AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iphoB_ctra_opreg_100.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ytgA 300 Solute Protein Binding Family #2 phnP 28 predicted metal dependent hydrolase (histidinic triad) #3 artJ 68 Arginine Binding Protein #4 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase Motif number 1 TCTCTTCGAGATGAGAAACGCGCTAGATTT 1 37 1 ATGAGAAACG 0.83955 -264 ATCCTCAACCAAAAGGAAAATCTAGCGCGT 1 54 0 AAAAGGAAAA 0.929776 -247 CTCCCCCTCCAAAAAAAGAACCTCGCTTAT 1 115 0 AAAAAAAGAA 0.888927 -186 ACATGGGATCATAAGAAAAACTCTATTTTA 1 170 0 ATAAGAAAAA 0.939834 -131 ATTCTTAAAAAAAATAAGAAT 3 2 0 AAAATAAGAA 0.819447 -67 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 4 15 0 AAGAGAAGAG 0.988002 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 4 26 1 AAGAGAAGAG 0.988002 -111 AGATTTTTCAATGAAAAAAACGCCCTCTTC 4 40 0 ATGAAAAAAA 0.837028 -97 ACACACAGGGAAGAGAAAAGAAATAGAAAG 4 68 0 AAGAGAAAAG 0.983965 -69 TTCATGAGTTAAGAGAAGAAACAAGGAAAA 4 109 1 AAGAGAAGAA 0.988771 -28 AAGAGAAGAAACAAGGAAAACAAATCTA 4 119 1 ACAAGGAAAA 0.778598 -18 ********** Masking position 4 Map Score: 15.4266 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 702 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 TGATCCCATGTGGCGATAGGCCGGGTCTAGCG 1 189 1 TGGCGTAGCC 0.979323 -112 TTTCTACTATCGGCGCTAGACCCGGCCTATCG 1 202 0 CGGCGTAGCC 0.99721 -99 AAATATCGGTTGGTTTTTGTCCTTAGGGGATC 1 231 1 TGGTTTTGCC 0.966545 -70 AGAATCATGTTGGGTATAGTCCCTGCCGTTAG 3 27 1 TGGGTTAGCC 0.99132 -42 GTATAGTCCCTGCCGTTAGACCATTGAGTCGG 3 40 1 TGCCGTAGCC 0.995692 -29 ***** *** ** Masking position 7 Map Score: 6.05342 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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 3 TTCTCATCTCGAAGAGACAATTCTAAATAATTTT 1 20 0 GAGAGAATCT 0.885025 -281 ATCTTTGCGATAAGCGAGGTTCTTTTTTTGGAGG 1 106 1 TAGCGAGTTT 0.887911 -195 TCTTTTTTTGGAGGGGGAGCTCCTTACAGGAGGC 1 126 1 GAGGGGGTCT 0.98567 -175 TTTTTGTCCTTAGGGGATCGTATACTTTTTCAAA 1 244 1 TAGGGACTTA 0.954671 -57 AGATAATCGATACGGGGACATACTTTGAAAAAGT 1 267 0 TAGGGGCTCT 0.990363 -34 AGAAAACGATTAAGGGGCCTTATT 2 15 1 TAGGGGCTTT 0.989409 -14 CTCTTGAAGAGAAGAGAACGTTTAATGATG 4 7 0 GAGAGACTTA 0.948883 -130 CTCTTCAAGAGAAGAGGGCGTTTTTTTCATTGAA 4 30 1 GAGAGGCTTT 0.987729 -107 ** **** * * ** Masking position 2 Map Score: 5.84391 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 4 TTAGTTGTTAAAATTATTTAGAATTGT 1 6 1 TGTTAAATAT 0.919045 -295 AAATTCATTCTGTTAAAAGTATCTTTGCGATA 1 86 1 TGTTAAAGAT 0.986556 -215 GAAAAACTCTATTTTAAAGGATACAAGCCTCC 1 154 0 ATTTAAAGAT 0.95619 -147 ATCGTATACTTTTTCAAAGTATGTCCCCGTAT 1 260 1 TTTTAAAGAT 0.988828 -41 ATTCTTATTTTTTTTAAGAATCATGTTGGGT 3 10 1 TTTTTAAGAT 0.953937 -59 ATAGAAAGATTTTTCAATGAAAAAAACGCCCT 4 44 0 TTTTAATGAA 0.843417 -93 **** **** ** Masking position 7 Map Score: 3.01061 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 97 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 5 TAAAATTATTTAGAATTGTCTCTTCGAGAT 1 19 1 TAGAATTGTC 0.943435 -282 AGAAACGCGCTAGATTTTCCTTTTGGTTGA 1 50 1 TAGATTTTCC 0.966665 -251 TCCTTTAAAATAGAGTTTTTCTTATGATCC 1 165 1 TAGAGTTTTT 0.909221 -136 AAGAAATAGAAAGATTTTTCAATGAAAAAA 4 51 0 AAGATTTTTC 0.949295 -86 CCCTGTGTGTATGATTTGCTGTTCATGAGT 4 88 1 ATGATTTGCT 0.793145 -49 TAGATTTGTTTTCCTTGTTT 4 127 0 TAGATTTGTT 0.972159 -10 ********** Masking position 6 Map Score: 1.91974 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 111 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 AGCCTCCTGTAAGGAGCTCCCCCTCCAAAAAA 1 129 0 AAGAGTCCCC 0.908473 -172 TTTTAAAGGATACAAGCCTCCTGTAAGGAGCT 1 143 0 TAAAGCTCCT 0.946252 -158 TTTGAAAAAGTATACGATCCCCTAAGGACAAA 1 246 0 TAACGTCCCC 0.986716 -55 TAAGGCCCCTTAATCGTTTTCTAAAA 2 5 0 TATCGTTTCT 0.782459 -24 AATAAGGCCCCTTAATCGTTTT 2 17 0 AAAAGCCCCT 0.980223 -12 CATCATTAAACGTTCTCTTCTCTTCAAG 4 7 1 TAACGTCTCT 0.981633 -130 TTCAATGAAAAAAACGCCCTCTTCTCTTGAAG 4 32 0 AAACGCCTCT 0.980209 -105 ** *** ***** Masking position 2 Map Score: 1.898 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 157 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 GGAAAATCTAGCGCGTTTCTCATCTCGAAG 1 40 0 GCGCGTTTCT 0.974714 -261 TTTGCGATAAGCGAGGTTCTTTTTTTGGAG 1 109 1 GCGAGGTTCT 0.989525 -192 TTTTTGGAGGGGGAGCTCCTTACAGGAGGC 1 130 1 GGGAGCTCCT 0.931436 -171 TGTGGCGATAGGCCGGGTCTAGCGCCGATA 1 197 1 GGCCGGGTCT 0.989533 -104 ATCGATTATCTGGAGGCTCTT 1 290 1 TGGAGGCTCT 0.928985 -11 ATGGTCTAACGGCAGGGACTATACCCAACA 3 34 0 GGCAGGGACT 0.950787 -35 CAAGAGAAGAGGGCGTTTTTTTCATTGAAA 4 35 1 GGGCGTTTTT 0.922176 -102 ********** Masking position 10 Map Score: 3.57006 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 155 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: 4.99812e-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: 4.99812e-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: 4.99812e-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