AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_bbur_reg_100.orf -o00970_bbur_100.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 BB0595 21 B. burgdorferi predicted coding region BB0595 BB0834 22 ATP-dependent Clp protease, subunit C (clpC) Input sequences: #1 BB0006 24 conserved hypothetical integral membrane protein #2 BB0007 96 B. burgdorferi predicted coding region BB0007 #3 BB0067 114 peptidase, putative #4 BB0101 156 asparaginyl-tRNA synthetase (asnS) #5 BB0135 129 histidyl-tRNA synthetase (hisS) #6 BB0224 68 B. burgdorferi predicted coding region BB0224 #7 BB0226 129 seryl-tRNA synthetase (serS) #8 BB0251 202 leucyl-tRNA synthetase (leuS) #9 BB0373 124 B. burgdorferi predicted coding region BB0373 #10 BB0402 52 prolyl-tRNA synthetase (proS) #11 BB0403 165 B. burgdorferi predicted coding region BB0403 #12 BB0446 243 aspartyl-tRNA synthetase (aspS) #13 BB0508 77 GTP-binding protein #14 BB0511 91 B. burgdorferi predicted coding region BB0511 #15 BB0587 154 methionyl-tRNA synthetase (metG) #16 BB0596 268 methyl-accepting chemotaxis protein (mcp-2) #17 BB0599 51 cysteinyl-tRNA synthetase (cysS) #18 BB0659 86 lysyl-tRNA synthetase #19 BB0660 89 GTP-binding protein (era) #20 BB0720 165 threonyl-tRNA synthetase (thrZ) #21 BB0735 66 rare lipoprotein A (rlpA) #22 BB0835 114 phosphomannomutase (cpsG) Motif number 1 TGCTTATTTATATATTTTATATTATACTAATATA 2 36 0 TATATTATTA 0.879179 -61 ACAATTTAATTTAATAATTACAAACTGTGCTTAT 2 63 0 TTAATTTAAA 0.652529 -34 ATTATTAAATTAAATTGTTTTTGAATTT 2 79 1 TAAATTTTTA 0.886395 -18 AATTTCAAGCTAAATTATATCAAATAATTTTTTT 3 30 1 TAAATTATAA 0.796374 -85 TATCAAATAATTTTTTTTTTTTAAATTGATAATT 3 47 1 TTTTTTTTTA 0.794194 -68 AAGTAAAGTATAAATATTAACAAAGTTAATATCA 4 35 1 TAAATTAAAA 0.748209 -122 CATTTAACAATTTTTATTATTTTAATTCTTGATA 4 64 0 TTTTTTATTA 0.745645 -93 TTGTTAAATGTTTTTTTTAAAAAAAGTTTTAAGC 4 88 1 TTTTTTAAAA 0.590762 -69 AGCTATAATAAAATTGATTTAACAATATTAATAA 4 119 1 AAATTTTTAA 0.534815 -38 TGATTTAACAATATTAATAAGTTAAGTATTTAGG 4 133 1 ATATTTAATA 0.347603 -24 TGGACCTCTTAAATTATTTTATGACTATATGAAA 5 17 1 AAATTTTTTA 0.635242 -113 AAATGAATAATTTTTTATTTCATATAGTCATAAA 5 34 0 TTTTTTTTAA 0.718026 -96 TCTATATTATTATATGTTATTATATTCTGAAAAA 5 77 1 TATATTATAA 0.827772 -53 TACCCTCTGCTATATAGTAATTTACTTTTTCAGA 5 102 0 TATATTAATA 0.830051 -28 TATATAATATGTTAGAATAAACGA 6 1 1 TATATTATTA 