AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icpxR_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 0.900543 -38 TATAAATAATATTTAAATATTTGATTAATT 1 17 0 ATTTAAATAT 0.835511 -23 TTTTATAAATAATATTTAAATA 1 28 0 TTATAAATAA 0.854321 -12 AATAAAATTATATAAATAAAAATATGTT 2 10 0 ATATAAATAA 0.93287 -19 AAAATTTTACATTTAAATCTAGTTAATAAA 3 17 0 ATTTAAATCT 0.822209 -63 AGATTTAAATGTAAAATTTTGTTAAATTAG 3 27 1 GTAAAATTTT 0.548243 -53 TTTAAAATTATAACATTTTA 4 1 1 TTTAAAATTA 0.779297 -136 AACCTGAATTATTTAATAAACAAGCTAAAA 4 26 0 ATTTAATAAA 0.715085 -111 AGTTTATTTAATAAAAATAAACTATTTAAC 4 53 0 ATAAAAATAA 0.844562 -84 CTATTGTATTGTATAATTCAATAAGTTTAT 4 98 1 GTATAATTCA 0.815294 -39 AACCTCCCTCATTTAAAATTGCTTTTAA 7 9 0 ATTTAAAATT 0.693571 -25 AGGGTGTTTTTTATAAATTTATAACTTGTT 11 11 1 TTATAAATTT 0.790683 -82 TTGTTAAAATATTTAATATATTTTTTGCTA 11 36 1 ATTTAATATA 0.80498 -57 TACTTTTTCATTATAATTCTTATT 13 5 0 TTATAATTCT 0.597729 -46 TAATGAAAAAGTATAATAAAGTGTATTAAA 13 22 1 GTATAATAAA 0.567789 -29 ATTAAATTTAATATAAAAAAGTTAACA 14 8 0 ATATAAAAAA 0.790439 -200 TTTATATTAAATTTAATTTAACCTACAACT 14 21 1 ATTTAATTTA 0.938455 -187 GAATTCTATCTTATAATTTAAGGTAGAAAG 14 49 0 TTATAATTTA 0.873244 -159 ATAGAATTCTGTTAAAATTATGTTTTTTAT 14 70 1 GTTAAAATTA 0.803548 -138 ACCAAAAACAATAAAAAACATAATTTTAAC 14 80 0 ATAAAAAACA 0.572532 -128 AGTTAATAAAATTTAATTTACCAAAAACAA 14 99 0 ATTTAATTTA 0.938455 -109 TCTATTTGCGATTTAAATTACATTCAAAGG 14 181 1 ATTTAAATTA 0.955439 -27 ATGATTATTATAATTTAATTATAAGGA 15 8 1 TTATAATTTA 0.873244 -35 TATTAGTAAAATTTAATTTA 16 1 0 ATTTAATTTA 0.938455 -70 AATTTTACTAATAAAAATAATTAAAAAACG 16 18 1 ATAAAAATAA 0.844562 -53 TAAATCTTTTATAAAATTTTCGTTTTTTAA 16 38 0 ATAAAATTTT 0.712708 -33 CTCCTTATATATATAAATCTTTTATAAAAT 16 51 0 ATATAAATCT 0.831865 -20 GTTTAAATTAATATGTAAAG 17 1 1 GTTTAAATTA 0.912961 -67 TGCTTTACATATTAAAATAATAGGAAATAG 17 45 1 ATTAAAATAA 0.835607 -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 ATTTTAAATTAATCAAATATTTAAATATTAT 1 10 1 TAATAAAATT 0.929151 -30 TAAAATTATATAAATAAAAATATGTT 2 5 0 TAAAAAAATA 0.66901 -24 TAAATCTAGTTAATAAAACATTT 3 2 0 TAATAAAATT 0.929151 -78 ACCCACTAATTTAACAAAATTTTACATTTAAA 3 30 0 TTAAAAATTT 0.928534 -50 ACATAACCTCTTATTAAAGAATCACTTACCCA 3 57 0 TTATAAAAAT 0.898587 -23 TTTAAAATTATAACATTTTAGCTTGTTTA 4 8 1 TTATACATTT 0.871077 -129 TTTAGCTTGTTTATTAAATAATTCAGGTTAAA 4 27 1 TTATAAAAAT 0.898587 -110 CTAAGTTTATTTAATAAAAATAAACTATTTAA 4 54 0 TTAAAAAATA 0.786338 -83 TCCTAAAGTCTTAATAAACTTATTGAATTATA 4 109 0 TTAAAAATTA 0.712966 -28 ATACTAAAAAAACAATCTTAGA 5 7 0 TAAAAAAAAT 0.796847 -16 AGCAAAAAATATATTAAATATTTTAACAAGTT 