AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_bbur_reg_100.orf -o00300_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 Purged sequences: BB0304 22 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase (murF) Input sequences: #1 BB0201 271 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) #2 BB0308 30 B. burgdorferi predicted coding region BB0308 #3 BB0309 92 B. burgdorferi predicted coding region BB0309 #4 BB0312 43 purine-binding chemotaxis protein (cheW-1) #5 BB0313 50 cell division protein (ftsJ) #6 BB0659 86 lysyl-tRNA synthetase #7 BB0660 89 GTP-binding protein (era) Motif number 1 ATATGTATTATTTTAATTTATC 1 1 1 ATATGTTTAT 0.757363 -271 AACTTAAAGCATTTTTATTAAAGATAAATTAA 1 23 0 ATTTTTTTAA 0.936266 -249 AGTCAAAAATATTTTTATACTTAAGGACATAA 1 53 0 ATTTTTTACT 0.764643 -219 ACAATTTTCTATTTTTTTAATAAACTAAGCAA 1 176 0 ATTTTTTAAA 0.936266 -96 AATAGAAAATATATTTACAATTTTCTATTTTT 1 192 0 ATATTTCAAT 0.853401 -80 TTTCTTAGCTATTTTTATTAGTTTTATGTAAA 1 240 1 ATTTTTTTAT 0.965797 -32 ACATTAAAATTTTACATAAAACTAATAAAA 1 252 0 ATTTTAATAA 0.884862 -20 CAAGTTATAAATTTATAAAAAACACCCT 3 7 0 ATTTATAAAA 0.512402 -86 TATATTAAATATTTTAACAAGTTATAAATTTA 3 24 0 ATTTTACAAT 0.880374 -69 TTGTTAAAATATTTAATATATTTTTTGCTAAA 3 36 1 ATTTAAATAT 0.782257 -57 TAATATATTGATTTTAGCAAAAAATATATTAA 3 48 0 ATTTTACAAA 0.880939 -45 GTTTATAACAATTTGATTAATTTG 4 3 0 ATTTGATAAT 0.838147 -41 ATTAAACTGCATTTTTTTAAATTCTTGAAACT 6 16 1 ATTTTTTAAT 0.546866 -71 ATTTTACTTAAAAATAAGTATT 7 1 1 ATTTTATTAA 0.937233 -89 ATTATATAGTATTTTAAATACTTATTTTTAAG 7 17 0 ATTTTAATAT 0.933546 -73 TTAAAATACTATATAATTAATTATAATAAAAA 7 32 1 ATATAATAAT 0.74142 -58 TAATATTCATATATTTTTTATTATAATTAATT 7 46 0 ATATTTTTAT 0.920794 -44 AAATATATGAATATTACATATTTAAGGAATAC 7 62 1 ATATTAATAT 0.856913 -28 ****** *** * Masking position 4 Map Score: 18.3747 Number of sites scoring better than the average of aligned sites = 3469 Number in coding regions = 2190 Number in noncoding regions = 1279 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 ATATGTATTATTTTAATTTATCTTTAATA 1 9 1 TATTTTATTT 0.962201 -263 TAACTTAAAGCATTTTTATTAAAGATAAATT 1 25 0 CATTTTATTA 0.735931 -247 ATATATTTACAATTTTCTATTTTTTTAATAA 1 185 0 AATTTTTATT 0.815297 -87 ATTGTAAATATATTTTCTATTGAAGCATAAT 1 203 1 TATTTTTATT 0.925552 -69 ATTGAAGCATAATTTTGAATTTCTTAGCTAT 1 221 1 AATTTTAATT 0.916362 -51 CTATTTTTATTAGTTTTATGTAAAATTTTAA 1 248 1 TAGTTTATGT 0.834441 -24 TTTTATGTAAAATTTTAATGT 1 261 1 AATTTTATGT 0.860131 -11 AGCTATCTAATATATTGATTTTAGCAAAAAA 3 56 0 TATATTATTT 0.724478 -37 TAAAAAAATGCAGTTTAATGTTTG 6 4 0 CAGTTTATGT 0.738061 -83 TAAACTGCATTTTTTTAAATTCTTGAAACTT 6 18 1 TTTTTTAATT 0.748509 -69 TAAATTTTAGCATTTTGTTTTTCAAGTTTCA 6 41 0 CATTTTTTTT 0.85955 -46 ATTTTATTCCTAATTTAAATTTAGGTAAATT 6 66 0 TAATTTAATT 0.750793 -21 TTTAAATACTTATTTTTAAGTAAAAT 7 6 0 TATTTTAAGT 0.951766 -84 AATTATATAGTATTTTAAATACTTATTTTTA 7 19 0 