0.896818 -94 GTCCTTTCTACTGCACTGTACCGGTCAGATATC 2 29 1 CGCACGTACG 0.859187 -71 GGGCGGCGGCGCGGTCACGTAGACCATTC 2 81 0 CGCGCGTCCG 0.92594 -19 CACCGCCGCGCCGCGCATTAGGGCATCCTAATA 3 60 0 CGCGCTTAGG 0.928568 -67 GCCACACGTTCGCCACCGCCGCGCCGCGCATTA 3 73 0 CCCACGCCCG 0.549658 -54 GTGTCAGCCAGCCAAGTCACGGTGGTTTGAC 3 106 0 CGCCAGTCCG 0.98297 -21 * **** *** ** Masking position 4 Map Score: 1.36244 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 348 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CAACCCGAGCACCTCCGCTG 1 241 0 CAACCCGAGC 0.99015 -10 GGTCAGATATCGACTTGAGCTGCTCTGGGA 2 51 1 CGACTTGAGC 0.95169 -49 GTAGACCATTCTCCCAGAGCAGCTCAAGTC 2 62 0 CTCCCAGAGC 0.977669 -38 GGAGAATGGTCTACGTGACCGCGCCGCCGC 2 78 1 CTACGTGACC 0.97954 -22 ATAGGTTAGGCTACCCTAGTTATTCCTGTG 3 31 0 CTACCCTAGT 0.882762 -96 GGCGTCAAACCACCGTGACTTGGCTGGCTG 3 103 1 CACCGTGACT 0.903478 -24 ********** Masking position 8 Map Score: 0.435709 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 420 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 ********** No masking Map Score: -6.51267e-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: -6.51267e-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 9 ********** No masking Map Score: -6.51267e-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