AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_bbur_reg_300.orf -o00290_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 Purged sequences: BB0736 51 B. burgdorferi predicted coding region BB0736 Input sequences: #1 BB0247 196 conserved hypothetical protein #2 BB0248 119 oligoendopeptidase F (pepF) #3 BB0251 202 leucyl-tRNA synthetase (leuS) #4 BB0735 66 rare lipoprotein A (rlpA) #5 BB0834 22 ATP-dependent Clp protease, subunit C (clpC) #6 BB0835 114 phosphomannomutase (cpsG) Motif number 1 TTAAAATAAATTTTTAATTTTCTTGTTTGATCA 1 35 0 TTTTAATTTT 0.986181 -162 TTTGTGTACTTATTAAGTATTTTTGTACCAGGT 1 103 0 TTTAAGTATT 0.830567 -94 AGTATTATTCTCTTTAATTTTGTGTACTTATTA 1 121 0 TTTTAATTTT 0.986181 -76 ATTATATTGGTTTTAAGTATTATTCTCTTTAAT 1 136 0 TTTAAGTATT 0.830567 -61 TGAGTTTAATTGTATAATTATATTGGTTTTAAG 1 152 0 TTATAATTTT 0.971019 -45 TCATAAATACTTTATTATTATATAG 1 182 1 TTATTATTTT 0.892936 -15 TCCTCTTCCTTTTTTTATTGTTTGAAAAGAAAT 2 90 0 TTTTTATTTT 0.946707 -30 TTGTTAATTTTATTTAATAATTTGCTAACAATT 3 119 0 TTTTAATATT 0.96152 -84 CAACTTATTCTCTAATATTCTTTTAGATTGCAT 3 154 0 TTAATATTTT 0.867525 -49 CTTTTTTCTTTTTATAATTAAATCAAAAAAAAT 4 19 1 TTATAATTAT 0.892783 -48 ATTTATTAAATTTTCTGTTATG 5 7 0 TTTAAATTTT 0.982446 -16 ATACACATTCTTATAAATTATATGATAATAAAT 6 17 1 TATAAATTTT 0.90025 -98 AATTATATGATAATAAATTCTATATCAAGTATA 6 32 1 TATAAATTTT 0.900529 -83 CTATATCAAGTATATAATTCATTATAAATCAAT 6 51 1 TTATAATTAT 0.892932 -64 AACAAAGATTAATTAAATTATATTGATTTATAA 6 72 0 ATTAAATTTT 0.824138 -43 AATTAATCTTTGTTTAATAAAATAAAAGGAAAT 6 91 1 TTTTAATAAT 0.861301 -24 * ******* * * Masking position 8 Map Score: 21.8812 Number of sites scoring better than the average of aligned sites = 1893 Number in coding regions = 1196 Number in noncoding regions = 697 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 CTAAGGTGTTAAAATAAATTTTTAATTTTCTTGTT 1 41 0 AAATAAATAA 0.947077 -156 TTAACACCTTAGACAAAAATCCAAATTTTTTCGAT 1 64 1 AGAAAAATAA 0.941007 -133 AACCTGGTACAAAAATACTTAATAAGTACACAAAA 1 102 1 AAAATACTAA 0.590311 -95 CTTAATAAGTACACAAAATTAAAGAGAATAATACT 1 119 1 ACAAAAATGA 0.852976 -78 AAATTAAAGAGAATAATACTTAAAACCAATATAAT 1 134 1 GAAAATATAA 0.635428 -63 TATAATTATACAATTAAACTCATAAATACTTTATT 1 163 1 CAATAAATAA 0.866826 -34 TTTTTATTTTACAATAAAGTCTAAACTTTATATAT 2 26 0 ACATAAATAA 0.874969 -94 CTTTATTGTAAAATAAAAAGCACAATGTTTATAAA 2 42 1 AAAAAAAGAA 0.968272 -78 GTTTGAAAAGAAATAATAAGTTGAAATTTTATAAA 2 69 0 AAAAATAGAA 0.868386 -51 TCTTTTCAAACAATAAAAAAAGGAAGAGGAGAATT 2 93 1 CAAAAAAAAA 0.680205 -27 AAAATATAATGGTTAATAGTGCTGTG 3 2 1 AAAATAAGAA 0.868386 -201 GCAAATTATTAAATAAAATTAACAAAAATGCAATC 3 127 1 AAAAAAATAA 0.983449 -76 ATGCAATCTAAAAGAATATTAGAGAATAAGTTGTT 3 154 1 AAAAATATGA 0.762335 -49 TGTCCTCTTGAAAATTAACTCATAACAACTTATTC 