AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -intrC_bbur_opreg_100.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 BB0068 114 conserved hypothetical protein #2 BB0074 46 peptide chain release factor 2 (prfB) #3 BB0076 36 cell division protein, putative #4 BB0079 70 B. burgdorferi predicted coding region BB0079 #5 BB0755 191 conserved hypothetical protein #6 BB0767 148 UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (murG) Motif number 1 TTAGTATACCAAATAATTATCAATTTAAAA 1 41 1 AAATAATTAT 0.715583 -74 TCAATTTAAAAAAAAAAAATTATTTGATAT 1 60 1 AAAAAAAAAT 0.965776 -55 TAGCGAGAAATAAAAATGAAAGAAAAA 2 8 1 AAATAAAAAT 0.921855 -39 AAATGAAAGAAAAAATAAATACATTGCTCA 2 24 1 AAAAATAAAT 0.976516 -23 TAAAAAGCTTTAAAATAAAATCAATTTTCA 4 13 1 TAAAATAAAA 0.852198 -58 GTAATTATGCAAAAATAAATGAAACTTTAA 4 46 1 AAAAATAAAT 0.976516 -25 AAAAATTAAAGTTTCATTTA 4 61 0 AAAAATTAAA 0.960576 -10 ATGAATTTAGAAATATTAATAGTAGTCGTT 5 43 0 AAATATTAAT 0.95183 -149 TAAATTCATAAAAAAATAATATAATGTTTA 5 64 1 AAAAAATAAT 0.969769 -128 ACAAAGCAAATAAAATTAATTGACACTTAC 5 149 1 TAAAATTAAT 0.927115 -43 ATTCAATCTTAAAAATTGAATTTAATGGAA 6 18 0 AAAAATTGAA 0.793582 -131 AATATATTATTAAAATAAAATGTGAAAAAA 6 82 1 TAAAATAAAA 0.852198 -67 TAAAATGTGAAAAAATTTATTACAAAGTAA 6 97 1 AAAAATTTAT 0.895557 -52 TTACTCATGAAAACAATAAAGCATTTACTT 6 121 0 AAACAATAAA 0.756777 -28 TTTCATGAGTAAATAAAAAT 6 139 1 AAATAAAAAT 0.921855 -10 ********** Masking position 5 Map Score: 24.0557 Number of sites scoring better than the average of aligned sites = 2595 Number in coding regions = 1671 Number in noncoding regions = 924 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 2 AATTTTTTTTTTTTAAATTGATAATTATTTGGTAT 1 46 0 TTAATTATAT 0.912153 -69 AGGAGTTAATTTCAAGCTAAATTATATCAAATAAT 1 78 0 TTAGTAATTT 0.722949 -37 TTATTTTTTCTTTCATTTTTATTTCTCGCTA 2 7 0 TTATTTATTC 0.783563 -40 TCCTATTTTATTGCAGATTATTAAAT 3 2 0 TTAGTTTTAA 0.937972 -35 TGATTTTATTTTAAAGCTTTTTATA 4 1 0 TTAGTTTTAA 0.937469 -70 ATAATTACTTTTGAAAATTGATTTTATTTTAAAGC 4 19 0 TTAATTATTT 0.938726 -52 AAAAATTAAAGTTTCATTTATTTTTGCATA 4 51 0 TTAGTTATTA 0.98315 -20 AATCAAAATTTTTAAATCCATACATACTGACAAA 5 10 1 TTAATCATAA 0.878182 -182 CTATTAATATTTCTAAATTCATAAAAAAATAATAT 5 51 1 TTAATTATAA 0.961269 -141 ATAAGAATTATTTTAGCTTAACTTAAACATTATAT 5 82 0 TTAGTTACTA 0.895358 -110 ATTTGCTTTGTTAAATCTTGTTTCACTCTTAGTTT 5 125 0 TTATTTTTTA 0.879886 -67 ATTTAAATTCCATTAAATTCAATTTT 6 2 1 TTAATCATTA 0.913468 -147 AAATTCAATTTTTAAGATTGAATCAATTTCTTGGT 6 25 1 TTAGTTAATA 0.852354 -124 TTTTTTCACATTTTATTTTAATAATATATTGCAAT 6 77 0 TTATTTATAT 0.844885 -72 ATTTACTTTGTAATAAATTTTTTCACATTTTATTT 6 94 0 TAAATTTTTA 0.560773 -55 ** ** ** *** * Masking position 5 Map Score: 11.8891 Number of sites scoring better than the average of aligned sites = 1720 Number in coding regions = 1109 Number in noncoding regions = 611 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 