AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icpxR9_bbur_opreg_300.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 BB0104 39 periplasmic serine protease DO (htrA) #2 BB0107 28 N-utilization substance protein B (nusB) #3 BB0108 79 basic membrane protein #4 BB0109 136 acetyl-CoA C-acetyltransferase (fadA) #5 BB0282 22 flagellar protein (flbD) #6 BB0293 23 flagellar basal-body rod protein (flgC) #7 BB0294 33 flagellar basal-body rod protein (flgB) #8 BB0301 35 cell division protein (divIB) #9 BB0304 22 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase (murF) #10 BB0308 30 B. burgdorferi predicted coding region BB0308 #11 BB0309 92 B. burgdorferi predicted coding region BB0309 #12 BB0312 43 purine-binding chemotaxis protein (cheW-1) #13 BB0313 50 cell division protein (ftsJ) #14 BB0565 207 purine-binding chemotaxis protein (cheW-2) #15 BB0665 42 B. burgdorferi predicted coding region BB0665 #16 BB0668 70 flagellar filament outer layer protein (flaA) #17 BB0669 67 chemotaxis histidine kinase (cheA-2) Motif number 1 ATTTTAAATTAATCAAATATT 1 2 1 TTTTAAATTA 0.90866 -38 TATAAATAATATTTAAATATTTGATTAATT 1 17 0 ATTTAAATAT 0.848015 -23 TTTTATAAATAATATTTAAATA 1 28 0 TTATAAATAA 0.865546 -12 AATAAAATTATATAAATAAAAATATGTT 2 10 0 ATATAAATAA 0.938484 -19 AAAATTTTACATTTAAATCTAGTTAATAAA 3 17 0 ATTTAAATCT 0.835551 -63 AGATTTAAATGTAAAATTTTGTTAAATTAG 3 27 1 GTAAAATTTT 0.571429 -53 TTTAAAATTATAACATTTTA 4 1 1 TTTAAAATTA 0.795056 -136 AACCTGAATTATTTAATAAACAAGCTAAAA 4 26 0 ATTTAATAAA 0.733861 -111 AGTTTATTTAATAAAAATAAACTATTTAAC 4 53 0 ATAAAAATAA 0.856492 -84 CTATTGTATTGTATAATTCAATAAGTTTAT 4 98 1 GTATAATTCA 0.829047 -39 AACCTCCCTCATTTAAAATTGCTTTTAA 7 9 0 ATTTAAAATT 0.713199 -25 AGGGTGTTTTTTATAAATTTATAACTTGTT 11 11 1 TTATAAATTT 0.80583 -82 TTGTTAAAATATTTAATATATTTTTTGCTA 11 36 1 ATTTAATATA 0.819331 -57 TACTTTTTCATTATAATTCTTATT 13 5 0 TTATAATTCT 0.620134 -46 TAATGAAAAAGTATAATAAAGTGTATTAAA 13 22 1 GTATAATAAA 0.59072 -29 ATTAAATTTAATATAAAAAAGTTAACA 14 8 0 ATATAAAAAA 0.805569 -200 TTTATATTAAATTTAATTTAACCTACAACT 14 21 1 ATTTAATTTA 0.943671 -187 GAATTCTATCTTATAATTTAAGGTAGAAAG 14 49 0 TTATAATTTA 0.883299 -159 ATAGAATTCTGTTAAAATTATGTTTTTTAT 14 70 1 GTTAAAATTA 0.81798 -138 ACCAAAAACAATAAAAAACATAATTTTAAC 14 80 0 ATAAAAAACA 0.595391 -128 AGTTAATAAAATTTAATTTACCAAAAACAA 14 99 0 ATTTAATTTA 0.943671 -109 TCTATTTGCGATTTAAATTACATTCAAAGG 14 181 1 ATTTAAATTA 0.959278 -27 ATGATTATTATAATTTAATTATAAGGA 15 8 1 TTATAATTTA 0.883299 -35 TATTAGTAAAATTTAATTTA 16 1 0 ATTTAATTTA 0.943671 -70 AATTTTACTAATAAAAATAATTAAAAAACG 16 18 1 ATAAAAATAA 0.856492 -53 TAAATCTTTTATAAAATTTTCGTTTTTTAA 16 38 0 ATAAAATTTT 0.731585 -33 CTCCTTATATATATAAATCTTTTATAAAAT 16 51 0 ATATAAATCT 0.844619 -20 GTTTAAATTAATATGTAAAG 17 1 1 GTTTAAATTA 0.920154 -67 TGCTTTACATATTAAAATAATAGGAAATAG 17 45 1 ATTAAAATAA 0.848123 -23 ********** Masking position 5 Map Score: 32.2239 Number of sites scoring better than the average of aligned sites = 3480 Number in coding regions = 2009 Number in noncoding regions = 1471 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 2 ATAATATTTAAATATTTGATTAATTTAAAAT 1 10 0 AATTTTGTTA 0.861017 -30 AACATATTTTTATTTATATAATTTTA 2 5 1 TATTTTATTA 0.732041 -24 AAATGTTTTATTAACTAGATTTA 3 2 1 AATTTTTTTA 0.863396 -78 TTTAAATGTAAAATTTTGTTAAATTAGTGGGT 3 30 1 AAATTTGTAA 0.921876 -50 TGGGTAAGTGATTCTTTAATAAGAGGTTATGT 3 57 1 ATTTTTATAA 0.913322 -23 TAAACAAGCTAAAATGTTATAATTTTAAA 4 8 0 AAATGTTTAA 0.843153 -129 TTTAACCTGAATTATTTAATAAACAAGCTAAA 4 27 0 ATTTTTATAA 0.913322 -110 TTAAATAGTTTATTTTTATTAAATAAACTTAG 4 54 1 TATTTTATAA 0.852129 -83 TATAATTCAATAAGTTTATTAAGACTTTAGGA 4 109 1 TAATTTATAA 0.838561 -28 TCTAAGATTGTTTTTTTAGTAT 5 7 1 ATTTTTTTTA 0.701074 -16 AACTTGTTAAAATATTTAATATATTTTTTGCT 11 33 1 AATTTTATAT 0.670144 -60 TATTTAATATATTTTTTGCTAAAATCAATATA 11 45 1 ATTTTTGTAA 0.829031 -48 CAAATTAATCAAATTGTTATAAACAGATTTAA 12 11 1 AAATGTTTAA 0.843153 -33 AAAGTATAATAAAGTGTATTAAAGGGATTGAT 13 29 1 AAATGTATAA 0.919658 -22 TTGGTAAATTAAATTTTATTAACTTCTAATTT 14 105 1 AAATTTATAA 0.962445 -103 ATTAACTTCTAATTTGTATTTATCAATATATG 14 122 1 AATTGTATTA 0.85737 -86 ATGATTATTATAATTTAATTATAAGGATTTT 15 10 1 ATATTTATTA 0.818441 -33 TAAATTAAATTTTACTAATAAAAATAAT 16 7 1 AAATTTATAA 0.962445 -64 TTAAAAAACGAAAATTTTATAAAAGATTTATA 16 38 1 AAATTTTTAA 0.923306 -33 *** **** *** Masking position 7 Map Score: 26.6188 Number of sites scoring better than the average of aligned sites = 1324 Number in coding regions = 825 Number in noncoding regions = 499 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 TTTATAAATAATATTTAAATATTTGATTAATTT 1 16 0 AATTAATATT 0.775237 -24 TAAACTATTTAACCTGAATTATTTAATAAACAA 4 33 0 ACCTATTATT 0.862426 -104 TTTACATTCCTTAAGATATTAAT 6 4 0 TCTTAATATT 0.968559 -20 TCAAACCTCATTCTAAAATCTT 9 1 0 ATCTAATCTT 0.658022 -22 AGGGTGTTTTTTATAAATTTATAACTTGT 11 7 1 TTTTAAAATT 0.671627 -86 CTTGTTAAAATATTTAATATATTTTTTGCTAAA 11 35 1 TTTTAATATT 0.949977 -58 ATTTATCAGCTATCTAATATATTGATTTTAGCA 11 61 0 TTCTAATATT 0.933772 -32 TGTTAACTTTTTTATATTAAATTTAATT 14 6 1 ATTTTATATT 0.637859 -202 ACAACTTTCTACCTTAAATTATAAGATAGAATT 14 45 1 ACTTATTATA 0.47603 -163 AGATTAATATTACCTCATATATTGATAAATACA 14 136 0 TCCTAATATT 0.95766 -72 AAAATTTTCGTTTTTTAATTATTTTTATTAGTA 16 23 0 TTTTATTATT 0.860708 -48 CCTTTTAGGTAGCTTTACATATTAATTTAAAC 17 10 0 ACTTAATATT 0.963754 -58 CTAAAAGGTTTGCTTTACATATTAAAATAATAG 17 35 1 TCTTAATATT 0.968559 -33 * *** * ***** Masking position 5 Map Score: 11.9509 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 368 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 AAATGTTTTATTAACTAGATTTAAATGTAAA 3 10 1 ATTAACGATT 0.968999 -70 TACCCACTAATTTAACAAAATTTTACATTTAA 3 31 0 TTTAACAATT 0.824028 -49 AAATAAACTATTTAACCTGAATTATTTAATAA 4 37 0 TTTAACGAAT 0.769902 -100 CTAAAGTCTTAATAAACTTATTGAATTATACA 4 107 0 AATAAATATT 0.57632 -30 TCAGCTATCTAATATATTGATTTTAGCAAAAA 11 57 0 AATATAGATT 0.831632 -36 ATCAAATTGTTATAAACAGATTTAAAGGTATA 12 18 1 TATAAAGATT 0.910566 -26 AATAAAGTGTATTAAAGGGATTGAT 13 36 1 ATTAAAGATT 0.955748 -15 AAAACATAATTTTAACAGAATTCTATCTTATA 14 64 0 TTTAACAATT 0.824032 -144 ATAGAATGCTAATATCAAGATTAATATTACCT 14 154 0 AATATCGATT 0.913818 -54 TTATAATTTAATTATAAGGATTTTAAAAGTAA 15 18 1 ATTATAGATT 0.908122 -25 ****** **** Masking position 4 Map Score: 6.28674 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 