AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icpxR_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 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 AATATTTGATTAATTTAAAAT 1 2 0 TAATTTAAAA 0.882711 -38 AATTAATCAAATATTTAAATATTATTTATA 1 17 1 ATATTTAAAT 0.927527 -23 TATTTAAATATTATTTATAAAA 1 28 1 TTATTTATAA 0.835692 -12 AACATATTTTTATTTATATAATT 2 4 1 ATATTTTTAT 0.701713 -25 AATAAAATTATATAAATAAAAAT 2 16 0 AAAATTATAT 0.9333 -13 TTTATTAACTAGATTTAAATGTAAAATTTT 3 17 1 AGATTTAAAT 0.855413 -63 TTTAAAATTATAACATTTTAGCT 4 4 1 AAAATTATAA 0.88271 -133 TTTTAGCTTGTTTATTAAATAATTCAGGTT 4 26 1 TTTATTAAAT 0.812565 -111 ATAGTTTATTTTTATTAAATAAACTTAGTT 4 58 1 TTTATTAAAT 0.812565 -79 TTAAAAGCAATTTTAAATGAGGGAGGTT 7 9 1 AATTTTAAAT 0.777121 -25 AACAAGTTATAAATTTATAAAAAACACCCT 11 11 0 AAATTTATAA 0.847543 -82 TAGCAAAAAATATATTAAATATTTTAACAA 11 36 0 TATATTAAAT 0.825174 -57 AATAAGAATTATAATGAAAAAGTA 13 5 1 AGAATTATAA 0.760881 -46 TGTTAACTTTTTTATATTAAATTTAAT 14 8 1 TTTTTTATAT 0.702289 -200 AGTTGTAGGTTAAATTAAATTTAATATAAA 14 21 0 TAAATTAAAT 0.949855 -187 CTTTCTACCTTAAATTATAAGATAGAATTC 14 49 1 TAAATTATAA 0.882711 -159 AATAAAAAACATAATTTTAACAGAATTCTA 14 71 0 ATAATTTTAA 0.632477 -137 TTGTTTTTGGTAAATTAAATTTTATTAACT 14 99 1 TAAATTAAAT 0.949855 -109 CCTTTGAATGTAATTTAAATCGCAAATAGA 14 181 0 TAATTTAAAT 0.933301 -27 TAAAATCCTTATAATTAAATTATAATAATC 15 13 0 ATAATTAAAT 0.945585 -30 TAAATTAAATTTTACTAATA 16 1 1 TAAATTAAAT 0.949855 -70 ACTAATAAAAATAATTAAAAAACGAAAATT 16 24 1 ATAATTAAAA 0.903403 -47 TTAAAAAACGAAAATTTTATAAAAGATTTA 16 38 1 AAAATTTTAT 0.777121 -33 ATTTTATAAAAGATTTATATATATAAGGAG 16 51 1 AGATTTATAT 0.81379 -20 GCTTTACATATTAATTTAAAC 17 2 0 TTAATTTAAA 0.699872 -66 CTATTTCCTATTATTTTAATATGTAAAGCA 17 45 0 TTATTTTAAT 0.761924 -23 ********** Masking position 5 Map Score: 33.0495 Number of sites scoring better than the average of aligned sites = 3175 Number in coding regions = 1891 Number in noncoding regions = 1284 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 ATTTTAAATTAATCAAATATTTAAATATTA 1 9 1 TTATCAAAAT 0.92099 -31 TTTTATAAATAATATTTAAATAT 1 27 0 TTTTAAATAT 0.679625 -13 CATATTTTTATTTATATAATTTTATT 2 13 1 TTTTATAATT 0.819428 -16 TTAAATCTAGTTAATAAAACATTT 3 3 0 TTATAAAAAT 0.982554 -77 ACCCACTAATTTAACAAAATTTTACATTTAAA 3 30 0 TTACAAAATT 0.933248 -50 ACATAACCTCTTATTAAAGAATCACTTACCCA 3 57 0 TTATAAAGAT 0.86295 -23 TTTAGCTTGTTTATTAAATAATTCAGGTTAAA 4 27 1 TTATAAATAT 0.882129 -110 CTAAGTTTATTTAATAAAAATAAACTATTTAA 4 54 0 TTATAAAATA 0.861112 -83 TTCAATAAGTTTATTAAGACTTTAGGAGTAAT 4 114 1 TTATAAGATT 0.831382 -23 AGGGTGTTTTTTATAAATTTATAACTTGT 11 8 1 TTTTATAATT 0.819354 -85 AATTTATAACTTGTTAAAATATTTAATATATT 11 26 1 TTGTAAAAAT 0.874871 -67 TATATTGATTTTAGCAAAAAATATATTAAATA 11 45 0 TTACAAAAAT 0.944395 -48 CAAATTAATCAAATTGTTATAAACAG 12 5 1 TTATCAAATG 0.518439 -39 TAAATTAAATTTAATATAAAAAAGTTAACA 14 9 0 TTATATAAAA 