11 33 0 ATATAAAATT 0.618314 -60 TATATTGATTTTAGCAAAAAATATATTAAATA 11 45 0 TTAGAAAAAT 0.754353 -48 TTAAATCTGTTTATAACAATTTGATTAATTTG 12 11 0 TTATACATTT 0.871077 -33 ATAAGAATTATAATGAAAAAGTATAATAAAGT 13 12 1 TAATAAAAGT 0.640208 -39 ATCAATCCCTTTAATACACTTTATTATACTTT 13 29 0 TTAAACATTT 0.844858 -22 AAATTAGAAGTTAATAAAATTTAATTTACCAA 14 105 0 TTAAAAATTT 0.928523 -103 CATATATTGATAAATACAAATTAGAAGTTAAT 14 122 0 TAAAACAATT 0.815858 -86 AAAATCCTTATAATTAAATTATAATAATCAT 15 10 0 TAATAAATAT 0.766597 -33 ATTATTTTTATTAGTAAAATTTAATTTA 16 7 0 TTAGAAATTT 0.848167 -64 AACGAAAATTTTATAAAAGATTTATATATATA 16 44 1 TTATAAAATT 0.959805 -27 **** *** *** Masking position 6 Map Score: 26.6496 Number of sites scoring better than the average of aligned sites = 1941 Number in coding regions = 1255 Number in noncoding regions = 686 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 AAATTAATCAAATATTTAAATATTATTTATAAA 1 16 1 AATATTAATT 0.793526 -24 TTGTTTATTAAATAATTCAGGTTAAATAGTTTA 4 33 1 AATAATAGGT 0.874766 -104 ATTAATATCTTAAGGAATGTAAA 6 4 1 AATATTAAGA 0.971692 -20 AAGATTTTAGAATGAGGTTTGA 9 1 1 AAGATTAGAT 0.681936 -22 ACAAGTTATAAATTTATAAAAAACACCCT 11 7 0 AATTTTAAAA 0.694971 -86 TTTAGCAAAAAATATATTAAATATTTTAACAAG 11 35 0 AATATTAAAA 0.95474 -58 TGCTAAAATCAATATATTAGATAGCTGATAAAT 11 61 1 AATATTAGAA 0.940126 -32 AATTAAATTTAATATAAAAAAGTTAACA 14 6 0 AATATAAAAT 0.662295 -202 AATTCTATCTTATAATTTAAGGTAGAAAGTTGT 14 45 0 TATAATAAGT 0.503059 -163 TGTATTTATCAATATATGAGGTAATATTAATCT 14 136 1 AATATTAGGA 0.961836 -72 TACTAATAAAAATAATTAAAAAACGAAAATTTT 16 23 1 AATAATAAAA 0.873181 -48 GTTTAAATTAATATGTAAAGCTACCTAAAAGG 17 10 1 AATATTAAGT 0.967348 -58 CTATTATTTTAATATGTAAAGCAAACCTTTTAG 17 35 0 AATATTAAGA 0.971692 -33 ***** * *** * Masking position 9 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 TTTACATTTAAATCTAGTTAATAAAACATTT 3 10 0 AATCGTTAAT 0.973149 -70 TTAAATGTAAAATTTTGTTAAATTAGTGGGTA 3 31 1 AATTGTTAAA 0.850507 -49 TTATTAAATAATTCAGGTTAAATAGTTTATTT 4 37 1 ATTCGTTAAA 0.802572 -100 TGTATAATTCAATAAGTTTATTAAGACTTTAG 4 107 1 AATATTTATT 0.608173 -30 TTTTTGCTAAAATCAATATATTAGATAGCTGA 11 57 1 AATCTATATT 0.843327 -36 TATACCTTTAAATCTGTTTATAACAATTTGAT 12 18 0 AATCTTTATA 0.925193 -26 ATCAATCCCTTTAATACACTTTATT 13 36 0 AATCTTTAAT 0.963114 -15 TATAAGATAGAATTCTGTTAAAATTATGTTTT 14 64 1 AATTGTTAAA 0.850513 -144 AGGTAATATTAATCTTGATATTAGCATTCTAT 14 154 1 AATCGATATT 0.927504 -54 TTACTTTTAAAATCCTTATAATTAAATTATAA 15 18 0 AATCTATAAT 0.923123 -25 **** ****** Masking position 9 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 