AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -imalT_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 BB0089 71 B. burgdorferi predicted coding region BB0089 #2 BB0093 21 V-type ATPase, subunit B (atpB) #3 BB0094 85 V-type ATPase, subunit A (atpA) #4 BB0096 183 V-type ATPase, subunit E, putative #5 BB0166 139 4-alpha-glucanotransferase (malQ) #6 BB0404 165 B. burgdorferi predicted coding region BB0404 #7 BB0642 78 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #8 BB0643 154 conserved hypothetical protein Motif number 1 TTTGATTTATTATTTCTTTTAATATTAAATT 1 12 1 TATTCTTTTA 0.872418 -60 GTTAATTTAATATATTTATTATT 1 59 1 TATATTATTA 0.894333 -13 TTTCCTTTTGTATTCATTTAAATTCCTTTT 3 10 0 TATTATTTAA 0.928968 -76 TGGTTGTATTATTTCTAATAGTTGAGA 4 7 1 TATTTTTCTA 0.830006 -177 AGAATAAGTATATTCTTTAAAGAAGTATTAT 4 35 1 TATTTTTAAA 0.852476 -149 GCCAACTTGATATGTTTTTTAATATTGTAAA 4 69 1 TATGTTTTTA 0.872413 -115 ATTGTAAAATTTTTGATATTAAAAATTTATT 4 92 1 TTTTATATTA 0.63408 -92 TGATATTAAAAATTTATTTTATGCTTTTTTA 4 105 1 AATTATTTTA 0.92903 -79 AGTGTTAGGTTATTATTTTTATCTTATATGA 4 154 1 TATTTTTTTA 0.965144 -30 TAATAGATTTTATCATAAAAGT 5 2 1 AATAATTTTA 0.888388 -138 TTTAATTTCTAATTTTTTTTAAAATTGCTAT 5 34 1 AATTTTTTTA 0.955609 -106 TGATATTTATTATAATTTATAACACAGTGGG 5 84 1 TATATTTATA 0.507644 -56 ACACAGTGGGAATTTATTTAAATTATTAATT 5 105 1 AATTATTTAA 0.839396 -35 GTAGATAATTTATTGTTATTAAACTTATACA 6 17 0 TATTTTATTA 0.933437 -149 AGTAAGGCTAAATTAATTATAAATAAGATTT 6 49 0 AATTATTATA 0.761403 -117 GCTGTTTTGATATTATTTTAAGTAAGGCTAA 6 69 0 TATTTTTTAA 0.952242 -97 ACTATTTGTTTATAGATTAAAAACTTAATAT 6 124 1 TATAATTAAA 0.671899 -42 ATCCCAAAAATTTAAATATTAAGTTTTTAAT 6 139 0 TTTAATATTA 0.482581 -27 AAATCAAGATTATACTTAATATTATTATTTA 7 25 0 TATATTAATA 0.640988 -54 TTTTTAAGAAAATAAATTTTACAGGAGGT 8 9 0 AATAATTTTA 0.887205 -146 TTTAAGTTTTTATATTTTTTAAGAAAATAAA 8 24 0 TATATTTTTA 0.969609 -131 AAATACAGATTATATTTTTTATTTAAAAAAA 8 52 1 TATATTTTTA 0.969609 -103 AAAAGAATTGTTTTTTTTTAAATAAAAAATA 8 64 0 TTTTTTTTAA 0.813215 -91 AAAAAAAAACAATTCTTTTAAAGAAAACTAA 8 76 1 AATTTTTTAA 0.895777 -79 GATAAATTGTTTTTGTTTTTAGTTTATGTTA 8 104 0 TTTTTTTTTA 0.915932 -51 **** ****** Masking position 7 Map Score: 35.4218 Number of sites scoring better than the average of aligned sites = 2880 Number in coding regions = 1785 Number in noncoding regions = 1095 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 ATATTAAAAGAAATAATAAATCAAAA 1 3 0 AAATAATCAA 0.969411 -69 AATTACGAGAAAATTTAATATTAAAAGAAATAAT 1 20 0 AAATTATTAA 0.965966 -52 AATAATAAATATATTAAATTAACTCATAAATT 1 50 0 ATATAATTAA 0.886861 -22 TTTAAAGAATATACTTATTCTCAACTATTAGAAA 4 22 0 ATACTTTCAA 0.43234 -162 GTTGGCACAATAATACTTCTTTAAAGAATATACT 