AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_bbur_reg_300.orf -o00970_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 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 BB0247 196 conserved hypothetical protein #9 BB0248 119 oligoendopeptidase F (pepF) #10 BB0251 202 leucyl-tRNA synthetase (leuS) #11 BB0373 124 B. burgdorferi predicted coding region BB0373 #12 BB0402 52 prolyl-tRNA synthetase (proS) #13 BB0403 165 B. burgdorferi predicted coding region BB0403 #14 BB0446 243 aspartyl-tRNA synthetase (aspS) #15 BB0452 90 B. burgdorferi predicted coding region BB0452 #16 BB0508 77 GTP-binding protein #17 BB0511 91 B. burgdorferi predicted coding region BB0511 #18 BB0587 154 methionyl-tRNA synthetase (metG) #19 BB0596 268 methyl-accepting chemotaxis protein (mcp-2) #20 BB0599 51 cysteinyl-tRNA synthetase (cysS) #21 BB0659 86 lysyl-tRNA synthetase #22 BB0660 89 GTP-binding protein (era) #23 BB0714 300 B. burgdorferi predicted coding region BB0714 #24 BB0720 165 threonyl-tRNA synthetase (thrZ) #25 BB0735 66 rare lipoprotein A (rlpA) #26 BB0835 114 phosphomannomutase (cpsG) Motif number 1 TATTAACCTATATTAGTATAATATAAAATA 2 28 1 TATTAGTATA 0.861419 -69 AAACTGTGCTTATTTATATATTTTATATTA 2 46 0 TATTTATATA 0.584001 -51 TTCAAAAACAATTTAATTTAATAATTACAA 2 74 0 ATTTAATTTA 0.56524 -23 CAAATAATTTTTTTTTTTTAAATTGATAAT 3 50 1 TTTTTTTTTA 0.882516 -65 ACCTTACTAATATTAGTATACCAAATAATT 3 77 0 TATTAGTATA 0.861419 -38 ATTTAACAATTTTTATTATTTTAATTCTTG 4 67 0 TTTTATTATT 0.882009 -90 TGTTAAATGTTTTTTTTAAAAAAAGTTTTA 4 89 1 TTTTTTTAAA 0.631845 -68 GTTAAATCAATTTTATTATAGCTTAAAACT 4 112 0 TTTTATTATA 0.928985 -45 ATACTTAACTTATTAATATTGTTAAATCAA 4 132 0 TATTAATATT 0.56616 -25 GGACCTCTTAAATTATTTTATGACTATATG 5 18 1 AATTATTTTA 0.676707 -112 AAAATGAATAATTTTTTATTTCATATAGTC 5 39 0 ATTTTTTATT 0.59734 -91 AAAATTATTCATTTTTTTTTGCATCTATAT 5 54 1 ATTTTTTTTT 0.580819 -76 TTTGCATCTATATTATTATATGTTATTATA 5 71 1 TATTATTATA 0.873873 -59 ATTATTTGTAATTTTGTTTAAAAATTTTAC 7 86 1 ATTTTGTTTA 0.684852 -44 TAAAATAAATTTTTAATTTTCTTGTTTGAT 8 37 0 TTTTAATTTT 0.696909 -160 AAAATTAAAAATTTATTTTAACACCTTAGA 8 47 1 ATTTATTTTA 0.797909 -150 ATAAATACTTTATTATTATATAG 8 184 1 TATTATTATA 0.873873 -13 ACTTAAAGGCTTTTTATATATAAAGTTTAG 9 11 1 TTTTTATATA 0.725893 -109 ACATTGTGCTTTTTATTTTACAATAAAGTC 9 40 0 TTTTATTTTA 0.924389 -80 CTCCTCTTCCTTTTTTTATTGTTTGAAAAG 9 94 0 TTTTTTTATT 0.821219 -26 TTTTTGTTAATTTTATTTAATAATTTGCTA 