ATATTAGTATACCAAATAATTATCAATTTAA 1 38 1 ACCAAAAATT 0.947731 -77 ATCAATTTAAAAAAAAAAAATTATTTGATAT 1 59 1 AAAAAAAAAT 0.952394 -56 AAAATGAAAGAAAAAATAAATACATTGCTCA 2 23 1 AAAAAAAAAT 0.952394 -24 ACAAGATTTAACAAAGCAAATAAAATTAATT 5 139 1 ACAAAGAAAT 0.992844 -53 ATTGACACTTACAAAACAAACCAGGAGAATA 5 167 1 ACAAAAAAAC 0.958731 -25 TTTCCTTTGTACCAAGAAATTGATTCAATCT 6 39 0 ACCAAGAATT 0.966398 -110 ATTTCTTGGTACAAAGGAAATACTGATATTG 6 50 1 ACAAAGAAAT 0.992844 -99 AAAATTTATTACAAAGTAAATGCTTTATTGT 6 108 1 ACAAAGAAAT 0.992844 -41 ****** **** Masking position 5 Map Score: 14.1209 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 120 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TTTTAAATTGATAATTATTTGGTATACTAA 1 41 0 ATAATTATTT 0.779331 -74 TTAAAAAAAAAAAATTATTTGATATAATTT 1 65 1 AAAATTATTT 0.964629 -50 AATTTCAAGCTAAATTATATCAAATAATTT 1 76 0 TAAATTATAT 0.654059 -39 GATTTTATTTTAAAGCTTTTTATA 4 5 0 TAAAGCTTTT 0.613378 -66 GCTTTAAAATAAAATCAATTTTCAAAAGTA 4 19 1 AAAATCAATT 0.959557 -52 ATCAATTTTCAAAAGTAATTATGCAAAAAT 4 32 1 AAAAGTAATT 0.921945 -39 ACTTAAACATTATATTATTTTTTTATGAAT 5 67 0 TATATTATTT 0.654051 -125 TCTTTGGATAAGAATTATTTTAGCTTAACT 5 94 0 AGAATTATTT 0.905965 -98 CAAAGCAAATAAAATTAATTGACACTTACA 5 150 1 AAAATTAATT 0.959932 -42 AAATTCCATTAAATTCAATTTTTAAGATTG 6 15 1 AAATTCAATT 0.7182 -134 TTTTTAAGATTGAATCAATTTCTTGGTACA 6 33 1 TGAATCAATT 0.84414 -116 AAAATGTGAAAAAATTTATTACAAAGTAAA 6 98 1 AAAATTTATT 0.830003 -51 ATGAAAACAATAAAGCATTTACTTTGTAAT 6 115 0 TAAAGCATTT 0.894947 -34 ********** Masking position 10 Map Score: 12.8558 Number of sites scoring better than the average of aligned sites = 1417 Number in coding regions = 903 Number in noncoding regions = 514 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 5 AGAAAAAATAAATACATTGCTCAAAC 2 31 1 AATACATTGC 0.895279 -16 TTGTTCTCCTATTTTATTGCAGATTATTAA 3 13 0 ATTTTATTGC 0.931248 -24 AATTGATTTTATTTTAAAGCTTTTTATA 4 9 0 ATTTTAAAGC 0.591501 -62 ATAAAAAAATAATATAATGTTTAAGTTAAG 5 71 1 AATATAATGT 0.860996 -121 AAGCAAATAAAATTAATTGACACTTACAAA 5 152 1 AATTAATTGA 0.762264 -40 TTAAAAATTGAATTTAATGGAATTTAAAT 6 10 0 AATTTAATGG 0.94204 -139 AGATTGAATCAATTTCTTGGTACAAAGGAA 6 39 1 AATTTCTTGG 0.784356 -110 TTATTTTAATAATATATTGCAATATCAGTA 6 70 0 AATATATTGC 0.969868 -79 ATATTATTAAAATAAAATGTGAAAAAATTT 6 85 1 AATAAAATGT 0.737206 -64 AATGTGAAAAAATTTATTACAAAGTAAATG 6 100 1 AATTTATTAC 0.81137 -49 ATTTATTACAAAGTAAATGCTTTATTGTTT 6 111 1 AAGTAAATGC 0.796641 -38 ********** Masking position 1 Map Score: 4.84848 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 674 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 ********** No masking Map Score: -5.51791e-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: -5.51791e-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 8 ********** No masking Map Score: -5.51791e-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