AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -iflhCD_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 BB0277 45 flagellar motor switch protein (fliN) #2 BB0278 37 flagellar motor switch protein (fliM) #3 BB0279 48 flagellar protein (fliL) #4 BB0282 22 flagellar protein (flbD) #5 BB0293 23 flagellar basal-body rod protein (flgC) #6 BB0294 33 flagellar basal-body rod protein (flgB) #7 BB0301 35 cell division protein (divIB) #8 BB0304 22 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase (murF) #9 BB0308 30 B. burgdorferi predicted coding region BB0308 #10 BB0309 92 B. burgdorferi predicted coding region BB0309 #11 BB0312 43 purine-binding chemotaxis protein (cheW-1) #12 BB0313 50 cell division protein (ftsJ) Motif number 1 AGTTGTTTTATTTATTAAAACTTAAATTATTAA 1 12 1 TTTTTAAATT 0.985296 -34 AATTCAACCTCTTAATAATTTAAGTTTTAAT 1 25 0 CTCTAAAATT 0.961961 -21 AAATTTAAAATTCTTTTAAATTTA 2 2 0 TTCTTTAATT 0.988671 -36 TTAAAATTCCTTTAAATTTAAAATTCTTT 2 19 0 TTCTTTAATT 0.988695 -19 GTAATTCTTTTTAACTTTAAAAAAGAA 3 5 1 TTCTTTAATT 0.988691 -44 TTTACATTCCTTAAGATATTAAT 5 5 0 TTCTTAGAAT 0.895167 -19 TGAAACCTCCCTCATTTAAAATTGCTTTTAA 6 9 0 CTCTTTAATT 0.984658 -25 TCAAACCTCATTCTAAAATCTT 8 4 0 CTCTTCAAAT 0.902799 -19 AGGGTGTTTTTTATAAATTTATAACTTGT 10 7 1 TTTTTAAATT 0.985253 -86 AAATTTATAACTTGTTAAAATATTTAATATATT 10 25 1 CTTTTAAAAT 0.940386 -68 TTTAAATCTGTTTATAACAATTTGATTAATTTG 11 11 0 TTTTAAAATT 0.93191 -33 ATTATACTTTTTCATTATAATTCTTATT 12 6 0 TTCTTAAATC 0.963765 -45 TTTAATACACTTTATTATACTTTTTCATTATAA 12 19 0 TTTTTAACTT 0.913563 -32 *** *** ** ** Masking position 5 Map Score: 23.48 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 486 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 TAGTTGTTTTATTTATTAAAACTTAA 1 7 1 TTTTATTTAT 0.713505 -39 TTTATTAAAACTTAAATTATTAAGAGGTTG 1 22 1 CTTAAATTAT 0.912824 -24 TCCTTTAAATTTAAAATTCTTTTAAATTTA 2 11 0 TTAAAATTCT 0.946001 -27 TTAAAATTCCTTTAAATTTA 2 28 0 TTAAAATTCC 0.913942 -10 AATTCCTCCCATTAATTTCTTTTTTAAAGT 3 24 0 ATTAATTTCT 0.946748 -25 AATAAAATTCCTCCCATTAAT 3 38 0 ATAAAATTCC 0.913684 -11 ATTAATATCTTAAGGAATGT 5 1 1 ATTAATATCT 0.842176 -23 CCTCCCTCATTTAAAATTGCTTTTAA 6 7 0 TTAAAATTGC 0.789809 -27 AACCTAACTCAATTTACACTACTAGAA 7 19 0 CTCAATTTAC 0.855691 -17 TTCTCCCCACCTTAATTTAT 9 1 0 CTTAATTTAT 0.915353 -30 GGTGTTTTTTATAAATTTATAACTTGTTAA 10 13 1 ATAAATTTAT 0.497908 -80 TGTTAAAATATTTAATATATTTTTTGCTAA 10 37 1 TTTAATATAT 0.794297 -56 TTTTGCTAAAATCAATATATTAGATAGCTG 10 58 1 ATCAATATAT 0.727622 -35 CAAATTAATCAAATTGTTATAAACAGA 11 8 1 ATCAAATTGT 0.83671 -36 TACTTTTTCATTATAATTCTTATT 12 5 0 TTATAATTCT 0.75303 -46 ********** Masking position 5 Map Score: 14.7271 Number of sites scoring better than the average of aligned sites = 2294 Number in coding regions = 1489 Number in noncoding regions = 805 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 TTTAATAAATAAAACAACTA 1 1 0 AAAACAACTA 0.855779 -45 AATTCAACCTCTTAATAATT 1 36 0 AATTCAACCT 0.802845 -10 TTAAAATTCCTTTAAATTTAAA 2 26 0 AAAATTCCTT 0.694452 -12 AATAAAATTCCTCCCATTAATTTCTT 3 33 0 ATTCCTCCCA 0.416814 -16 ATACTAAAAAAACAATCTTAGA 4 5 0 AAAACAATCT 0.928287 -18 TTAAAAGCAATTTTAAATGAGGG 6 4 1 AAAGCAATTT 0.70403 -30 ATTGAAACCTCCCTCATTTAAAAT 6 20 0 AAACCTCCCT 0.971388 -14 TCAAACCTCATTCTAAAATCTT 8 11 0 AAACCTCATT 0.706647 -12 TATAACTACTTTCTCCCCACC 9 20 0 ATAACTACTT 0.856322 -11 AAATTTATAAAAAACACCCT 10 1 0 AAAACACCCT 0.986776 -92 GATAGCTGATAAATCACCCTTTT 10 80 1 AAATCACCCT 0.959313 -13 AAATCTGTTTATAACAATTTGATTAATTTG 11 11 0 ATAACAATTT 0.750514 -33 CAATCCCTTTAATACACTTTATTATACTTT 12 29 0 AATACACTTT 0.848247 -22 ********** Masking position 1 Map Score: 10.6941 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 676 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 AATTCAACCTCTTAATAATTT 1 35 0 ATTCAACCTC 0.921706 -11 ATTGAAACCTCCCTCATTTAAAATT 6 19 0 AACCTCCCTC 0.996463 -15 AACCTAACTCAATTTACACT 7 26 0 AACCTAACTC 0.982292 -10 TCAAACCTCATTCTAAAATCTT 8 10 0 AACCTCATTC 0.959938 -13 ATAGCTGATAAATCACCCTTTT 10 81 1 AATCACCCTT 0.943573 -12 ********** Masking position 9 Map Score: 2.44951 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 36 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 ********** No masking Map Score: -6.86222e-14 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 6 ********** No masking Map Score: -6.86222e-14 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 7 ********** No masking Map Score: -6.86222e-14 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