10 125 0 TTTTATTTAA 0.722923 -78 TTAGATTGCATTTTTGTTAATTTTATTTAA 10 135 0 TTTTTGTTAA 0.589497 -68 ATGTATATCATATTATTTATTAATTGTCTA 11 41 1 TATTATTTAT 0.441352 -84 ATTGTCTATCTATTAGTATAATGTATTTAT 11 63 1 TATTAGTATA 0.861419 -62 AGTATAATGTATTTATTATATCTCAATTTT 11 77 1 ATTTATTATA 0.808674 -48 ATATAATTATTTAGTTTTTTAAAGAAGT 12 9 1 ATTTAGTTTT 0.668882 -44 TTTGATATACTATTTGTTTATAGATTAAAA 13 41 0 TATTTGTTTA 0.781053 -125 GCTGTTTTGATATTATTTTAAGTAAGGCTA 13 87 1 TATTATTTTA 0.866334 -79 TCTTATTTATAATTAATTTAGCCTTACTTA 13 105 0 AATTAATTTA 0.408024 -61 GTGGTGTCTAATTTTTTTTACCCAAGCATT 14 77 0 ATTTTTTTTA 0.70811 -167 AATATTCAAGTTTTATTTTTTCTGCGATCT 14 183 0 TTTTATTTTT 0.87473 -61 GCTATAATTCAATTAATTTATGTAAAGCCC 15 27 0 AATTAATTTA 0.408024 -64 TAATAGCAAATATTAGTATTTATGCCAATT 16 19 0 TATTAGTATT 0.780237 -59 CTATAATATATTTTATTTAACAAAAAAGCA 17 31 0 TTTTATTTAA 0.722923 -61 ATAAATATTCTTTTATTATAAGGAGTGTGA 18 15 0 TTTTATTATA 0.928985 -140 AATTTTGGCTTTTTTGTAAAAAATGATATA 18 42 0 TTTTTGTAAA 0.605909 -113 TTTGAAAGAATTTTTGTAAAAGATATTGAA 18 80 1 TTTTTGTAAA 0.605909 -75 ATGGATAGGATATTTTTTTTCAATATCTTT 18 98 0 TATTTTTTTT 0.694616 -57 TTTTTTATGCTATTAATATTGTAATATGGA 18 123 0 TATTAATATT 0.56616 -32 TATTAGTAATTATTTATATATGATTTATGA 19 70 0 TATTTATATA 0.584001 -199 TGCCAATTGTTATTAGTAATTATTTATATA 19 80 0 TATTAGTAAT 0.431073 -189 CAAATAATTATTTTATTATTTAGCTACATG 19 160 1 TTTTATTATT 0.882009 -109 ATTCTACATGTTTTATTATATAATTATATA 19 192 0 TTTTATTATA 0.928985 -77 AACATTAAATTTTTAGTATTCTACATGTTT 19 209 0 TTTTAGTATT 0.870078 -60 TCTCCTCAAAATTTTGTTTTTTCATAAAAT 19 245 0 ATTTTGTTTT 0.55381 -24 AAAAAATCTAATTTATTATTAAGTACGT 20 9 0 ATTTATTATT 0.707119 -43 AAATTAGATTTTTTATTTTTTCAATTTTGA 20 25 1 TTTTATTTTT 0.87473 -27 TTAAACTGCATTTTTTTAAATTCTTGAAAC 21 17 1 TTTTTTTAAA 0.631845 -70 AAATTTTAGCATTTTGTTTTTCAAGTTTCA 21 41 0 ATTTTGTTTT 0.55381 -46 TTCATATATTTTTTATTATAATTAATTATA 22 43 0 TTTTATTATA 0.928985 -47 GTTTTAGTATTCCTTAAATAT 22 79 0 TTTTAGTATT 0.870078 -11 TCATCTCTCTTATTTTTTTATCGCTAAAAA 23 215 0 TATTTTTTTA 0.799292 -86 TATTTTCAGGTTTTTGTTTTCTTATCTCTA 24 16 1 TTTTTGTTTT 0.793529 -150 TTCTTATCTCTATTTTTTTAGAAAATTTTT 24 34 1 TATTTTTTTA 0.799292 -132 TTAGAAAATTTTTTTGTATATTTTAATTTA 24 51 1 TTTTTGTATA 0.878112 -115 TTTTTGTATATTTTAATTTAGTAATTATAA 24 61 1 TTTTAATTTA 0.801024 -105 GCCTTTCGCTTTTTATTAAAAAATTAAAAT 24 133 0 TTTTATTAAA 0.736328 -33 TATTTCCTTTTATTTTATTAAACAAAG 26 98 0 TTTTATTTTA 0.924389 -17 ********** Masking