AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_bbur_reg_300.orf -o00300_bbur_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: BB0304 22 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase (murF) Input sequences: #1 BB0201 271 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) #2 BB0308 30 B. burgdorferi predicted coding region BB0308 #3 BB0309 92 B. burgdorferi predicted coding region BB0309 #4 BB0312 43 purine-binding chemotaxis protein (cheW-1) #5 BB0313 50 cell division protein (ftsJ) #6 BB0659 86 lysyl-tRNA synthetase #7 BB0660 89 GTP-binding protein (era) Motif number 1 TAAAGATAAATTAAAATAATACATAT 1 3 0 TTAAATATAT 0.983149 -269 TAAGATCAAGTCAAAAATATTTTTATACTTAAGG 1 59 0 TCAAAATTTT 0.733198 -213 GAAAATATATTTACAATTTTCTATTTTTTTAATA 1 186 0 TTAAATTTAT 0.978989 -86 GCTAAGAAATTCAAAATTATGCTTCAATAGAAAA 1 215 0 TCAAATTTTT 0.959557 -57 ACATTAAAATTTTACATAAAACTAATA 1 255 0 TTAAATTTAT 0.983066 -17 TTATAACTTGTTAAAATATTTAATATATTTTTTG 3 29 1 TTAAATATAT 0.982256 -64 TTTGCTAAAATCAATATATTAGATAGCTGATAAA 3 59 1 TCATATATAT 0.928621 -34 TACTTTTTCATTATAATTCTTATT 5 1 0 TTAAATTTTT 0.97698 -50 TTAATACACTTTATTATACTTTTTCATTATAATT 5 17 0 TTATATATTT 0.944147 -34 TAGGTAAATTTTAGCATTTTGTTTTTCAAGTTTC 6 42 0 TTACATTTTT 0.908386 -45 AAATAAGTATTTAAAATACTATATAATTAATTAT 7 22 1 TTAAATATAT 0.982256 -68 CATATATTTTTTATTATAATTAATTATATAGTAT 7 37 0 TTATATATAT 0.958799 -53 *** **** * ** Masking position 6 Map Score: 19.6614 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 289 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 ACTTAAAGCATTTTTATTAAAGATAAATTAAAATA 1 19 0 TTTTTTAAAA 0.990235 -253 ATTTTCTATTTTTTTAATAAACTAAGCAATGTTAC 1 170 0 TTTTTTAAAA 0.990494 -102 ACATTAAAATTTTACATAAAACTAATAAAAATAG 1 248 0 TTTTATAAAA 0.976728 -24 AGGGTGTTTTTTATAAATTTATAACTTGTTA 3 7 1 TTTTTTAAAA 0.990597 -86 TTTAATATATTTTTTGCTAAAATCAATATATTAGA 3 47 1 TTTTTTAAAA 0.990587 -46 AATTAATCAAATTGTTATAAACAGATTTAAAGGTA 4 13 1 ATTGTTAAAA 0.959638 -31 AGTATAATAAAGTGTATTAAAGGGATTGAT 5 31 1 AGTGTTAAAA 0.817862 -20 ATTAAACTGCATTTTTTTAAATTCTTGAAACTTGA 6 16 1 ATTTTTAAAT 0.887531 -71 AAATGCTAAAATTTACCTAAATTTAAATTAGGAAT 6 57 1 ATTTATAAAA 0.961159 -30 ATTTTACTTAAAAATAAGTATTTAAA 7 2 1 TTTTATAAAA 0.976659 -88 ATTCATATATTTTTTATTATAATTAATTATATAGT 7 39 0 TTTTTTATAA 0.930219 -51 ***** **** * Masking position 9 Map Score: 19.2022 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 397 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 ATATGTATTATTTTAATTTATCTTT 1 6 1 TATTATTTTA 0.635946 -266 AAGTCAAAAATATTTTTATACTTAAGGACA 1 56 0 TATTTTTATA 0.838174 -216 TACAATTTTCTATTTTTTTAATAAACTAAG 1 179 0 TATTTTTTTA 0.941828 -93 AAATTGTAAATATATTTTCTATTGAAGCAT 1 201 1 TATATTTTCT 0.875603 -71 ATTTCTTAGCTATTTTTATTAGTTTTATGT 1 239 1 TATTTTTATT 0.860752 -33 TAACAAGTTATAAATTTATAAAAAACACCC 3 12 0 TAAATTTATA 0.49744 -81 AAAAATATATTAAATATTTTAACAAGTTAT 3 31 0 TAAATATTTT 0.665276 -62 AAATATTTAATATATTTTTTGCTAAAATCA 3 42 1 TATATTTTTT 0.955641 -51 CACTTTATTATACTTTTTCATTATAATTCT 5 15 0 TACTTTTTCA 0.830906 -36 AACATTAAACTGCATTTTTTTAAATTCTTG 6 13 1 TGCATTTTTT 0.767017 -74 GTATTTTAAATACTTATTTTTAAGTAAAAT 7 11 0 TACTTATTTT 0.852603 -79 GTAATATTCATATATTTTTTATTATAATTA 7 49 0 TATATTTTTT 0.955641 -41 ATATGAATATTACATATTTAAGGAATACTA 7 66 1 TACATATTTA 0.808187 -24 ********** Masking position 7 Map Score: 11.502 Number of sites scoring better than the average of aligned sites = 2344 Number in coding regions = 1495 Number in noncoding regions = 849 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 TTATCTTTAATAAAAATGCTTTAAGTTATGTC 1 28 1 TAAAATCTTT 0.946572 -244 TCCTTAAGTATAAAAATATTTTTGACTTGATC 1 58 1 TAAAATTTTT 0.606987 -214 CAGCGCCTTGTAACATTGCTTAGTTTATTAAA 1 161 1 TACATTCTTA 0.835712 -111 AAGCATAATTTTGAATTTCTTAGCTATTTTTA 1 225 1 TTAATTCTTA 0.954686 -47 TCTTAGCTATTTTTATTAGTTTTATGTAAAAT 1 242 1 TTTATTGTTT 0.564582 -30 TATAACTACTTTCTCCCCACCT 2 19 0 TAAACTCTTT 0.945588 -12 TTTATAAATTTATAACTTGTTAAAATATTTAA 3 20 1 TAAACTGTTA 0.849835 -73 TACTTTTTCATTATAATTCTTATT 5 3 0 TTTAATCTTA 0.880768 -48 CAAACATTAAACTGCATTTTTTTAAATT 6 7 1 TTAACTCATT 0.614846 -80 ACTGCATTTTTTTAAATTCTTGAAACTTGAAA 6 21 1 TTAAATCTTG 0.848388 -66 TATATAGTATTTTAAATACTTATTTTTAAGTA 7 15 0 TTAAATCTTA 0.954683 -75 TATTTTTTATTATAATTAATTATATAGTATTT 7 35 0 TAAATTATTA 0.680728 -55 GTTTTAGTATTCCTTAAATATGTAAT 7 74 0 TATATTCTTA 0.896668 -16 ** **** **** Masking position 5 Map Score: 7.8359 Number of sites scoring better than the average of aligned sites = 1179 Number in coding regions = 760 Number in noncoding regions = 419 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 ********** No masking Map Score: 2.86649e-13 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: 2.86649e-13 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: 2.86649e-13 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