AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_fla_operon_bbur_reg_100.orf -o259_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RBB00453 18 3615 RBB00448 23 3615 RBB00447 33 3615 RBB00792 20 3615 Input sequences: #1 RBB00465 45 3615 #2 RBB00464 37 3615 #3 RBB00463 48 3615 #4 RBB00459 22 3615 #5 RBB00440 35 3615 #6 RBB00437 22 3615 #7 RBB00433 30 3615 #8 RBB00432 92 3615 #9 RBB00430 43 3615 #10 RBB00429 50 3615 #11 RBB00737 178 3615 Motif number 1 TAGTTGTTTTATTTATTAAAACTTAAAT 1 8 1 TTTATTTTTA 0.781981 -38 ATTCAACCTCTTAATAATTTAAGTTTTAATA 1 24 0 TTAATAATTA 0.896316 -22 ATTTAAAATTCTTTTAAATTTA 2 2 0 CTTTTAATTT 0.870349 -36 ATTTAAAAGAATTTTAAATTTAAAGGAATTT 2 14 1 ATTTTAATTT 0.888723 -24 GTAATTCTTTTTAACTTTAAAAAAGAAA 3 8 1 TTTTTAATTT 0.977044 -41 ATTCCTCCCATTAATTTCTTTTTTAAAGTTA 3 22 0 TTAATTTTTT 0.65188 -27 AGGGTGTTTTTTATAAATTTATAACTTGTT 8 10 1 TTTATAATTT 0.984324 -83 GTTAAAATATTTAATATATTTTTTGCTAAAA 8 38 1 TTAATATTTT 0.915178 -55 ATTTTATACCTTTAAATCTGTTT 9 31 0 TTTATACTTT 0.964288 -13 AATACACTTTATTATACTTTTTCATTATAAT 10 18 0 ATTATACTTT 0.835172 -33 TATAGCTCTTTTTTTAAATTACTCATGTAAG 11 29 1 TTTTTAATTA 0.956363 -150 TTGTGGCTAATTTTTAAATTAGCTGCCTTAC 11 55 0 TTTTTAATTA 0.956363 -124 TACAACTTATTTTATAATTTTAATTATTAAG 11 95 1 TTTATAATTT 0.984323 -84 TTTGTCTAGGTTTTTATCTTAATAATTAAAA 11 112 0 TTTTTATTTA 0.933365 -67 TTTGCTTAATTTTATATTTTTTTGTCTAGGT 11 132 0 TTTATATTTT 0.975685 -47 ******* *** Masking position 5 Map Score: 25.9761 Number of sites scoring better than the average of aligned sites = 1725 Number in coding regions = 1055 Number in noncoding regions = 670 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 AATTCAACCTCTTAATAATTTAAG 1 32 0 AATTCTCTTA 0.923348 -14 AATAAAATTCCTCCCATTAATTTCTTTTT 3 30 0 AATTCCATTA 0.840593 -19 ATACTAAAAAAACAATCTTAGA 4 3 0 AAAAATCTTA 0.919878 -20 TCAAACCTCATTCTAAAATCTT 6 7 0 AAACCTCTAA 0.787532 -16 TTGATTTTAGCAAAAAATATATTAAATATTTTAA 8 39 0 CAAAATATTA 0.716239 -54 TTTTTTGCTAAAATCAATATATTAGATAGCTGAT 8 56 1 AAATCTATTA 0.947647 -37 TTATACCTTTAAATCTGTTTATAACAATTTGATT 9 17 0 AAATCTATAA 0.947823 -27 AATAAGAATTATAATGAAAAAGTA 10 1 1 AATAATATAA 0.945406 -50 CAATCCCTTTAATACACTTTATTATACTTTTTCA 10 25 0 AATACTATTA 0.95464 -26 AGTAATTTAAAAAAAGAGCTATAATTTGGTTTTA 11 18 0 AAAAATATAA 0.945402 -161 CTAATTTTTAAATTAGCTGCCTTACATGAGTAAT 11 46 0 AATTACCTTA 0.74207 -133 AAAATTATAAAATAAGTTGTATAATGATGTTTGT 11 82 0 AATAATATAA 0.945406 -97 TTATCTTAATAATTAAAATTATAAAATAAGTTGT 11 96 0 AATTATATAA 0.937282 -83 AAACCTAGACAAAAAAATATAAAATTAAGCAAAA 11 130 1 AAAAATAAAA 0.630227 -49 ***** ***** Masking position 2 Map Score: 12.9309 Number of sites scoring better than the average of aligned sites = 1510 Number in coding regions = 914 Number in noncoding regions = 596 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TAGTTGTTTTATTTATTAAA 1 1 1 TAGTTGTTTT 0.786661 -45 AATTATTAAGAGGTTGAATT 1 36 1 AGGTTGAATT 0.867682 -10 TCTAAGATTGTTTTTTTAGTAT 4 5 1 AGATTGTTTT 0.937219 -18 CTTTCTCCCCACCTTAATTTAT 7 3 0 ACCTTAATTT 0.75794 -28 AGGGTGTTTTTTATAAATTT 8 1 1 AGGGTGTTTT 0.948431 -92 GCTATCTAATATATTGATTTTAGCAAAAAA 8 56 0 ATATTGATTT 0.737115 -37 