AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ilexA_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 BB0022 44 Holliday junction DNA helicase (ruvB) #2 BB0023 79 Holliday junction DNA helicase (ruvA) #3 BB0132 37 transcription elongation factor (greA) #4 BB0133 162 B. burgdorferi predicted coding region BB0133 #5 BB0260 206 B. burgdorferi predicted coding region BB0260 #6 BB0346 183 B. burgdorferi predicted coding region BB0346 #7 BB0605 70 serine-type D-Ala-D-Ala carboxypeptidase (dacA) #8 BB0836 114 excinuclease ABC, subunit B (uvrB) Motif number 1 GTTTCTGTGTAATATAATTTATAATTTAATTA 2 57 1 AATAATTTAT 0.978035 -23 AATCTTATATTATAATATTAAAAAGAAAATT 4 10 0 TATAATTAAA 0.942009 -153 AAAATAACAATATTTCATTTATTATTCTTTTA 4 48 0 TATTATTTAT 0.901124 -115 TTTATATAATTATATCATTTATCAATTTTTAG 4 99 0 TATAATTTAT 0.981535 -64 GGGGTTTGTATATATTGTTTAAAATGGTGGGA 4 139 1 TATAGTTTAA 0.775211 -24 AAATTAAAAATATCCCATTAATTTGCATCATC 5 24 1 TATCATTAAT 0.817429 -183 AGTTACTTTTAATAAAAGTTATTTACTTAAAA 5 58 1 AATAAGTTAT 0.926776 -149 ATTTACTTAAAATAAAAGTAATTTGTAAGTTG 5 78 1 AATAAGTAAT 0.913707 -129 ACTATAATATAATATAAATAATGTGATATTCA 5 108 0 AATAAATAAT 0.824709 -99 ATATTATAGTTATAATAATAATGATAACTATA 5 130 1 TATAAATAAT 0.846539 -77 CTTACGCACTAATTATAGTTATCATTATTATT 5 143 0 AATTAGTTAT 0.684511 -64 GTTTGGTTTCAATAAAATTAACAAAGCAAAGA 5 174 1 AATAATTAAC 0.816162 -33 GTATTAAACTAGTACTATTAATAATAGTTTAT 6 62 1 AGTAATTAAT 0.860374 -122 GTATTATGGAAATAAAGTTTATTGACAATAAA 6 108 1 AATAGTTTAT 0.881882 -76 AAACTACATTTAAACTATTTATTGTCAATAAA 6 125 0 TAAAATTTAT 0.757351 -59 TGTTAATTACAATACAATTAAAAAGGAGCCAT 7 15 0 AATAATTAAA 0.935152 -56 ATTAAAATTATATATTATTTATTGATTGTTAA 7 41 0 TATAATTTAT 0.981519 -30 GTTGTAATATTAAAATTATATATT 7 57 0 TGTAATTAAA 0.740384 -14 TATTTCCTTTTATTTTATTAAACAAAGATTAA 8 11 1 TATTATTAAA 0.747026 -104 ATTATAAATCAATATAATTTAATTAATCTTTG 8 33 0 AATAATTTAA 0.945137 -82 CTATATCAAGTATATAATTCATTATAAATCAA 8 53 0 TATAATTCAT 0.893456 -62 ATATACTTGATATAGAATTTATTATCATATAA 8 70 1 TATAATTTAT 0.981539 -45 AATTTATTATCATATAATTTATAAGAATGTGT 8 85 1 CATAATTTAT 0.893456 -30 **** ****** Masking position 9 Map Score: 29.2705 Number of sites scoring better than the average of aligned sites = 942 Number in coding regions = 588 Number in noncoding regions = 354 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 TTATTAGTTTTTTATAGTTATAAAATAGTT 1 10 1 TTTTATATTA 0.815545 -35 GTAATATAATTTATAATTTAATTAT 2 65 1 TTATAATTAA 0.615438 -15 AAATAAAATCTTATATTATAATATTAAAAAG 4 17 0 TTATATTTAA 0.528377 -146 TAATATAAGATTTTATTTTAAAAGAATAATA 4 30 1 TTTTATTTAA 0.957013 -133 CCGTTACACTTTATATAATTATATCATTTAT 4 109 0 TTATATATTA 0.769288 -54 AGTAAATAACTTTTATTAAAAGTAACTATGA 5 54 0 TTTTATTAAA 0.570541 -153 TACAAATTACTTTTATTTTAAGTAAATAACT 5 74 0 TTTTATTTAA 0.957013 -133 ATCACATTATTTATATTATATTATAGTTATA 5 113 1 TTATATTTAT 0.85976 -94 TAGTTATCATTATTATTATAACTATAATATA 5 129 0 TATTATTTAA 0.62467 -78 GCTTTGTTAATTTTATTGAAACCAAACTTAC 5 170 0 TTTTATTAAA 0.897321 -37 AGCTTTAAATTTTTATTTTATGTATTAAACT 6 41 1 TTTTATTTAT 0.959033 -143 TCCTTTTTAATTGTATTGTAATTAACAATCA 7 20 1 TTGTATTTAA 0.917387 -51 AATATTAAAATTATATATTATTTATTGATTG 7 45 0 TTATATATAT 0.822206 -26 TAATATATAATTTTAATATTACAAC 7 56 1 TTTTAATTTA 0.527306 -15 TATTTCCTTTTATTTTATTAAACAAAGA 8 8 1 TTTTATTTAT 0.959033 -107 ATTAATTAAATTATATTGATTTATAATGAAT 8 38 1 TTATATTATT 0.582014 -77 TTCTTATAAATTATATGATAATAAATTCTAT 8 81 0 TTATATGTAA 0.7825 -34 ******* *** Masking position 5 Map Score: 24.9971 Number of sites scoring better than the average of aligned sites = 1318 Number in coding regions = 750 Number in