ATTTTAAATGAGGGAGGTTTCAAT 7 20 1 AGGGAGGTTT 0.991362 -14 AGGGTGTTTTTTATAAATTT 11 1 1 AGGGTGTTTT 0.976786 -92 AAAAGGGTGATTTATCAGCTATC 11 80 0 AGGGTGATTT 0.976785 -13 TTACATTCAAAGGGGCGTTT 14 198 1 AGGGGCGTTT 0.964782 -10 CAAACCTTTTAGGTAGCTTTACATATTAAT 17 17 0 AGGTAGCTTT 0.92278 -51 ********** Masking position 8 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 AATTTTGTTAAATTAGTGGGTAAGTGATTCTT 3 41 1 ATTAGTGGTA 0.839293 -39 GTGATTCTTTAATAAGAGGTTATGTT 3 64 1 ATAAGAGTTA 0.954761 -16 TATTAAATAAACTTAGTTTTTATATGATCTAT 4 70 1 ATTAGTTTTA 0.928615 -67 CAATAAGTTTATTAAGACTTTAGGAGTAATT 4 116 1 ATAAGATTTA 0.947969 -21 TAAGGTGGGGAGAAAGTAGTTATA 10 17 1 AAAAGTGTTA 0.850238 -14 GCTATCTAATATATTGATTTTAGCAAAAAATA 11 54 0 AATTGATTTA 0.62305 -39 TAAATTTAATATAAAAAAGTTAACA 14 4 0 AAAAAAGTTA 0.779278 -204 GTTTTTGGTAAATTAAATTTTATTAACTTCTA 14 101 1 ATTAAATTTA 0.889986 -107 GATAAATACAAATTAGAAGTTAATAAAATTTA 14 114 0 ATTAGAGTTA 0.966727 -94 TAATTTAATTATAAGGATTTTAAAAGTAATTT 15 21 1 AAAGGATTTA 0.640224 -22 TAAATTAAATTTTACTAATAAAAA 16 3 1 ATTAAATTTA 0.889986 -68 GTTTAAATTAATATGTAAAGCTACCTA 17 6 1 ATTAATTGTA 0.592525 -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 7 TAAATATTTGATTAATTTAAAAT 1 4 0 ATTAATTTAA 0.813998 -36 ATATTTAAATATTATTTATAAAA 1 27 1 ATTATTTATA 0.55256 -13 TTAACAAAATTTTACATTTAAATCTAGTTA 3 22 0 TTTACATTTA 0.430859 -58 GGTTAAATAGTTTATTTTTATTAAATAAAC 4 52 1 TTTATTTTTA 0.698791 -85 AATTACTCCTAAAGTCTTAAT 4 126 0 ATTACTCCTA 0.200953 -11 TCTAAGATTGTTTTTTTAGTAT 5 7 1 ATTGTTTTTT 0.480426 -16 CTCATTTAAAATTGCTTTTAA 7 2 0 ATTGCTTTTA 0.925775 -32 TATCTAATATATTGATTTTAGCAAAAAATA 11 54 0 ATTGATTTTA 0.938123 -39 ACTTTTTTATATTAAATTTAATTTAACCTA 14 16 1 ATTAAATTTA 0.859134 -192 TATGTTTTTTATTGTTTTTGGTAAATTAAA 14 88 1 ATTGTTTTTG 0.578139 -120 AGTTAATAAAATTTAATTTACCAAAAACAA 14 99 0 ATTTAATTTA 0.554701 -109 TAATATCAAGATTAATATTACCTCATATAT 14 147 0 ATTAATATTA 0.75341 -61 TAATATTAATCTTGATATTAGCATTCTATT 14 157 1 CTTGATATTA 0.224867 -51 AAATTACTTTTAAAATCCTTAT 15 31 0 ATTACTTTTA 0.943371 -12 TATTAGTAAAATTTAATTTA 16 1 0 ATTTAATTTA 0.554701 -70 TCGTTTTTTAATTATTTTTATTAGTAAAAT 16 19 0 ATTATTTTTA 0.938935 -52 AGCTTTACATATTAATTTAAAC 17 3 0 ATTAATTTAA 0.813998 -65 ACTATTTCCTATTATTTTAATATGTAAAGC 17 46 0 ATTATTTTAA 0.768732 -22 ********** Masking position 3 Map Score: 10.5941 Number of sites scoring better than the average of aligned sites = 2353 Number in coding regions = 1513 Number in noncoding regions = 840 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 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