AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -imalT_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 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 BB0100 156 glutamate racemase (murI) #6 BB0166 139 4-alpha-glucanotransferase (malQ) #7 BB0404 165 B. burgdorferi predicted coding region BB0404 #8 BB0642 78 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #9 BB0643 154 conserved hypothetical protein Motif number 1 AAATTTAATATTAAAAGAAATAATAAATCAA 1 13 0 TTAAAAAAAT 0.80957 -59 AATAATAAATATATTAAATTAAC 1 59 0 TAATAATATA 0.859362 -13 AAAAGGAATTTAAATGAATACAAAAGGAAA 3 10 1 TTAAATAATA 0.919383 -76 TCTCAACTATTAGAAATAATACAACCA 4 7 0 TAGAAAAATA 0.780088 -177 ATAATACTTCTTTAAAGAATATACTTATTCT 4 35 0 TTTAAAAATA 0.856143 -149 TTTACAATATTAAAAAACATATCAAGTTGGC 4 69 0 TAAAAACATA 0.816625 -115 AATAAATTTTTAATATCAAAAATTTTACAAT 4 92 0 TAATATAAAA 0.684805 -92 TAAAAAAGCATAAAATAAATTTTTAATATCA 4 105 0 TAAAATAATT 0.919441 -79 TCATATAAGATAAAAATAATAACCTAACACT 4 154 0 TAAAAAAATA 0.969629 -30 ATTAATATTGTTAAATCAATTTTATTATAGC 5 27 1 TTAAATAATT 0.852807 -130 TAAAACTTTTTTTAAAAAAAACATTTAACAA 5 59 1 TTTAAAAAAA 0.692785 -98 ATATCAAGAATTAAAATAATAAAAATTGTTA 5 84 0 TTAAAAAATA 0.954361 -73 TTAACTTTGTTAATATTTATACTTTACTTTT 5 114 1 TAATATTATA 0.684777 -43 TAATCACCCCTAAAAAGTAAAGTATAAATAT 5 126 0 TAAAAATAAA 0.897892 -31 ACTTTTATGATAAAATCTATTA 6 2 0 TAAAATTATT 0.859028 -138 ATAGCAATTTTAAAAAAAATTAGAAATTAAA 6 34 0 TAAAAAAATT 0.957417 -106 CCCACTGTGTTATAAATTATAATAAATATCA 6 84 0 TATAAATATA 0.513873 -56 AATTAATAATTTAAATAAATTCCCACTGTGT 6 105 0 TTAAATAATT 0.852807 -35 TGTATAAGTTTAATAACAATAAATTATCTAC 7 17 1 TAATAAAATA 0.919826 -149 AAATCTTATTTATAATTAATTTAGCCTTACT 7 49 1 TATAATAATT 0.743128 -117 TTAGCCTTACTTAAAATAATATCAAAACAGC 7 69 1 TTAAAAAATA 0.954361 -97 GTTTTTAATCTATAAACAAATAGTATATCAA 7 117 0 TATAAAAAAT 0.693881 -49 ATTAAAAACTTAATATTTAAATTTTTGGGAT 7 139 1 TAATATTAAA 0.508788 -27 TAAATAATAATATTAAGTATAATCTTGATTT 8 25 1 TATTAATATA 0.590843 -54 ACCTCCTGTAAAATTTATTTTCTTAAAAA 9 9 1 TAAAATTATT 0.858459 -146 TTTATTTTCTTAAAAAATATAAAAACTTAAA 9 24 1 TAAAAATATA 0.959103 -131 TTTTTTTAAATAAAAAATATAATCTGTATTT 9 52 0 TAAAAATATA 0.959103 -103 TATTTTTTATTTAAAAAAAAACAATTCTTTT 9 64 1 TTAAAAAAAA 0.893315 -91 TTAGTTTTCTTTAAAAGAATTGTTTTTTTTT 9 76 0 TTAAAAAATT 0.919442 -79 TAACATAAACTAAAAACAAAAACAATTTATC 9 104 1 TAAAAAAAAA 0.942807 -51 ****** **** Masking position 5 Map Score: 44.9438 Number of sites scoring better than the average of aligned sites = 3878 Number in coding regions = 2435 Number in noncoding regions = 1443 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 2 AATATTAAAAGAAATAATAAATCAAAA 