AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_bbur_reg_300.orf -o00620_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 Input sequences: #1 BB0087 120 L-lactate dehydrogenase (ldh) #2 BB0088 159 GTP-binding membrane protein (lepA) #3 BB0089 71 B. burgdorferi predicted coding region BB0089 #4 BB0093 21 V-type ATPase, subunit B (atpB) #5 BB0094 85 V-type ATPase, subunit A (atpA) #6 BB0096 183 V-type ATPase, subunit E, putative #7 BB0100 156 glutamate racemase (murI) #8 BB0109 136 acetyl-CoA C-acetyltransferase (fadA) #9 BB0347 183 fibronectin/fibrinogen-binding protein, putative #10 BB0348 97 pyruvate kinase (pyk) #11 BB0588 154 pfs protein (pfs-2) #12 BB0589 84 phosphate acetyltransferase (pta) #13 BB0623 96 transcription-repair coupling factor (mfd) Motif number 1 TAAGTAATGATAAAAATATTCTATCGCATTTCTA 1 53 0 TAAAAAATAT 0.941118 -68 TACTCCATTAAATTAAAACTATATACAAAACTAA 1 94 0 AATTAAATAT 0.924711 -27 ATATTAAAAGAAATAATAAATCAAAA 3 3 0 AAATAAACAA 0.897299 -69 AATAATAAATATATTAAATTAACTCAT 3 55 0 AATAAAATAA 0.945264 -17 TTACAATATTAAAAAACATATCAAGTTGGCACAA 6 65 0 AAAAAAACAA 0.897299 -119 AAATTTTTGATATTAAAAATTTATTTTATGCTTT 6 98 1 TATTAAATAT 0.897272 -86 ACTTATTAGCAAACAAAACTTTAAAAAAGCATAA 6 123 0 AAACAAATAA 0.926731 -61 TATAAGATAAAAATAATAACCTAACACTTATTAG 6 148 0 AAATAAATAA 0.970012 -36 GATTTAACAATATTAATAAGTTAAGTATTTAGG 7 10 0 TATTAAATAA 0.924711 -147 TGTTTTTTTTAAAAAAAGTTTTAAGCTATAATAA 7 48 0 AAAAAAGTAA 0.808605 -109 AACTTTTTTTAAAAAAAACATTTAACAATTTTTA 7 62 1 AAAAAAATTA 0.846348 -95 TAATATCAAGAATTAAAATAATAAAAATTGTTAA 7 83 0 AATTAAATAA 0.945268 -74 AAAGTATAAATATTAACAAAGTTAATATCAAGAA 7 105 0 TATTAAATTA 0.676532 -52 TGAATTATTTAATAAACAAGCTAAAATGTTATAA 8 18 0 AATAAAATAA 0.945268 -119 GTTTATTTAATAAAAATAAACTATTTAACCTGAA 8 48 0 TAAAAAATAT 0.942393 -89 TTAAGCTTAATAATAAGAGTTCATAGA 9 4 0 TAATAAACAT 0.815451 -180 CTTAAGCTATTAACAAAACTACATTTAAACTATT 9 33 1 TAACAAACAT 0.633412 -151 GTTTATTGACAATAAATAGTTTAAATGTAGTTTT 9 47 0 AATAAAATAA 0.945264 -137 CTAGTACTATTAATAATAGTTTATTTCCATGATA 9 101 0 TAATAAATAT 0.941813 -83 TTAATACATAAAATAAAAATTTAAAGCTTAGATA 9 136 1 AAATAAATAA 0.970009 -48 TTTTTTATGCTATTAATATTGTAATATGGATAGG 11 23 1 TATTAAATAA 0.924527 -132 AGATATTGAAAAAAAATATCCTATCCATATTACA 11 42 0 AAAAAAATAT 0.95833 -113 GCTTTTTTGTAAAAAATGATATAAATATTCTTTT 11 111 1 AAAAAAGTAA 0.808624 -44 ACACTCCTTATAATAAAAGAATATTTATATCATT 