173 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 ATTGAAACCTCCCTCATTTAAAAT 7 20 0 AAACCTCCCT 0.992285 -14 AAATTTATAAAAAACACCCT 11 1 0 AAAACACCCT 0.979233 -92 GATAGCTGATAAATCACCCTTTT 11 80 1 AAATCACCCT 0.979232 -13 AAACGCCCCTTTGAATGTAA 14 198 0 AAACGCCCCT 0.968453 -10 ATTAATATGTAAAGCTACCTAAAAGGTTTG 17 17 1 AAAGCTACCT 0.930515 -51 ********** Masking position 3 Map Score: 2.10353 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 25 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TAAATATTTGATTAATTTAAAAT 1 4 0 ATTAATTTAA 0.860231 -36 ATATTTAAATATTATTTATAAAA 1 27 1 ATTATTTATA 0.579213 -13 TTAACAAAATTTTACATTTAAATCTAGTTA 3 22 0 TTTACATTTA 0.507775 -58 GGTTAAATAGTTTATTTTTATTAAATAAAC 4 52 1 TTTATTTTTA 0.719698 -85 AATTACTCCTAAAGTCTTAAT 4 126 0 ATTACTCCTA 0.219571 -11 TCTAAGATTGTTTTTTTAGTAT 5 7 1 ATTGTTTTTT 0.53038 -16 CTCATTTAAAATTGCTTTTAA 7 2 0 ATTGCTTTTA 0.948149 -32 TATCTAATATATTGATTTTAGCAAAAAATA 11 54 0 ATTGATTTTA 0.947215 -39 AATTAATCAAATTGTTATAAACAGATTTAA 12 13 1 ATTGTTATAA 0.474195 -31 ACTTTTTTATATTAAATTTAATTTAACCTA 14 16 1 ATTAAATTTA 0.883532 -192 TATGTTTTTTATTGTTTTTGGTAAATTAAA 14 88 1 ATTGTTTTTG 0.626011 -120 AGTTAATAAAATTTAATTTACCAAAAACAA 14 99 0 ATTTAATTTA 0.587382 -109 TAATATCAAGATTAATATTACCTCATATAT 14 147 0 ATTAATATTA 0.816139 -61 TAATATTAATCTTGATATTAGCATTCTATT 14 157 1 CTTGATATTA 0.290016 -51 TGCGATTTAAATTACATTCAAAGGGGCGTT 14 187 1 ATTACATTCA 0.495034 -21 AAATTACTTTTAAAATCCTTAT 15 31 0 ATTACTTTTA 0.95706 -12 TATTAGTAAAATTTAATTTA 16 1 0 ATTTAATTTA 0.587382 -70 TCGTTTTTTAATTATTTTTATTAGTAAAAT 16 19 0 ATTATTTTTA 0.950594 -52 AGCTTTACATATTAATTTAAAC 17 3 0 ATTAATTTAA 0.860231 -65 ACTATTTCCTATTATTTTAATATGTAAAGC 17 46 0 ATTATTTTAA 0.844133 -22 ********** Masking position 3 Map Score: 10.6197 Number of sites scoring better than the average of aligned sites = 2844 Number in coding regions = 1805 Number in noncoding regions = 1039 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 7 AATTTTGTTAAATTAGTGGGTAAGTGATTCTT 3 41 1 ATTAGTGGTA 0.814294 -39 GTGATTCTTTAATAAGAGGTTATGTT 3 64 1 ATAAGAGTTA 0.946581 -16 TATTAAATAAACTTAGTTTTTATATGATCTAT 4 70 1 ATTAGTTTTA 0.916122 -67 CAATAAGTTTATTAAGACTTTAGGAGTAATT 4 116 1 ATAAGATTTA 0.938639 -21 TAAGGTGGGGAGAAAGTAGTTATA 10 17 1 AAAAGTGTTA 0.82659 -14 GCTATCTAATATATTGATTTTAGCAAAAAATA 11 54 0 AATTGATTTA 0.581199 -39 TAAATTTAATATAAAAAAGTTAACA 14 4 0 AAAAAAGTTA 0.74775 -204 GTTTTTGGTAAATTAAATTTTATTAACTTCTA 14 101 1 ATTAAATTTA 0.871667 -107 GATAAATACAAATTAGAAGTTAATAAAATTTA 14 114 0 ATTAGAGTTA 0.960621 -94 TAATTTAATTATAAGGATTTTAAAAGTAATTT 15 21 1 AAAGGATTTA 0.599053 -22 TAAATTAAATTTTACTAATAAAAA 16 3 1 ATTAAATTTA 0.871667 -68 GTTTAAATTAATATGTAAAGCTACCTA 17 6 1 ATTAATTGTA 0.549734 -62 * ***** **** Masking position 1 Map Score: 6.41565 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 310 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ********** No masking Map Score: -1.29076e-12 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: -1.29076e-12 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 10 ********** No masking Map Score: -1.29076e-12 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