position 4 Map Score: 56.0139 Number of sites scoring better than the average of aligned sites = 3840 Number in coding regions = 2313 Number in noncoding regions = 1527 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 2 ACAGTTTGTAATTATTAAATTAAATTGTTTTTGAA 2 69 1 ATTATTAAAT 0.836304 -28 ACAAAGTTAATATCAAGAATTAAAATAATAAAAAT 4 54 1 TTAATTAAAA 0.831198 -103 TTTTTTTGCATCTATATTATTATATGTTATTATAT 5 67 1 TTTATTATAT 0.942822 -63 GTTATTATATTCTGAAAAAGTAAATTACTATATAG 5 92 1 TTAAGTAAAT 0.651273 -38 GCTCGTTTATTCTAACATATTATATA 6 2 0 TTAATTATAT 0.958136 -67 CTAATCCTGTTATAAGATATTATATAATAACCTTA 7 39 1 TTAATTATAT 0.958136 -91 TATGAGTTTAATTGTATAATTATATTGGTTTTAAG 8 152 0 ATTATTATAT 0.909301 -45 ACTCATAAATACTTTATTATTATATAG 8 180 1 ATTATTATAT 0.909301 -17 ACCACAGCACTATTAACCATTATATTTT 10 4 0 TTAATTATAT 0.95813 -199 ATTAATTGTCTATCTATTAGTATAATGTATTTATT 11 59 1 TTTAGTATAA 0.527245 -66 TCTTTAAAAAACTAAATAATTATAT 12 1 0 ATAATTATAT 0.932951 -52 ATAAAACTTGAATATTGCATTAAAATTCAAGGACT 14 197 1 ATTATTAAAA 0.683291 -47 TAAATACTAATATTTGCTATTATAATGGAAATATC 16 27 1 TTTATTATAA 0.874426 -51 TGATATAAATATTCTTTTATTATAAGGAGTGTGAT 18 14 0 ATTATTATAA 0.808958 -141 TTGGCTTTTTTGTAAAAAATGATATAAATATTCTT 18 33 0 TTAATGATAT 0.655923 -122 TCTTTCTAAATCTTAAAGATTAAATCCTTCAAATA 19 121 1 TTAATTAAAT 0.920569 -148 TACATGTTTTATTATATAATTATATATGCATGTAG 19 183 0 ATTATTATAT 0.909301 -86 TCATAAAATTTTTAAAACATTAAATTTTTAGTATT 19 219 0 TTAATTAAAT 0.920569 -50 TATTTTTTATTATAATTAATTATATAGTATTTTAA 22 32 0 TTAATTATAT 0.958136 -58 GTATATTTTAATTTAGTAATTATAAATATTTGAGG 24 66 1 ATAATTATAA 0.852837 -100 TTCGCTTTTTATTAAAAAATTAAAATTCACACTCA 24 124 0 ATAATTAAAA 0.748242 -42 GACTTTTTTCTTTTTATAATTAAATCAAAAAAAAT 25 17 1 TTTATTAAAT 0.860814 -50 TAATACACATTCTTATAAATTATATGATAATAAAT 26 15 1 TTAATTATAT 0.958136 -100 TATATTGATTTATAATGAATTATATACTTGATATA 26 52 0 TTAATTATAT 0.958136 -63 * * * ******* Masking position 3 Map Score: 30.0945 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 166 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 GTGCTTATTTATATATTTTATATTATACTA 2 41 0 ATATATTTTA 0.759951 -56 AAATTATTTGATATAATTTAGCTTGAAATT 3 30 0 ATATAATTTA 0.880088 -85 AAATTATATCAAATAATTTTTTTTTTTTAA 3 41 1 AAATAATTTT 0.860075 -74 TTAGTATACCAAATAATTATCAATTTAAAA 3 65 0 AAATAATTAT 0.871908 -50 CCTAAATACTTAACTTATTAATA 4 144 0 AAATACTTAA 0.848278 -13 TATAGTCATAAAATAATTTAAGAGGTCCAA 5 16 0 AAATAATTTA 0.880088 -114 AAAAAAGAATAAATAATTGTTAAATCAGCT 