AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00040_bbur_reg_300.orf -o00040_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 BB0207 52 UTP--glucose-1-phosphate uridylyltransferase (gtaB) #2 BB0541 283 B. burgdorferi predicted coding region BB0541 #3 BB0542 214 B. burgdorferi predicted coding region BB0542 #4 BB0543 114 B. burgdorferi predicted coding region BB0543 #5 BB0544 202 phosphoribosyl pyrophosphate synthetase (prs) Motif number 1 TGAATATATAAAATTAAATTTTTGCTATA 1 8 1 ATAAAAAAAT 0.978204 -45 TTAAAATAAGATTATAGCAAAAATTTAATTTT 1 20 0 ATTATAAAAA 0.779324 -33 AGATAGATTTTTAAAAAAAAATTTTGTAAAAT 2 63 0 TTAAAAAAAT 0.963071 -221 CAAATATTTAATAATATAAAACGATATAAGAT 2 91 0 ATAATAAAAC 0.914975 -193 TTTAAACTATTTTATATGAAATTTGACAGTTT 2 127 1 TTTATAAAAT 0.649251 -157 GTTTTAATCAATAAAATCAAAATCTACTAAAT 2 208 0 ATAAAAAAAA 0.980289 -76 TCTTAGGAGTATAATAATAAAGTAAGAGTTAA 2 255 0 ATAATAAAAG 0.85396 -29 TAATACTATCTAAAAAACAAATTAAAGCTTTT 3 25 0 TAAAAAAAAT 0.825007 -190 TGTTTTTTAGATAGTATTAAAAGCCCTTTTGC 3 38 1 ATAGTAAAAA 0.738832 -177 CCCTCCTGCTTTAAAAGCAAAAGGGCTTTTAA 3 54 0 TTAAAAAAAA 0.966533 -161 AAAGCTAGTCATAAACATAAATAAGCCCTCCT 3 79 0 ATAAACAAAT 0.927356 -136 CTTGATGATTATAAAACAAAATTTATTACTCT 3 112 0 ATAAAAAAAT 0.978217 -103 CTGTTGAATTTTAAAATTAAATAAACCATCTT 3 141 0 TTAAAAAAAT 0.963056 -74 AATAATAATCAAAATACAAAACTTCAATGCTG 3 170 0 AAAATAAAAC 0.660483 -45 AGCAGCAAAATAACACTAAATCTAATAATAA 3 194 0 ATAACAAAAT 0.867567 -21 AAGTAAACAAAAAAACTTAAAAA 4 2 0 AAAAACAAAA 0.718754 -113 CAAAAATTTATGAAAAATAAAACAGGGTTTAT 4 84 0 TGAAAAAAAA 0.753845 -31 AATCCTAAAAATAAAATTAAATAAA 5 4 0 ATAAAAAAAT 0.978204 -199 ATACTATAACATAATCCTAAAAATAAAATTAA 5 16 0 ATAATCAAAA 0.898231 -187 AAAAATTCTATTAATAGCAAAAACAAATACTA 5 42 0 TTAATAAAAA 0.947455 -161 AGCTTTAATAATAAAAATAAAAATCTAAAAAT 5 68 0 ATAAAAAAAA 0.980289 -135 ATTTTTATTATTAAAGCTAAAATATTTTAATG 5 82 1 TTAAAGAAAA 0.753844 -121 ****** **** Masking position 9 Map Score: 30.9837 Number of sites scoring better than the average of aligned sites = 1941 Number in coding regions = 1221 Number in noncoding regions = 720 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 TGAATATATAAAATTAAATTTTTG 1 1 1 TATATAAAAT 0.931008 -52 TCTTAAAATAAGATTATAGCAAAAATTTAATTTT 1 20 0 AATATCAAAA 0.916593 -33 TTTTAAAAAAAAATTTTGTAAAATTACTAAGATA 2 53 0 AATTTAAAAT 0.87118 -231 GATATAAGATAGATTTTTAAAAAAAAATTTTGTA 2 67 0 AATTTAAAAA 0.912503 -217 ATATCGTTTTATATTATTAAATATTTGGAAGTTT 2 96 1 AATATAATAT 0.550228 -188 ATAAGGATATACATTAATGCAAATTTAATCAAGC 2 159 0 AATAACAAAT 0.851301 -125 