AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_bbur_reg_100.orf -o00190_bbur_100.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 BB0093 21 V-type ATPase, subunit B (atpB) #2 BB0094 85 V-type ATPase, subunit A (atpA) #3 BB0096 183 V-type ATPase, subunit E, putative #4 BB0293 23 flagellar basal-body rod protein (flgC) #5 BB0294 33 flagellar basal-body rod protein (flgB) #6 BB0301 35 cell division protein (divIB) #7 BB0308 30 B. burgdorferi predicted coding region BB0308 #8 BB0309 92 B. burgdorferi predicted coding region BB0309 #9 BB0312 43 purine-binding chemotaxis protein (cheW-1) #10 BB0313 50 cell division protein (ftsJ) Motif number 1 GGGGTTTGGAGAAATATATAT 1 5 1 TTTAATAAAT 0.936017 -17 GACTTTTCCTTTTGTATTCATTTAAATTCCTTTT 2 8 0 TTTATTTAAT 0.978909 -78 GGTTGTATTATTTCTAATAGTTGAGAATAAGTATATT 3 12 1 TTTATTTAAA 0.975016 -172 TATCAAAAATTTTACAATATTAAAAAACATATCAAGT 3 73 0 TTTATTAAAA 0.912428 -111 ATAAAATAAATTTTTAATATCAAAAATTTTACAATAT 3 90 0 TTTATCAAAT 0.936007 -94 CAAACAAAACTTTAAAAAAGCATAAAATAAATTTTTA 3 111 0 TTTAACAAAA 0.878798 -73 TTTACATTCCTTAAGATATTAAT 4 7 0 TTTATTTAAT 0.980604 -17 ACCTCCCTCATTTAAAATTGCTTTTAA 5 1 0 TTTATCTTAA 0.783328 -33 CCTAACTCAATTTACACTACTAGAAAAATCTAA 6 7 0 TTTATTAAAA 0.980364 -29 AGGGTGTTTTTTATAAATTTATAACTTGTTAAAA 8 8 1 TTTAATTAAA 0.914833 -85 TTTATAACTTGTTAAAATATTTAATATATTTTTTGCT 8 28 1 GTTATTTAAT 0.896635 -65 ATTTTATACCTTTAAATCTGTTTATAACAATTTGATT 9 17 0 TTTACTTAAA 0.940604 -27 *** * * ** * ** Masking position 6 Map Score: 16.9775 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 570 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 GTATTCATTTAAATTCCTTTT 2 1 0 AAATTCTTTT 0.89641 -85 TCTTTAAAGAATATACTTATTCTCAACTATT 3 27 0 ATATACTATT 0.724716 -157 GTTGGCACAATAATACTTCTTTAAAGAATAT 3 44 0 TAATACTCTT 0.933064 -140 TGTGCCAACTTGATATGTTTTTTAATATTGT 3 66 1 TGATATTTTT 0.728333 -118 AAAAAGCATAAAATAAATTTTTAATATCAAA 3 103 0 AAATAATTTT 0.921981 -81 TTTTGTTTGCTAATAAGTGTTAGGTTATTAT 3 139 1 TAATAATGTT 0.799326 -45 AAGTGTTAGGTTATTATTTTTATCTTATATG 3 153 1 TTATTATTTT 0.898388 -31 CCCTCATTTAAAATTGCTTTTAA 5 3 0 AAATTGTTTT 0.753756 -31 TTTTAACAAGTTATAAATTTATAAAAAACAC 8 14 0 TTATAATTTA 0.801067 -79 TTAAAATATTTAATATATTTTTTGCTAAAAT 8 39 1 TAATATTTTT 0.909545 -54 GCTATCTAATATATTGATTTTAGCAAAAAAT 8 55 0 ATATTGTTTT 0.753904 -38 ATTTTATACCTTTAAATCTGTTTA 9 30 0 TTATACTTTA 0.884514 -14 TACTTTTTCATTATAATTCTTATT 10 4 0 TTATAATCTT 0.879958 -47 ATACACTTTATTATACTTTTTCATTATAATT 10 17 0 TTATACTTTT 0.97783 -34 TCAATCCCTTTAATACACTTTATTATACTTT 10 29 0 TAATACCTTT 0.856691 -22 ****** **** Masking position 3 Map Score: 11.6608 Number of sites scoring better than the average of aligned sites = 2225 Number in coding regions = 1404 Number in noncoding regions = 821 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 3 AGAAACTGAACCTTCTACCTCAATAGTA 2 68 0 AACCTTCTAC 0.953941 -18 TAAAAATAATAACCTAACACTTATTAGCAA 3 145 0 AACCTAACAC 0.989452 -39 ATTGAAACCTCCCTCATTTAAAATT 5 19 0 AACCTCCCTC 0.991867 -15 AACCTAACTCAATTTACACT 6 26 0 AACCTAACTC 0.989447 -10 ********** Masking position 5 Map Score: 2.48506 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TGGTTGTATTATTTCTAATAGTTGAGAATA 3 11 1 ATTTCTAATA 0.728854 -173 ACTTGATATGTTTTTTAATATTGTAAAATT 3 73 1 TTTTTTAATA 0.914365 -111 ATATTGTAAAATTTTTGATATTAAAAATTT 3 90 1 ATTTTTGATA 0.96384 -94 TAAAAATTTATTTTATGCTTTTTTAAAGTT 3 111 1 TTTTATGCTT 0.609863 -73 TTTTAAAGTTTTGTTTGCTAATAAGTGTTA 3 131 1 TTGTTTGCTA 0.908296 -53 TATTTTTATCTTATATGATAAGGAGTT 3 167 1 TTATATGATA 0.882274 -17 ACTTGTTAAAATATTTAATATATTTTTTGC 8 34 1 ATATTTAATA 0.844863 -59 ATTTAATATATTTTTTGCTAAAATCAATAT 8 46 1 TTTTTTGCTA 0.964392 -47 TAAAATCAATATATTAGATAGCTGATAAAT 8 64 1 ATATTAGATA 0.723723 -29 ********** Masking position 4 Map Score: 4.28743 Number of sites scoring better than the average of aligned sites = 1210 Number in coding regions = 773 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 ********** No masking Map Score: -9.07063e-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: -9.07063e-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: -9.07063e-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