AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icpxR9_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 0.921476 -38 AATTAATCAAATATTTAAATATTATTTATA 1 17 1 ATATTTAAAT 0.839732 -23 TATTTAAATATTATTTATAAAA 1 28 1 TTATTTATAA 0.865497 -12 AACATATTTTTATTTATATAATTTTATT 2 10 1 TTATTTATAT 0.921454 -19 TTTATTAACTAGATTTAAATGTAAAATTTT 3 17 1 AGATTTAAAT 0.830518 -63 CTAATTTAACAAAATTTTACATTTAAATCT 3 27 0 AAAATTTTAC 0.67236 -53 TAAAATGTTATAATTTTAAA 4 1 0 TAATTTTAAA 0.856713 -136 GTTAAATAGTTTATTTTTATTAAATAAACT 4 53 1 TTATTTTTAT 0.857178 -84 ATAAACTTATTGAATTATACAATACAATAG 4 98 0 TGAATTATAC 0.800323 -39 AACAAGTTATAAATTTATAAAAAACACCCT 11 11 0 AAATTTATAA 0.858962 -82 AATATATTAAATATTTTAACAAGTTATAAA 11 28 0 ATATTTTAAC 0.629424 -65 AATAAGAATTATAATGAAAAAGTA 13 5 1 AGAATTATAA 0.624201 -46 AGTTGTAGGTTAAATTAAATTTAATATAAA 14 21 0 TAAATTAAAT 0.924222 -187 CTTTCTACCTTAAATTATAAGATAGAATTC 14 49 1 TAAATTATAA 0.878674 -159 ATAAAAAACATAATTTTAACAGAATTCTAT 14 70 0 TAATTTTAAC 0.873834 -138 TTGTTTTTGGTAAATTAAATTTTATTAACT 14 99 1 TAAATTAAAT 0.924222 -109 TATTAACTTCTAATTTGTATTTATCAATAT 14 121 1 TAATTTGTAT 0.733346 -87 CCTTTGAATGTAATTTAAATCGCAAATAGA 14 181 0 TAATTTAAAT 0.955291 -27 TCCTTATAATTAAATTATAATAATCAT 15 8 0 TAAATTATAA 0.878674 -35 TAAATTAAATTTTACTAATA 16 1 1 TAAATTAAAT 0.924222 -70 CGTTTTTTAATTATTTTTATTAGTAAAATT 16 18 0 TTATTTTTAT 0.857178 -53 TTAAAAAACGAAAATTTTATAAAAGATTTA 16 38 1 AAAATTTTAT 0.763344 -33 ATTTTATAAAAGATTTATATATATAAGGAG 16 51 1 AGATTTATAT 0.841221 -20 CTTTACATATTAATTTAAAC 17 1 0 TAATTTAAAC 0.931477 -67 CTATTTCCTATTATTTTAATATGTAAAGCA 17 45 0 TTATTTTAAT 0.847585 -23 ********** Masking position 5 Map Score: 30.1562 Number of sites scoring better than the average of aligned sites = 2184 Number in coding regions = 1232 Number in noncoding regions = 952 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 ATTTTAAATTAATCAAATATTTAAATATT 1 9 1 TTAATAAATA 0.957155 -31 CATATTTTTATTTATATAATTTTATT 2 13 1 TTTATTAATT 0.828552 -16 AAATGTTTTATTAACTAGATTTAAATG 3 7 1 TTTATAACTA 0.945943 -73 AATGTAAAATTTTGTTAAATTAGTGGGTAAG 3 34 1 TTTGTAAATT 0.929484 -46 TTTTAGCTTGTTTATTAAATAATTCAGGTTA 4 26 1 TTTATAAATA 0.969209 -111 ATAGTTTATTTTTATTAAATAAACTTAGTTT 4 58 1 TTTATAAATA 0.969209 -79 TCCTAAAGTCTTAATAAACTTATTGAATTAT 4 110 0 TTAATAACTT 0.956969 -27 AGGGTGTTTTTTATAAATTTATAACTTGTT 11 10 1 TTTATAATTT 0.857354 -83 TAGCAAAAAATATATTAAATATTTTAACAAG 11 35 0 TATATAAATA 0.824714 -58 AAAAGGGTGATTTATCAGCTATCTAATATAT 11 72 0 TTTATAGCTA 0.675658 -21 CAAATTAATCAAATTGTTATAAACA 12 5 1 TTAATAAATT 0.975636 -39 ATCAATCCCTTTAATACACTTTATTATACTT 13 30 0 TTAATCACTT 0.738241 -21 TTAACTTTTTTATATTAAATTTAATTTAACC 14 13 1 TATATAAATT 0.894846 -195 AAATTAGAAGTTAATAAAATTTAATTTACCA 