AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_bbur_reg_300.orf -o00190_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: BB0304 22 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase (murF) Input sequences: #1 BB0093 21 V-type ATPase, subunit B (atpB) #2 BB0094 85 V-type ATPase, subunit A (atpA) #3 BB0096 183 V-type ATPase, subunit E, putative #4 BB0100 156 glutamate racemase (murI) #5 BB0293 23 flagellar basal-body rod protein (flgC) #6 BB0294 33 flagellar basal-body rod protein (flgB) #7 BB0301 35 cell division protein (divIB) #8 BB0308 30 B. burgdorferi predicted coding region BB0308 #9 BB0309 92 B. burgdorferi predicted coding region BB0309 #10 BB0312 43 purine-binding chemotaxis protein (cheW-1) #11 BB0313 50 cell division protein (ftsJ) Motif number 1 AAAGGAATTTAAATGAATACAAAAGGAAAAGTC 2 12 1 AAAGATACAA 0.88422 -74 TACAATATTAAAAAACATATCAAGTTGGCACAA 3 65 0 AAAAATATAA 0.756853 -119 TTTAATATCAAAAATTTTACAATATTAAAAAAC 3 82 0 AAATTTACAT 0.920109 -102 AGCATAAAATAAATTTTTAATATCAAAAATTTT 3 97 0 AAATTTAAAT 0.977469 -87 AAAACTTTAAAAAAGCATAAAATAAATTTTTAA 3 110 0 AAAGATAAAT 0.96834 -74 ATATAAGATAAAAATAATAACCTAACACTTATT 3 150 0 AAATATAACT 0.940006 -34 AATTGATTTAACAATATTAATAAGTTAAGTATT 4 15 0 ACATTTAAAA 0.909909 -142 TTTTTTAAAAAAAGTTTTAAGCTATAATAAAAT 4 45 0 AAATTTAACT 0.940046 -112 TTTTTAAAAAAAACATTTAACAATTTTTATTAT 4 67 1 AAAATTAAAA 0.950697 -90 ATCAAGAATTAAAATAATAAAAATTGTTAAATG 4 80 0 AAATATAAAA 0.97878 -77 ATAAATATTAACAAAGTTAATATCAAGAATTAA 4 101 0 ACAATTAAAT 0.808591 -56 CCTAAAAAGTAAAGTATAAATATTAACAAAGTT 4 116 0 AAATTAAAAT 0.773912 -41 TACAAAATAATAATCACCCCTAAAAA 4 141 0 AAATATAACA 0.940006 -16 AACAAGTTATAAATTTATAAAAAACACCCT 9 8 0 AAATATAAAA 0.97878 -85 TAACTTGTTAAAATATTTAATATATTTTTTGCT 9 32 1 AAAATTAAAT 0.950676 -61 CAAATTAATCAAATTGTTATAAACAGATTTAAA 10 11 1 AAATTTATAA 0.881601 -33 AAACAGATTTAAAGGTATAAAAT 10 31 1 AAAGATAAAT 0.96834 -13 ATTATAATGAAAAAGTATAATAAAGTGTATTAA 11 18 1 AAAGATAAAA 0.96834 -33 *** * **** ** Masking position 9 Map Score: 27.0885 Number of sites scoring better than the average of aligned sites = 1838 Number in coding regions = 1179 Number in noncoding regions = 659 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 2 ATATATATTTCTCCAAACCC 1 12 0 ATATATATTT 0.746232 -10 GTATTCATTTAAATTCCTTTT 2 2 0 AAATTCCTTT 0.615832 -84 GAGTTAATGGAAACTTAGTTACTATTGAGG 2 49 1 AAACTTAGTT 0.851674 -37 TTTAAAGAATATACTTATTCTCAACTATTA 3 26 0 ATACTTATTC 0.787325 -158 TGGCACAATAATACTTCTTTAAAGAATATA 3 43 0 