0.879065 -68 AAAGAATAAATAATTGTTAAATCAGCTCGTTTAT 6 27 0 TAATTTAATA 0.773899 -42 TTAACAATTATTTATTCTTTTTTAGGAGGAATTG 6 41 1 TTTATTTTTA 0.835451 -28 TTAAGGTTATTATATAATATCTTATAACAGGATT 7 41 0 TATATTATTA 0.879065 -89 AATATGAATTAATATTATTTGTAATTTTGTTTAA 7 73 1 AATATTTTTA 0.737856 -57 TGTCTTAAGTAAAATTTTTAAACAAAATTACAAA 7 90 0 AAAATTTAAA 0.534815 -40 TGCATTTTTGTTAATTTTATTTAATAATTTGCTA 8 125 0 TTAATTATTA 0.758579 -78 CTTATTCTCTAATATTCTTTTAGATTGCATTTTT 8 150 0 AATATTTTAA 0.650121 -53 AGACAATTAATAAATAATATGATATACATGGTTA 9 36 0 TAAATTATAA 0.796203 -89 TAATAAATACATTATACTAATAGATAGACAATTA 9 61 0 ATTATTAAAA 0.362543 -64 GTATAATGTATTTATTATATCTCAATTTTTGAAT 9 78 1 TTTATTATTA 0.794229 -47 ATATAATTATTTAGTTTTTTAAAGAAGTGAA 10 8 1 TATTTTTTTA 0.879138 -45 TTTGATATACTATTTGTTTATAGATTAAAAACTT 11 37 0 TATTTTTAAA 0.785036 -129 AGCCTTACTTAAAATAATATCAAAACAGCATTTC 11 82 0 AAAATTATAA 0.534815 -84 TAAGGCTAAATTAATTATAAATAAGATTTAGTAG 11 109 1 TTAATTAATA 0.467515 -57 TAGTAGATAATTTATTGTTATTAAACTTATACAA 11 137 1 TTTATTTATA 0.787697 -29 TAAATACTAATATTTGCTATTATAATGGAAATAT 13 27 1 TATTTTATAA 0.785037 -51 TTGACTATAATATATTTTATTTAACAAAAAAGCA 14 31 0 TATATTATTA 0.879196 -61 AATGATATAAATATTCTTTTATTATAAGGAGTGT 15 17 0 ATATTTTTTA 0.480054 -138 AAAGAATATTTATATCATTTTTTACAAAAAAGCC 15 32 1 TATATTTTTA 0.905323 -123 ATCTTTTACAAAAATTCTTTCAAAAGCAATTCAA 15 70 0 AAAATTTTAA 0.602081 -85 TAGTATGATTAAAATCTTAAAACAAAACTTTCAC 16 34 1 AAAATTAAAA 0.466259 -235 TAATTATTTATATATGATTTATGAAGGTGAAAGT 16 60 0 TATATTTTTA 0.905497 -209 AAATCATATATAAATAATTACTAATAACAATTGG 16 74 1 TAAATTTATA 0.832134 -195 TGCAAATAATTATTTTATTATTTAGCTACATGCA 16 158 1 TATTTTTATA 0.510438 -111 CATGTTTTATTATATAATTATATATGCATGTAGC 16 182 0 TATATTTAAA 0.485169 -87 TACTAAAAATTTAATGTTTTAAAAATTTTATGAA 16 221 1 TTAATTTTAA 0.731954 -48 TCTCCTCAAAATTTTGTTTTTTCATAAAATTTTT 16 241 0 ATTTTTTTTA 0.531359 -28 ATAAAAAATCTAATTTATTATTAAGTACGT 17 7 0 TAATTTTATA 0.508446 -45 TAAATTAGATTTTTTATTTTTTCAATTTTGAGAA 17 24 1 TTTTTTTTTA 0.794229 -28 ATTTTATTCCTAATTTAAATTTAGGTA 18 70 0 TTATTTAATA 0.644522 -17 TTTTAAATACTTATTTTTAAGTAAAAT 19 4 0 TTATTTAATA 0.644635 -86 TTTAAAATACTATATAATTAATTATAATAAAAAA 19 31 1 TATATTTATA 0.523791 -59 GTAATATTCATATATTTTTTATTATAATTAATTA 19 45 0 TATATTTTTA 0.905441 -45 TATTTTCAGGTTTTTGTTTTCTTATCTCTATTTT 20 16 1 TTTTTTTTTA 0.79423 -150 TTCTTATCTCTATTTTTTTAGAAAATTTTTTTGT 