11 125 0 TAATAAATAT 0.942393 -30 ATCATGTATGAAAAAAGATTTTTTATTTTAAAAT 12 37 1 AAAAAAATTT 0.76444 -48 ATAATGCATAAAAAAAGACATTTTAAAATAAAAA 12 56 0 AAAAAAATTT 0.79663 -29 ACACATTATATATAAAGAAAGTAATAATACCTAT 13 31 1 TATAAAATAA 0.924711 -66 TAATTTAGTATAATAATATACTATAGGTATTATT 13 53 0 TAATAAATAT 0.942379 -44 TAAATTAATTAAACAAAAAGGTAAAAA 13 80 1 AAACAAATAA 0.926734 -17 ****** * *** Masking position 6 Map Score: 41.7144 Number of sites scoring better than the average of aligned sites = 2096 Number in coding regions = 1260 Number in noncoding regions = 836 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 2 ATTTGTTTTTAATTTTTAAAGGTATGT 1 6 1 TTTTATTTTT 0.972341 -115 ATTTTTAAATTTTGACTTGTAGT 2 2 1 TTTTAATTTT 0.833107 -158 TAAGAAAAACTTTTGCATTATTGCACACATTG 2 61 1 TTTTATTATT 0.94406 -99 TCAGATATTATTTTAGCTTTTTGAATAAATCG 2 119 0 TTTTCTTTTT 0.976101 -41 TTTTGATTTATTATTTCTTTTA 3 1 1 TTTTTTTATT 0.731492 -71 TATGAGTTAATTTAATATATTTATTATT 3 54 1 TTTAATATTT 0.759353 -18 ACTTGATATGTTTTTTAATATTGTAAAATTTT 6 73 1 TTTTAATATT 0.705574 -111 TATTGTAAAATTTTTGATATTAAAAATTTATT 6 91 1 TTTTATATTA 0.607978 -93 AAAAATTTATTTTATGCTTTTTTAAAGTTTTG 6 112 1 TTTACTTTTT 0.962712 -72 AGGTTATTATTTTTATCTTATATGATAAGGAG 6 160 1 TTTTCTTATA 0.858745 -24 ATAAAATTGATTTAACAATATTAATAAGTTAA 7 20 0 TTTAAATATT 0.602362 -137 TTATTATAGCTTAAAACTTTTTTTAAAAAAAA 7 48 1 TTAACTTTTT 0.571972 -109 TTTAACAATTTTTATTATTTTAATTCTTGATA 7 82 1 TTTAATTTTA 0.873469 -75 TTTAAAATTATAACATTTTAGC 8 1 1 TTTAATTATA 0.767968 -136 AATTATAACATTTTAGCTTGTTTATTAAATAA 8 16 1 TTTTCTTGTT 0.820826 -121 GGTTAAATAGTTTATTTTTATTAAATAAACTT 8 52 1 TTTATTTATT 0.632634 -85 CAAAACTACATTTAAACTATTTATTGTCAATA 9 46 1 TTTACTATTT 0.78569 -138 TATATCTAAGCTTTAAATTTTTATTTTATGTA 9 140 0 CTTTATTTTT 0.729492 -44 CAAAGTAAAGTTTTGAATTTTTTACAAAATAT 10 24 1 TTTTATTTTT 0.972341 -74 TTTTATAAATTTTATGCTTTTTGTCATTGAAT 10 60 0 TTTACTTTTT 0.962712 -38 TCAGTTTTCCCTTTTTTTATGCTATT 11 5 1 TTTTCTTTTT 0.976101 -150 AGCAATTCAATTTTGGCTTTTTTGTAAAAAAT 11 96 1 TTTTCTTTTT 0.976101 -59 AAAGAATATTTATATCATTTTTTACAAAAAAG 11 112 0 TATAATTTTT 0.534919 -43 TCATACATGATTTTCAATTATAAAAATTAAAT 12 16 0 TTTTATTATA 0.839826 -69 TGAAAAAAGATTTTTTATTTTAAAATGTCTTT 12 45 1 TTTTATTTTA 0.916118 -40 TTTTTACCTTTTTGTTTAATTAA 13 84 0 TTTTCTTTTT 0.976101 -13 **** ****** Masking position 11 Map Score: 34.9279 Number of sites scoring better than the average of