ATACTTCTTT 0.913671 -141 TGCCAACTTGATATGTTTTTTAATATTGTA 3 68 1 ATATGTTTTT 0.660197 -116 TTGATATTAAAAATTTATTTTATGCTTTTT 3 104 1 AAATTTATTT 0.867387 -80 AATTTATTTTATGCTTTTTTAAAGTTTTGT 3 115 1 ATGCTTTTTT 0.834803 -69 TGCTTTTTTAAAGTTTTGTTTGCTAATAAG 3 126 1 AAGTTTTGTT 0.623532 -58 AGCTATAATAAAATTGATTTAACAATATTA 4 29 0 AAATTGATTT 0.910068 -128 TTATAGCTTAAAACTTTTTTTAAAAAAAAC 4 51 1 AAACTTTTTT 0.936876 -106 AAATTGTTAAATGTTTTTTTTAAAAAAAGT 4 63 0 ATGTTTTTTT 0.8297 -94 CCCTCATTTAAAATTGCTTTTAA 6 4 0 AAATTGCTTT 0.875085 -30 CTAGTAGTGTAAATTGAGTTAGGTT 7 21 1 AAATTGAGTT 0.791951 -15 AAAATATTTAATATATTTTTTGCTAAAATC 9 41 1 ATATATTTTT 0.766908 -52 GCTATCTAATATATTGATTTTAGCAAAAAA 9 56 0 ATATTGATTT 0.917941 -37 AAATTGTTATAAACAGATTTAAAGGTATAA 10 21 1 AAACAGATTT 0.719598 -23 ACACTTTATTATACTTTTTCATTATAATTC 11 16 0 ATACTTTTTC 0.765068 -35 ********** Masking position 9 Map Score: 16.9828 Number of sites scoring better than the average of aligned sites = 1919 Number in coding regions = 1261 Number in noncoding regions = 658 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 ATATATATTTCTCCAAACCCC 1 10 0 TATATATTCT 0.840764 -12 TTTGTATTCATTTAAATTCCTTTT 2 4 0 TTTAAATTCT 0.892833 -82 TTCTTTAAAGAATATACTTATTCTCAACTAT 3 28 0 AATATACTAT 0.740444 -156 AGTTGGCACAATAATACTTCTTTAAAGAATA 3 45 0 ATAATACTCT 0.842137 -139 TATCAAAAATTTTACAATATTAAAAAACATA 3 79 0 TTTACAATTT 0.525811 -105 TTTTTGATATTAAAAATTTATTTTATGCTTT 3 101 1 TAAAAATTAT 0.718266 -83 ATCATATAAGATAAAAATAATAACCTAACAC 3 155 0 ATAAAAATAT 0.623092 -29 ACTTAACTTATTAATATTGTTAAATCAATTT 4 18 1 TTAATATTTT 0.779657 -139 TTAAGCTATAATAAAATTGATTTAACAATAT 4 31 0 ATAAAATTAT 0.81829 -126 TTATTATAGCTTAAAACTTTTTTTAAAAAAA 4 48 1 TTAAAACTTT 0.681046 -109 AATATCAAGAATTAAAATAATAAAAATTGTT 4 85 0 ATTAAAATAT 0.674894 -72 ATTAACTTTGTTAATATTTATACTTTACTTT 4 113 1 TTAATATTAT 0.860799 -44 TACAAAATAATAATCACCCCTAAA 4 143 0 AAAATAATAT 0.56009 -14 TTTACATTCCTTAAGATATTA 5 13 0 TTTACATTCT 0.839178 -11 CCTCCCTCATTTAAAATTGCTTTTAA 6 6 0 TTAAAATTCT 0.86303 -28 CCTAACTCAATTTACACTACTAGAAAAATCT 7 13 0 TTTACACTCT 0.796202 -23 GGGTGTTTTTTATAAATTTATAACTTGTTAA 9 12 1 TATAAATTAT 0.771138 -81 TAAAATATTTAATATATTTTTTGCTAAAATC 9 40 1 AATATATTTT 0.679326 -53 TCAGCTATCTAATATATTGATTTTAGCAAAA 9 58 0 AATATATTAT 0.79206 -35 ATACTTTTTCATTATAATTCTTATT 11 5 0 ATTATAATCT 0.814947 -46 AATACACTTTATTATACTTTTTCATTATAAT 11 18 0 ATTATACTTT 0.761072 -33 ******** ** Masking position 8 Map Score: 19.2599 Number of sites scoring better than the average of aligned sites = 