4 41 0 TAATATTTAA 0.567132 -143 TTACAATATTAAAAAACATATCAAGTTGGCACAA 4 65 0 AAAAAATCAA 0.730583 -119 AAAAAGCATAAAATAAATTTTTAATATCAAAAAT 4 100 0 AAATATTTAA 0.948221 -84 ACTTATTAGCAAACAAAACTTTAAAAAAGCATAA 4 123 0 AAACAATTAA 0.929239 -61 TATAAGATAAAAATAATAACCTAACACTTATTAG 4 148 0 AAATAACTAA 0.803773 -36 ATTTTAAAAAAAATTAGAAATTAAATACTTTTAT 5 25 0 AAATTATTAA 0.965966 -115 ATTTTTTTTAAAATTGCTATTTAATATGTTGTTC 5 45 1 AAATTTTTAA 0.930822 -95 AAATTATAATAAATATCAGATCAGAACAACATAT 5 68 0 AAATAATCAG 0.770673 -72 GAATTTATTTAAATTATTAATTAATAGAGGTTTT 5 114 1 AAATTTTTAA 0.930822 -26 AAGTAAGGCTAAATTAATTATAAATAAGATTTAG 6 47 0 AAATTTTAAA 0.588798 -119 AATAATATCAAAACAGCATTTCAAATTCAAAACT 6 83 1 AAACAATCAA 0.915066 -83 ATCTATAAACAAATAGTATATCAAAGTTTTGAAT 6 107 0 AAATAATCAA 0.969411 -59 TTATCCCAAAAATTTAAATATTAAGTTTTTAATC 6 138 0 AATTTATTAA 0.670035 -28 TTCTTAAAAAATATAAAAACTTAAATACAGATTA 8 30 1 ATATAATTAA 0.88687 -125 GCCTAAATTATAGCTTAATGTGTATTGA 8 137 0 AAATTATTAA 0.965966 -18 ***** * **** Masking position 13 Map Score: 26.0192 Number of sites scoring better than the average of aligned sites = 1121 Number in coding regions = 688 Number in noncoding regions = 433 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 ATTTAATATTAAAAGAAATAATAAATCAAA 1 12 0 AAAAGAAATA 0.90999 -60 AAAAGGAATTTAAATGAATA 3 1 1 AAAAGGAATT 0.9677 -85 AAATGAATACAAAAGGAAAAGTCGTTGGAG 3 22 1 AAAAGGAAAA 0.733502 -64 TTACAATATTAAAAAACATATCAAGTTGGC 4 69 0 AAAAAACATA 0.879304 -115 CAAAACTTTAAAAAAGCATAAAATAAATTT 4 114 0 AAAAAGCATA 0.949077 -70 CATATAAGATAAAAATAATAACCTAACACT 4 154 0 AAAAATAATA 0.797019 -30 TAGCAATTTTAAAAAAAATTAGAAATTAAA 5 34 0 AAAAAAAATT 0.919959 -106 CAACATATTAAATAGCAATTTTAAAAAAAA 5 46 0 AATAGCAATT 0.828252 -94 GTATAAGTTTAATAACAATAAATTATCTAC 6 18 1 AATAACAATA 0.807128 -148 AATAATATCAAAACAGCATTTCAAATTCAA 6 83 1 AAACAGCATT 0.773009 -83 AAAAGGCATTTACATAAATA 7 1 1 AAAAGGCATT 0.956521 -78 TTATTTAAAAAAAAACAATTCTTTTAAAGA 8 70 1 AAAAACAATT 0.959559 -85 AACTAAAAACAAAAACAATTTATCATTCAA 8 111 1 AAAAACAATT 0.959559 -44 ********** Masking position 8 Map Score: 14.4267 Number of sites scoring better than the average of aligned sites = 1547 Number in coding regions = 1085 Number in noncoding regions = 462 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 ATTATTTCTTTTAATATTAAATTTTCTCGT 1 20 1 TTAATATTAA 0.411265 -52 GTCGTTGGAGTTAATGGAAACTTAGTTACT 3 42 1 TTAATGGAAA 0.756113 -44 ATTTTTATCTTATATGATAAGGAGTT 4 168 1 TATATGATAA 0.691742 -16 ATTAAATACTTTTATGATAAAATCTATTA 5 10 0 TTTATGATAA 0.957157 -130 AAATAGCAATTTTAAAAAAAATTAGAAATT 5 37 0 TTTAAAAAAA 0.550455 -103 TGATCTGATATTTATTATAATTTATAACAC 5 79 1 TTTATTATAA 0.857431 -61 ACAGTGGGAATTTATTTAAATTATTAATTA 