AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ifis_bbur_opreg_300.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 BB0649 194 heat shock protein (groEL) #4 BB0650 23 B. burgdorferi predicted coding region BB0650 #5 BB0652 85 protein-export membrane protein (secD) #6 BB0797 163 DNA mismatch repair protein (mutS) #7 BB0799 49 conserved hypothetical protein #8 BB0804 198 ribosomal protein S15 (rpsO) #9 BB0809 26 tRNA-guanine transglycosylase (tgt) Motif number 1 ACTATTTTATAACTATAAAAAACTAATAA 1 10 0 AACTATAAAA 0.816467 -35 ATTCCTTAAAAACTATTTTATAACTATAAA 1 21 0 AACTATTTTA 0.85722 -24 AGAAACATTCAACAATTTAAAGCAAAAGCC 2 33 0 AACAATTTAA 0.956516 -47 TTAAATTATAAATTATATTACACAGAAACA 2 56 0 AATTATATTA 0.866894 -24 TAATATAATTTATAATTTAATTAT 2 66 1 TATAATTTAA 0.901559 -14 TCTTTGTCTTTATAATTTAAAGATTAGTCA 3 15 1 TATAATTTAA 0.901559 -180 TAAAAATTTTTATTATATAATGTAAATATT 3 44 0 TATTATATAA 0.826204 -151 CTATGCATCAAAAAATACAAAATATACAAA 3 79 0 AAAAATACAA 0.766771 -116 ATTTACATATAACAATATAAGATTAACATA 3 143 0 AACAATATAA 0.945615 -52 TATAAATAAAAATAATTTACATATAACAAT 3 157 0 AATAATTTAC 0.718661 -38 AAAAATTTTACCCCTTTCTA 3 185 0 AAAAATTTTA 0.867872 -10 GGTATTTTTTAAAAATTTTAAGGATTTGTA 5 64 1 AAAAATTTTA 0.867872 -22 TAGGCTTTTTAATAATTAAATAGCGTTTAA 6 32 1 AATAATTAAA 0.934445 -132 ACCATAAAAAAAATATTTTACGCAATTAAA 6 57 0 AAATATTTTA 0.813992 -107 AAGAATATAAAATAATAAAAAGACCATAAA 6 79 0 AATAATAAAA 0.918702 -85 ATTAAAAAGAAAGAATATAAAATAATAAAA 6 89 0 AAGAATATAA 0.799435 -75 ATAAAATAAATATAATTCAATTAAAAAGAA 6 108 0 TATAATTCAA 0.703952 -56 TTACAATTGATATTATAAAATAAATATAAT 6 122 0 TATTATAAAA 0.681519 -42 TTATAAATATATTATGACATTTTA 8 5 1 AAATATATTA 0.790467 -194 TTAAAAAAACAAATATAAAATTAAAATGTC 8 26 0 AAATATAAAA 0.793112 -173 TGTTTTTTTAAACAATTTAATAATTTATTA 8 45 1 AACAATTTAA 0.956516 -154 TTTAATAATTTATTATTAAAAATAACCCGA 8 60 1 TATTATTAAA 0.722137 -139 ATTTTTAAGAAAAAATATTATAATCTATCG 8 111 1 AAAAATATTA 0.858997 -88 AACCTCTTGCCATAATTTAAAATAACTACT 8 142 0 CATAATTTAA 0.772124 -57 AAATATCCCAAATAATTATATATA 9 5 0 AATAATTATA 0.84833 -22 ********** Masking position 6 Map Score: 29.1732 Number of sites scoring better than the average of aligned sites = 3738 Number in coding regions = 2353 Number in noncoding regions = 1385 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 2 AAACTATTTTATAACTATAAAAAACTAATAA 1 8 0 ATAACAAAAA 0.713824 -37 ATAAATTATATTACACAGAAACATTCAACAATTT 2 45 0 TTACAAAAAT 0.811225 -35 TCTTTAAATTATAAAGACAAAGAATTT 3 4 0 ATAAAAAAAA 0.961252 -191 AATACAAAATATACAAAACCAGTAAAAATTTTTA 3 62 0 ATACAACCTA 0.636607 -133 TTCTATGCATCAAAAAATACAAAATATACAAAAC 3 77 0 CAAAAAACAA 0.637534 -118 AATATAAGATTAACATAAACTTAATACATTCGCT 3 126 0 TAACAAACAA 0.823403 -69 TAAAAATAATTTACATATAACAATATAAGATTAA 3 147 0 TTACAAAAAT 0.811223 -48 ACCCCTTTCTATAAATAAAAATAATTTACATATA 3 162 0 ATAAAAAAAA 0.961248 -33 AGTTAAAAAAAAGGTATTGTTTAAAG 5 3 1 TTAAAAAATA 0.749339 -83 AAAATTTTTAAAAAATACCATTATTAGCTAACAG 5 49 0 AAAAAACAAT 0.724526 -37 TATACAAATCCTTAAAATTTTTAAA 5 71 0 ATACAACCAA 0.929148 -15 GCCTAATGTTTTAAATTTAATTAACT 6 3 0 TTAAATAAAA 0.597798 -161 TATTTAATTATTAAAAAGCCTAATGTTTTAAATT 6 20 0 TTAAAACCAT 0.881424 -144 ATAAAATAATAAAAAGACCATAAAAAAAATATTT 6 69 0 AAAAAACAAA 0.883496 -95 TATAATTCAATTAAAAAGAAAGAATATAAAATAA 6 94 0 TTAAAAAAAA 0.957268 -70 ATATTATAAAATAAATATAATTCAATTAAAAAGA 6 109 0 ATAAAAAACA 0.735582 -55 ATTAAATTGTTTAAAAAAACAAATATAAAATTAA 8 32 0 TTAAAAACAT 0.894 -167 