AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_aquae_reg_100.orf -o071_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAA00901 53 Aquifex_aeolicus #2 RAA01386 43 Aquifex_aeolicus #3 RAA01389 44 Aquifex_aeolicus #4 RAA01390 25 Aquifex_aeolicus #5 RAA01403 300 Aquifex_aeolicus #6 RAA01490 30 Aquifex_aeolicus #7 RAA00515 38 Aquifex_aeolicus #8 RAA00516 48 Aquifex_aeolicus #9 RAA00518 62 Aquifex_aeolicus #10 RAA00712 40 Aquifex_aeolicus #11 RAA00715 130 Aquifex_aeolicus #12 RAA01685 18 Aquifex_aeolicus Motif number 1 ATAATATTTCTACAAGCTTACTTTTTAAAGGCT 1 18 1 TACAAGCCTT 0.959922 -36 ACACTTTTATAATAGCCTTTAAAAAGTAAG 1 34 0 TATAATATTT 0.95486 -20 ATTTTTAATATACAATCAAGTTTT 4 2 0 TACAATCTTT 0.982956 -24 CAATTTGTGCTTCAAGCTCTTTTATCTTCTTCT 5 49 1 TTCAAGCTTT 0.834683 -252 CTGAACTTCATACAACCTCTTTTAAGCGAAAAG 5 152 0 TACAACCTTT 0.930915 -149 ATTATCAATTTAAAATAAGGCTT 6 18 1 TAAAATACTT 0.848524 -13 TTCGGGCGGGTATAATCCTCTTT 7 26 1 TATAATCTTT 0.981558 -13 AAAATTATAATATTCTTTTATAAGAAAG 8 6 1 TATAATATTT 0.95486 -43 AATATTCTTTTATAAGAAAGTTTGTTAAGGAGG 8 19 1 TATAAGATTT 0.945658 -30 CCTTTGTCGTTAAAATCATGTTTA 9 2 0 TAAAATCTTT 0.965416 -61 CAAAGGGCGGTATGATACTATTTTAAAGGTCTC 9 29 1 TATGATATTT 0.879968 -34 GACCACACATTAAGAGCGTGCTTCCACATTCTA 11 23 0 TAAGAGCCTT 0.800762 -108 CCGCCGAACTTATTATCCTTTTTACACTTTTGA 11 85 1 TATTATCTTT 0.871189 -46 ******* *** Masking position 5 Map Score: 14.3439 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 150 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 TATAATAGCCTTTAAAAAGTAAGCTTGTAGAA 1 25 0 TTAAAAGTAA 0.924451 -29 AATTCCGTTTGAAAAATTTATCCCCCAGAC 3 9 1 TTAAAATTTA 0.914688 -36 ATCCCCCAGACTAAAAATGTTATTT 3 30 1 CTAAAAGTTA 0.911487 -15 TTAGTAATTCCTCAAGAGATAAATCCTTAGTC 5 16 1 CTAAGAATAA 0.811242 -285 GAAGAGGAGCTTGAAAACTTAAGGGCAACACA 5 111 0 TTAAAATTAA 0.936457 -190 ACAAAAAATTTTAAAATTTAATGGAGAGGGG 5 280 0 TTAAAATTAA 0.932984 -21 AACAAACTTTCTTATAAAAGAATATTATAATT 8 13 0 CTATAAAGAA 0.770593 -36 CTCCGAGACCTTTAAAATAGTATCATACCGCC 9 34 0 TTAAAAAGTA 0.947875 -29 CTTCCACATTCTAAAATGAGTATAC 11 4 0 CTAAATAGTA 0.825173 -127 AAAGAGAAAGTTCAAAAGTGTAAAAAGGATAA 11 97 0 TTAAAATGTA 0.925426 -34 TACAGGAATTAAAAAGAGAAAGTTCAAAAG 11 111 0 TTAAAAAGAA 0.96153 -20 AATCTAAAATAATAAAGC 12 4 0 CTAAATATAA 0.848491 -15 ** **** **** Masking position 4 Map Score: 9.72794 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 473 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 TTAATTTCAGGGAGGAAGAGA 2 33 1 GGAGGAAGAG 0.968707 -11 TTTTTAGTCTGGGGGATAAATTTTTCAAAC 3 17 0 GGGGGATAAA 0.881172 -28 AGCTTGCTCTGGAGAAGAAGATAAAAGAGC 5 64 0 GGAGAAGAAG 0.668492 -237 AGAGAAAACTGGAAGAGGAGCTTGAAAACT 5 124 0 GGAAGAGGAG 0.793191 -177 TTCGCTTAAAAGAGGTTGTATGAAGTTCAG 5 155 1 AGAGGTTGTA 0.765178 -146 GAAAGGACTCAGAGGGAAAAAATACTACTT 5 221 0 AGAGGGAAAA 0.764028 -80 CCCGCCCGAAGGCGGGTGAAAGGAA 7 6 0 GGCGGGTGAA 0.978567 -33 CCCGCCTTCGGGCGGGTATAATCCTCTTT 7 20 1 GGCGGGTATA 0.905318 -19 AGTTTGTTAAGGAGGTGGTATC 8 37 1 GGAGGTGGTA 0.953985 -12 TAAAGGTCTCGGAGGTAGAAA 9 52 1 GGAGGTAGAA 0.970675 -11 TAATAAGTTCGGCGGTTAAGCGGAAATTTT 11 70 0 GGCGGTTAAG 0.948955 -61 ********** Masking position 2 Map Score: 6.37516 Number of sites scoring better than the average of aligned sites = 1900 Number in coding regions = 1666 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 4 TTGTAGAAATATTATTAATAAG 1 3 0 ATTATTAATA 0.951758 -51 AGTCGTTATTATTAATAAAGGTTTAAT 2 8 1 ATTATTAATA 0.951758 -36 TGGGGGATAAATTTTTCAAACGGAATT 3 8 0 ATTTTTCAAA 0.782065 -37 AATTTTTAATATACAATCAAG 4 15 0 ATTTTTAATA 0.962521 -11 CATTCAAAGAATTTTCCATAGTCCCCTCTC 5 258 1 ATTTTCCATA 0.920838 -43 ACACAAAATTATCAATTTAAAATAAGG 6 8 1 ATTATCAATT 0.852396 -23 TGAACTTTCTCTTTTTAATTCCTGTA 11 115 1 CTTTTTAATT 0.774686 -16 ********** Masking position 8 Map Score: 3.32994 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 61 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 ATAGCCTTTAAAAAGTAAGCTTGTAGAAATA 1 22 0 AAAAGAAGCT 0.901728 -32 AAAGAGCTTGAAGCACAAATTGAGACTAAGG 5 40 0 AAGCAAAATT 0.903322 -261 TCTTCTTCTCCAGAGCAAGCTTCTTCGCAAT 5 73 1 CAGAGAAGCT 0.956077 -228 TTTAAGCGAAAAGAGAAAACTGGAAGAGGAG 5 134 0 AAGAGAAACT 0.983216 -167 CATAAAACGAAGGCAAAAACTAACGGGATAA 5 186 1 AGGCAAAACT 0.855865 -115 TTCGGCGGTTAAGCGGAAATTTTGGAAAAGT 11 62 0 AAGCGAAATT 0.971632 -69 AGGAATTAAAAAGAGAAAGTTCAAAAGTGTA 11 107 0 AAGAGAAGTT 0.971632 -24 ***** ***** Masking position 7 Map Score: 3.09924 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 254 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ********** No masking Map Score: -1.00654e-12 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 7 ********** No masking Map Score: -1.00654e-12 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: -1.00654e-12 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