14 106 0 TTAATAAATT 0.975636 -102 TAAAATCCTTATAATTAAATTATAATAATCA 15 12 0 ATAATAAATT 0.76283 -31 ATTATTTTTATTAGTAAAATTTAATTTA 16 8 0 TTAGTAAATT 0.903345 -63 ATATAAATCTTTTATAAAATTTTCGTTTTTT 16 40 0 TTTATAAATT 0.9826 -31 ***** ***** Masking position 5 Map Score: 26.9575 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 533 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 AATAAAATTATATAAATAAAAATATGTT 2 8 0 TTATAATAAA 0.542812 -21 GCTTGTTTATTAAATAATTCAGGTTAAATAGTT 4 31 1 TAATAATAGG 0.943528 -106 AATAAGTTTATTAAGACTTTAGGAGTAATT 4 117 1 TAAGACTAGG 0.706811 -20 ATTAATATCTTAAGGAATGTAAA 6 2 1 TAATATTAAG 0.983088 -22 TAACAAGTTATAAATTTATAAAAAACACCCT 11 9 0 TAATTTTAAA 0.712124 -84 AAAAATATATTAAATATTTTAACAAGTTATAAA 11 28 0 TAATATTAAC 0.905847 -65 TTTGCTAAAATCAATATATTAGATAGCTGATAA 11 59 1 TAATATTAGA 0.961138 -34 TAAATTAAATTTAATATAAAAAAGTTAACA 14 8 0 TAATATAAAA 0.712117 -200 TTTGTATTTATCAATATATGAGGTAATATTAAT 14 134 1 TAATATTAGG 0.985367 -74 ATAAAAGATTTATATATATAAGGAG 16 56 1 TTATATTAGG 0.937839 -15 GTTTAAATTAATATGTAAAGCTACCTAAAA 17 8 1 TAATATTAAG 0.983088 -60 TCCTATTATTTTAATATGTAAAGCAAACCTTTT 17 37 0 TAATATTAAG 0.983088 -31 * ***** * *** Masking position 4 Map Score: 13.0399 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 194 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 ACATTTAAATCTAGTTAATAAAACATTT 3 9 0 CTAGTTAATA 0.862778 -71 ATTTAATAAACAAGCTAAAATGTTATAATT 4 16 0 CAAGCTAAAA 0.936597 -121 ACTAAAAAAACAATCTTAGA 5 1 0 CAATCTTAGA 0.822611 -22 TTAAAAGCAATTTTAAATGAGGGAGGT 7 8 1 CAATTTTAAA 0.847027 -26 TCAAACCTCATTCTAAAATCTT 9 5 0 CATTCTAAAA 0.877049 -18 AAATTTATAACTTGTTAAAATATTTAATAT 11 25 1 CTTGTTAAAA 0.785707 -68 GATTTATCAGCTATCTAATATATTGATTTT 11 65 0 CTATCTAATA 0.954017 -28 TGTTAACTTTTTTATATTAAATTTAA 14 7 1 CTTTTTTATA 0.718709 -201 CTACAACTTTCTACCTTAAATTATAAGATA 14 43 1 CTACCTTAAA 0.935378 -165 TAACAGAATTCTATCTTATAATTTAAGGTA 14 54 0 CTATCTTATA 0.945827 -154 ATATGTAAAGCTACCTAAAAGGTTTGCTTT 17 21 1 CTACCTAAAA 0.945056 -47 ********** Masking position 8 Map Score: 8.16015 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 282 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 ATATTTAAATATTATTTATAAAA 1 27 1 ATTTTTATAA 0.667887 -13 TTAAATGTAAAATTTTGTTAAATTAGTGGGT 3 31 1 AATTTGTTAA 0.721522 -49 GCTAAAATGTTATAATTTTAAA 4 2 0 TATATTTTAA 0.626168 -135 CTCATTTAAAATTGCTTTTAA 7 1 0 ATTCTTTTAA 0.95167 -33 AAATTAATCAAATTGTTATAAACAGATTTAA 12 12 1 AATGTTATAA 0.765203 -32 ATTTTATACCTTTAAATCTGTTTAT 12 29 0 TATCCTTTAA 0.826251 -15 ATCAATCCCTTTAATACACTTTAT 13 37 0 AATCCTTTAA 0.955005 -14 TATAAGATAGAATTCTGTTAAAATTATGTTT 14 64 1 AATCTGTTAA 0.929368 -144 TTACTTTTAAAATCCTTATAATTAAATTATA 15 19 0 AATCTTATAA 0.95167 -24 