AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -irpoN_bbur_opreg_100.orf -g0.282 -x5 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 = 0.282 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 BB0068 114 conserved hypothetical protein #2 BB0074 46 peptide chain release factor 2 (prfB) #3 BB0076 36 cell division protein, putative #4 BB0079 70 B. burgdorferi predicted coding region BB0079 #5 BB0755 191 conserved hypothetical protein #6 BB0767 148 UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (murG) Motif number 1 ATATCAAATAATTTTTTTTTTTTAAATTGA 1 60 0 ATTTTTTTTT 0.977402 -55 TATTTGATATAATTTAGCTTGAAATTAACT 1 80 1 AATTTAGCTT 0.926629 -35 TTTTTCTTTCATTTTTATTTCTCGCTA 2 8 0 ATTTTTATTT 0.972195 -39 CAATGTATTTATTTTTTCTTTCATTTTTAT 2 20 0 ATTTTTTCTT 0.969475 -27 TTGAAAATTGATTTTATTTTAAAGCTTTTT 4 14 0 ATTTTATTTT 0.960927 -57 AGTTTCATTTATTTTTGCATAATTACTTTT 4 42 0 ATTTTTGCAT 0.904775 -29 AATAAATGAAACTTTAATTTTT 4 59 1 ACTTTAATTT 0.806234 -12 TGGATTTAAAAATTTTGATT 5 1 0 AATTTTGATT 0.814623 -191 ACATTATATTATTTTTTTATGAATTTAGAA 5 61 0 ATTTTTTTAT 0.890311 -131 GATAAGAATTATTTTAGCTTAACTTAAACA 5 88 0 ATTTTAGCTT 0.965797 -104 TGCTTTGTTAAATCTTGTTTCACTCTTAGT 5 127 0 AATCTTGTTT 0.823126 -65 AGTGTCAATTAATTTTATTTGCTTTGTTAA 5 146 0 AATTTTATTT 0.941466 -46 ATTTTTTCACATTTTATTTTAATAATATAT 6 83 0 ATTTTATTTT 0.960927 -66 ATTTTTATTTACTCATGAAA 6 139 0 ATTTTTATTT 0.972195 -10 ********** Masking position 1 Map Score: 21.6492 Number of sites scoring better than the average of aligned sites = 1997 Number in coding regions = 1361 Number in noncoding regions = 636 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 2 CAAATAATTTTTTTTTTTTAAATTGATAATTATTTGGTAT 1 46 0 TTTTTATAAT 0.983487 -69 GTTTTATCCTTTAGGAGTTAATTTCAAGCTAA 1 93 0 TTTCTAAAAT 0.965902 -22 ATGTATTTATTTTTTCTTTCATTTTTATTTCTCGCTA 2 8 0 TTTCTATTTT 0.723069 -39 GTTCTCCTATTTTATTGCAGATTATTAAAT 3 1 0 TTTTCAAAAT 0.933711 -36 GAAAATTGATTTTATTTTAAAGCTTTTTATA 4 2 0 TTTTTATTAT 0.954935 -69 ATTATATTATTTTTTTATGAATTTAGAAATATTAATAGTA 5 49 0 TTTTTATAAT 0.983473 -143 ATTCTCCTGGTTTGTTTTGTAAGTGTCAATTAATTTTATT 5 157 0 TTTTTATAAT 0.980473 -35 TTCCATTAAATTCAATTTTTAAGATTGAATCAATTTCTTG 6 18 1 TTCTTAAAAT 0.933703 -131 AATATCAGTATTTCCTTTGTACCAAGAAATTGATTCAATC 6 40 0 TTTTTAAAAT 0.986554 -109 TTTTTTCACATTTTATTTTAATAATATATTGCAATATCAG 6 72 0 TTTTTAAATT 0.966852 -77 CAATAAAGCATTTACTTTGTAATAAATTTTTTCACATTTT 6 98 0 TTTTTAATTT 0.912056 -51 GTAAATGCTTTATTGTTTTCATGAGTAAATAAAAAT 6 123 1 TATTTAAAAT 0.90477 -26 *** * * * * *** Masking position 11 Map Score: 15.6758 Number of sites scoring better than the average of aligned sites = 757 Number in coding regions = 491 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 CAAATAATTTTTTTTTTTTAAATTGATAAT 1 56 0 TTTTTTTTTA 0.955419 -59 TTTTCTTTCATTTTTATTTCTCGCTA 2 7 0 TTTTTATTTC 0.917186 -40 ATGTATTTATTTTTTCTTTCATTTTTATTT 2 18 0 TTTTTCTTTC 0.958114 -29 TGAAAATTGATTTTATTTTAAAGCTTTTTA 4 13 0 TTTTATTTTA 0.895138 -58 TAAAGTTTCATTTATTTTTGCATAATTACT 4 45 0 TTTATTTTTG 0.864514 -26 CATTATATTATTTTTTTATGAATTTAGAAA 5 60 0 TTTTTTTATG 0.853301 -132 TCACTCTTAGTTTCTCTTTGGATAAGAATT 5 108 0 TTTCTCTTTG 