AAAAGGGTGATTTATCAGCTATC 8 80 0 AGGGTGATTT 0.972571 -13 TATAACAATTTGATTAATTTG 9 2 0 TGATTAATTT 0.927143 -42 CTGCCTTACATGAGTAATTTAAAAAAAGAG 11 34 0 TGAGTAATTT 0.891136 -145 ATGATGTTTGTGGCTAATTTTTAAATTAGC 11 63 0 TGGCTAATTT 0.857214 -116 ATCATTATACAACTTATTTTATAATTTTAA 11 88 1 AACTTATTTT 0.658859 -91 GTTGTGTTTTTGCTTAATTTTATATTTTTT 11 141 0 TGCTTAATTT 0.940402 -38 ********** Masking position 5 Map Score: 8.5197 Number of sites scoring better than the average of aligned sites = 1015 Number in coding regions = 704 Number in noncoding regions = 311 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TTAATAATTTAAGTTTTAATAAATAAAACAAC 1 13 0 AATTTTAAAA 0.94959 -33 ATTAAAACTTAAATTATTAAGAGGTTGAATT 1 25 1 AATTATTAGA 0.7322 -21 TAAATTTAAAAGAATTTTAAATT 2 2 1 AATTTAAAGA 0.93704 -36 AAAGAATTTTAAATTTAAAGGAATTTTAA 2 19 1 AATTTAAAGA 0.93704 -19 AATTCTTTTTAACTTTAAAAAAGAAATTAATG 3 13 1 AATTTAAAAA 0.96715 -36 AAGATTTTAGAATGAGGTTTGA 6 1 1 AAATTTTAAA 0.909952 -22 AACAAGTTATAAATTTATAAAAAACACCCT 8 9 0 AATTTATAAA 0.971558 -84 ATAAATTTATAACTTGTTAAAATATTTAATAT 8 23 1 AATTGTTAAA 0.893363 -70 CAAATTAATCAAATTGTTATAAACAGATTTAA 9 11 1 AATTGTTAAA 0.893363 -33 TTACATGAGTAATTTAAAAAAAGAGCTATAAT 11 27 0 AATTAAAAAA 0.879727 -152 AGCCACAAACATCATTATACAACTTATTTTAT 11 78 1 ATATTATAAA 0.627272 -101 CTTAATAATTAAAATTATAAAATAAGTTGTAT 11 94 0 AAATTATAAA 0.940527 -85 AAAAAAATATAAAATTAAGCAAAAACACAACA 11 140 1 AAATTAAGAA 0.68285 -39 ** ****** ** Masking position 1 Map Score: 17.319 Number of sites scoring better than the average of aligned sites = 1651 Number in coding regions = 1038 Number in noncoding regions = 613 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 5 AATAATTTAAGTTTTAATAAATAAAACAAC 1 13 0 GTTTTAATAA 0.860755 -33 TAAATTTAAAAGAATTTTAAATTT 2 5 1 TTTAAAAGAA 0.738092 -33 AGAATTTTAAATTTAAAGGAATTTTAA 2 21 1 ATTTAAAGGA 0.770701 -17 CTTTTTTAAAGTTAAAAAGAATTAC 3 6 0 GTTAAAAAGA 0.551662 -43 AAGATTTTAGAATGAGGTTTGA 6 6 1 TTTAGAATGA 0.694488 -17 AAGTTATAAATTTATAAAAAACACCCT 8 8 0 TTTATAAAAA 0.677202 -85 TATATTAAATATTTTAACAAGTTATAAATT 8 26 0 ATTTTAACAA 0.82456 -67 TAATATATTGATTTTAGCAAAAAATATATT 8 50 0 ATTTTAGCAA 0.374608 -43 TTTAAATCTGTTTATAACAATTTGATTAAT 9 14 0 TTTATAACAA 0.844703 -30 AATAAGAATTATAATGAAAAAGTATAA 10 8 1 ATTATAATGA 0.912431 -43 ATAATGAAAAAGTATAATAAAGTGTATTAA 10 21 1 AGTATAATAA 0.653156 -30 CTATAATTTGGTTTTAAGGAGGA 11 4 0 GTTTTAAGGA 0.843316 -175 ATAGCTCTTTTTTTAAATTACTCATGTAAG 11 30 1 TTTTAAATTA 0.670773 -149 TGTGGCTAATTTTTAAATTAGCTGCCTTAC 11 55 0 TTTTAAATTA 0.670773 -124 TAAAATAAGTTGTATAATGATGTTTGTGGC 11 79 0 TGTATAATGA 0.750875 -100 TTATTTTATAATTTTAATTATTAAGATAAA 11 101 1 ATTTTAATTA 0.773481 -78 ********** Masking position 6 Map Score: 8.48635 Number of sites scoring better than the average of aligned sites = 3379 Number in coding regions = 2118 Number in noncoding regions = 1261 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 6 ********** No masking Map Score: 1.50878e-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: 1.50878e-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: 1.50878e-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