2932 Number in coding regions = 1840 Number in noncoding regions = 1092 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 4 TTACTTTTTAGGGGTGATTATTATTTTGTA 4 137 1 GGGGTGATTA 0.969562 -20 ATTTTAAATGAGGGAGGTTTCAAT 6 20 1 AGGGAGGTTT 0.978561 -14 AGGGTGTTTTTTATAAATTT 9 1 1 AGGGTGTTTT 0.987312 -92 AAAAGGGTGATTTATCAGCTATC 9 80 0 AGGGTGATTT 0.992765 -13 ********** Masking position 8 Map Score: 2.6413 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 AATGAATACAAAAGGAAAAGTCGTTGGAGTT 2 23 1 AAAGAAAAGT 0.777353 -63 TTAAAAAAGCATAAAATAAATTTTTAATATC 3 106 0 ATAAATAAAT 0.742426 -78 TTTTTATCTTATATGATAAGGAGTT 3 169 1 ATAGATAAGG 0.962314 -15 AACAATATTAATAAGTTAAGTATTTAGG 4 8 0 ATAGTTAAGT 0.976631 -149 ATCACCCCTAAAAAGTAAAGTATAAATATTA 4 124 0 AAAGTAAAGT 0.848509 -33 ATTAATATCTTAAGGAATGTAAA 5 5 1 ATACTTAAGG 0.92085 -19 ATAAATTAAGGTGGGGAGAAA 8 1 1 ATAATTAAGG 0.952002 -30 TTAGCAAAAAATATATTAAATATTTTAACAA 9 36 0 ATAATTAAAT 0.819054 -57 *** ******* Masking position 8 Map Score: 2.90186 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 127 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TTATTCTCAACTATTAGAAATAATACAACC 3 12 0 CTATTAGAAA 0.875486 -172 AAATTTTACAATATTAAAAAACATATCAAG 3 74 0 ATATTAAAAA 0.968993 -110 AAAATTTTTGATATTAAAAATTTATTTTAT 3 97 1 ATATTAAAAA 0.968993 -87 AACCTAACACTTATTAGCAAACAAAACTTT 3 135 0 TTATTAGCAA 0.869364 -49 ACTCCTTATCATATAAGATAAAAATAATAA 3 163 0 ATATAAGATA 0.690874 -21 TGATTTAACAATATTAATAAGTTAAGTATT 4 15 0 ATATTAATAA 0.821057 -142 CTTAAAACTTTTTTTAAAAAAAACATTTAA 4 57 1 TTTTTAAAAA 0.458631 -100 AAGAATTAAAATAATAAAAATTGTTAAATG 4 80 0 ATAATAAAAA 0.801619 -77 AACAAAGTTAATATCAAGAATTAAAATAAT 4 95 0 ATATCAAGAA 0.595408 -62 TAAAGTATAAATATTAACAAAGTTAATATC 4 110 0 ATATTAACAA 0.957332 -47 AGTTATAAATTTATAAAAAACACCCT 9 7 0 TTATAAAAAA 0.723993 -86 AGCAAAAAATATATTAAATATTTTAACAAG 9 35 0 ATATTAAATA 0.923107 -58 TAATATATTGATTTTAGCAAAAAATATATT 9 50 0 ATTTTAGCAA 0.796714 -43 TAAAATCAATATATTAGATAGCTGATAAAT 9 64 1 ATATTAGATA 0.916262 -29 ********** Masking position 6 Map Score: 16.2631 Number of sites scoring better than the average of aligned sites = 1454 Number in coding regions = 922 Number in noncoding regions = 532 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 ********** No masking Map Score: 1.57984e-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: 1.57984e-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 9 ********** No masking Map Score: 1.57984e-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