6 34 0 AAATAATTGT 0.774596 -35 CCTGGTACAAAAATACTTAATAAGTACACA 8 104 1 AAATACTTAA 0.848278 -93 CTTAAAACCAATATAATTATACAATTAAAC 8 152 1 ATATAATTAT 0.871908 -45 TTAAACTCATAAATACTTTATTATTATATA 8 176 1 AAATACTTTA 0.834676 -21 ATATAATTATTTAGTTTTTT 12 1 1 ATATAATTAT 0.871908 -52 TTTGACTATAATATATTTTATTTAACAAAA 17 36 0 ATATATTTTA 0.759951 -56 AATTATTTGCAAATATTTGAAGGATTTAAT 19 139 0 AAATATTTGA 0.638976 -130 CTAAATAATAAAATAATTATTTGCAAATAT 19 153 0 AAATAATTAT 0.871908 -116 ATGTTTTATTATATAATTATATATGCATGT 19 185 0 ATATAATTAT 0.871908 -84 ATAGTATTTTAAATACTTATTTTTAAGTAA 22 14 0 AAATACTTAT 0.82402 -76 TTAAAATACTATATAATTAATTATAATAAA 22 32 1 ATATAATTAA 0.890444 -58 TGTAATATTCATATATTTTTTATTATAATT 22 50 0 ATATATTTTT 0.725733 -40 TACGCACCTCAAATATTTATAATTACTAAA 24 77 0 AAATATTTAT 0.745577 -89 ATTTATTATCATATAATTTATAAGAATGTG 26 20 0 ATATAATTTA 0.880088 -95 ATAATGAATTATATACTTGATATAGAATTT 26 46 0 ATATACTTGA 0.73839 -69 TTATAAATCAATATAATTTAATTAATCTTT 26 72 1 ATATAATTTA 0.880088 -43 ********** Masking position 4 Map Score: 25.0063 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 402 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 AGCTAAATTATATCAAATAATTTTTTTTTTTTAA 3 37 1 TATATAATTT 0.581014 -78 AAATGTTTTTTTTAAAAAAAGTTTTAAGCTATAA 4 93 1 TTTAAAATTT 0.881414 -64 TTTGTAATTTTGTTTAAAAATTTTACTTAAGACA 7 90 1 TGTAAAATTT 0.847675 -40 TCATGGTAATTTTTAGTAAGGTTTGTT 8 4 0 TTTTAAGTTT 0.773254 -193 ACCAGGTTTTTATCGAAAAAATTTGGATTTTTGT 8 76 0 TATAAAATTT 0.889987 -121 AAAGGCTTTTTATATATAAAGTTTAGACTTTATT 9 15 1 TATTAAATTT 0.940865 -105 AAAAGCACAATGTTTATAAAATTTCAACTTATTA 9 57 1 TGTTAAATTT 0.91628 -63 TTAGATTGCATTTTTGTTAATTTTATTTAATAAT 10 131 0 TTTTTAATTT 0.714751 -72 AATAAGTTGTTATGAGTTAATTTTCAAGAGGACA 10 178 1 TATTTAATTT 0.731706 -25 ATGTATTTATTATATCTCAATTTTTGAATTAAGC 11 83 1 TATTCAATTT 0.89272 -42 AAATTTATCCCAAAAATTTAAATATTAAG 13 6 1 TATAAAATTT 0.889987 -160 AAACAAATAGTATATCAAAGTTTTGAATTTGAAA 13 52 1 TATAAAGTTT 0.653655 -114 CTAAATTAATTATAAATAAGATTTAGTAGATAAT 13 114 1 TATTAAGTTT 0.787765 -52 GATAATTTATTGTTATTAAACTTATACAAAGCTT 13 142 1 TGTTAAATTA 0.490033 -24 GTTATGTTTAAAGTTATCAAATGTAA 14 3 1 TATTAAATTA 0.5827 -241 TCAACTTTTTTGTCTATCAATTTTTCATTCAATT 14 39 0 TGTTCAATTT 0.851283 -205 TACCCAAGCATTTATTTCAACTTTTTTGTCTATC 14 55 0 TTTTCAATTT 0.884332 -189 TAAAATATATTATAGTCAAATTTTTAGCGATAAG 17 46 1 TATCAAATTT 0.627855 -46 TAAAAGAATATTTATATCATTTTTTACAAAAAAG 18 30 1 TTTTCATTTT 0.531463 -125 