0.924102 -84 GTGTCAATTAATTTTATTTGCTTTGTTAAA 5 145 0 ATTTTATTTG 0.917557 -47 CAATATCAGTATTTCCTTTGTACCAAGAAA 6 51 0 ATTTCCTTTG 0.84303 -98 TTTTTTCACATTTTATTTTAATAATATATT 6 82 0 TTTTATTTTA 0.895138 -67 ACAATAAAGCATTTACTTTGTAATAAATTT 6 109 0 ATTTACTTTG 0.901535 -40 ATTTTTATTTACTCATGAAAA 6 138 0 TTTTTATTTA 0.930358 -11 ********** Masking position 7 Map Score: 13.1666 Number of sites scoring better than the average of aligned sites = 1873 Number in coding regions = 1308 Number in noncoding regions = 565 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 TTTTAAATTGATAATTATTTGGTATACTAA 1 41 0 ATAATTATTT 0.724501 -74 ATTATATCAAATAATTTTTTTTTTTTAAAT 1 63 0 ATAATTTTTT 0.87288 -52 TTATTTTTTCTTTCATTTTTATTTCTCGCT 2 12 0 TTTCATTTTT 0.669648 -35 GAGCAATGTATTTATTTTTTCTTTCATTTT 2 23 0 TTTATTTTTT 0.853138 -24 TTAAAATAAAATCAATTTTCAAAAGTAATT 4 22 1 ATCAATTTTC 0.860369 -49 TTAAAGTTTCATTTATTTTTGCATAATTAC 4 46 0 ATTTATTTTT 0.782043 -25 TAAATGAAACTTTAATTTTT 4 61 1 TTTAATTTTT 0.932855 -10 AATCAAAATTTTTAAATCCAT 5 2 1 ATCAAAATTT 0.595729 -190 AACGACTACTATTAATATTTCTAAATTCAT 5 43 1 ATTAATATTT 0.932855 -149 TAAACATTATATTATTTTTTTATGAATTTA 5 64 0 ATTATTTTTT 0.938426 -128 GTAAGTGTCAATTAATTTTATTTGCTTTGT 5 149 0 ATTAATTTTA 0.782043 -43 TTCCATTAAATTCAATTTTTAAGATTGAAT 6 18 1 TTCAATTTTT 0.941497 -131 TTAAGATTGAATCAATTTCTTGGTACAAAG 6 36 1 ATCAATTTCT 0.851315 -113 ATATTGCAATATCAGTATTTCCTTTGTACC 6 57 0 ATCAGTATTT 0.751949 -92 TTACTTTGTAATAAATTTTTTCACATTTTA 6 97 0 ATAAATTTTT 0.936166 -52 ********** Masking position 8 Map Score: 17.3483 Number of sites scoring better than the average of aligned sites = 2254 Number in coding regions = 1482 Number in noncoding regions = 772 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 5 CCAAATAATTATCAATTTAAAAAAAAAAAA 1 49 1 ATCAATTTAA 0.900414 -66 ATAATTTAGCTTGAAATTAACTCCTAAAGG 1 88 1 TTGAAATTAA 0.885472 -27 GAAAATTGATTTTATTTTAAAGCTTTTTAT 4 12 0 TTTATTTTAA 0.805812 -59 GTCAGTATGTATGGATTTAAAAATTTTGAT 5 12 0 ATGGATTTAA 0.900837 -180 TTATTTTTTTATGAATTTAGAAATATTAAT 5 53 0 ATGAATTTAG 0.900667 -139 TAATATAATGTTTAAGTTAAGCTAAAATAA 5 80 1 TTTAAGTTAA 0.859707 -112 AACAAAGCAAATAAAATTAATTGACACTTA 5 148 1 ATAAAATTAA 0.630233 -44 TTGAATTTAATGGAATTTAAAT 6 3 0 TGGAATTTAA 0.922094 -146 ATCTTAAAAATTGAATTTAATGGAATTTAA 6 13 0 TTGAATTTAA 0.801476 -136 TTTTTCACATTTTATTTTAATAATATATTG 6 81 0 TTTATTTTAA 0.805812 -68 ********** Masking position 7 Map Score: 7.97222 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 655 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 AAGTTTGTTCTCCTATTTTATTGCAGATT 3 18 0 CTCCTATTTT 0.980341 -19 TCTTGTTTCACTCTTAGTTTCTCTTTGGAT 5 115 0 CTCTTAGTTT 0.980341 -77 AGATTATTCTCCTGGTTTGTTTTGTAAG 5 174 0 CTCCTGGTTT 0.991327 -18 ********** Masking position 5 Map Score: 0.422512 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ********** No masking Map Score: -5.51791e-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 8 ********** No masking Map Score: -5.51791e-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 9 ********** No masking Map Score: -5.51791e-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