AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_bbur_reg_100.orf -o00271_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 BB0067 114 peptidase, putative #2 BB0374 124 B. burgdorferi predicted coding region BB0374 #3 BB0375 22 pfs protein (pfs-1) #4 BB0587 154 methionyl-tRNA synthetase (metG) Motif number 1 GTTTTATCCTTTAGGAGTTAAT 1 3 1 TTTATCCTTT 0.968514 -112 CAAGCTAAATTATATCAAATAATTTTTTTT 1 35 1 TATATCAAAT 0.923224 -80 ATACCAAATAATTATCAATTTAAAAAAAAA 1 60 0 ATTATCAATT 0.902598 -55 CTAATATTAGTATACCAAATAATTATCAAT 1 71 0 TATACCAAAT 0.835641 -44 AAAAATCCCCTTTATACAACCTT 1 102 0 AATCCCCTTT 0.876525 -13 GTATTTATTATATCTCAATTTTTGAATTAA 2 31 0 TATCTCAATT 0.950183 -94 TTATTAATTGTCTATCTATTAGTATAATGT 2 59 0 TCTATCTATT 0.74873 -66 TATCATATTATTTATTAATTGTCTATCTAT 2 70 0 TTTATTAATT 0.658919 -55 ATTAACCATGTATATCATATTATTTATTAA 2 82 0 TATATCATAT 0.946644 -43 ATTTTTTCTCCTTTTAAGTGTC 3 9 0 TTTCTCCTTT 0.948962 -14 AAATGATATAAATATTCTTTTATTATAAGG 4 22 0 AATATTCTTT 0.748842 -133 AAAGAATATTTATATCATTTTTTACAAAAA 4 32 1 TATATCATTT 0.978973 -123 ATTTTTTTTCAATATCTTTTACAAAAATTC 4 87 0 AATATCTTTT 0.915617 -68 ATTGAAAAAAAATATCCTATCCATATTACA 4 104 1 AATATCCTAT 0.913683 -51 TCAGTTTTCCCTTTTTTTATGCTAT 4 140 0 TTTCCCTTTT 0.754475 -15 ********** Masking position 3 Map Score: 18.4693 Number of sites scoring better than the average of aligned sites = 1692 Number in coding regions = 1134 Number in noncoding regions = 558 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 ATAATTTAGCTTGAAATTAACTCCTAAAGG 1 18 0 TTGAAATTAA 0.896936 -97 AATTATCAATTTAAAAAAAAAAAATTATTT 1 51 0 TTAAAAAAAA 0.94109 -64 ATTAGTAAGGTTGTATAAAGGGGATTTTT 1 96 1 TTGTATAAAG 0.900132 -19 AAAAATCTCTTCAAAAAAGCTTAATTCAA 2 10 1 TTCAAAAAAG 0.881509 -115 ATCTCAATTTTTGAATTAAGCTTTTTTGAA 2 20 0 TTGAATTAAG 0.900132 -105 AAAAATTGAGATATAATAAATACATTATAC 2 38 1 ATATAATAAA 0.711492 -87 TTATTCCCTTGAAATTAAGCTCTATTAA 2 107 0 TTGAAATTAA 0.896936 -18 ATCACACTCCTTATAATAAAAGAATATTTA 4 14 1 TTATAATAAA 0.922481 -141 TTTGGCTTTTTTGTAAAAAATGATATAAAT 4 39 0 TTGTAAAAAA 0.977336 -116 GAAAGAATTTTTGTAAAAGATATTGAAAAA 4 83 1 TTGTAAAAGA 0.881597 -72 GTAAAAGATATTGAAAAAAAATATCCTATC 4 95 1 TTGAAAAAAA 0.980376 -60 GCTATTAATATTGTAATATGGATAGGATAT 4 115 0 TTGTAATATG 0.815464 -40 TATTAATAGCATAAAAAAAGGGAAAACTGA 4 135 1 ATAAAAAAAG 0.771327 -20 ********** Masking position 5 Map Score: 16.5799 Number of sites scoring better than the average of aligned sites = 2862 Number in coding regions = 1973 Number in noncoding regions = 889 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 3 AATTAACTCCTAAAGGATAAAAC 1 4 0 TAAAGGATAA 0.929115 -111 GGAGTTAATTTCAAGCTAAATTATATCAAA 1 24 1 TCAAGCTAAA 0.893329 -91 ATCTCTTCAAAAAAGCTTAATTCAAAAATT 2 15 1 AAAAGCTTAA 0.979222 -110 ACATGGTTAATAGAGCTTAATTTCAAGGGA 2 101 1 TAGAGCTTAA 0.935984 -24 TTTTTTACAAAAAAGCCAAAATTGAATTGC 4 49 1 AAAAGCCAAA 0.963123 -106 TTACAATATTAATAGCATAAAAAAAGGGAA 4 129 1 AATAGCATAA 0.908917 -26 ATAGCATAAAAAAAGGGAAAACTGA 4 140 1 AAAAGGGAAA 0.916894 -15 ********** Masking position 4 Map Score: 3.51478 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 427 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 ATTATATCAAATAATTTTTTTTTTTTAAAT 1 43 1 ATAATTTTTT 0.972595 -72 TTTTAAATTGATAATTATTTGGTATACTAA 1 65 1 ATAATTATTT 0.867018 -50 TTATTATATCTCAATTTTTGAATTAAGCTT 2 27 0 TCAATTTTTG 0.937365 -98 GAATATTTATATCATTTTTTACAAAAAAGC 4 35 1 ATCATTTTTT 0.906275 -120 CAAAAGCAATTCAATTTTGGCTTTTTTGTA 4 54 0 TCAATTTTGG 0.894213 -101 TGCTTTTGAAAGAATTTTTGTAAAAGATAT 4 76 1 AGAATTTTTG 0.928794 -79 TATGGATAGGATATTTTTTTTCAATATCTT 4 99 0 ATATTTTTTT 0.867018 -56 TTTTATGCTATTAATATTGTAATATGGATA 4 121 0 TTAATATTGT 0.688775 -34 ********** Masking position 5 Map Score: 4.14434 Number of sites scoring better than the average of aligned sites = 1647 Number in coding regions = 1132 Number in noncoding regions = 515 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 ********** No masking Map Score: 5.42445e-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: 5.42445e-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: 5.42445e-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