aligned sites = 3289 Number in coding regions = 2153 Number in noncoding regions = 1136 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 3 TGTGTGCAATAATGCAAAAGTTTTTCTTAC 2 60 0 AATGCAAAAG 0.657519 -100 ATTTATTCAAAAAGCTAAAATAATATCTGA 2 121 1 AAAGCTAAAA 0.968167 -39 AATGAATACAAAAGGAAAAGTCGTTGGAGT 5 23 1 AAAGGAAAAG 0.772234 -63 AAACTTTAAAAAAGCATAAAATAAATTTTT 6 112 0 AAAGCATAAA 0.974834 -72 CAATTTTATTATAGCTTAAAACTTTTTTTA 7 43 1 ATAGCTTAAA 0.931329 -114 CCTAAAAAGTAAAGTATAAATATTAACAAA 7 119 0 AAAGTATAAA 0.830537 -38 ATTTAATAAACAAGCTAAAATGTTATAATT 8 16 0 CAAGCTAAAA 0.794115 -121 AGTTTTGTTAATAGCTTAAGCTTAATAATA 9 23 0 ATAGCTTAAG 0.841355 -161 TTGACAATAAATAGTTTAAATGTAGTTTTG 9 46 0 ATAGTTTAAA 0.631805 -138 ATAAAAATTTAAAGCTTAGATATAAACACC 9 148 1 AAAGCTTAGA 0.830863 -36 TCAATGACAAAAAGCATAAAATTTATAAAA 10 62 1 AAAGCATAAA 0.974834 -36 TAGCATAAAAAAAGGGAAAACTGA 11 5 0 AAAGGGAAAA 0.697237 -150 TACAATATTAATAGCATAAAAAAAGGGAAA 11 16 0 ATAGCATAAA 0.931329 -139 TTTTTACAAAAAAGCCAAAATTGAATTGCT 11 96 0 AAAGCCAAAA 0.889846 -59 AATTGATAATGCATAAAAAAAGACATT 12 68 0 AATGCATAAA 0.862125 -17 AATTAAACAAAAAGGTAAAAA 13 86 1 AAAGGTAAAA 0.896592 -11 ********** Masking position 8 Map Score: 16.0736 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 416 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 ATTTGTTTTTAATTTTTAAAGGTAT 1 6 1 TTTTTAATTT 0.30368 -115 AATTACTCCATTAAATTAAAACTATATA 1 103 0 CATTAAATTA 0.653443 -18 ATTTTTAAATTTTGACTTGTAG 2 3 1 TTTTAAATTT 0.718115 -157 TTTCTTTTAATATTAAATTTTCTCGTAATT 3 24 1 TATTAAATTT 0.891702 -48 ATAATAAATATATTAAATTAACTCATAAAT 3 51 0 TATTAAATTA 0.826643 -21 AAAAAGCATAAAATAAATTTTTAATATCAA 6 104 0 AAATAAATTT 0.761391 -80 AAGATAAAAATAATAACCTAACACTTATTA 6 149 0 TAATAACCTA 0.497716 -35 TTTTAAGCTATAATAAAATTGATTTAACAA 7 34 0 TAATAAAATT 0.583742 -123 TAATATCAAGAATTAAAATAATAAAAATTG 7 87 0 AATTAAAATA 0.317066 -70 TAATTCTTGATATTAACTTTGTTAATATTT 7 102 1 TATTAACTTT 0.605793 -55 TATTTAATAAAAATAAACTATTTAACCTGA 8 49 0 AAATAAACTA 0.717056 -88 TATTTTTATTAAATAAACTTAGTTTTTATA 8 64 1 AAATAAACTT 0.813649 -73 CCTAAAGTCTTAATAAACTTATTGAATTAT 8 110 0 TAATAAACTT 0.902044 -27 GAACTCTTATTATTAAGCTTAAGCTATTAA 9 16 1 TATTAAGCTT 0.525408 -168 ACAAAACTACATTTAAACTATTTATTGTCA 9 45 1 ATTTAAACTA 0.481825 -139 TATTTATTGTCAATAAACTTTATTTCCATA 9 63 1 CAATAAACTT 0.782888 -121 CATATCATGGAAATAAACTATTATTAATAG 9 99 1 AAATAAACTA 