ATAAAAAGTTTTAATCAATAAAATCAAAATCTAC 2 213 0 TATCAAAAAT 0.611745 -71 AAGAGTTAATTCACTAAATAAAAAGTTTTAATCA 2 230 0 TATAAAAAAA 0.943918 -54 AGGGCTTTTAATACTATCTAAAAAACAAATTAAA 3 31 0 AATATAAAAA 0.969958 -184 ACCATCTTGATGATTATAAAACAAAATTTATTAC 3 115 0 TATATAACAA 0.752485 -100 ACTAAATCTAATAATAATCAAAATACAAAACTTC 3 177 0 AATAAAAAAT 0.943915 -38 CCACAAGCAAAAAGTAAACAAAAAAACTTAAAAA 4 11 0 AATAAAAAAA 0.963039 -104 TTTATGGTAATTATTATATAATAAGGTGTGCAAT 4 50 1 TATATAATAA 0.491709 -65 TCTCCTACAAAAATTTATGAAAAATAAAACAGGG 4 89 0 AATTAAAAAA 0.893907 -26 GCAAAAACAAATACTATAACATAATCCTAAAAAT 5 24 0 AATATCATAA 0.780322 -179 TATTTTAGCTTTAATAATAAAAATAAAAATCTAA 5 72 0 TATAAAAAAT 0.915143 -131 CAATCTTAATTTACTAATTAATAAAACTTATACA 5 147 0 TATAAAATAA 0.78011 -56 AAGATTGTTAAGATTTTCTAAAAAAGAACGAGGA 5 174 1 AATTTAAAAA 0.912767 -29 * * *** ***** Masking position 5 Map Score: 22.0645 Number of sites scoring better than the average of aligned sites = 1945 Number in coding regions = 1230 Number in noncoding regions = 715 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 AGATTATAGCAAAAATTTAATTTTATATAT 1 14 0 AAAAATTTAA 0.854964 -39 GTAGAAGATTAACTATCTTAGTAATTTTAC 2 40 1 AACTATCTTA 0.942094 -244 ATTTTTAAAAAAAAATTTTGTAAAATTACT 2 59 0 AAAAATTTTG 0.811061 -225 TTTTTTAAAAATCTATCTTATATCGTTTTA 2 77 1 ATCTATCTTA 0.75327 -207 TTAAACTTCCAAATATTTAATAATATAAAA 2 102 0 AAATATTTAA 0.820422 -182 TGGAAGTTTAAACTATTTTATATGAAATTT 2 121 1 AACTATTTTA 0.947043 -163 TCACTAAATAAAAAGTTTTAATCAATAAAA 2 224 0 AAAAGTTTTA 0.902685 -60 ATAATTATCTTAGGAGTATAAT 2 272 0 AATTATCTTA 0.757141 -12 AAAGTAAACAAAAAAACTTAAAAA 4 5 0 AAAAAACTTA 0.741716 -110 ATAAAAATCTAAAAATTCTATTAATAGCAA 5 54 0 AAAAATTCTA 0.823493 -149 AAGGTCATTAAAATATTTTAGCTTTAATAA 5 89 0 AAATATTTTA 0.960051 -114 CCTTGCTTTAAAAAATTTTAGTCATATTTG 5 115 1 AAAAATTTTA 0.954574 -88 ATTTGTGTGTATAAGTTTTATTAATTAGTA 5 140 1 ATAAGTTTTA 0.635976 -63 AGAAAATCTTAACAATCTTAATTTACTAAT 5 163 0 AACAATCTTA 0.955396 -40 ********** Masking position 1 Map Score: 15.0413 Number of sites scoring better than the average of aligned sites = 1193 Number in coding regions = 806 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 ATTTTGTAAAATTACTAAGATAGTTAATCT 2 45 0 ATTACTAAGA 0.864394 -239 CCAAATATTTAATAATATAAAACGATATAA 2 94 0 AATAATATAA 0.775633 -190 AAAAGTTTTAATCAATAAAATCAAAATCTA 2 214 0 ATCAATAAAA 0.711266 -70 CAAATATGACCAAGAAAAGCTTTAA 3 6 1 ATGACCAAGA 0.702637 -209 AAAGCTAGTCATAAACATAAATAAGCCCTC 3 81 0 ATAAACATAA 0.524282 -134 AACAAAATTTATTACTCTAAAAGCTAGTCA 3 100 0 ATTACTCTAA 0.762099 -115 AACCATCTTGATGATTATAAAACAAAATTT 