AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_Glycolysis___PPS_bbur_reg_100.orf -o017_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 Input sequences: #1 RBB00632 156 3615 #2 RBB00123 129 3615 #3 RBB00036 16 3615 #4 RBB00034 263 3615 Motif number 1 TACAAAATAATAATCACCCCTAAAAA 1 6 1 AATAATAATA 0.907023 -151 AAGTATAAATATTAACAAAGTTAATATCAAG 1 40 1 ATTAACAAAT 0.863117 -117 TATCAAGAATTAAAATAATAAAAATTGTTAA 1 64 1 TAAAATAATA 0.797358 -93 AAAAAAAACATTTAACAATTTTTATTATTTT 1 75 0 TTTAACAATT 0.923139 -82 TAAAACTTTTTTTAAAAAAAACATTTAACAA 1 88 0 TTTAAAAAAA 0.839009 -69 AGTTTTAAGCTATAATAAAATTGATTTAACA 1 112 1 TATAATAAAT 0.949388 -45 ATAAAATTGATTTAACAATATTAATAAGTTA 1 126 1 TTTAACAATT 0.923139 -31 AAAACTAGTATATAATAAGGAGA 2 3 0 TATAATAAGA 0.811014 -127 TAGTTTTGTTTATAAAAAAATGATATTTAAT 2 27 1 TATAAAAAAT 0.906794 -103 CAAAAAACATATTCATAAAGATTAGCAGACA 2 72 0 ATTCATAAAA 0.588872 -58 ATTTATTATATATCACAAAAAACATATTCAT 2 87 0 TATCACAAAA 0.91679 -43 TTTTGTGATATATAATAAATTGACCAGATTG 2 98 1 TATAATAAAT 0.949387 -32 ATCATAATAAAGAGGT 3 3 1 CATAATAAAA 0.76874 -14 TAAAACTGTTTAAAACAATTTGAAGCT 4 7 0 TAAAACAATT 0.838927 -257 GTTTTACACAAATAAAAAAGTTTAAAACAAT 4 32 1 AATAAAAAAT 0.821819 -232 TAAAAAAGTTTAAAACAATTAAGCTATAAAC 4 44 1 TAAAACAATA 0.863523 -220 CTACCCTTAAAATCAAAAACATACCATCATC 4 99 1 AATCAAAAAA 0.627523 -165 AGTGTAAAATTATAACAATAATTTTACACTA 4 182 1 TATAACAATA 0.970665 -82 AATTTTACACTATAACAATCAACCCATAACA 4 201 1 TATAACAATA 0.970665 -63 GTGCATAAGAATTAATAATGTTATGGGTTGA 4 219 0 ATTAATAATT 0.779782 -45 ********* * Masking position 5 Map Score: 25.1485 Number of sites scoring better than the average of aligned sites = 2372 Number in coding regions = 1394 Number in noncoding regions = 978 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 CCCTAAAAAGTAAAGTATAAATATTAACAAA 1 28 1 TAAAGTTAAA 0.943234 -129 TCAATTTTATTATAGCTTAAAACTTTTTTTA 1 105 0 TATAGCTAAA 0.981866 -52 CAGACAAAAATTAAGCTCAAATTAAATATCA 2 47 0 TTAAGCCAAA 0.915654 -83 CAATTTATTATATATCACAAAAAACATATTC 2 89 0 TATATCCAAA 0.784564 -41 AGAATTTAGTCCAATCTGGTCAATT 2 115 0 TTTAGTCAAT 0.830128 -15 ACACAAATAAAAAAGTTTAAAACAATTAAGC 4 37 1 AAAAGTTAAA 0.723959 -227 TAAGCGTGTTTATAGCTTAATTGTTTTAAAC 4 51 0 TATAGCTAAT 0.93283 -213 TATAAACACGCTTAGCCAAAAATCAATAAAT 4 68 1 CTTAGCAAAA 0.837844 -196 ATGCTGTTTACATAGTGTAAAATTATAACAA 4 169 1 CATAGTTAAA 0.947237 -95 GGTTGATTGTTATAGTGTAAAATTATTGTTA 4 194 0 TATAGTTAAA 0.976015 -70 TATAGTATACTTTAGTAAAAAGT 4 251 1 TTTAGTAAAA 0.897816 -13 ****** **** Masking position 4 Map Score: 10.5043 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 245 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 TTTTATTATAGCTTAAAACTTTTTTTAAAA 1 102 0 GCTTAAAACT 0.983095 -55 AGCTTCAAATTGTTTTAAACA 4 2 1 GCTTCAAATT 0.943391 -262 TTTTTTATTTGTGTAAAACTGTTTAAAACA 4 21 0 GTGTAAAACT 0.991018 -243 TAGCTTAATTGTTTTAAACTTTTTTATTTG 