AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_Glycyl_TRNA_synthase_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glyQ 300 glycine tRNA synthetase, alpha subunit Motif number 1 ATCCTTGCATAACGCTTCCATATTCAACGAA 1 24 0 AACGCTTCCT 0.992694 -277 CGCGCATTTCATAGCTTCCCTGGAACTGTTC 1 109 0 ATAGCTTCCT 0.997638 -192 ATGCGCGGTTATACCTTCCGTAAAGAGCAGT 1 133 1 ATACCTTCCT 0.99765 -168 TTCGTACTGTATATCTTCCATCCAGCGGGTA 1 234 1 ATATCTTCCT 0.993612 -67 GGGTATACTGATCCCTTCCTTTAAATCCACA 1 260 1 ATCCCTTCCT 0.997821 -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 GCCTGATCCTTGCATAACGCTTCCATATTC 1 30 0 TGCATAACGC 0.981806 -271 AGGATCAGGCGGCAAAACGTTATAACACCG 1 50 1 GGCAAAACGT 0.993117 -251 AACACCGGCGAGCAAAAAATCGACGTCACC 1 73 1 AGCAAAAAAT 0.886414 -228 CATGGAAAGATGCAAAAAATGGCCATCCGC 1 181 0 TGCAAAAAAT 0.932254 -120 GAAAAAGCAGGGCTTAACGCATGGAAAGAT 1 200 0 GGCTTAACGC 0.967189 -101 AGTACGAAACGGGAAAAAGCAGGGCTTAAC 1 212 0 GGGAAAAAGC 0.970656 -89 ********** Masking position 6 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 0.978258 -297 GATGGAAGATATACAGTACGAAACGGGAAA 1 226 0 ATACAGTACG 0.980233 -75 TATATCTTCCATCCAGCGGGTATACTGATC 1 243 1 ATCCAGCGGG 0.994345 -58 ATCCACACGTATCCAGCACGAAATAAT 1 284 1 ATCCAGCACG 0.996729 -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 0.946234 -294 GTTTTGCCGCCTGATCCTTGCATAACGCTTCC 1 36 0 CTGATCTTCA 0.968467 -265 AAATCGACGTCACCGCCTTCGAACAGTTCCAG 1 89 1 CACCGCTTGA 0.971509 -212 GAAGGTATAACCGCGCATTTCATAGCTTCCCT 1 119 0 CCGCGCTTCA 0.991881 -182 AACAGACAAACTGCTCTTTACGGAAGGTATAA 1 141 0 CTGCTCTTCG 0.978079 -160 AGCAGTTTGTCTGTTCTTTTGACGCGGATGGC 1 158 1 CTGTTCTTGA 0.987278 -143 GTATACTGATCCCTTCCTTTAAATCCACACGT 1 262 1 CCCTTCTTAA 0.924971 -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 0.992633 -253 TTTACGGAAGGTATAACCGCGCATTTCATA 1 127 0 GTATAACCGC 0.99647 -174 GAAGGGATCAGTATACCCGCTGGATGGAAG 1 248 0 GTATACCCGC 0.99762 -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 TTCCCTGGAACTGTTCGAAGGCGGTGACGT 1 95 0 CTGTTCGAAG 0.977444 -206 ACAAACTGCTCTTTACGGAAGGTATAACCG 1 138 0 CTTTACGGAA 0.965394 -163 GGAAGATATACAGTACGAAACGGGAAAAAG 1 223 0 CAGTACGAAA 0.99474 -78 CACACGTATCCAGCACGAAATAAT 1 287 1 CAGCACGAAA 0.991046 -14 ********** Masking position 9 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