20 34 1 TATTTTTAAA 0.784962 -132 AATTTTTTTGTATATTTTAATTTAGTAATTATAA 20 57 1 TATATTAATA 0.833965 -109 GTGTGAATTTTAATTTTTTAATAAAAAGCGAAAG 20 127 1 TAATTTTATA 0.810609 -39 TTTTTAGACTTTTTTCTTTTTATAATTAAATCAA 21 11 1 TTTTTTTTAA 0.718154 -56 TTAAGCTTGCAAATTGCTTATTTACATTTTTTTT 21 43 0 AAATTTTATA 0.569573 -24 CACATTCTTATAAATTATATGATAATAAATTCTA 22 20 1 TAAATTATAA 0.796272 -95 TATATGATAATAAATTCTATATCAAGTATATAAT 22 35 1 TAAATTATTA 0.855669 -80 ATCAAGTATATAATTCATTATAAATCAATATAAT 22 55 1 TAATTTTAAA 0.723551 -60 TATTTCCTTTTATTTTATTAAACAAAGATTAATT 22 91 0 TATTTTTAAA 0.768267 -24 ***** *** * * Masking position 8 Map Score: 63.4099 Number of sites scoring better than the average of aligned sites = 3370 Number in coding regions = 1934 Number in noncoding regions = 1436 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 TTAAAAAAAAAAAATTATTTGATATAATTTA 3 40 0 AAAATATTTG 0.823975 -75 TTTTAAATTGATAATTATTTGGTATACTAAT 3 65 1 ATAATATTTG 0.919093 -50 ATATTTATACTTTACTTTTTAGGGGTGATTA 4 21 0 TTTATTTTTA 0.823195 -136 TATTAATAAGTTAAGTATTTAGG 4 144 1 TTAATATTTA 0.945388 -13 AAAAAAATGAATAATTTTTTATTTCATATAG 5 41 0 ATAATTTTTA 0.908322 -89 AGCTGATTTAACAATTATTTATTCTTTTTTA 6 34 1 ACAATATTTA 0.867899 -35 AATATGAATTAATATTATTTGTAATTTTGTT 7 73 1 AATATATTTG 0.651471 -57 ATGTCTTAAGTAAAATTTTTAAACAAAATTA 7 94 0 TAAATTTTTA 0.784654 -36 ATATAATTATTTAGTTTTTTAAA 10 3 1 ATAATATTTA 0.936351 -50 AACTTAATATTTAAATTTTTGGGATAAATTT 11 11 0 TTAATTTTTG 0.900012 -155 AATTTAAATATTAAGTTTTTAATCTATAAAC 11 25 1 TTAATTTTTA 0.921004 -141 AAAACTTTGATATACTATTTGTTTATAGATT 11 45 0 TATATATTTG 0.687475 -121 AATAGCAAATATTAGTATTTATGCCAATTAC 13 17 0 ATTATATTTA 0.854546 -61 TATATTATAGTCAAATTTTTAGCGATAAGTT 14 51 1 TCAATTTTTA 0.838299 -41 TTTTAATCATACTAATATTTATGTTTGGAGA 16 17 0 ACTATATTTA 0.724012 -252 ATTGTTATTAGTAATTATTTATATATGATTT 16 74 0 GTAATATTTA 0.716397 -195 ATTAAATCCTTCAAATATTTGCAAATAATTA 16 139 1 TCAATATTTG 0.856503 -130 AAATAATAAAATAATTATTTGCAAATATTTG 16 150 0 ATAATATTTG 0.919093 -119 AAATAATTATTTTATTATTTAGCTACATGCA 16 161 1 TTTATATTTA 0.873629 -108 TTTTAAAACATTAAATTTTTAGTATTCTACA 16 214 0 TTAATTTTTA 0.920361 -55 TGTTTTTTCATAAAATTTTTAAAACATTAAA 16 230 0 TAAATTTTTA 0.784654 -39 TTACTTAAAAATAAGTATTTAAAATACTATA 19 14 1 ATAATATTTA 0.936369 -76 GTAATATTCATATATTTTTTATTATAATTAA 19 48 0 TATATTTTTA 0.656708 -42 TTTAGTAATTATAAATATTTGAGGTGCGTAT 