1 7 0 GAAATATAAA 0.718835 -65 TAAATTACGAGAAAATTTAATATTAAAAGAA 1 25 0 GAAAATTAAT 0.857629 -47 AATAATAAATATATTAAATTAACTCATA 1 54 0 AATATTTAAA 0.761879 -18 CAAAAATTTTACAATATTAAAAAACATATCA 4 76 0 ACAATTTAAA 0.931328 -108 AGCATAAAATAAATTTTTAATATCAAAAATT 4 99 0 AAATTTTAAT 0.844466 -85 ATTAGCAAACAAAACTTTAAAAAAGCATAAA 4 122 0 AAAACTTAAA 0.75238 -62 ATATAAGATAAAAATAATAACCTAACACTTA 4 152 0 AAAATATAAC 0.703541 -32 CCTAAATACTTAACTTATTAATAT 5 4 1 AAATATTAAC 0.63172 -153 AATTGATTTAACAATATTAATAAGTTAAGTA 5 17 0 ACAATTTAAT 0.931324 -140 AAAATAATAAAAATTGTTAAATGTTTTTTTT 5 72 0 AAATTTTAAA 0.844466 -85 ATAAATATTAACAAAGTTAATATCAAGAATT 5 103 0 ACAAATTAAT 0.925155 -54 TACAAAATAATAATCACCCCTAAA 5 143 0 AAAATATAAT 0.872567 -14 ATATTAAATAGCAATTTTAAAAAAAATTAGA 6 41 0 GCAATTTAAA 0.83508 -99 AGATCAGAACAACATATTAAATAGCAATTTT 6 54 0 AACATTTAAA 0.652395 -86 GAATTTATTTAAATTATTAATTAATAGAGGT 6 114 1 AAATTTTAAT 0.844466 -26 TTTAAGTAAGGCTAAATTAATTATAAATAAG 7 53 0 GCTAATTAAT 0.454742 -113 TTTATAGATTAAAAACTTAATATTTAAATTT 7 132 1 AAAAATTAAT 0.941627 -34 AATTTATCCCAAAAATTTAAATATTAAGTTT 7 144 0 AAAAATTAAA 0.941638 -22 AAAGGCATTTACATAAATAATAATATTAAGT 8 12 1 ACATAATAAT 0.594682 -67 TAAAAAATATAAAAACTTAAATACAGATTAT 9 34 1 AAAAATTAAA 0.941638 -121 TTTTTAAATAAAAAATATAATCTGTATTTAA 9 50 0 AAAAAATAAT 0.861908 -105 TTTAAAGAAAACTAACATAAACTAAAAACAA 9 92 1 ACTAAATAAA 0.463694 -63 ***** ***** Masking position 8 Map Score: 23.441 Number of sites scoring better than the average of aligned sites = 3104 Number in coding regions = 2033 Number in noncoding regions = 1071 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 GTATTCATTTAAATTCCTTTT 3 1 0 AAATTCCTTT 0.730083 -85 ATACAAAAGGAAAAGTCGTTGGAGTTAATGG 3 28 1 AAAAGTCTTG 0.754614 -58 TTGGCACAATAATACTTCTTTAAAGAATATA 4 43 0 AATACTTTTT 0.903668 -141 TGCCAACTTGATATGTTTTTTAATATTGTAA 4 68 1 ATATGTTTTT 0.773594 -116 TTTGATATTAAAAATTTATTTTATGCTTTTT 4 103 1 AAAATTTTTT 0.885968 -81 ATTATAGCTTAAAACTTTTTTTAAAAAAAAC 5 50 1 AAAACTTTTT 0.951893 -107 AAAAATTGTTAAATGTTTTTTTTAAAAAAAG 5 64 0 AAATGTTTTT 0.968173 -93 TTAGAAATTAAATACTTTTATGATAAAATCT 6 15 0 AATACTTTAT 0.602275 -125 TTTTTTTTAAAATTGCTATTTAATATGTTGT 6 46 1 AATTGCTTTT 0.933666 -94 ATAAAACCTCTATTAATTAATAA 6 127 0 AAAACCTTAT 0.707162 -13 ATTATCTACTAAATCTTATTTATAATTAATT 7 39 1 AAATCTTTTT 0.961617 -127 TTTGAATTTGAAATGCTGTTTTGATATTATT 7 83 0 AAATGCTTTT 0.967488 -83 TTATTTATGTAAATGCCTTTT 8 1 0 AAATGCCTTT 0.738901 -78 ACCTCCTGTAAAATTTATTTTCTTAAAAAA 9 10 1 AAAATTTTTT 0.885968 -145 TCTTTAAAAGAATTGTTTTTTTTTAAATAAA 9 69 0 AATTGTTTTT 0.949489 -86 TTGAATGATAAATTGTTTTTGTTTTTAGTTT 9 110 0 AATTGTTTTG 0.824793 -45 ******* *** Masking