ATTTATTATTAAAAATAACCCGAAAAGGATAAAT 8 67 1 AAAAAACCAA 0.89168 -132 ATATTTTTTCTTAAAAATAACAAAAGCAATTTAT 8 95 0 TTAAAAAAAA 0.957268 -104 ATAAATATCCCAAATAATTATATA 9 13 0 ATAAAACCAA 0.95957 -14 ***** * ** ** Masking position 3 Map Score: 19.0205 Number of sites scoring better than the average of aligned sites = 2799 Number in coding regions = 1750 Number in noncoding regions = 1049 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 3 TTATTAGTTTTTTATAGTTAT 1 2 1 TATTAGTTTT 0.710109 -43 TTAGTGTCCTTTTTTTACTTAAGGCT 2 7 1 TCCTTTTTTT 0.904447 -73 AAATTCTTTGTCTTTATAATTTAA 3 5 1 TCTTTGTCTT 0.783665 -190 AACCAGTAAAAATTTTTATTATATAATGTA 3 50 0 AATTTTTATT 0.679962 -145 TAAAAATTTTTACTGGTTTTGTATATTTTG 3 62 1 TACTGGTTTT 0.754585 -133 ATATGTAAATTATTTTTATTTATAGAAAGG 3 163 1 TATTTTTATT 0.878936 -32 TTTAAACAATACCTTTTTTTTAACT 5 6 0 ACCTTTTTTT 0.734759 -80 TTGCGTAAAATATTTTTTTTATGGTCTTTT 6 62 1 TATTTTTTTT 0.957652 -102 TTTTTTATGGTCTTTTTATTATTTTATATT 6 76 1 TCTTTTTATT 0.868481 -88 TATTTTATATTCTTTCTTTTTAATTGAATT 6 95 1 TCTTTCTTTT 0.909535 -69 AATTGAATTATATTTATTTTATAATATCAA 6 116 1 TATTTATTTT 0.802081 -48 TTTAATTTTATATTTGTTTTTTTAAACAAT 8 31 1 TATTTGTTTT 0.95485 -168 GAAAAGGATAAATTGCTTTTGTTATTTTTA 8 88 1 AATTGCTTTT 0.505447 -111 TAGATTATAATATTTTTTCTTAAAAATAAC 8 108 0 TATTTTTTCT 0.767376 -91 ********** Masking position 4 Map Score: 11.5607 Number of sites scoring better than the average of aligned sites = 2136 Number in coding regions = 1407 Number in noncoding regions = 729 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 AAAATAGTTTTTAAGGAATATTT 1 32 1 TTAAGGATAT 0.874658 -13 CTTTTTTTACTTAAGGCTTTTGCTTTAAATT 2 19 1 TTAAGGTTTT 0.97661 -61 TCTTTATAATTTAAAGATTAGTCAATATTTA 3 21 1 TTAAAGTTAG 0.948974 -174 TTTAAAAATTTTAAGGATTTGTATA 5 71 1 TTAAGGTTTG 0.989024 -15 ATTTAAAACATTAGGCTTTTTAATAATTAAA 6 21 1 TTAGGCTTTT 0.849884 -143 TAACCTTGACTTAAGGTTTAGTTT 7 36 1 TTAAGGTTAG 0.978997 -14 AAGAGGTTTGTTAGAGCTTTGCTATAATGGT 8 164 1 TTAGAGTTTG 0.943134 -35 ****** **** Masking position 3 Map Score: 4.89644 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 96 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 ATAATTAAATTATAAATTATATT 2 67 0 ATTAAATTAT 0.704882 -13 TTGACTAATCTTTAAATTATAAAGACAAAG 3 16 0 TTTAAATTAT 0.701929 -179 TTAGTCAATATTTACATTATATAATAAAAA 3 38 1 TTTACATTAT 0.904896 -157 TAATTTACATATAACAATATAAGATTAACA 3 145 0 ATAACAATAT 0.689405 -50 CCTTTAAACAATACCTTTTTTTTAACT 5 8 0 ATACCTTTTT 0.432421 -78 TTTTTAAAAAATACCATTATTAGCTAACAG 5 49 0 ATACCATTAT 0.937113 -37 ATACAAATCCTTAAAATTTTTAAAAAATAC 5 65 0 TTAAAATTTT 0.675707 -21 TGAATTACAATTGATATTATAAAATAAATA 6 126 0 TTGATATTAT 0.771356 -38 TGTTGACATTATTTTTGCTAAG 7 3 1 TTGACATTAT 0.951636 -47 TAAATATATTATGACATTTTAATTTTATAT 8 14 1 ATGACATTTT 0.913479 -185 ACGATAGATTATAATATTTTTTCTTAAAAA 8 112 0 ATAATATTTT 0.584021 -87 AACAAACCTCTTGCCATAATTTAAAATAAC 8 146 0 TTGCCATAAT 0.606186 -53 AGCAACTCCTATACCATTATAGCAAAGCTC 8 177 0 ATACCATTAT 0.937113 -22 ********** Masking position 2 Map Score: 7.8851 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 399 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 ********** No masking Map Score: -1.58208e-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 7 ********** No masking Map Score: -1.58208e-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 8 ********** No masking Map Score: -1.58208e-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