20 77 1 ATAATATTTG 0.919093 -89 AGTGTGAATTTTAATTTTTTAATAAAAAGCG 20 126 1 TTAATTTTTA 0.92004 -40 **** ****** Masking position 6 Map Score: 31.0672 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 579 Number in noncoding regions = 418 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 3 ACTGTGCTTATTTATATATTTTATATTATACTAA 2 40 0 TTATATTTTT 0.72937 -57 AAAAAAACATTTAACAATTTTTATTATTTTAATT 4 71 0 TTAATTTTTT 0.739645 -86 TTATTATAGCTTAAAACTTTTTTTAAAAAAAACA 4 96 0 TTACTTTTTT 0.70493 -61 AAATAAAAAATTATTCATTTTTTTTTGCATCTAT 5 48 1 TTCATTTTTT 0.834256 -82 TAACAATTATTTATTCTTTTTTAGGAGGAATTGT 6 42 1 TTCTTTTTTG 0.817352 -27 TTAATATTATTTGTAATTTTGTTTAAAAATTTTA 7 81 1 TTATTTTGTT 0.814699 -49 AATTTTTGAATTAAGCTTTTTTGAAGAGATTTTT 9 101 1 TTCTTTTTTA 0.884111 -24 AAGCATTTATTTCAACTTTTTTGTCTATCAATTT 12 50 0 TTCTTTTTTT 0.975548 -194 TTTCCGTGGTGTCTAATTTTTTTTACCCAAGCAT 12 78 0 GTATTTTTTT 0.864942 -166 TTACCAGAACTTGAGCTTTTTCATATCTGTCTCT 12 131 0 TTCTTTTTCT 0.80046 -113 CAATATTCAAGTTTTATTTTTTCTGCGATCTTTA 12 180 0 GTATTTTTTT 0.864942 -64 ATGAGAATCGGTGTGCTTTTTTGTTAAATAAAAT 14 18 1 GTCTTTTTTT 0.918969 -74 GCAATTCAATTTTGGCTTTTTTGTAAAAAATGAT 15 45 0 TTCTTTTTTT 0.975548 -110 TCAGTTTTCCCTTTTTTTATGCTATTAAT 15 136 0 TTCTTTTTTA 0.884112 -19 AATTGGCAAATTAGACTTTTCTTTCTAAATCTTA 16 102 1 TTCTTTTCTT 0.808818 -167 TAAATTAGATTTTTTATTTTTTCAATTTTGAGAA 17 24 1 TTATTTTTTA 0.811609 -28 TAGGTAAATTTTAGCATTTTGTTTTTCAAGTTTC 18 42 0 TTATTTTGTT 0.814699 -45 ATATGTAATATTCATATATTTTTTATTATAATTA 19 49 0 TTATATTTTT 0.729377 -41 ACCTTTTGCCTTTCGCTTTTTATTAAAAAATTAA 20 136 0 TTCTTTTTAT 0.730212 -30 TTTTTAGACTTTTTTCTTTTTATAATT 21 4 1 TTCTTTTTTT 0.975548 -63 AAATTGCTTATTTACATTTTTTTTGATTTAATTA 21 33 0 TTATTTTTTT 0.957501 -34 ** ******* * Masking position 9 Map Score: 24.9296 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 566 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 CCTTTAGGAGTTAATTTCAAGCTAAATTATA 3 18 1 TTATTTCAAG 0.971558 -97 ATTAACAAAGTTAATATCAAGAATTAAAATA 4 50 1 TTATATCAAG 0.82778 -107 TGTTATGAGTTAATTTTCAAGAGGACAA 8 185 1 TAATTTCAAG 0.971558 -18 TTAATAGAGCTTAATTTCAAGGGAATAA 9 8 0 TTATTTCAAG 0.971558 -117 AATTTTAATGCAATATTCAAGTTTTATTTTT 12 193 0 CAAATTCAAG 0.871148 -51 AATATTGCATTAAAATTCAAGGACTGTTGAT 12 207 1 TAAATTCAAG 0.904721 -37 TTTTGTTTTTCAAGTTTCAAGAATTTAAAAA 18 29 0 CAATTTCAAG 0.960507 -58 