AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -iflhCD_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 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 0.984535 -34 AATTCAACCTCTTAATAATTTAAGTTTTAAT 1 25 0 CTCTAAAATT 0.960042 -21 AAATTTAAAATTCTTTTAAATTTA 2 2 0 TTCTTTAATT 0.988086 -36 TTAAAATTCCTTTAAATTTAAAATTCTTT 2 19 0 TTCTTTAATT 0.988108 -19 GTAATTCTTTTTAACTTTAAAAAAGAA 3 5 1 TTCTTTAATT 0.988104 -44 TTTACATTCCTTAAGATATTAAT 5 5 0 TTCTTAGAAT 0.890262 -19 TGAAACCTCCCTCATTTAAAATTGCTTTTAA 6 9 0 CTCTTTAATT 0.983865 -25 TCAAACCTCATTCTAAAATCTT 8 4 0 CTCTTCAAAT 0.898211 -19 AGGGTGTTTTTTATAAATTTATAACTTGT 10 7 1 TTTTTAAATT 0.984494 -86 AAATTTATAACTTGTTAAAATATTTAATATATT 10 25 1 CTTTTAAAAT 0.937457 -68 TTTAAATCTGTTTATAACAATTTGATTAATTTG 11 11 0 TTTTAAAATT 0.928587 -33 ATTATACTTTTTCATTATAATTCTTATT 12 6 0 TTCTTAAATC 0.961933 -45 TTTAATACACTTTATTATACTTTTTCATTATAA 12 19 0 TTTTTAACTT 0.909432 -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 0.720844 -39 TTTATTAAAACTTAAATTATTAAGAGGTTG 1 22 1 CTTAAATTAT 0.915687 -24 TCCTTTAAATTTAAAATTCTTTTAAATTTA 2 11 0 TTAAAATTCT 0.947832 -27 TTAAAATTCCTTTAAATTTA 2 28 0 TTAAAATTCC 0.916783 -10 AATTCCTCCCATTAATTTCTTTTTTAAAGT 3 24 0 ATTAATTTCT 0.948169 -25 AATAAAATTCCTCCCATTAAT 3 38 0 ATAAAATTCC 0.916513 -11 ATTAATATCTTAAGGAATGT 5 1 1 ATTAATATCT 0.84693 -23 CCTCCCTCATTTAAAATTGCTTTTAA 6 7 0 TTAAAATTGC 0.795831 -27 AACCTAACTCAATTTACACTACTAGAA 7 19 0 CTCAATTTAC 0.860137 -17 TTCTCCCCACCTTAATTTAT 9 1 0 CTTAATTTAT 0.917641 -30 TTAACAAGTTATAAATTTATAAAAAACACC 10 13 0 ATAAATTTAT 0.498046 -80 TGTTAAAATATTTAATATATTTTTTGCTAA 10 37 1 TTTAATATAT 0.80015 -56 TTTTGCTAAAATCAATATATTAGATAGCTG 10 58 1 ATCAATATAT 0.732721 -35 CAAATTAATCAAATTGTTATAAACAGA 11 8 1 ATCAAATTGT 0.841651 -36 TACTTTTTCATTATAATTCTTATT 12 5 0 TTATAATTCT 0.759784 -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 0.853542 -45 AATTCAACCTCTTAATAATT 1 36 0 AATTCAACCT 0.79998 -10 TTAAAATTCCTTTAAATTTAAA 2 26 0 AAAATTCCTT 0.69062 -12 AATAAAATTCCTCCCATTAATTTCTT 3 33 0 ATTCCTCCCA 0.412444 -16 ATACTAAAAAAACAATCTTAGA 4 5 0 AAAACAATCT 0.92708 -18 TTAAAAGCAATTTTAAATGAGGG 6 4 1 AAAGCAATTT 0.700545 -30 ATTGAAACCTCCCTCATTTAAAAT 6 20 0 AAACCTCCCT 0.970883 -14 TCAAACCTCATTCTAAAATCTT 8 11 0 AAACCTCATT 0.702901 -12 TATAACTACTTTCTCCCCACC 9 20 0 ATAACTACTT 0.854092 -11 AAATTTATAAAAAACACCCT 10 1 0 AAAACACCCT 0.986539 -92 GATAGCTGATAAATCACCCTTTT 10 80 1 AAATCACCCT 0.958605 -13 AAATCTGTTTATAACAATTTGATTAATTTG 11 11 0 ATAACAATTT 0.747128 -33 CAATCCCTTTAATACACTTTATTATACTTT 12 29 0 AATACACTTT 0.845917 -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 AAATTATTAAGAGGTTGAATT 1 35 1 GAGGTTGAAT 0.914842 -11 AATTTTAAATGAGGGAGGTTTCAAT 6 19 1 GAGGGAGGTT 0.996125 -15 AGTGTAAATTGAGTTAGGTT 7 26 1 GAGTTAGGTT 0.98063 -10 AAGATTTTAGAATGAGGTTTGA 8 10 1 GAATGAGGTT 0.956267 -13 AAAAGGGTGATTTATCAGCTAT 10 81 0 AAGGGTGATT 0.938499 -12 ********** Masking position 2 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