AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_bbur_reg_300.orf -o00860_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 BB0196 300 peptide chain release factor 1 (prfA) #2 BB0373 124 B. burgdorferi predicted coding region BB0373 Motif number 1 TCAAACACACCGCAAATAATAATACGTAAAGCTC 1 22 1 CGAAATAATA 0.797449 -279 ATATAAATACAACAAAACCTAATTTAACTTTAAT 1 63 1 AAAAATAATT 0.962785 -238 TTTTTTATATAATAAATGTTATTAAGTTGGATAT 1 95 0 AAAAATATTA 0.980889 -206 TTTATTATATAAAAAAACATGAAAAAATATAATT 1 113 1 AAAAATGAAA 0.89294 -188 AAGCGTGATTAAAAAAATCAATTATATTTTTTCA 1 132 0 AAAAAAATTA 0.943901 -169 GCTTTTATTAAATAAATAGAATAAGCGTGATTAA 1 154 0 AAAAAAATAA 0.854886 -147 CTATTTATTTAATAAAAGCAGTTTTAAAAAAGAA 1 169 1 AAAAAAGTTT 0.8282 -132 AAGCAGTTTTAAAAAAGAATGTTAAAATAAAACA 1 184 1 AAAAATGTTA 0.96388 -117 AGAATGTTAAAATAAAACATAAATATGGGAATCT 1 199 1 AAAAATAAAT 0.900591 -102 TGGGAATCTACACAAAACTTATTAAAAAGTCTAA 1 224 1 CAAAATATTA 0.949746 -77 AAAGTCTAACAAAAAAATCTAAAATTAATATAAA 1 249 1 AAAAATAAAA 0.941991 -52 ATCTAAAATTAATATAAACTATTACTATCTTTCA 1 265 1 AAATATATTA 0.893479 -36 ATACATGGTTAATAGAGCTTAATTTCAAGGGAAT 2 13 0 AAAGATAATT 0.778118 -112 ATAGACAATTAATAAATAATATGATATACATGGT 2 38 0 AAAAATATGA 0.891252 -87 TCTATCTATTAGTATAATGTATTTATTATATCTC 2 67 1 AGATATATTT 0.522031 -58 AAGCTTAATTCAAAAATTGAGATATAATAAATAC 2 85 0 CAAAAAGATA 0.737234 -40 AAATCTCTTCAAAAAAGCTTAATTCAAAAATTGA 2 99 0 AAAAATAATT 0.95143 -26 ** *** ***** Masking position 6 Map Score: 21.0614 Number of sites scoring better than the average of aligned sites = 3212 Number in coding regions = 1993 Number in noncoding regions = 1219 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 CATGTTTTTTTATATAATAAATGTTATTAA 1 104 0 TATATAATAA 0.968067 -197 ATAATTGATTTTTTTAATCACGCTTATTCT 1 141 1 TTTTTAATCA 0.908643 -160 TTATTCTATTTATTTAATAAAAGCAGTTTT 1 164 1 TATTTAATAA 0.966862 -137 AATAAAAGCAGTTTTAAAAAAGAATGTTAA 1 179 1 GTTTTAAAAA 0.721337 -122 AAAAAAGAATGTTAAAATAAAACATAAATA 1 194 1 GTTAAAATAA 0.843318 -107 TTTGTTAGACTTTTTAATAAGTTTTGTGTA 1 232 0 TTTTTAATAA 0.810299 -69 ATAGTAATAGTTTATATTAATTTTAGATTT 1 263 0 TTTATATTAA 0.873162 -38 TATATCATATTATTTATTAATTGTCTATCT 2 44 1 TATTTATTAA 0.92161 -81 CAAAAATTGAGATATAATAAATACATTATA 2 79 0 GATATAATAA 0.965091 -46 ********** Masking position 6 Map Score: 12.1864 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 319 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 AATACGTAAAGCTCAATTTATATATAAATA 1 42 1 GCTCAATTTA 0.981879 -259 ATACAACAAAACCTAATTTAACTTTAATAT 1 69 1 ACCTAATTTA 0.912149 -232 TTTTAATCACGCTTATTCTATTTATTTAAT 1 152 1 GCTTATTCTA 0.942755 -149 GGTTAATAGAGCTTAATTTCAAGGGAATAA 2 11 0 GCTTAATTTC 0.981879 -114 CTTCAAAAAAGCTTAATTCAAAAATTGAGA 2 97 0 GCTTAATTCA 0.981879 -28 ********** Masking position 5 Map Score: 1.93868 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 124 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AATATGGGAATCTACACAAAACTTATTAAA 1 220 1 TCTACACAAA 0.921169 -81 TATGGTTTCTCCTGAAAGATAGTAATA 1 284 0 TCTCCTGAAA 0.988492 -17 TTATTCCCTTGAAATTAAGCTCTA 2 5 1 TCCCTTGAAA 0.977124 -120 AAAAATCTCTTCAAAAAAGCTTAAT 2 110 0 TCTCTTCAAA 0.986233 -15 ********** Masking position 8 Map Score: 1.23727 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 58 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GAGCTTTACGTATTATTATTTGCGGTGTGTT 1 25 0 TATATTATTT 0.938997 -276 GGTTTTGTTGTATTTATATATAAATTGAGCT 1 51 0 TATTATATAT 0.958155 -250 ATATCCAACTTAATAACATTTATTATATAAA 1 95 1 TATAACATTT 0.841759 -206 TTTTTTCATGTTTTTTTATATAATAAATGTT 1 109 0 TTTTTTATAT 0.687583 -192 TTAAAAAAATCAATTATATTTTTTCATGTTT 1 127 0 CATTATATTT 0.826377 -174 TAGATTCCCATATTTATGTTTTATTTTAACA 1 203 0 TATTATGTTT 0.826859 -98 TAGTTTATATTAATTTTAGATTTTTTTGTTA 1 255 0 TATTTTAGAT 0.917495 -46 TCCTGAAAGATAGTAATAGTTTATATTAATT 1 271 0 TATAATAGTT 0.941587 -30 AATTAATAAATAATATGATATACATGGTTAA 2 35 0 TATATGATAT 0.785007 -90 AAATACATTATACTAATAGATAGACAATTAA 2 60 0 TATAATAGAT 0.940738 -65 ** ******** Masking position 4 Map Score: 6.33748 Number of sites scoring better than the average of aligned sites = 892 Number in coding regions = 504 Number in noncoding regions = 388 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 ********** No masking Map Score: -4.02005e-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: -4.02005e-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: -4.02005e-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