TTTTAAATACTTATTTTTAAGTAAAAT 19 7 0 TTATTTTAAG 0.749021 -83 AAATTTATTTTCAGGTTTTTGTTTT 20 5 1 TTATTTCAGG 0.876906 -161 TGTAAATAAGCAATTTGCAAGCTTAA 21 51 1 CAATTGCAAG 0.835315 -16 *** ******* Masking position 3 Map Score: 8.22653 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 74 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 CTGTGCTTATTTATATATTTTATATTATACTAAT 2 39 0 TTTTTTTATA 0.735836 -58 TAAGCACAGTTTGTAATTATTAAATTAAATTGTT 2 64 1 TTTATATAAA 0.434389 -33 ATCAAATAATTTTTTTTTTTTAAATTGATAATTA 3 48 1 TTTTTTTAAA 0.880132 -67 TTTTTATTATTTTAATTCTTGATATTAACTTTGT 4 54 0 TTATCTTATA 0.876471 -103 AAATTGTTAAATGTTTTTTTTAAAAAAAGTTTTA 4 85 1 ATTTTTTAAA 0.511106 -72 AATCAATTTTATTATAGCTTAAAACTTTTTTTAA 4 104 0 ATAACTTAAA 0.590307 -53 AAATGAATAATTTTTTATTTCATATAGTCATAAA 5 34 0 TTTTTTTATA 0.735941 -96 TTATATGTTATTATATTCTGAAAAAGTAAATTAC 5 86 1 TTTTCTGAAA 0.514963 -44 TCAAGTCCAGTTCACAGCATCAAAATTGTTAGCA 8 96 1 TTAACATAAA 0.662555 -107 TTGTCCTCTTGAAAATTAACTCAT 8 189 0 TTTCCTTAAA 0.824784 -14 TTATTCCCTTGAAATTAAGCTCTA 9 1 1 TTTCCTTAAA 0.824784 -124 AATAAAGCATTTCACTTCTTTAAAAAACTAAATA 10 18 0 TTATCTTAAA 0.949328 -35 TGTTTATAGATTAAAAACTTAATATTTAAATTTT 11 23 0 TTAACTTATA 0.793434 -143 TATATCAAAGTTTTGAATTTGAAATGCTGTTTTG 11 62 1 TTTATTTAAA 0.798774 -104 TTCATTACATTTGATAACTTTAAACATAAC 12 7 0 TTAACTTAAA 0.909795 -237 GATATGGCTTGAGTTTTTTAAACTTATCGCTA 14 70 0 TTATTTTAAA 0.908806 -22 TATTACAATATTAATAGCATAAAAAAAGGGAAAA 15 127 1 TTAACATAAA 0.661464 -28 ATTAGTATGATTAAAATCTTAAAACAAAACTTTC 16 32 1 TTAACTTAAA 0.909428 -237 ATCTTAAAGATTAAATCCTTCAAATATTTGCAAA 16 130 1 TTATCTTAAA 0.949345 -139 ATACTAAAAATTTAATGTTTTAAAAATTTTATGA 16 220 1 TTATTTTAAA 0.560491 -49 CTGCATTTTTTTAAATTCTTGAAACTTGAAAAAC 18 22 1 TTATCTTAAA 0.949345 -65 TTACTTAAAAATAAGTATTTAAAATACTATATAA 19 14 1 ATATTTTAAA 0.58595 -76 AGTGTGAATTTTAATTTTTTAATAAAAAGCGAAA 20 126 1 TTATTTTATA 0.790478 -40 TTTTTAGACTTTTTTCTTTTTATAATTAAATCAA 21 11 1 TTTCTTTATA 0.486516 -56 TTATAATGAATTATATACTTGATATAGAATTTAT 22 44 0 TTTTCTTATA 0.839787 -71 TATTTCCTTTTATTTTATTAAACAAAGATTAA 22 93 0 TTATTATAAA 0.657766 -22 ** * * *** *** Masking position 2 Map Score: 28.0981 Number of sites scoring better than the average of aligned sites = 1487 Number in coding regions = 996 Number in noncoding regions = 491 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 