3 177 0 AAATTAATAA 0.794622 -26 AATTATAAAAAGAAAAAAGTCTAAAAA 4 3 0 AGAAAAATAA 0.941007 -64 ATAATTAAATCAAAAAAAATGTAAATAAGCAATTT 4 32 1 CAAAAAATAA 0.955774 -35 CATAACAGAAAATTTAATAAAT 5 5 1 ACAAAAATTA 0.789502 -18 TTGTTTAATAAAATAAAAGGAAATA 6 100 1 AAAAAAAGTA 0.831264 -15 *** **** * ** Masking position 3 Map Score: 17.5357 Number of sites scoring better than the average of aligned sites = 3841 Number in coding regions = 2485 Number in noncoding regions = 1356 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 3 GTCTAAGGTGTTAAAATAAATTTTTAATTTTCTT 1 44 0 TTAAAAATTT 0.530255 -153 ACACCTTAGACAAAAATCCAAATTTTTTCGATAA 1 67 1 CAAAACAAAT 0.707477 -130 AAACCTGGTACAAAAATACTTAATAAGTACACAA 1 101 1 CAAAACTTAT 0.707476 -96 GAGAATAATACTTAAAACCAATATAATTATACAA 1 142 1 CTTAACAATT 0.906375 -55 CAATTAAACTCATAAATACTTTATTATTATATAG 1 173 1 CATAACTTTT 0.880253 -24 ACTTAAAGGCTTTTTATATATAAAG 2 2 1 CTTAACTTTT 0.906375 -118 AAGTTGAAATTTTATAAACATTGTGCTTTTTATT 2 53 0 TTTAACATTT 0.91362 -67 CACCACAGCACTATTAACCATTATATTTT 3 6 0 CTATACATTT 0.925596 -197 ATAAAATTAACAAAAATGCAATCTAAAAGAATAT 3 139 1 CAAAACAATT 0.927998 -64 TTTTTAGACTTTTTTCTTTTTATA 4 1 1 TTTTACTTTT 0.716056 -66 AAAAAAAATGTAAATAAGCAATTTGCAAGCTTAA 4 43 1 TAAAACAATT 0.889271 -24 AATTTAATACACATTCTTATAAATTAT 6 4 1 TTAAACATTT 0.948834 -111 ATATAATTCATTATAAATCAATATAATTTAATTA 6 62 1 TTATACAATT 0.815549 -53 CAATATAATTTAATTAATCTTTGTTTAATAAAAT 6 80 1 TAATACTTTT 0.770503 -35 **** * **** * Masking position 6 Map Score: 10.9758 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 534 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 TGTTTGATCATGGTAATTTTTAGTAAGGTTT 1 14 0 TGTAATTTTT 0.873205 -183 AACAAGAAAATTAAAAATTTATTTTAACACC 1 41 1 TTAAAATTTA 0.77738 -156 TAGACAAAAATCCAAATTTTTTCGATAAAAA 1 73 1 TCAAATTTTT 0.950295 -124 TACAATAAAGTCTAAACTTTATATATAAAAA 2 21 0 TCAAACTTTA 0.862214 -99 AACATTGTGCTTTTTATTTTACAATAAAGTC 2 40 0 TTTTATTTTA 0.647148 -80 AAATAATAAGTTGAAATTTTATAAACATTGT 2 63 0 TTAAATTTTA 0.951188 -57 GTTCACAGCATCAAAATTGTTAGCAAATTAT 3 105 1 TCAAATTGTT 0.817077 -98 ATTGCATTTTTGTTAATTTTATTTAATAATT 3 130 0 TGTAATTTTA 0.894564 -73 AAATTGCTTATTTACATTTTTTTTGATTTAA 4 36 0 TTACATTTTT 0.807917 -31 ** ******** Masking position 6 Map Score: 1.07333 Number of sites scoring better than the average of aligned sites = 1528 Number in coding regions = 1048 Number in noncoding regions = 480 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 ********** No masking Map Score: -5.16264e-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 6 ********** No masking Map Score: -5.16264e-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: -5.16264e-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