0.66576 -199 AAATTAGAAGTTAATAAAATTTAATTTACCAA 14 105 0 TTATAAAATT 0.97894 -103 TAATTTGTATTTATCAATATATGAGGTAATAT 14 131 1 TTACAATAAT 0.548561 -77 ATGATTATTATAATTTAATTATAAGG 15 5 1 TTATATAATT 0.94104 -38 ATTATTTTTATTAGTAAAATTTAATTTA 16 7 0 TTATAAAATT 0.978946 -64 AAACGAAAATTTTATAAAAGATTTATATATAT 16 43 1 TTTTAAAAAT 0.940827 -28 CTATTTCCTATTATTTTAATATGTAAAGCAAA 17 43 0 TTATTTAAAT 0.544661 -25 *** ***** ** Masking position 2 Map Score: 22.3154 Number of sites scoring better than the average of aligned sites = 1858 Number in coding regions = 1140 Number in noncoding regions = 718 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 AATAAAATTATATAAATAAAAATATGTT 2 8 0 TTATAATAAA 0.688136 -21 GCTTGTTTATTAAATAATTCAGGTTAAATAGTT 4 31 1 TAATAATAGG 0.951192 -106 ATTAATATCTTAAGGAATGTAAA 6 2 1 TAATATTAAG 0.988233 -22 TAACAAGTTATAAATTTATAAAAAACACCCT 11 9 0 TAATTTTAAA 0.819953 -84 AAAAATATATTAAATATTTTAACAAGTTATAAA 11 28 0 TAATATTAAC 0.941678 -65 TTTGCTAAAATCAATATATTAGATAGCTGATAA 11 59 1 TAATATTAGA 0.971006 -34 TAAATTAAATTTAATATAAAAAAGTTAACA 14 8 0 TAATATAAAA 0.819931 -200 TTTGTATTTATCAATATATGAGGTAATATTAAT 14 134 1 TAATATTAGG 0.987428 -74 ATAAAAGATTTATATATATAAGGAG 16 56 1 TTATATTAGG 0.951192 -15 GTTTAAATTAATATGTAAAGCTACCTAAAA 17 8 1 TAATATTAAG 0.988233 -60 TCCTATTATTTTAATATGTAAAGCAAACCTTTT 17 37 0 TAATATTAAG 0.988233 -31 * ***** * *** Masking position 4 Map Score: 14.4771 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 163 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TTTTATAAATAATATTTAAATAT 1 27 0 TATAAATAAT 0.542798 -13 AATAAAATTATATAAATAAAAATATGTT 2 9 0 TATAAATAAA 0.61039 -20 AATCTAGTTAATAAAACATTT 3 2 0 ATAAAACATT 0.277747 -78 TAACTAGATTTAAATGTAAAATTTTGTTAA 3 22 1 TAAATGTAAA 0.500253 -58 TTTAAAATTATAACATTTTAGC 4 3 1 TAAAATTATA 0.504076 -134 GTTTATTTAATAAAAATAAACTATTTAACC 4 52 0 TAAAAATAAA 0.929042 -85 ATAGATCATATAAAAACTAAGTTTATTTAA 4 72 0 TAAAAACTAA 0.787133 -65 ATACTAAAAAAACAATCTTAGA 5 7 0 AAAAAACAAT 0.908042 -16 TTAAAAGCAATTTTAAATGAG 7 2 1 TAAAAGCAAT 0.902973 -32 ACACTACTAGAAAAATCTAA 8 1 0 AAAAATCTAA 0.382955 -35 TGATTTTAGCAAAAAATATATTAAATATTT 11 42 0 AAAAAATATA 0.741416 -51 TATTTTTTGCTAAAATCAATATATTAGATA 11 54 1 TAAAATCAAT 0.784357 -39 AATTATAATGAAAAAGTATAATAAAGTGTA 13 17 1 AAAAAGTATA 0.647663 -34 ATTTAATATAAAAAAGTTAACA 14 3 0 AAAAAGTTAA 0.519205 -205 CAAAAACAATAAAAAACATAATTTTAACAG 14 78 0 AAAAAACATA 0.80953 -130 TTTAATTTACCAAAAACAATAAAAAACATA 14 88 0 CAAAAACAAT 0.697629 -120 CATATATTGATAAATACAAATTAGAAGTTA 14 124 0 TAAATACAAA 0.698217 -84 ATAAGGATTTTAAAAGTAATTT 15 31 1 TAAAAGTAAT 0.863563 -12 ATTTTACTAATAAAAATAATTAAAAAACGA 16 19 1 TAAAAATAAT 0.90847 -52 AAAAATAATTAAAAAACGAAAATTTTATAA 16 30 1 AAAAAACGAA 0.594241 -41 GCTTTACATATTAAAATAATAGGAAATAGT 17 46 1 TTAAAATAAT 0.543072 -22 ********** Masking position 4 Map Score: 13.1947 Number of sites scoring better than the