ATTCAAAAACAATTTAATTTAATAATTACA 2 75 0 AATTTAATTT 0.554762 -22 AGTTAATTTCAAGCTAAATTATATCAAATA 3 26 1 AAGCTAAATT 0.849828 -89 ATATAGTCATAAAATAATTTAAGAGGTCCA 5 17 0 AAAATAATTT 0.48111 -113 AATTACAAATAATATTAATTCATATTAAGG 7 69 0 AATATTAATT 0.731545 -61 CATTTTTGTTAATTTTATTTAATAATTTGC 8 127 0 AATTTTATTT 0.657567 -76 CTCTTCAAAAAAGCTTAATTCAAAAATTGA 9 99 0 AAGCTTAATT 0.787216 -26 TGCTTTATTGAGGATAATTT 10 43 1 AGGATAATTT 0.664372 -10 ATTTTAAGTAAGGCTAAATTAATTATAAAT 11 101 1 AGGCTAAATT 0.732235 -65 TTATCTACTAAATCTTATTTATAATTAATT 11 117 0 AATCTTATTT 0.790519 -49 TATATTTAGAAAGATAAATTTTCCGTGGTG 12 101 0 AAGATAAATT 0.804194 -143 GCAATATTCAAGTTTTATTTTTTCTGCGAT 12 185 0 AGTTTTATTT 0.486756 -59 TAGAAAGAAAAGTCTAATTTGCCAATTGTT 16 99 0 AGTCTAATTT 0.736136 -170 AAAAATAAAAAATCTAATTTATTATTAAGT 17 15 0 AATCTAATTT 0.844183 -37 AATTTACCTAAATTTAAATTAGGAATAAAA 18 66 1 AATTTAAATT 0.469855 -21 CAAAAACCTGAAAATAAATTT 20 2 0 AAAATAAATT 0.464745 -164 GATGAGTGTGAATTTTAATTTTTTAATAAA 20 122 1 AATTTTAATT 0.634487 -44 ATTATAAATCAATATAATTTAATTAATCTT 22 71 1 AATATAATTT 0.799607 -44 TTATTAAACAAAGATTAATTAAATTATATT 22 81 0 AAGATTAATT 0.728103 -34 ********** Masking position 5 Map Score: 13.0283 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 506 Number in noncoding regions = 319 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 TATTAACCTATATTAGTATAATATAAAATA 2 28 1 TATTAGTATA 0.916578 -69 ACCTTACTAATATTAGTATACCAAATAATT 3 77 0 TATTAGTATA 0.916578 -38 ATTTAACAATTTTTATTATTTTAATTCTTG 4 67 0 TTTTATTATT 0.870981 -90 GTTAAATCAATTTTATTATAGCTTAAAACT 4 112 0 TTTTATTATA 0.928999 -45 ATACTTAACTTATTAATATTGTTAAATCAA 4 132 0 TATTAATATT 0.393674 -25 TTTGCATCTATATTATTATATGTTATTATA 5 71 1 TATTATTATA 0.883692 -59 TATTATTATATGTTATTATATTCTGAAAAA 5 81 1 TGTTATTATA 0.59832 -49 ATTGTCTATCTATTAGTATAATGTATTTAT 9 63 1 TATTAGTATA 0.916578 -62 AGTATAATGTATTTATTATATCTCAATTTT 9 77 1 ATTTATTATA 0.388957 -48 TAATAGCAAATATTAGTATTTATGCCAATT 13 19 0 TATTAGTATT 0.848266 -59 ATAAATATTCTTTTATTATAAGGAGTGTGA 15 15 0 TTTTATTATA 0.928999 -140 AATTTTGGCTTTTTTGTAAAAAATGATATA 15 42 0 TTTTTGTAAA 0.427115 -113 TTTGAAAGAATTTTTGTAAAAGATATTGAA 15 80 1 TTTTTGTAAA 0.427115 -75 TTTTTTATGCTATTAATATTGTAATATGGA 15 123 0 TATTAATATT 0.393674 -32 CAAACATAAATATTAGTATGATTAAAATCT 16 21 1 TATTAGTATG 0.538299 -248 TGCCAATTGTTATTAGTAATTATTTATATA 16 80 0 TATTAGTAAT 0.560153 -189 