AAATTACTTTTAAAATCCTTATA 15 30 0 ATTCTTTTAA 0.95167 -13 TTCGTTTTTTAATTATTTTTATTAGTAAAAT 16 19 0 AATATTTTTA 0.62617 -52 ATACTATTTCCTATTATTTTAATATG 17 52 0 ATTCCTATTA 0.561253 -16 *** ******* Masking position 11 Map Score: 6.02934 Number of sites scoring better than the average of aligned sites = 1237 Number in coding regions = 857 Number in noncoding regions = 380 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TTTTATAAATAATATTTAAATATTT 1 25 0 TATAAATAAT 0.749893 -15 ATTATATAAATAAAAATATGTT 2 1 0 TAAAAATATT 0.874309 -28 TAACTAGATTTAAATGTAAAATTTTGTTAAAT 3 22 1 TAAATGTAAT 0.665336 -58 TGAATTATTTAATAAACAAGCTAAAATGTTAT 4 20 0 AATAAACAAT 0.771282 -117 GTTTATTTAATAAAAATAAACTATTTAACCTG 4 50 0 TAAAAATAAT 0.952088 -87 TAGATCATATAAAAACTAAGTTTATTTAATAA 4 69 0 AAAAACTAAT 0.860085 -68 ATACTAAAAAAACAATCTTAGA 5 5 0 AAAAAACAAT 0.95717 -18 TTAAAAGCAATTTTAAATGAGGG 7 2 1 TAAAAGCAAT 0.943173 -32 ATAAATTTATAAAAAACACCCT 11 1 0 AAAAAACACT 0.779011 -92 TGATTTTAGCAAAAAATATATTAAATATTTTA 11 40 0 AAAAAATATT 0.859139 -53 TATTTTTTGCTAAAATCAATATATTAGATAGC 11 54 1 TAAAATCAAT 0.760854 -39 AATTATAATGAAAAAGTATAATAAAGTGTATT 13 17 1 AAAAAGTATT 0.80456 -34 CAAAAACAATAAAAAACATAATTTTAACAGAA 14 76 0 AAAAAACATT 0.886661 -132 CATATATTGATAAATACAAATTAGAAGTTAAT 14 122 0 TAAATACAAT 0.790601 -86 ATAAGGATTTTAAAAGTAATTT 15 31 1 TAAAAGTAAT 0.929433 -12 ATTTTACTAATAAAAATAATTAAAAAACGAAA 16 19 1 TAAAAATAAA 0.614787 -52 AAAATAATTAAAAAACGAAAATTTTATAAAAG 16 31 1 AAAAACGAAT 0.561788 -40 ********* * Masking position 8 Map Score: 17.0893 Number of sites scoring better than the average of aligned sites = 1676 Number in coding regions = 1096 Number in noncoding regions = 580 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 7 AATAATTCAGGTTAAATAGTTTATTTTTAT 4 43 1 GTTAAATAGT 0.879587 -94 AATTAAGGTGGGGAGAAAGTAGTTATA 10 14 1 GGGAGAAAGT 0.975629 -17 AAGAATTATAATGAAAAAGTATAATAAAGT 13 14 1 ATGAAAAAGT 0.95129 -37 TAAATTTAATATAAAAAAGTTAACA 14 6 0 ATAAAAAAGT 0.830953 -202 TATAATTTAAGGTAGAAAGTTGTAGGTTAA 14 38 0 GGTAGAAAGT 0.946716 -170 TTAAAATAATAGGAAATAGTAT 17 56 1 AGGAAATAGT 0.942721 -12 ********** Masking position 6 Map Score: 1.28083 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 65 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ATTGAAACCTCCCTCATTTAAAATT 7 19 0 AACCTCCCTC 0.991484 -15 AACCTAACTCAATTTACACT 8 26 0 AACCTAACTC 0.979859 -10 TCAAACCTCATTCTAAAATCTT 9 10 0 AACCTCATTC 0.965028 -13 AATTTAATTTAACCTACAACTTTCTACCTT 14 30 1 AACCTACAAC 0.916114 -178 ********** Masking position 5 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 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 Motif number 11 ********** 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