AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_bbur_reg_100.orf -o00260_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 BB0226 129 seryl-tRNA synthetase (serS) #2 BB0373 124 B. burgdorferi predicted coding region BB0373 #3 BB0599 51 cysteinyl-tRNA synthetase (cysS) #4 BB0720 165 threonyl-tRNA synthetase (thrZ) Motif number 1 TATAACAGGATTAGAATAAATATTGCAGGGAG 1 21 0 TAAATAAATA 0.938218 -109 TGTTATAAGATATTATATAATAACCTTAATAT 1 46 1 TTATATAATA 0.488807 -84 TTAAACAAAATTACAAATAATATTAATTCATA 1 75 0 TAAAATAATA 0.966764 -55 TTTGTAATTTTGTTTAAAAATTTTACTTAAGA 1 90 1 TTTAAAAATT 0.887061 -40 GATAGACAATTAATAAATAATATGATATACAT 2 41 0 TAAAATAATA 0.938632 -84 ATTCAAAAATTGAGATATAATAAATACATTAT 2 80 0 TAATATAATA 0.886636 -45 ACGTACTTAATAATAAATTAGATTT 3 4 1 TCTAATAATA 0.86552 -48 ATTTCTCAAAATTGAAAAAATAAAAAATCTAA 3 28 0 ATAAAAAATA 0.789691 -24 AACAAAAACCTGAAAATAAATTT 4 2 0 TAAATAAATT 0.852709 -164 AAAAAAATTTTCTAAAAAAATAGAGATAAGAA 4 34 0 TTAAAAAATA 0.975899 -132 AATTAAAATATACAAAAAAATTTTCTAAAAAA 4 47 0 TCAAAAAATT 0.938735 -119 TTATAATTACTAAATTAAAATATACAAAAAAA 4 59 0 TATTAAAATA 0.884622 -107 TTTAATTTAGTAATTATAAATATTTGAGGTGC 4 72 1 TATATAAATA 0.804708 -94 TCATCACTTTTACGTAAAAATACGCACCTCAA 4 95 0 TCTAAAAATA 0.95336 -71 TTTCGCTTTTTATTAAAAAATTAAAATTCACA 4 128 0 TTAAAAAATT 0.880947 -38 * * ******** Masking position 9 Map Score: 21.7297 Number of sites scoring better than the average of aligned sites = 2271 Number in coding regions = 1425 Number in noncoding regions = 846 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 2 TATAACAGGATTAGAATAAATATTGCAGGG 1 23 0 TTAGAATAAA 0.898005 -107 ATAACCTTAATATGAATTAATATTATTTGT 1 65 1 TATGAATTAA 0.854677 -65 TGTTTAAAAATTTTACTTAAGACATATCTT 1 100 1 TTTTACTTAA 0.897205 -30 ATAGATAGACAATTAATAAATAATATGATA 2 46 0 AATTAATAAA 0.847431 -79 AAAAATTGAGATATAATAAATACATTATAC 2 78 0 ATATAATAAA 0.793896 -47 TATCTCAATTTTTGAATTAAGCTTTTTTGA 2 95 1 TTTGAATTAA 0.926986 -30 ATTAAGCTTTTTTGAAGAGATTTTT 2 110 1 TTTGAAGAGA 0.76066 -15 ACGTACTTAATAATAAATTAGATTTTT 3 8 1 TAATAATAAA 0.84743 -44 ATTTTTTCAATTTTGAGAAATGT 3 39 1 TTTTGAGAAA 0.82291 -13 TATCTCTATTTTTTTAGAAAATTTTTTTGT 4 38 1 TTTTTAGAAA 0.75707 -128 AAATATTTATAATTACTAAATTAAAATATA 4 67 0 AATTACTAAA 0.73712 -99 AGGTGCGTATTTTTACGTAAAAGTGATGAG 4 98 1 TTTTACGTAA 0.865048 -68 AATTTTAATTTTTTAATAAAAAGCGAAAGG 4 132 1 TTTTAATAAA 0.973799 -34 ********** Masking position 10 Map Score: 10.9972 Number of sites scoring better than the average of aligned sites = 3013 Number in coding regions = 1869 Number in noncoding regions = 1144 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 ATTATTTGTAATTTTGTTTAAAAATTTTAC 1 86 1 ATTTTGTTTA 0.75058 -44 TATATCTCAATTTTTGAATTAAGCTTTTTT 2 93 1 TTTTTGAATT 0.966188 -32 GAATTAAGCTTTTTTGAAGAGATTTTT 2 108 1 TTTTTGAAGA 0.962818 -17 GATTTTTTATTTTTTCAATTTTGAGAAATG 3 31 1 TTTTTCAATT 0.867638 -21 TATTTTCAGGTTTTTGTTTTCTTATCTCTA 4 16 1 TTTTTGTTTT 0.912797 -150 CTTATCTCTATTTTTTTAGAAAATTTTTTT 4 36 1 TTTTTTTAGA 0.876322 -130 TTAGAAAATTTTTTTGTATATTTTAATTTA 4 51 1 TTTTTGTATA 0.97866 -115 TGAATTTTAATTTTTTAATAAAAAGCGAAA 4 130 1 TTTTTTAATA 0.925891 -36 ********** Masking position 5 Map Score: 8.03833 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 456 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 TTATATAATAACCTTAATATGAATTAATAT 1 58 1 ACCTTAATAT 0.94119 -72 TGGTTAATAGAGCTTAATTTCAAGGGAATA 2 12 0 AGCTTAATTT 0.961328 -113 TATTTATTATATCTCAATTTTTGAATTAAG 2 86 1 ATCTCAATTT 0.979423 -39 TCTTCAAAAAAGCTTAATTCAAAAATTGAG 2 98 0 AGCTTAATTC 0.853406 -27 ACATTTCTCAAAATTGAAAAAATA 3 38 0 TTCTCAAAAT 0.578633 -14 GAAAACAAAAACCTGAAAATAAATTT 4 7 0 ACCTGAAAAT 0.730972 -159 TTGTTTTCTTATCTCTATTTTTTTAGAAAA 4 29 1 ATCTCTATTT 0.870261 -137 TTTTTTGTATATTTTAATTTAGTAATTATA 4 60 1 ATTTTAATTT 0.856185 -106 AAAAATACGCACCTCAAATATTTATAATTA 4 82 0 ACCTCAAATA 0.769339 -84 ATGAGTGTGAATTTTAATTTTTTAATAAAA 4 123 1 ATTTTAATTT 0.856185 -43 ********** Masking position 4 Map Score: 5.26206 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 486 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 ********** No masking Map Score: -4.80737e-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: -4.80737e-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 7 ********** No masking Map Score: -4.80737e-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