CAAATAATTATTTTATTATTTAGCTACATG 16 160 1 TTTTATTATT 0.870981 -109 ATTCTACATGTTTTATTATATAATTATATA 16 192 0 TTTTATTATA 0.928999 -77 AACATTAAATTTTTAGTATTCTACATGTTT 16 209 0 TTTTAGTATT 0.903719 -60 CAAAATTTTGTTTTTTCATAAAATTTTTAA 16 239 0 TTTTTTCATA 0.326242 -30 TTTAGGTAAATTTTAGCATTTTGTTTTTCA 18 48 0 TTTTAGCATT 0.658727 -39 TTCATATATTTTTTATTATAATTAATTATA 19 43 0 TTTTATTATA 0.928999 -47 GTTTTAGTATTCCTTAAATAT 19 79 0 TTTTAGTATT 0.903719 -11 TTAGAAAATTTTTTTGTATATTTTAATTTA 20 51 1 TTTTTGTATA 0.765963 -115 GCCTTTCGCTTTTTATTAAAAAATTAAAAT 20 133 0 TTTTATTAAA 0.750261 -33 TTTTTTTTGATTTAATTATAAAAAGAAAAA 21 21 0 TTTAATTATA 0.363459 -46 ATATAGAATTTATTATCATATAATTTATAA 22 27 0 TATTATCATA 0.618628 -88 TTTCCTTTTATTTTATTAAACAAAGATTAA 22 93 0 TTTTATTAAA 0.750261 -22 ********** Masking position 3 Map Score: 32.5717 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 449 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 8 AAATTCAAAAACAATTTAATTTAATAATT 2 78 0 AAAAACTTAA 0.80749 -19 AAGCTATAATAAAATTGATTTAACAATATTAAT 4 118 1 AAAATTTTAA 0.561141 -39 AAATTAACAAAAATGCAATCTAAAAGAATATTA 8 142 1 AAATGCTCAA 0.802935 -61 AAAAATCTCTTCAAAAAAGCTTAA 9 111 0 AAAATCTTAA 0.880903 -14 ATAATATCAAAACAGCATTTCAAATTCAAAACT 11 70 0 AACAGCTTAA 0.942599 -96 GTAAATGAAGAAAAGCTTCTAAAGATCGCAGAA 12 161 1 AAAAGCCTAA 0.889595 -83 TCTTTTGATCAACAGTCCTTGAATTTTAATGCA 12 212 0 AACAGTTTAA 0.739499 -32 AAATTCTTTCAAAAGCAATTCAATTTTGGCTTT 15 60 0 AAAAGCTTAA 0.977162 -95 GAATTTTTGTAAAAGATATTGAAAAAAAATATC 15 87 1 AAAAGATTAA 0.807491 -68 AAAAGCTCTCCAAACATAAATAT 16 1 1 AAAAGCTCAA 0.942599 -268 GAATTTAAAAAAATGCAGTTTAATGTTTG 18 7 0 AAATGCTTAA 0.913913 -80 ****** ** ** Masking position 2 Map Score: 4.72665 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 258 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAAAAATTATTTGATATAATTTAGCTTGAAA 3 32 0 TTGAATAATT 0.735577 -83 ATATAATATGTTAGAATAAACGAGCTGATTT 6 12 1 TTAGATAAAC 0.706963 -57 TATAACAGGATTAGAATAAATATTGCAGGGA 7 22 0 TTAGATAAAT 0.900825 -108 ATTTAAATTTTTGGGATAAATTT 11 3 0 TTGGATAAAT 0.975437 -163 GACAAAAAAGTTGAAATAAATGCTTGGGTAA 12 59 1 TTGAATAAAT 0.939478 -185 TCATGTGTAATTGGCATAAATACTAATATTT 13 11 1 TTGGATAAAT 0.975437 -67 AATGGAAATATCGGAATAAATAAAGAGGTGT 13 50 1 TCGGATAAAT 0.913403 -28 TTTGTAAAAAATGATATAAATATTCTTTTAT 15 29 0 ATGAATAAAT 0.735577 -126 **** ****** Masking position 