AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_ecoli_mtub_300.orf -o226_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 glyQ 300 glycine tRNA synthetase, alpha subunit Motif number 1 TTCGTTGAATATGGAAGCGTTATGCAAGGAT 1 24 1 AGGAAGCGTT 0.992596 -277 GAACAGTTCCAGGGAAGCTATGAAATGCGCG 1 109 1 AGGAAGCTAT 0.997605 -192 ACTGCTCTTTACGGAAGGTATAACCGCGCAT 1 133 0 AGGAAGGTAT 0.997617 -168 TACCCGCTGGATGGAAGATATACAGTACGAA 1 234 0 AGGAAGATAT 0.993521 -67 TGTGGATTTAAAGGAAGGGATCAGTATACCC 1 260 0 AGGAAGGGAT 0.99779 -41 * ********* Masking position 6 Map Score: 11.5188 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 42 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 2 GAATATGGAAGCGTTATGCAAGGATCAGGC 1 30 1 GCGTTATGCA 0.982782 -271 CGGTGTTATAACGTTTTGCCGCCTGATCCT 1 50 0 ACGTTTTGCC 0.99349 -251 GGTGACGTCGATTTTTTGCTCGCCGGTGTT 1 73 0 ATTTTTTGCT 0.891947 -228 GCGGATGGCCATTTTTTGCATCTTTCCATG 1 181 1 ATTTTTTGCA 0.935716 -120 ATCTTTCCATGCGTTAAGCCCTGCTTTTTC 1 200 1 GCGTTAAGCC 0.968864 -101 GTTAAGCCCTGCTTTTTCCCGTTTCGTACT 1 212 1 GCTTTTTCCC 0.972213 -89 ********** Masking position 5 Map Score: 4.88962 Number of sites scoring better than the average of aligned sites = 1737 Number in coding regions = 1597 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 3 TTGATCCTCTGCGTTCGTTGAAT 1 4 1 ATCCTCTGCG 0.978184 -297 GATGGAAGATATACAGTACGAAACGGGAAA 1 226 0 ATACAGTACG 0.980165 -75 TATATCTTCCATCCAGCGGGTATACTGATC 1 243 1 ATCCAGCGGG 0.994326 -58 ATCCACACGTATCCAGCACGAAATAAT 1 284 1 ATCCAGCACG 0.996718 -17 ********** Masking position 2 Map Score: 2.78338 Number of sites scoring better than the average of aligned sites = 777 Number in coding regions = 747 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TTGATCCTCTGCGTTCGTTGAATATGGA 1 7 1 CTCTGCTTGT 0.950189 -294 GTTTTGCCGCCTGATCCTTGCATAACGCTTCC 1 36 0 CTGATCTTCA 0.970838 -265 AAATCGACGTCACCGCCTTCGAACAGTTCCAG 1 89 1 CACCGCTTGA 0.973657 -212 GAAGGTATAACCGCGCATTTCATAGCTTCCCT 1 119 0 CCGCGCTTCA 0.992505 -182 AACAGACAAACTGCTCTTTACGGAAGGTATAA 1 141 0 CTGCTCTTCG 0.979742 -160 AGCAGTTTGTCTGTTCTTTTGACGCGGATGGC 1 158 1 CTGTTCTTGA 0.988251 -143 GTATACTGATCCCTTCCTTTAAATCCACACGT 1 262 1 CCCTTCTTAA 0.930377 -39 ****** ** ** Masking position 8 Map Score: 2.99161 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 540 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 GTGTTATAACGTTTTGCCGCCTGATCCTTG 1 48 0 GTTTTGCCGC 0.991583 -253 TTTACGGAAGGTATAACCGCGCATTTCATA 1 127 0 GTATAACCGC 0.995966 -174 GAAGGGATCAGTATACCCGCTGGATGGAAG 1 248 0 GTATACCCGC 0.997278 -53 ********** Masking position 4 Map Score: 2.6404 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ACGTCACCGCCTTCGAACAGTTCCAGGGAA 1 95 1 CTTCGAACAG 0.978385 -206 CGGTTATACCTTCCGTAAAGAGCAGTTTGT 1 138 1 TTCCGTAAAG 0.966857 -163 CTTTTTCCCGTTTCGTACTGTATATCTTCC 1 223 1 TTTCGTACTG 0.994969 -78 ATTATTTCGTGCTGGATACGTGTG 1 287 0 TTTCGTGCTG 0.991433 -14 ********** Masking position 2 Map Score: 2.1866 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 144 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: 7.91135e-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: 7.91135e-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: 7.91135e-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