4 40 0 GTTTTAAACT 0.955084 -224 TGTTTACATAGTGTAAAATTATAACAATAA 4 173 1 GTGTAAAATT 0.98595 -91 GATTGTTATAGTGTAAAATTATTGTTATAA 4 191 0 GTGTAAAATT 0.98595 -73 ********** Masking position 6 Map Score: 8.41059 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 25 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TTTTTAGGGGTGATTATTATTTTGTA 1 7 0 TGATTATTAT 0.849409 -150 ATTTATACTTTACTTTTTAGGGGTGATTAT 1 20 0 TACTTTTTAG 0.763074 -137 TTAACTTTGTTAATATTTATACTTTACTTT 1 34 0 TAATATTTAT 0.881801 -123 TTTATTATTTTAATTCTTGATATTAACTTT 1 56 0 TAATTCTTGA 0.740722 -101 AAACATTTAACAATTTTTATTATTTTAATT 1 71 0 CAATTTTTAT 0.841978 -86 TATAAAAAAATGATATTTAATTTGAGCTTA 2 37 1 TGATATTTAA 0.692275 -93 AATTTGAGCTTAATTTTTGTCTGCTAATCT 2 55 1 TAATTTTTGT 0.97078 -75 TTTTGTCTGCTAATCTTTATGAATATGTTT 2 69 1 TAATCTTTAT 0.862457 -61 TTTATGAATATGTTTTTTGTGATATATAAT 2 84 1 TGTTTTTTGT 0.811206 -46 GTAGATTTATTGATTTTTGGCTAAGCGTGT 4 73 0 TGATTTTTGG 0.957578 -191 GGTATGTTTTTGATTTTAAGGGTAGATTTA 4 94 0 TGATTTTAAG 0.709519 -170 CAGCATTTTGTAAGTTTTGTTAATTGAAAG 4 145 0 TAAGTTTTGT 0.828952 -119 TGTTATGGGTTGATTGTTATAGTGTAAAAT 4 202 0 TGATTGTTAT 0.893161 -62 ATAACATTATTAATTCTTATGCACTTATAG 4 226 1 TAATTCTTAT 0.926788 -38 ********** Masking position 7 Map Score: 9.9868 Number of sites scoring better than the average of aligned sites = 2051 Number in coding regions = 1313 Number in noncoding regions = 738 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 5 TTTACTTTTTAGGGGTGATTATTATTTTGT 1 12 0 AGGGGTGATT 0.992605 -145 TTTGATTTTAAGGGTAGATTTATTGATTTT 4 86 0 AGGGTAGATT 0.989069 -178 AATAATGTTATGGGTTGATTGTTATAGTGT 4 207 0 TGGGTTGATT 0.989079 -57 ********** Masking position 8 Map Score: 1.42486 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TTTTTTAAAAAAAACATTTAACAATTTTTA 1 82 0 AAAACATTTA 0.927837 -75 ATTATAGCTTAAAACTTTTTTTAAAAAAAA 1 98 0 AAAACTTTTT 0.848712 -59 TAATATTGTTAAATCAATTTTATTATAGCT 1 119 0 AAATCAATTT 0.889468 -38 CTCAAATTAAATATCATTTTTTTATAAACA 2 33 0 ATATCATTTT 0.854867 -97 TATATCACAAAAAACATATTCATAAAGATT 2 80 0 AAAACATATT 0.881481 -50 AAAACTGTTTAAAACAATTTGAAGCT 4 7 0 AAAACAATTT 0.93328 -257 AAAAAAGTTTAAAACAATTAAGCTATAAAC 4 45 1 AAAACAATTA 0.887509 -219 TCCACCTCTCACAGCATCTTTCAATTAACA 4 128 1 ACAGCATCTT 0.820787 -136 CACTATGTAAACAGCATTTTGTAAGTTTTG 4 156 0 ACAGCATTTT 0.956292 -108 TAAAATTATAACAATAATTTTACACTATAA 4 186 1 ACAATAATTT 0.65105 -78 CAATCAACCCATAACATTATTAATTCTTAT 4 216 1 ATAACATTAT 0.712768 -48 ********** Masking position 3 Map Score: 9.90302 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 627 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 ********** No masking Map Score: -1.01364e-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: -1.01364e-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: -1.01364e-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