6 Map Score: 2.33246 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 81 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ACCAAATAATTATCAATTTAAAAAAAAAAA 3 58 0 TATCAATTTA 0.677704 -57 AAAAAACATTTAACAATTTTTATTATTTTA 4 74 0 TAACAATTTT 0.800357 -83 AATATTGTTAAATCAATTTTATTATAGCTT 4 118 0 AATCAATTTT 0.800362 -39 AATAATTTGCTAACAATTTTGATGCTGTGA 8 107 0 TAACAATTTT 0.800357 -96 ATTTATTATATCTCAATTTTTGAATTAAGC 9 87 1 TCTCAATTTT 0.923653 -38 AAACTTAATATTTAAATTTTTGGGATAAAT 11 13 0 TTTAAATTTT 0.584578 -153 CTTTTTTGTCTATCAATTTTTCATTCAATT 12 39 0 TATCAATTTT 0.955286 -205 CAAGCATTTATTTCAACTTTTTTGTCTATC 12 55 0 TTTCAACTTT 0.771151 -189 AGAATATTTATATCATTTTTTACAAAAAAG 15 34 1 TATCATTTTT 0.677703 -121 TTCAAAAGCAATTCAATTTTGGCTTTTTTG 15 56 0 ATTCAATTTT 0.800363 -99 TTTTTTATTTTTTCAATTTTGAGAAATGT 17 33 1 TTTCAATTTT 0.955286 -19 GCATTTTGTTTTTCAAGTTTCAAGAATTTA 18 33 0 TTTCAAGTTT 0.771151 -54 TGTTTTCTTATCTCTATTTTTTTAGAAAAT 20 30 1 TCTCTATTTT 0.543529 -136 TGAGTGTGAATTTTAATTTTTTAATAAAAA 20 124 1 TTTTAATTTT 0.584578 -42 ********** Masking position 8 Map Score: 9.56603 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 131 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TATACTAATATAGGTTAATAAGTACAGTGT 2 18 0 TAGGTTAATA 0.914862 -79 TAACCTATATTAGTATAATATAAAATATAT 2 31 1 TAGTATAATA 0.583193 -66 TTAACTCCTAAAGGATAAAAC 3 2 0 AAGGATAAAA 0.643012 -113 AAATATTAACAAAGTTAATATCAAGAATTA 4 46 1 AAAGTTAATA 0.589497 -111 AATTCATATTAAGGTTATTATATAATATCT 7 53 0 AAGGTTATTA 0.698408 -77 ATTTGTAATTTTGTTTAAAAATTTTACTTA 7 89 1 TTGTTTAAAA 0.57023 -41 AAAATATAATGGTTAATAGTGCTGTGGT 8 9 1 ATGGTTAATA 0.914863 -194 TATGATATACATGGTTAATAGAGCTTAATT 9 23 0 ATGGTTAATA 0.914863 -102 AGCTTTGTATAAGTTTAATAACAATAAATT 11 145 0 AAGTTTAATA 0.905503 -21 TTTTAGCGATAAGTTTAAAAAACTCAAGCC 14 67 1 AAGTTTAAAA 0.792393 -25 TAATTAATCTTTGTTTAATAAAATAAAAGG 22 90 1 TTGTTTAATA 0.769107 -25 ********** Masking position 7 Map Score: 3.94827 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 144 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ********** No masking Map Score: -4.72978e-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 13 ********** No masking Map Score: -4.72978e-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 14 ********** No masking Map Score: -4.72978e-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