position 9 Map Score: 15.8457 Number of sites scoring better than the average of aligned sites = 1450 Number in coding regions = 1013 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 AAGGAATTTAAATGAATACAAAAGGAAAAG 3 13 1 AATGAATACA 0.67497 -73 ACTTATTAGCAAACAAAACTTTAAAAAAGC 4 127 0 AAACAAAACT 0.947634 -57 AACTTTTTTTAAAAAAAACATTTAACAATT 5 62 1 AAAAAAAACA 0.787642 -95 AAAATTAGAAATTAAATACTTTTATGATAA 6 20 0 ATTAAATACT 0.725895 -120 TATTAAACTTATACAAAGCTT 7 2 0 ATACAAAGCT 0.79053 -164 CTTAAAATAATATCAAAACAGCATTTCAAA 7 78 1 TATCAAAACA 0.603579 -88 AGCATTTCAAATTCAAAACTTTGATATACT 7 97 1 ATTCAAAACT 0.947634 -69 TTGTTTATAGATTAAAAACTTAATATTTAA 7 129 1 ATTAAAAACT 0.836227 -37 GGCTGTATTAATACAAATCAAGATTATACT 8 40 0 ATACAAATCA 0.765347 -39 ATTTAAAAAAAAACAATTCTTTTAAAGAAA 9 72 1 AAACAATTCT 0.699591 -83 CAATTCTTTTAAAGAAAACTAACATAAACT 9 85 1 AAAGAAAACT 0.846437 -70 ACAATTTATCATTCAATACACATTAAGCTA 9 125 1 ATTCAATACA 0.872087 -30 ********** Masking position 5 Map Score: 6.32101 Number of sites scoring better than the average of aligned sites = 709 Number in coding regions = 472 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 ATTAAAAGAAATAATAAATCAAAA 1 5 0 ATAATAAATC 0.852131 -67 ATTTCTTTTAATATTAAATTTTCTCGTAAT 1 23 1 ATATTAAATT 0.863382 -49 AATAATAAATATATTAAATTA 1 61 0 ATAATAAATA 0.95594 -11 AAATTTTACAATATTAAAAAACATATCAAG 4 74 0 ATATTAAAAA 0.736755 -110 AAAAAAGCATAAAATAAATTTTTAATATCA 4 105 0 AAAATAAATT 0.872922 -79 CTTATCATATAAGATAAAAATAATAACCTA 4 159 0 AAGATAAAAA 0.522646 -25 GTTTTAAGCTATAATAAAATTGATTTAACA 5 35 0 ATAATAAAAT 0.938982 -122 AAGAATTAAAATAATAAAAATTGTTAAATG 5 80 0 ATAATAAAAA 0.92369 -77 AAATACTTTTATGATAAAATCTATTA 6 7 0 ATGATAAAAT 0.848629 -133 TCAGAACAACATATTAAATAGCAATTTTAA 6 52 0 ATATTAAATA 0.833825 -88 GTTATAAATTATAATAAATATCAGATCAGA 6 77 0 ATAATAAATA 0.95594 -63 AAGTTTAATAACAATAAATTATCTACTAAA 7 22 1 ACAATAAATT 0.801227 -144 AATCTTATTTATAATTAATTTAGCCTTACT 7 50 1 ATAATTAATT 0.689384 -116 ATTTACATAAATAATAATATTAAGTATAAT 8 18 1 ATAATAATAT 0.550425 -61 ATTTTTTAAGAAAATAAATTTTACAGGAGG 9 12 0 AAAATAAATT 0.872922 -143 TTTTTTTTAAATAAAAAATATAATCTGTAT 9 54 0 ATAAAAAATA 0.635388 -101 TGTGTATTGAATGATAAATTGTTTTTGTTT 9 117 0 ATGATAAATT 0.9095 -38 ********** Masking position 7 Map Score: 24.1444 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 635 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 ********** No masking Map Score: 6.13499e-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: 6.13499e-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 8 ********** No masking Map Score: 6.13499e-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