TATTTTAATA 0.77197 -71 AATATTCATATATTTTTTATTATAATTAATT 7 46 0 TATTTTTATT 0.925552 -44 ****** **** Masking position 6 Map Score: 17.2887 Number of sites scoring better than the average of aligned sites = 1772 Number in coding regions = 1166 Number in noncoding regions = 606 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 ATTAAAGATAAATTAAAATAATACATAT 1 9 0 AATTAAAATA 0.623986 -263 TTATGTCCTTAAGTATAAAAATATTTTTGA 1 53 1 AAGTATAAAA 0.942987 -219 ACATAAAACTAATAAAAATAGCTAAGAAAT 1 239 0 AATAAAAATA 0.565814 -33 GTGGGGAGAAAGTAGTTATA 2 21 1 AGTAGTTATA 0.495673 -10 CAAGTTATAAATTTATAAAAAACACCCT 3 9 0 ATTTATAAAA 0.584767 -84 AAATTAATCAAATTGTTATAAACAGATTTA 4 12 1 AATTGTTATA 0.653672 -32 ACAGATTTAAAGGTATAAAAT 4 33 1 AGGTATAAAA 0.916626 -11 AATAAGAATTATAATGAAAAAGT 5 4 1 AAGAATTATA 0.908773 -47 TATAATGAAAAAGTATAATAAAGTGTATTA 5 20 1 AAGTATAATA 0.963789 -31 AAGTATAATAAAGTGTATTAAAGGGATTGA 5 30 1 AAGTGTATTA 0.801479 -21 TTCAAGTTTCAAGAATTTAAAAAAATGCAG 6 22 0 AAGAATTTAA 0.69964 -65 AATTTAAATTAGGAATAAAAT 6 76 1 AGGAATAAAA 0.896187 -11 ACTTAAAAATAAGTATTTAAAATACTATAT 7 16 1 AAGTATTTAA 0.747895 -74 CTATATAATTAATTATAATAAAAAATATAT 7 40 1 AATTATAATA 0.908008 -50 TAAAAAATATATGAATATTACATATTTAAG 7 58 1 ATGAATATTA 0.644919 -32 TACATATTTAAGGAATACTAAAAC 7 76 1 AGGAATACTA 0.70771 -14 ********** Masking position 1 Map Score: 11.7437 Number of sites scoring better than the average of aligned sites = 1680 Number in coding regions = 1058 Number in noncoding regions = 622 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 4 ATATGTATTATTTTAATTTATCTTTA 1 7 1 ATTATTTTAA 0.771147 -265 CTTTAATAAAAATGCTTTAAGTTATGTCCT 1 32 1 AATGCTTTAA 0.896429 -240 TAAACTAAGCAATGTTACAAGGCGCTGTAC 1 158 0 AATGTTACAA 0.886361 -114 CATTGCTTAGTTTATTAAAAAAATAGAAAA 1 174 1 TTTATTAAAA 0.739249 -98 AATTCAAAATTATGCTTCAATAGAAAATAT 1 212 0 TATGCTTCAA 0.802834 -60 AAATATATTAAATATTTTAACAAGTTATAA 3 29 0 AATATTTTAA 0.8161 -64 TAATATATTTTTTGCTAAAATCAATATATT 3 49 1 TTTGCTAAAA 0.846872 -44 AATTAATCAAATTGTTATAAACAGATTTAA 4 13 1 ATTGTTATAA 0.877755 -31 TGAAAAACAAAATGCTAAAATTTACCTAAA 6 48 1 AATGCTAAAA 0.92738 -39 ATTTTACTTAAAAATAAGTATT 7 3 1 TTTACTTAAA 0.720806 -87 AAGTATTTAAAATACTATATAATTAATTAT 7 26 1 AATACTATAT 0.700877 -64 TCATATATTTTTTATTATAATTAATTATAT 7 42 0 TTTATTATAA 0.77115 -48 AAAATATATGAATATTACATATTTAAGGAA 7 61 1 AATATTACAT 0.546345 -29 ATATTTAAGGAATACTAAAAC 7 79 1 AATACTAAAA 0.913101 -11 ********** Masking position 9 Map Score: 12.1949 Number of sites scoring better than the average of aligned sites = 1428 Number in coding regions = 900 Number in noncoding regions = 528 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 ********** No masking Map Score: 2.86649e-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: 2.86649e-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: 2.86649e-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