AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i298_mixed13_ecoli_reg_100.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 yicC 126 putative alpha helix protein #2 gmk 251 guanylate kinase #3 priA 202 primosomal protein N'(= factor Y)(putative helicase) Motif number 1 CCGTATAATGCGCAGCCACATTTGTTTCAA 1 26 0 CGCAGCCACA 0.947666 -101 TTATAGCCATCGATGCCTTGTCAGGATAGG 1 72 0 CGATGCCTTG 0.826425 -55 GTTTTTGCCACTCGGCTTTGCTTTCATCAC 2 43 0 CTCGGCTTTG 0.981314 -209 ATTTTCAGGAAGCGTCCTCGCAGACTCCGT 2 71 0 AGCGTCCTCG 0.9772 -181 CTTCCTGAAAATCGTCTTTATTGCAGTGAA 2 89 1 ATCGTCTTTA 0.584177 -163 CAAATGCGGAAGCAGCTACGCAAAACGCAA 2 126 1 AGCAGCTACG 0.928892 -126 TTATACACGGCGCGGCCATGTGACGTAGCC 2 183 0 CGCGGCCATG 0.982579 -69 GGAAGAGCGACGCGGCCTTAAACCGAGGTT 3 16 0 CGCGGCCTTA 0.987054 -187 TGTATGATTTCGCGCCTTCGTACGAAATGA 3 96 0 CGCGCCTTCG 0.974614 -107 CTGATCCGCACTCTTCTACGGCAATGTGTA 3 148 1 CTCTTCTACG 0.814688 -55 ********** Masking position 6 Map Score: 9.50052 Number of sites scoring better than the average of aligned sites = 4792 Number in coding regions = 4570 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 2 CCATCGATGCCTTGTCAGGATAGGAATAAC 1 66 0 CTTGTCAGGA 0.987758 -61 CTCTCCTTTTATAAACAGGAACGTCT 1 111 1 ATAAACAGGA 0.909054 -16 TCCGCTGTAGATAGTCAGGCAGATATACAA 2 12 1 ATAGTCAGGC 0.987758 -240 AATAAAGACGATTTTCAGGAAGCGTCCTCG 2 81 0 ATTTTCAGGA 0.949109 -171 TATTGCAGTGAATGACAGGCAAATGCGGAA 2 107 1 AATGACAGGC 0.958639 -145 CACCGAATTTCAAGTCAGGATGATGCT 3 186 1 CAAGTCAGGA 0.977398 -17 ********** Masking position 7 Map Score: 4.87286 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 159 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 GCCGGAAGTCCGTATAATGCGCAGCCACATTTGT 1 31 0 CGTAAAGCGG 0.937319 -96 GTGGAAGGATTATAGCCATCGATGCCTTGTCAGG 1 77 0 TATACCTCGG 0.963831 -50 CGTTCCTGTTTATAAAAGGAGAGGTGGAAGGATT 1 100 0 TATAAAGAGG 0.967993 -27 TCTGCCTGACTATCTACAGCGGAG 2 1 0 TATCACGCGG 0.990136 -251 GTCAGGCAGATATACAACGTGATGAAAGCAAAGC 2 25 1 TATAAAGTGG 0.981607 -227 ACGAGCTTATTATACACGGCGCGGCCATGTGACG 2 188 0 TATAACGCGG 0.996944 -64 GGTGGGTTAGTATACACATTGCCGTAGAAGAGTG 3 156 0 TATAACTTGG 0.96782 -47 **** ** *** * Masking position 3 Map Score: 3.83423 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 226 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GATAGGAATAACCGCCGGAAGTCCGTATAAT 1 47 0 ACGCCGGAAG 0.99099 -80 TTATAAAAGGAGAGGTGGAAGGATTATAGCC 1 94 0 AGGGTGGAAG 0.990281 -33 AGATATACAACGTGATGAAAGCAAAGCCGAG 2 32 1 CGGATGAAAG 0.890566 -220 AATGACAGGCAAATGCGGAAGCAGCTACGCA 2 117 1 AATGCGGAAG 0.931626 -135 TTCGCTAATCACATACGAAAGATACTC 2 235 1 ACTACGAAAG 0.890335 -17 GTCTGGCGTTAGGGCTGGAAGAGCGACGCGG 3 31 0 AGGCTGGAAG 0.990281 -172 ** ******** Masking position 9 Map Score: 1.16232 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 1137 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 ACTCCGTTTTTGCCACTCGGCTTTGCTTTC 2 48 0 TGCCACTCGG 0.979104 -204 GCTTATTATACACGGCGCGGCCATGTGACG 2 188 0 CACGGCGCGG 0.994691 -64 GGGCTGGAAGAGCGACGCGGCCTTAAACCG 3 21 0 AGCGACGCGG 0.994657 -182 TAACGCCAGACACCACGCGATGTTAAAAGT 3 51 1 CACCACGCGA 0.988004 -152 ********** Masking position 6 Map Score: 0.679414 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 650 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 AATGCGCAGCCACATTTGTTTCAAGCCGGAGA 1 18 0 CACATTTTTC 0.970581 -109 TCCTCGCAGACTCCGTTTTTGCCACTCGGCTT 2 55 0 CTCCTTTTGC 0.986588 -197 TCCTGAAAATCGTCTTTATTGCAGTGAATGAC 2 91 1 CGTCTTTTGC 0.96484 -161 ACTTTTTGCGCAAAGTTGTTGCGTTTTGCGTA 2 142 0 CAAATTTTGC 0.977442 -110 AGCCCTTGCTCACACTTTTTGCGCAAAGTTGT 2 155 0 CACATTTTGC 0.994226 -97 **** ** **** Masking position 6 Map Score: 1.82295 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 151 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 TATAATAAGCTCGTATGTAGGCTTTATTTC 2 208 1 TCGTATGTAG 0.973266 -44 GAGTATCTTTCGTATGTGATTAGCGAAAT 2 233 0 TCGTATGTGA 0.970404 -19 TACGAAATGATCGTATTGAAGCTATACTTT 3 76 0 TCGTATTGAA 0.928573 -127 TTTCGCGCCTTCGTACGAAATGATCGTATT 3 89 0 TCGTACGAAA 0.953808 -114 AAATTAACCAGCGTATGCAAACTGATCCGC 3 127 1 GCGTATGCAA 0.968156 -76 ********** Masking position 5 Map Score: 0.373331 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 55 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ********** No masking Map Score: 9.90086e-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: 9.90086e-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 10 ********** No masking Map Score: 9.90086e-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