0.717056 -85 TTATTTTATGTATTAAACTAGTACTATTAA 9 122 0 TATTAAACTA 0.864702 -62 TATATCTAAGCTTTAAATTTTTATTTTATG 9 142 0 CTTTAAATTT 0.499057 -42 TCCTCCACTTTTATAAATTTTATGCTTTTT 10 70 0 TTATAAATTT 0.680849 -28 GAAATATTTAATTTTTATAATTGA 12 5 1 TATTTAATTT 0.554051 -80 CCTTTTTGTTTAATTAATTTAGTATAATAA 13 71 0 TAATTAATTT 0.451449 -26 ********** Masking position 4 Map Score: 16.1316 Number of sites scoring better than the average of aligned sites = 1985 Number in coding regions = 1269 Number in noncoding regions = 716 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 ACTATATACAAAACTAATTTTAAATAAGTAA 1 80 0 AAACAATTTT 0.688752 -41 ACCTCAATAGTAACTAAGTTTCCATTAACTC 5 49 0 TAACAAGTTT 0.616397 -37 AAAAAGCATAAAATAAATTTTTAATATCAAA 6 103 0 AAATAATTTT 0.902341 -81 CAATATTAATAAGTTAAGTATTTAGG 7 6 0 AAGTAAGTAT 0.911963 -151 TAATATTGTTAAATCAATTTTATTATAGCTT 7 29 1 AAATAATTTT 0.906003 -128 TGTTTTTTTTAAAAAAAGTTTTAAGCTATAA 7 51 0 AAAAAAGTTT 0.741796 -106 CACCCCTAAAAAGTAAAGTATAAATATTAAC 7 122 0 AAGTAAGTAT 0.912005 -35 TATTTAATAAAAATAAACTATTTAACCTGAA 8 48 0 AAATAACTAT 0.863309 -89 GATCATATAAAAACTAAGTTTATTTAATAAA 8 68 0 AAACAAGTTT 0.589676 -69 TAAATAGTTTAAATGTAGTTTTGTTAATAGC 9 38 0 AAATTAGTTT 0.716534 -146 AACTACATTTAAACTATTTATTGTCAATAAA 9 49 1 AAACATTTAT 0.423768 -135 AGTATTATGGAAATAAAGTTTATTGACAATA 9 67 0 AAATAAGTTT 0.948453 -117 CATATCATGGAAATAAACTATTATTAATAGT 9 99 1 AAATAACTAT 0.863309 -85 GCTTATAGCAAAGTAAAGTTTTGAATTTTTT 10 16 1 AAGTAAGTTT 0.929149 -82 TCAATTATAAAAATTAAATATTTC 12 4 0 AAATAAATAT 0.695107 -81 TTATAATTGAAAATCATGTATGAAAAAAGAT 12 25 1 AAATATGTAT 0.810517 -60 **** ****** Masking position 9 Map Score: 16.6168 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 364 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 AATTTTAAATAAGTAATGATAAAAATATTCT 1 65 0 AAGTATGATA 0.867668 -56 TTCAGGGGGGAAGTAGTATTAGTATTCGTAA 2 33 1 AAGTATATTA 0.928176 -127 TTAATATTAAAAGAAATAATAAATCAAAA 3 9 0 AAGAATAATA 0.891615 -63 TTACGAGAAAATTTAATATTAAAAGAAATAA 3 21 0 ATTTATATTA 0.429738 -51 TCTCAACTATTAGAAATAATACAACCA 6 7 0 TAGAATAATA 0.779355 -177 ATATTCTTTAAAGAAGTATTATTGTGCCAAC 6 44 1 AAGAATATTA 0.936464 -140 TTTGTTTGCTAATAAGTGTTAGGTTATTATT 6 140 1 AATAATGTTA 0.76535 -44 TCATATAAGATAAAAATAATAACCTAACACT 6 154 0 TAAAATAATA 0.604352 -30 CTTAACTTATTAATATTGTTAAATCAATTTT 7 19 1 TAATATGTTA 0.648573 -138 TTAAAATAATAAAAATTGTTAAATGTTTTTT 7 74 0 