3 120 0 ATGATTATAA 0.578228 -95 TACCATAAAGATTACCACAAGCAAAAAGTA 4 29 0 ATTACCACAA 0.817535 -86 TTATATAATAATTACCATAAAGATTACCAC 4 41 0 ATTACCATAA 0.935738 -74 AGCAAAAACAAATACTATAACATAATCCTA 5 29 0 AATACTATAA 0.865355 -174 TGTTTTTGCTATTAATAGAATTTTTAGATT 5 49 1 ATTAATAGAA 0.784231 -154 TTTTAGCTTTAATAATAAAAATAAAAATCT 5 74 0 AATAATAAAA 0.775632 -129 ACACACAAATATGACTAAAATTTTTTAAAG 5 120 0 ATGACTAAAA 0.924681 -83 TAATTTACTAATTAATAAAACTTATACACA 5 145 0 ATTAATAAAA 0.921947 -58 ********** Masking position 4 Map Score: 7.86422 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 621 Number in noncoding regions = 381 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 TGAATATATAAAATTAAATTTTTGC 1 6 1 ATATAAAATT 0.926504 -47 TTCTCTCTTAAAATAAGATTATAGCAAAAA 1 29 0 AAATAAGATT 0.875626 -24 AAAAAAAATTTTGTAAAATTACTAAGATAG 2 52 0 TTGTAAAATT 0.676224 -232 TAGATTTTTAAAAAAAAATTTTGTAAAATT 2 62 0 AAAAAAAATT 0.549238 -222 ATATAAAACGATATAAGATAGATTTTTAAA 2 80 0 ATATAAGATA 0.839019 -204 TCGTTTTATATTATTAAATATTTGGAAGTT 2 99 1 TTATTAAATA 0.616856 -185 GTCAAATTTCATATAAAATAGTTTAAACTT 2 124 0 ATATAAAATA 0.827715 -160 TTTAATTTGTTTTTTAGATAGTATTAAAAG 3 31 1 TTTTTAGATA 0.421627 -184 GATGATTATAAAACAAAATTTATTACTCTA 3 111 0 AAACAAAATT 0.505737 -104 TGCTGTTGAATTTTAAAATTAAATAAACCA 3 145 0 TTTTAAAATT 0.822446 -70 ATTTTGATTATTATTAGATTTAGTGTTATT 3 187 1 TTATTAGATT 0.82092 -28 ATAATCCTAAAAATAAAATTAAATAAA 5 8 0 AAATAAAATT 0.866182 -195 ATTAATAGAATTTTTAGATTTTTATTTTTA 5 59 1 TTTTTAGATT 0.656312 -144 TGACCTTGCTTTAAAAAATTTTAGTCATAT 5 112 1 TTAAAAAATT 0.675448 -91 TTAATTAGTAAATTAAGATTGTTAAGATTT 5 160 1 AATTAAGATT 0.744048 -43 ********** Masking position 6 Map Score: 9.93418 Number of sites scoring better than the average of aligned sites = 1808 Number in coding regions = 1128 Number in noncoding regions = 680 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 6 ATAATCTTATTTTAAGAGAGAAAAAT 1 37 1 TTTAAGAGAG 0.804391 -16 CCCACATATCATCAGGAGGGACAAAGTCTA 2 11 0 ATCAGGAGGG 0.990625 -273 CTGCTTTAAAAGCAAAAGGGCTTTTAATAC 3 51 0 AGCAAAAGGG 0.942352 -164 TTGCTTTTAAAGCAGGAGGGCTTATTTATG 3 66 1 AGCAGGAGGG 0.994017 -149 TTTTATAATCATCAAGATGGTTTATTTAAT 3 128 1 ATCAAGATGG 0.912249 -87 CATAAATTTTTGTAGGAGAGT 4 104 1 TGTAGGAGAG 0.910456 -11 ********** Masking position 4 Map Score: 3.11997 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 45 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 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 Motif number 9 ********** 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