AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_aquae_reg_300.orf -o071_aquae_300.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 AGCCTTTAAAAAGTAAGCTTGTAGAAATATTAT 1 18 0 AAGGCTTGTA 0.961597 -36 CTTACTTTTTAAAGGCTATTATAAAAGTGT 1 34 1 AAATATTATA 0.956737 -20 AAAACTTGATTGTATATTAAAAAT 4 2 1 AAAGATTGTA 0.983685 -24 AGAAGAAGATAAAAGAGCTTGAAGCACAAATTG 5 49 0 AAAGCTTGAA 0.840724 -252 CTTTTCGCTTAAAAGAGGTTGTATGAAGTTCAG 5 152 1 AAAGGTTGTA 0.933718 -149 AAGCCTTATTTTAAATTGATAAT 6 18 0 AAGTATTTTA 0.854147 -13 AAAGAGGATTATACCCGCCCGAA 7 26 0 AAAGATTATA 0.982345 -13 CTTTCTTATAAAAGAATATTATAATTTT 8 6 0 AAATATTATA 0.956737 -43 CCTCCTTAACAAACTTTCTTATAAAAGAATATT 8 19 0 AAATCTTATA 0.947897 -30 TAAACATGATTTTAACGACAAAGG 9 2 1 AAAGATTTTA 0.966869 -61 GAGACCTTTAAAATAGTATCATACCGCCCTTTG 9 29 0 AAATATCATA 0.884583 -34 TAGAATGTGGAAGCACGCTCTTAATGTGTGGTC 11 23 1 AAGGCTCTTA 0.807756 -108 TCAAAAGTGTAAAAAGGATAATAAGTTCGGCGG 11 85 0 AAAGATAATA 0.876093 -46 *** ******* Masking position 2 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 TTAATTTCAGGGAGGAAGAGA 2 33 1 GGAGGAAGAG 0.887587 -11 TTTTTAGTCTGGGGGATAAATTTTTCAAAC 3 17 0 GGGGGATAAA 0.815961 -28 AGAAGATAAAAGAGCTTGAAGCACAAATTG 5 49 0 AGAGCTTGAA 0.879894 -252 AACTGGAAGAGGAGCTTGAAAACTTAAGGG 5 118 0 GGAGCTTGAA 0.967294 -183 TTCGCTTAAAAGAGGTTGTATGAAGTTCAG 5 155 1 AGAGGTTGTA 0.9245 -146 GAAAGGACTCAGAGGGAAAAAATACTACTT 5 221 0 AGAGGGAAAA 0.808373 -80 CCCGCCCGAAGGCGGGTGAAAGGAA 7 6 0 GGCGGGTGAA 0.986466 -33 CCCGCCTTCGGGCGGGTATAATCCTCTTT 7 20 1 GGCGGGTATA 0.914284 -19 AGTTTGTTAAGGAGGTGGTATC 8 37 1 GGAGGTGGTA 0.929229 -12 TAAAGGTCTCGGAGGTAGAAA 9 52 1 GGAGGTAGAA 0.982516 -11 TAATAAGTTCGGCGGTTAAGCGGAAATTTT 11 70 0 GGCGGTTAAG 0.925707 -61 ********** Masking position 4 Map Score: 11.2643 Number of sites scoring better than the average of aligned sites = 890 Number in coding regions = 766 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 CTTATTAATAATATTTCTACAAG 1 4 1 ATTAATAATA 0.932366 -50 TATAATAGCCTTTAAAAAGTAAGCTTGTAG 1 27 0 TTTAAAAAGT 0.660739 -27 ACACTTTTATAATAGCCTTTAAAA 1 40 0 TTTTATAATA 0.885143 -14 TTAAACCTTTATTAATAATAACGACT 2 7 0 ATTAATAATA 0.932366 -37 TTGATTGTATATTAAAAATT 4 16 1 ATTAAAAATT 0.881496 -10 AAAAAATACTACTTATAATTATCCCGTTAG 5 205 0 ACTTATAATT 0.4852 -96 CTCCATTAAATTTTAAAATTTTTTGT 5 285 1 TTTTAAAATT 0.856422 -16 AAAATTATCAATTTAAAATAAGGCTT 6 15 1 ATTTAAAATA 0.961353 -16 AAAATTATAATATTCTTTTATA 8 3 1 AATTATAATA 0.538982 -46 TATAATATTCTTTTATAAGAAAGTTTGTTA 8 16 1 TTTTATAAGA 0.806516 -33 CCTCCGAGACCTTTAAAATAGTATCATACC 9 37 0 CTTTAAAATA 0.854543 -26 TACAGGAATTAAAAAGAGAAAGTTCAA 11 114 0 ATTAAAAAGA 0.890251 -17 AATCTAAAATAATAAAGC 12 8 0 ATCTAAAATA 0.798652 -11 ********** Masking position 5 Map Score: 11.3976 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 163 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 TCTGGGGGATAAATTTTTCAAACGGAATT 3 9 0 AAATTTTCAA 0.982988 -36 GTGTTGCCCTTAAGTTTTCAAGCTCCTCTTC 5 112 1 TAATTTTCAA 0.923053 -189 AACCATTCAAAGAATTTTCCATAGTCCCCTC 5 255 1 AGATTTTCCA 0.945992 -46 ACAAAAAATTTTAAAATTTAATGGA 5 286 0 AAATTTTAAA 0.899386 -15 ACACAAAATTATCAATTTAAAATAA 6 5 1 AAATTATCAA 0.923053 -26 GTGGTCCATCACACTTTTCCAAAATTTCCGC 11 50 1 ACATTTTCCA 0.969911 -81 TATCCTTTTTACACTTTTGAACTTTCTCTTT 11 98 1 ACATTTTGAA 0.916553 -33 *** ******* Masking position 3 Map Score: 3.95819 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 113 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TATTTCTACAAGCTTACTTTTTAAAGGCTAT 1 22 1 AGCTTCTTTT 0.902132 -32 CCTTAGTCTCAATTTGTGCTTCAAGCTCTTT 5 40 1 AATTTTGCTT 0.90372 -261 ATTGCGAAGAAGCTTGCTCTGGAGAAGAAGA 5 73 0 AGCTTCTCTG 0.956268 -228 CTCCTCTTCCAGTTTTCTCTTTTCGCTTAAA 5 134 1 AGTTTCTCTT 0.983291 -167 TTATCCCGTTAGTTTTTGCCTTCGTTTTATG 5 186 0 AGTTTTGCCT 0.856428 -115 ACTTTTCCAAAATTTCCGCTTAACCGCCGAA 11 62 1 AATTTCGCTT 0.971758 -69 TACACTTTTGAACTTTCTCTTTTTAATTCCT 11 107 1 AACTTCTCTT 0.971758 -24 ***** ***** Masking position 1 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 TAAATTTTTCAAACGGAATT 3 1 0 AAACGGAATT 0.943225 -44 GATTTATCTCTTGAGGAATTACTAAATATA 5 11 0 TTGAGGAATT 0.95337 -290 CTTCTTCGCAATCAGGAATTGTGTTGCCCT 5 92 1 ATCAGGAATT 0.966992 -209 TTCGGCGGTTAAGCGGAAATTTTGGAAAAG 11 63 0 AAGCGGAAAT 0.93231 -68 TACAGGAATTAAAAAGAGAA 11 121 0 TACAGGAATT 0.966992 -10 ********** Masking position 7 Map Score: 0.196037 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 100 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 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 Motif number 9 ********** 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