5 107 1 TTTATTTAAA 0.570456 -33 TAAGGCTAAATTAATTATAAATAAGATTTA 6 48 0 TTAATTATAA 0.763476 -118 TTGATATTATTTTAAGTAAGGCTAAATTAA 6 64 0 TTTAAGTAAG 0.666083 -102 AATATTATTATTTATGTAAATGCCTTTT 7 9 0 TTTATGTAAA 0.884074 -70 TTTTATATTTTTTAAGAAAATAAATTTTAC 8 18 0 TTTAAGAAAA 0.905237 -137 GATTATATTTTTTATTTAAAAAAAAACAAT 8 59 1 TTTATTTAAA 0.570456 -96 AACAATTCTTTTAAAGAAAACTAACATAAA 8 83 1 TTAAAGAAAA 0.833432 -72 TTGTTTTTAGTTTATGTTAGTTTTCTTTAA 8 93 0 TTTATGTTAG 0.822233 -62 TAATGTGTATTGAATGATAAATTGTTTTTG 8 120 0 TGAATGATAA 0.631403 -35 ********** Masking position 4 Map Score: 11.5647 Number of sites scoring better than the average of aligned sites = 1372 Number in coding regions = 897 Number in noncoding regions = 475 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 5 TCTTTTAATATTAAATTTTCTCGTAATTTA 1 26 1 TTAAATTTTC 0.939674 -46 AATAAATATATTAAATTAACTCATAAATTA 1 49 0 TTAAATTAAC 0.612859 -23 TTTAATATTGTAAAATTTTTGATATTAAAA 4 86 1 TAAAATTTTT 0.859189 -98 AAAGCATAAAATAAATTTTTAATATCAAAA 4 102 0 ATAAATTTTT 0.656496 -82 TTATGCTTTTTTAAAGTTTTGTTTGCTAAT 4 123 1 TTAAAGTTTT 0.910032 -61 GATTTTATCATAAAAGTATTTAATTTCTAA 5 16 1 TAAAAGTATT 0.688201 -124 GGGAATTTATTTAAATTATTAATTAATAGA 5 112 1 TTAAATTATT 0.955381 -28 TTTAATAACAATAAATTATCTACTAAATCT 6 25 1 ATAAATTATC 0.709505 -141 AATTTAAATATTAAGTTTTTAATCTATAAA 6 132 0 TTAAGTTTTT 0.836621 -34 AACTTAATATTTAAATTTTTGGGATAAATT 6 145 1 TTAAATTTTT 0.95829 -21 AGATTATACTTAATATTATTATTTATGTAA 7 20 0 TAATATTATT 0.688547 -59 ACCTCCTGTAAAATTTATTTTCTTAAAA 8 9 1 TAAAATTTAT 0.601113 -146 ATTTAAGTTTTTATATTTTTTAAGAAAATA 8 26 0 TTATATTTTT 0.910184 -129 TAAATACAGATTATATTTTTTATTTAAAAA 8 51 1 TTATATTTTT 0.910184 -104 GTATTGAATGATAAATTGTTTTTGTTTTTA 8 114 0 ATAAATTGTT 0.670683 -41 ********** Masking position 3 Map Score: 18.5555 Number of sites scoring better than the average of aligned sites = 2013 Number in coding regions = 1355 Number in noncoding regions = 658 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 TGGTTGTATTATTTCTAATAG 4 2 1 GGTTGTATTA 0.945632 -182 TTTTAAGTAAGGCTAAATTAATTATAAATA 6 55 0 GGCTAAATTA 0.978106 -111 ACCTCCTTATGGCTGTATTAATACAAATCA 7 50 0 GGCTGTATTA 0.985735 -29 GCCTAAATTATAGCTTAATG 8 145 0 GCCTAAATTA 0.943393 -10 ********** Masking position 4 Map Score: 0.773704 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 11 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ********** No masking Map Score: -1.80235e-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 8 ********** No masking Map Score: -1.80235e-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 9 ********** No masking Map Score: -1.80235e-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