average of aligned sites = 4707 Number in coding regions = 3073 Number in noncoding regions = 1634 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 5 AAATGTTTTATTAACTAGATTTAAATGT 3 9 1 TATTAACTAG 0.699485 -71 AATTATAACATTTTAGCTTGTTTATTAAAT 4 16 1 TTTTAGCTTG 0.938993 -121 TCTAAGATTGTTTTTTTAGT 5 1 1 TCTAAGATTG 0.871605 -22 ACCTCCCTCATTTAAAATTGCTTTTAA 7 8 0 TTTAAAATTG 0.785216 -26 AAGATTTTAGAATGAGGTTTGA 9 5 1 TTTTAGAATG 0.78288 -18 AAAATCAATATATTAGATAGCTGATAAATC 11 65 1 TATTAGATAG 0.946139 -28 TATCTTATAATTTAAGGTAGAAAGTTGTAG 14 43 0 TTTAAGGTAG 0.938993 -165 TACCTTAAATTATAAGATAGAATTCTGTTA 14 54 1 TATAAGATAG 0.934461 -154 AAAGCAAACCTTTTAGGTAGCTTTACATAT 17 21 0 TTTTAGGTAG 0.949907 -47 ********** Masking position 5 Map Score: 5.85376 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 169 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ATTTTAAATTAATCAAATATTTAAATATTA 1 11 1 AATCAAATAT 0.680661 -29 TTTTATAAATAATATTTAAATATTTGA 1 23 0 AATAATATTT 0.674169 -17 AAATTATATAAATAAAAATATGTT 2 5 0 AATAAAAATA 0.798922 -24 AATAAAATTATATAAATAAA 2 19 0 AATAAAATTA 0.941031 -10 AAATCTAGTTAATAAAACATTT 3 3 0 AATAAAACAT 0.53665 -77 CCACTAATTTAACAAAATTTTACATTTAAA 3 30 0 AACAAAATTT 0.900723 -50 TGAATTATTTAATAAACAAGCTAAAATGTT 4 22 0 AATAAACAAG 0.329677 -115 ATTTAATAAAAATAAACTATTTAACCTGAA 4 48 0 AATAAACTAT 0.834746 -89 ATTTTTATTAAATAAACTTAGTTTTTATAT 4 65 1 AATAAACTTA 0.886448 -72 TGAATTATACAATACAATAGATCATATAAA 4 88 0 AATACAATAG 0.614594 -49 CTAAAGTCTTAATAAACTTATTGAATTATA 4 109 0 AATAAACTTA 0.886448 -28 AACCTAACTCAATTTACACTACTAG 8 21 0 AACTCAATTT 0.406588 -15 CAAATTAATCAAATTGTTATAAACAG 12 7 1 AATCAAATTG 0.730972 -37 CAATCCCTTTAATACACTTTATTATACTTT 13 29 0 AATACACTTT 0.866724 -22 TTGTAGGTTAAATTAAATTTAATATAAAAA 14 19 0 AATTAAATTT 0.865427 -189 AACAATAAAAAACATAATTTTAACAGAATT 14 74 0 AACATAATTT 0.407098 -134 ATTAGAAGTTAATAAAATTTAATTTACCAA 14 105 0 AATAAAATTT 0.971147 -103 TATATTGATAAATACAAATTAGAAGTTAAT 14 122 0 AATACAAATT 0.767959 -86 AAATCCTTATAATTAAATTATAATAATCAT 15 11 0 AATTAAATTA 0.753171 -32 TATTTTTATTAGTAAAATTTAATTTA 16 7 0 AGTAAAATTT 0.754112 -64 AAATTTTACTAATAAAAATAATTAAAAAAC 16 17 1 AATAAAAATA 0.798922 -54 ATAAATCTTTTATAAAATTTTCGTTTTTTA 16 39 0 TATAAAATTT 0.674188 -32 ********** Masking position 6 Map Score: 19.9842 Number of sites scoring better than the average of aligned sites = 3415 Number in coding regions = 2229 Number in noncoding regions = 1186 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 7 AATTTTAAATGAGGGAGGTTTCAAT 7 19 1 GAGGGAGGTT 0.991938 -15 AGTGTAAATTGAGTTAGGTT 8 26 1 GAGTTAGGTT 0.980922 -10 AAGATTTTAGAATGAGGTTTGA 9 10 1 GAATGAGGTT 0.966848 -13 AAGGTAGAAAGTTGTAGGTTAAATTAAATT 14 30 0 GTTGTAGGTT 0.920271 -178 ********** Masking position 6 Map Score: 0.261252 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 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