AAAAATGTTA 0.861426 -83 AAAAGTAAAGTATAAATATTAACAAAGTTAA 7 114 0 TATAATATTA 0.589127 -43 TTTCCATGATATGTAGTATTATGGAAATAAA 9 81 0 ATGTATATTA 0.752751 -103 TATCATGGAAATAAACTATTATTAATAGTAC 9 101 1 ATAAATATTA 0.616962 -83 TGTATTAAACTAGTACTATTAATAATAGTTT 9 113 0 TAGTATATTA 0.796386 -71 ATTTTTTACAAAATATTGTTATTCAATGACA 10 40 1 AAATATGTTA 0.845831 -58 GCTTTTTTGTAAAAAATGATATAAATATTCT 11 111 1 AAAAATGATA 0.776238 -44 TATATAAAGAAAGTAATAATACCTATAGTAT 13 39 1 AAGTATAATA 0.879548 -58 ***** ***** Masking position 5 Map Score: 15.0086 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 493 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 CTAATTTTAAATAAGTAATGATAAAAATAT 1 68 0 ATAAGTAATG 0.872569 -53 AAAAGGAATTTAAATGAATA 5 1 1 AAAAGGAATT 0.902654 -85 ATCTTATATGATAAGGAGTT 6 174 1 ATAAGGAGTT 0.964545 -10 TTACTTTGCTATAAGCAGTGT 10 2 0 ATAAGCAGTG 0.96707 -96 AAATTCTTTCAAAAGCAATTCAATTTTGGC 11 83 1 AAAAGCAATT 0.86418 -72 TTCTTTTATTATAAGGAGTGTGATTTT 11 138 1 ATAAGGAGTG 0.977158 -17 ********** Masking position 4 Map Score: 2.28072 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 21 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 AGTTTTGTATATAGTTTTAATTTAATGGAG 1 96 1 ATAGTTTTAA 0.729216 -25 TAGCTGATCGATTTATTCAAAAAGCTAAAA 2 111 1 ATTTATTCAA 0.564112 -49 TGATTTATTATTTCTTTTAATATTAAATTT 3 14 1 TTTCTTTTAA 0.729818 -58 TTCCTTTTGTATTCATTTAAATTCCTTTT 5 10 0 ATTCATTTAA 0.923543 -76 GAATAAGTATATTCTTTAAAGAAGTATTAT 6 36 1 ATTCTTTAAA 0.924429 -148 CTATAATAAAATTGATTTAACAATATTAAT 7 27 0 ATTGATTTAA 0.861668 -130 AACAATTTTTATTATTTTAATTCTTGATAT 7 85 1 ATTATTTTAA 0.842044 -72 TTGACAATAAATAGTTTAAATGTAGTTTTG 9 46 0 ATAGTTTAAA 0.585507 -138 ATCCTAATTCTTTCAAGGTGTTTATA 9 168 0 ATTCTTTCAA 0.950587 -16 TTTTACAAAAATTCTTTCAAAAGCAATTCA 11 75 1 ATTCTTTCAA 0.950587 -80 TGATATAAATATTCTTTTATTATAAGGAGT 11 127 1 ATTCTTTTAT 0.729818 -28 ATTATACTAAATTAATTAAACAAAAAGGTA 13 73 1 ATTAATTAAA 0.581109 -24 ********** Masking position 9 Map Score: 6.96755 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 424 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 ********** No masking Map Score: 1.26009e-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 10 ********** No masking Map Score: 1.26009e-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 11 ********** No masking Map Score: 1.26009e-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