TTCAATATCTTTTACAAAAATTCTTTCAAAAGCA 18 76 0 TTTAAAATCT 0.604501 -79 TAAATATTAGTATGATTAAAATCTTAAAACAAAA 19 27 1 TATTAAATCT 0.765906 -242 AAATTTTTAGTATTCTACATGTTTTATTATATAA 19 199 0 TATACATTTT 0.385655 -70 AAATTTTGTTTTTTCATAAAATTTTTAAAACATT 19 233 0 TTTTAAATTT 0.935971 -36 TTAAACTGCATTTTTTTAAATTCTTGAAACTTGA 21 17 1 TTTTAAATCT 0.750375 -70 TTTAGCATTTTGTTTTTCAAGTTTCAAGAATTTA 21 33 0 TGTTCAATTT 0.851283 -54 CTAATTTAAATTTAGGTAAATTTTAGCATTTTGT 21 54 0 TTTTAAATTT 0.935971 -33 ATCTCTATTTTTTTAGAAAATTTTTTTGTATATT 24 39 1 TTTAAAATTT 0.881414 -127 ATCAATATAATTTAATTAATCTTTGTTTAATAAA 26 78 1 TTTTAATTTT 0.68442 -37 *** **** *** Masking position 9 Map Score: 22.4617 Number of sites scoring better than the average of aligned sites = 1190 Number in coding regions = 791 Number in noncoding regions = 399 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 TTAAAAAAAGTTTTAAGCTATAATAAAATTGA 4 104 1 TTTTAGCATA 0.971701 -53 TTGTACCAGGTTTTTATCGAAAAAATTTGGAT 8 82 0 TTTTATCAAA 0.530643 -115 AATATTAAGTTTTTAATCTATAAACAAATAGT 13 31 1 TTTTATCATA 0.898785 -135 AAGTTTTATTTTTTCTGCGATCTTTAGAAGCT 14 174 0 TTTTTGCATC 0.804451 -70 GTCCTTGAATTTTAATGCAATATTCAAGTTTT 14 199 0 TTTATGCATA 0.719653 -45 TTGGGGGGTCTTTTGATCAACAGTCCTTGAAT 14 221 0 TTTTATCACA 0.796105 -23 CTTGTTTGTTTTTTGTGCTATAATTCAATTAA 15 41 0 TTTTTGCATA 0.963022 -50 TATAGTCAAATTTTTAGCGATAAGTTTAAAAA 17 56 1 TTTTAGCATA 0.971708 -36 GATAGGATATTTTTTTTCAATATCTTTTACAA 18 93 0 TTTTTTCATA 0.87098 -62 TTTTCCCTTTTTTTATGCTATTAATATTGTAA 18 129 0 TTTTTGCATT 0.735142 -26 ATTATTTTATTATTTAGCTACATGCATATATA 19 166 1 TATTAGCACA 0.764916 -103 ACGGCGGTAATTTTCTGCGACACTTTCTTAGG 23 39 0 TTTTTGCACA 0.929413 -262 GCTCACCGCTTATTTAGCAATAAATACAGGCA 23 101 1 TATTAGCATA 0.864973 -200 TCGCACGATTTTTTTAGCGATAAAAAAATAAG 23 205 1 TTTTAGCATA 0.971708 -96 **** *** *** Masking position 10 Map Score: 13.9986 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 92 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TAATATTTATACTTTACTTTTTAGGGGTGATT 4 22 0 ACTTTATTTT 0.507593 -135 GCTATATAGTAATTTACTTTTTCAGAATATAA 5 96 0 AATTTATTTT 0.795127 -34 TTATCGAAAAAATTTGGATTTTTGTCTAAGGT 8 69 0 AATTTGTTTT 0.875045 -128 TCAATTTTTGAATTAAGCTTTTTTGAAGAGAT 11 99 1 AATTAATTTT 0.845533 -26 ATATAATTATTTAGTTTTTTAAAGAAGTGA 12 9 1 ATTTAGTTTT 0.926358 -44 AAAACTTAATATTTAAATTTTTGGGATAAATT 13 12 0 ATTTAATTTT 0.874554 -154 TGTTTTAATTAGGGTTTTTATTGGAAGG 15 73 0 AATTAGTTTT 0.908062 -18 