noncoding regions = 568 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 TTTTTATAGTTATAAAATAGTTTTTAAGGAATAT 1 19 1 TATATGTTTT 0.793644 -26 TAATATAATTTATAATTTAATTAT 2 66 1 TATATATTAT 0.960554 -14 TGCTTGATGCTAAAAAATCGATATTAGGAGAGTT 3 12 1 TAAATGATAT 0.927073 -26 GAATAATAAATGAAATATTGTTATTTTGCCCTAA 4 53 1 TGAATGTTAT 0.952987 -110 AAAAGTAATTTGTAAGTTGAATATCACATTATTT 5 91 1 TGTATAATAT 0.926646 -116 TTATTTATATTATATTATAGTTATAATAATAATG 5 119 1 TATATGTTAT 0.97504 -88 AATAAAAATTTAAAGCTTAGATATAAACACCTTG 6 24 0 TAAATGATAT 0.927073 -160 ATCATGGAAATAAACTATTATTAATAGTACTAGT 6 69 0 TAAATATTAA 0.828644 -115 ATAGTTTAAATGTAGTTTTGTTAATAGCTTAAGC 6 139 1 TGTATGTTAA 0.936943 -45 TCTATGAACTCTTATTATTAAGCTTAAG 6 166 0 TGAATATTAT 0.926643 -18 CCTTTTTAATTGTATTGTAATTAACAATCAATAA 7 21 1 TGTATATTAA 0.902523 -50 ATAAATAATATATAATTTTAATATTACAAC 7 51 1 TATATAATAT 0.932835 -20 TATAAATCAATATAATTTAATTAATCTTTGTTTA 8 29 0 TATATATTAA 0.910552 -86 TATAATGAATTATATACTTGATATAGAATTTATT 8 59 1 TATATGATAT 0.957061 -56 **** * ***** Masking position 4 Map Score: 20.1369 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 87 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AAAATAGTTTTTAAGGAATATTT 1 32 1 TAAGGAATAT 0.524242 -13 AGCAAAAGCCTTAAGTAAAAAAAGGACACTA 2 12 0 TAAGTAAAAA 0.928119 -68 ATTCAACAATTTAAAGCAAAAGCCTTAAGTA 2 26 0 TAAAGCAAAA 0.84524 -54 TTATAATATTAAAAAGAAAATT 4 2 0 AAAAGAAAAT 0.329731 -161 GATTTTATTTTAAAAGAATAATAAATGAAAT 4 38 1 TAAAGAATAA 0.828719 -125 AAAAGAATAATAAATGAAATATTGTTATTTT 4 49 1 TAATGAAATA 0.847101 -114 AAACAAGAAATTAGGGCAAAATAACAATATT 4 66 0 TAGGGCAAAA 0.561617 -97 CCGTTACACTTTATATAATTATATCATTTAT 4 109 0 TATATAATTA 0.492732 -54 GTATTGCTCCTAAATTAAAAATATCCCATTA 5 13 1 TAATTAAAAA 0.690603 -194 TACTTTTATTTTAAGTAAATAACTTTTATTA 5 67 0 TAAGTAAATA 0.941243 -140 AACTATAATATAATATAAATAATGTGATATT 5 110 0 TATATAAATA 0.763372 -97 ATAAACACCTTGAAAGAATTAGGAT 6 5 0 TAAAGAATTA 0.857211 -179 GTTTAATACATAAAATAAAAATTTAAAGCTT 6 40 0 TAAATAAAAA 0.889259 -144 ATACTACATATCATGGAAATAAACTATTATT 6 81 0 TATGGAAATA 0.912116 -103 ATATGTAGTATTATGGAAATAAAGTTTATTG 6 101 1 TATGGAAATA 0.912075 -83 TTAATAAAATAAAAGGAAATA 8 1 0 AAAGGAAATA 0.873888 -114 ATAATTCATTATAAATCAATATAATTTAATT 8 41 0 AAAATCAATA 0.422712 -74 AAATTCTATATCAAGTATATAATTCATTATA 8 59 0 TAAGTATATA 0.548 -56 * ********* Masking position 3 Map Score: 11.8122 Number of sites scoring better than the average of aligned sites = 2304 Number in coding regions = 1508 Number in noncoding regions = 796 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 5 AATTTTCTTTTTAATATTATAATAT 4 6 1 TCTTTTTAAT 0.881302 -157 ATAAATGAAATATTGTTATTTTGCCCTAAT 4 58 1 TATTGTTATT 0.885425 -105 ATTAATGGGATATTTTTAATTTAGGAGCAA 5 16 0 TATTTTTAAT 0.965462 -191 TCATCATAGTTACTTTTAATAAAAGTTATT 5 51 1 TACTTTTAAT 0.86722 -156 AACCTCTTTGCTTTGTTAATTTTATTGAAA 5 180 0 CTTTGTTAAT 0.802176 -27 GGAAATAAACTATTATTAATAGTACTAGTT 6 68 0 TATTATTAAT 0.894697 -116 TTAAACTATTTATTGTCAATAAACTTTATT 6 118 0 TATTGTCAAT 0.919703 -66 TTAAATGTAGTTTTGTTAATAGCTTAAGCT 6 144 1 TTTTGTTAAT 0.94552 -40 ATTATTTATTGATTGTTAATTACAATACAA 7 30 0 GATTGTTAAT 0.927704 -41 AAATAATATATAATTTTAATATTACAAC 7 53 1 TAATTTTAAT 0.815044 -18 ********** Masking position 6 Map Score: 8.58982 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 412 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 ********** No masking Map Score: -3.30951e-14 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: -3.30951e-14 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: -3.30951e-14 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