AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_bbur_reg_100.orf -o00380_bbur_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 BB0006 24 conserved hypothetical integral membrane protein #2 BB0007 96 B. burgdorferi predicted coding region BB0007 #3 BB0109 136 acetyl-CoA C-acetyltransferase (fadA) #4 BB0590 36 dimethyladenosine transferase (ksgA) #5 BB0591 115 competence locus E, putative Motif number 1 CTAATATAGGTTAATAAGTACAGTGTTTTCAC 2 12 0 TTAATAAACA 0.994095 -85 CTTATTAACCTATATTAGTATAATATAAAATA 2 26 1 TATATTAATA 0.731719 -71 ATAAAATATATAAATAAGCACAGTTTGTAATT 2 50 1 TAAATAAACA 0.987334 -47 ACAATTTAATTTAATAATTACAAACTGTGCTT 2 65 0 TTAATAAACA 0.994085 -32 TTTAAAATTATAACATTTTAGC 3 1 1 TTTAAAAATA 0.83496 -136 AGCTTGTTTATTAAATAATTCAGGTTAAATAG 3 30 1 TTAAATATCA 0.70542 -107 CTAAGTTTATTTAATAAAAATAAACTATTTAA 3 54 0 TTAATAAATA 0.991843 -83 TCCTAAAGTCTTAATAAACTTATTGAATTATA 3 109 0 TTAATAATTA 0.961291 -28 ATTATTCTTAATAATGACAGATATTTTAA 4 18 0 TTAATAAACA 0.994096 -19 TAATAATTATTTAATTACAATACTTT 5 5 0 TTAATTAATA 0.977422 -111 TATTGATTGATTAATCAAAACAAATTAAAATT 5 53 1 TTAATCAACA 0.972312 -63 TTTTTATTTATAAATAATTATATTTTGAATTT 5 80 0 TAAATAAATA 0.978706 -36 TAATTATTTATAAATAAAAATAAGAATATTAT 5 92 1 TAAATAAATA 0.982141 -24 ******* *** Masking position 7 Map Score: 29.2361 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 324 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 GTATAATATAAAATATATAAATAAGCACAG 2 43 1 AAATATATAA 0.83963 -54 AAAACAATTTAATTTAATAATTACAAACTG 2 70 0 AATTTAATAA 0.962617 -27 AAATTCAAAAACAATTTAATT 2 86 0 AATTCAAAAA 0.905063 -11 TTTAAAATTATAACATTTTAGCT 3 4 1 AAAATTATAA 0.908938 -133 ATTTAATAAACAAGCTAAAATGTTATAATT 3 16 0 CAAGCTAAAA 0.579985 -121 TAACCTGAATTATTTAATAAACAAGCTAAA 3 27 0 TATTTAATAA 0.909738 -110 AAACTAAGTTTATTTAATAAAAATAAACTA 3 59 0 TATTTAATAA 0.909738 -78 TACAATAGATCATATAAAAACTAAGTTTAT 3 76 0 CATATAAAAA 0.914488 -61 TGTATTGTATAATTCAATAAGTTTATTAAG 3 102 1 AATTCAATAA 0.944713 -35 AATAATTTTAAAATATCTGTCAT 4 4 1 AATTTTAAAA 0.910656 -33 AAAGTATTGTAATTAAATAATTATTAATTG 5 11 1 AATTAAATAA 0.892147 -105 CATTCGTTGACAATTAATAATTATTTAATT 5 21 0 CAATTAATAA 0.965413 -95 TTTGATTAATCAATCAATAATCATTCGTTG 5 42 0 CAATCAATAA 0.948812 -74 TTAATCAAAACAAATTAAAATTCAAAATAT 5 63 1 CAAATTAAAA 0.871267 -53 AATTAAAATTCAAAATATAATTATTTATAA 5 75 1 CAAAATATAA 0.795694 -41 TAATTATTTATAAATAAAAATAAGAATATT 5 92 1 TAAATAAAAA 0.757735 -24 TAAAAATAAGAATATTATAA 5 106 1 AATATTATAA 0.917916 -10 ********** Masking position 7 Map Score: 25.382 Number of sites scoring better than the average of aligned sites = 2355 Number in coding regions = 1433 Number in noncoding regions = 922 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 TTATACTAATATAGGTTAATAAGTACAGTG 2 19 0 ATAGGTTAAT 0.781542 -78 TTAACCTATATTAGTATAATATAAAATATA 2 30 1 TTAGTATAAT 0.929656 -67 ACTGTGCTTATTTATATATTTTATATTATA 2 44 0 TTTATATATT 0.681587 -53 CAAAAACAATTTAATTTAATAATTACAAAC 2 72 0 TTAATTTAAT 0.862334 -25 AACATTTTAGCTTGTTTATTAAATAATTCA 3 22 1 CTTGTTTATT 0.755177 -115 TTCAGGTTAAATAGTTTATTTTTATTAAAT 3 48 1 ATAGTTTATT 0.94971 -89 ATATAAAAACTAAGTTTATTTAATAAAAAT 3 65 0 TAAGTTTATT 0.944309 -72 GATCTATTGTATTGTATAATTCAATAAGTT 3 95 1 ATTGTATAAT 0.84498 -42 TATAATTCAATAAGTTTATTAAGACTTTAG 3 109 1 TAAGTTTATT 0.944309 -28 ACAGATATTTTAAAATTATT 4 1 0 TAAAATTATT 0.717176 -36 CTGTCATTATTAAGAATAAT 4 27 1 TAAGAATAAT 0.842387 -10 ACAATTAATAATTATTTAATTACAATACTT 5 12 0 ATTATTTAAT 0.533122 -104 ATTGTCAACGAATGATTATTGATTGATTAA 5 37 1 AATGATTATT 0.804359 -79 ATGATTATTGATTGATTAATCAAAACAAAT 5 48 1 ATTGATTAAT 0.830442 -68 ATTAAAATTCAAAATATAATTATTTATAAA 5 76 1 AAAATATAAT 0.700294 -40 TAAATAAAAATAAGAATATTATAA 5 102 1 TAAGAATATT 0.842391 -14 ********** Masking position 7 Map Score: 20.6273 Number of sites scoring better than the average of aligned sites = 1671 Number in coding regions = 1054 Number in noncoding regions = 617 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 4 ********** No masking Map Score: -6.79689e-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 5 ********** No masking Map Score: -6.79689e-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 6 ********** No masking Map Score: -6.79689e-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