AAGCAATTCAATTTTGGCTTTTTTGTAAAAAA 18 49 0 ATTTTGTTTT 0.899182 -106 GAAAGTTTTGTTTTAAGATTTTAATCATACTA 19 34 0 TTTTAATTTT 0.693016 -235 ACAATTGGCAAATTAGACTTTTCTTTCTAAAT 19 100 1 AATTAGTTTT 0.908062 -169 AATACTAAAAATTTAATGTTTTAAAAATTTTA 19 219 1 ATTTAATTTT 0.874554 -50 TCTCCTCAAAATTTTGTTTTTTCATAAAATTT 19 243 0 ATTTTGTTTT 0.899182 -26 CTTAATAATAAATTAGATTTTTTATTTTTTCA 20 16 1 AATTAGTTTT 0.908062 -36 TTTAGGTAAATTTTAGCATTTTGTTTTTCAAG 21 46 0 TTTTAGTTTT 0.802891 -41 ATGAGTGTGAATTTTAATTTTTTAATAAAAAG 24 123 1 ATTTTATTTT 0.831734 -43 TTTTTAGACTTTTTTCTTTTTAT 25 2 1 TTTTAGTTTT 0.802891 -65 GCAAATTGCTTATTTACATTTTTTTTGATTTA 25 37 0 TATTTATTTT 0.556888 -30 ****** **** Masking position 4 Map Score: 21.4645 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 377 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 AAACAATTTAATTTAATAATTACAAACTGT 2 69 0 ATTTAATAAT 0.937287 -28 TAAAAAAAACATTTAACAATTTTTATTATT 4 77 0 ATTTAACAAT 0.913535 -80 TGTTAAATCAATTTTATTATAGCTTAAAAC 4 113 0 ATTTTATTAT 0.579351 -44 AATAAAATTGATTTAACAATATTAATAAGT 4 125 1 ATTTAACAAT 0.913535 -32 TAAATACTTAACTTATTAATATTGTTAAAT 4 135 0 ACTTATTAAT 0.388125 -22 ATATAATAACATATAATAATATAGATGCAA 5 72 0 ATATAATAAT 0.65473 -58 AAACGAGCTGATTTAACAATTATTTATTCT 6 29 1 ATTTAACAAT 0.913535 -40 CTATATAATAATAAAGTATTTA 8 185 0 ATATAATAAT 0.65473 -12 TGTGCTTTTTATTTTACAATAAAGTCTAAA 9 36 0 ATTTTACAAT 0.784987 -84 ATAAGTTGAAATTTTATAAACATTGTGCTT 9 59 0 ATTTTATAAA 0.499269 -61 TGTTAATTTTATTTAATAATTTGCTAACAA 10 121 0 ATTTAATAAT 0.937287 -82 ATATCATATTATTTATTAATTGTCTATCTA 11 45 1 ATTTATTAAT 0.763916 -80 AATATATTTTATTTAACAAAAAAGCACACC 17 27 0 ATTTAACAAA 0.66986 -65 GCAAATAATTATTTTATTATTTAGCTACAT 19 159 1 ATTTTATTAT 0.579351 -110 ACGTACTTAATAATAAATTAGATT 20 5 1 ACTTAATAAT 0.745805 -47 CTCACCGCTTATTTAGCAATAAATACAGGC 23 102 1 ATTTAGCAAT 0.712339 -199 GTATATTTTAATTTAGTAATTATAAATATT 24 66 1 ATTTAGTAAT 0.778203 -100 GTGAATTTTAATTTTTTAATAAAAAGCGAA 24 129 1 ATTTTTTAAT 0.527344 -37 ATTTTTTTTGATTTAATTATAAAAAGAAAA 25 22 0 ATTTAATTAT 0.79888 -45 AATCAATATAATTTAATTAATCTTTGTTTA 26 77 1 ATTTAATTAA 0.43173 -38 ********** Masking position 4 Map Score: 18.4853 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 394 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 ATTTAGCTTGAAATTAACTCCTAAAGGATAAAA 3 12 0 AAAACTCCTA 0.587714 -103 AAAAATCCCCTTTATACAACCTTA 3 101 0 AAACCCTTTA 0.84307 -14 TACAAAATAATAATCACCCCTAAAAAGTAAAG 4 10 1 ATACCCCCTA 0.876953 -147 TAAATTCTCCTCTTCCTTTTTTTA 9 106 0 AAACCCTCTT 0.896516 -14 AAAAATCTCTTCAAAAAAGCTTAA 11 111 0 AAACCTTCAA 0.925769 -14 AAATTATCCTCAATAAAGCATTT 12 40 0 AAAACCTCAA 0.843071 -13 CTGTTGATCAAAAGACCCCCCAAC 14 230 1 AAACCCCCAA 0.969521 -14 AGCAAATACACCTCTTTATTTATTCC 16 62 0 AAACCCTCTT 0.896516 -16 AAAAGCTCTCCAAACATAAATAT 19 1 1 AAACCTCCAA 0.911188 -268 TAAGTCTCCTCAAAATTTTGTTT 19 256 0 TAACCCTCAA 0.817471 -13 TTAAAACTCTCTTTTAGGTCAATGAA 23 285 0 AAACCTTTTA 0.634074 -16 TTACGTAAAAATACGCACCTCAAATATTTATAA 24 85 0 ATACCCTCAA 0.896516 -81 *** * ****** Masking position 3 Map Score: 4.6375 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 112 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TTTTTAATTTTCTTGTTTGATCATGGTAAT 8 28 0 TCTTGTTTGA 0.595957 -169 TAAAGTTTAGACTTTATTGTAAAATAAAAA 9 31 1 ACTTTATTGT 0.711119 -89 CTTTTAGATTGCATTTTTGTTAATTTTATT 10 138 0 GCATTTTTGT 0.863539 -65 TTTGAATTAAGCTTTTTTGAAGAGATTTTT 11 105 1 GCTTTTTTGA 0.968473 -20 GAAGTGAAATGCTTTATTGAGGATAATTT 12 34 1 GCTTTATTGA 0.895168 -19 AATTTGAAATGCTGTTTTGATATTATTTTA 13 77 1 GCTGTTTTGA 0.86498 -89 ATTTATTTCAACTTTTTTGTCTATCAATTT 14 50 0 ACTTTTTTGT 0.898537 -194 TTATTGGAAGGCTTGTTTGTTTTTTGTGCT 15 54 0 GCTTGTTTGT 0.95083 -37 GAATCGGTGTGCTTTTTTGTTAAATAAAAT 17 22 1 GCTTTTTTGT 0.978248 -70 TTCAATTTTGGCTTTTTTGTAAAAAATGAT 18 45 0 GCTTTTTTGT 0.978248 -110 ********** Masking position 7 Map Score: 10.4008 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 58 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 CTAAACAAAAGTAAGTTACATGAA 1 8 0 AAAGTAAGTT 0.73792 -17 TTGTAATTATTAAATTAAATTGTTTTTGAAT 2 74 1 TAATTAAATT 0.511467 -23 TTTAATTCTTGATATTAACTTTGTTAATATT 4 47 0 GAATTAACTT 0.419264 -110 ATTTAACAATATTAATAAGTTAAGTATTTAG 4 135 1 ATAATAAGTT 0.365015 -22 TATATTCTGAAAAAGTAAATTACTATATAGC 5 97 1 AAAGTAAATT 0.721745 -33 TCTAAGGTGTTAAAATAAATTTTTAATTTTC 8 46 0 TAAATAAATT 0.587613 -151 CTATATAATAATAAAGTATTTATGAGT 8 180 0 AAAATAAAGT 0.510091 -17 TTTGAAAAGAAATAATAAGTTGAAATTTTAT 9 72 0 AAAATAAGTT 0.899114 -48 AAGAATATTAGAGAATAAGTTGTTATGAGTT 10 165 1 GAAATAAGTT 0.871175 -38 TTATTCCCTTGAAATTAAGCTCTATTAACCA 11 11 1 GAATTAAGCT 0.628136 -114 CAAAAATTTAAATATTAAGTTTTTAATCTAT 13 21 1 AAATTAAGTT 0.867503 -145 TAAGTTTAATAACAATAAATTATCTACTAAA 13 135 0 AAAATAAATT 0.891424 -31 CATGTAGCTAAATAATAAAATAATTATTTGC 19 159 0 AAAATAAAAT 0.553325 -110 AAATTTTTAAAACATTAAATTTTTAGTATTC 19 218 0 AAATTAAATT 0.857784 -51 ACGTACTTAATAATAAATTAGATTTTTTA 20 9 1 AAAATAAATT 0.891424 -43 CAAACATTAAACTGCATTTTTTT 21 3 1 AAATTAAACT 0.672212 -84 ATTTTACTTAAAAATAAGTATTTAAAATAC 22 10 1 AAAATAAGTA 0.365015 -80 TTAGGTCAATGAAATTAAGCTGACACCCATA 23 267 0 GAATTAAGCT 0.628136 -34 ACAAAAACCTGAAAATAAATTT 24 2 0 GAAATAAATT 0.861683 -164 TTTTTATTAAAAAATTAAAATTCACACTCAT 24 123 0 AAATTAAAAT 0.476489 -43 TAAATTATATGATAATAAATTCTATATCAAG 26 30 1 GAAATAAATT 0.861683 -85 ** ******** Masking position 6 Map Score: 12.8383 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 384 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 TGTGAAAACACTGTACTTATTAACCTATAT 2 6 1 ATGTACTTAT 0.873008 -91 TTTAATAATTACAAACTGTGCTTATTTATATATTT 2 53 0 ATGTGCTTAT 0.949232 -44 ATGAATTAATATTATTTGTAATTTTGTTTAAAAAT 7 76 1 ATGTAATTTT 0.829666 -54 ATTCTCTTTAATTTTGTGTACTTATTAAGTATTTT 8 113 0 ATGTACTTAT 0.873043 -84 GAAATTTTATAAACATTGTGCTTTTTATTTTACAA 9 47 0 ATGTGCTTTT 0.979148 -73 AAAAGAAATAATAAGTTGAAATTTTATAAACATTG 9 64 0 ATGAAATTTT 0.697785 -56 TTCATTTACCAGAACTTGAGCTTTTTCATATCTGT 14 135 0 ATGAGCTTTT 0.964999 -109 CCTTGATGAGAATCGGTGTGCTTTTTTGTTAAATA 17 13 1 ATGTGCTTTT 0.979162 -79 GATATGGCTTGAGTTTTTTAAACTTATC 17 74 0 ATGAGTTTTT 0.755727 -18 CTTTTATTATAAGGAGTGTGATTTT 18 1 0 ATGTGATTTT 0.929867 -154 ATTGCTAAATAAGCGGTGAGCTCTTACCTCACCTT 23 87 0 ATGAGCTCTT 0.839111 -214 * ********* Masking position 1 Map Score: 5.21708 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 57 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 ATTAGTATAATATAAAATATATAAATAAGC 2 39 1 TATAAAATAT 0.546857 -58 CAAGCTAAATTATATCAAATAATTTTTTTT 3 35 1 TATATCAAAT 0.537343 -80 AATACTTAACTTATTAATATTGTTAAATCA 4 133 0 TTATTAATAT 0.202861 -24 AATAATTTTTTATTTCATATAGTCATAAAA 5 33 0 TATTTCATAT 0.858389 -97 TATATAATATGTTAGAATAA 6 1 1 TATATAATAT 0.869719 -68 TTAAGGTTATTATATAATATCTTATAACAG 7 45 0 TATATAATAT 0.869719 -85 CAAATAATATTAATTCATATTAAGGTTATT 7 64 0 TAATTCATAT 0.755886 -66 CTATATAATAATAAAGTATTT 8 186 0 TATATAATAA 0.546834 -11 TTGTTAATTTTATTTAATAATTTGCTAACA 10 122 0 TATTTAATAA 0.429547 -81 ATTAACCATGTATATCATATTATTTATTAA 11 34 1 TATATCATAT 0.906618 -91 TAGTATAATGTATTTATTATATCTCAATTT 11 76 1 TATTTATTAT 0.332707 -49 AATTATCTACTAAATCTTATTTATAATTAA 13 119 0 TAAATCTTAT 0.37237 -47 GAACTTGAGCTTTTTCATATCTGTCTCTTA 14 129 0 TTTTTCATAT 0.420333 -115 AAAGAATATTTATATCATTTTTTACAAAAA 18 32 1 TATATCATTT 0.385076 -123 TTCACCTTCATAAATCATATATAAATAATT 19 63 1 TAAATCATAT 0.832202 -206 CATATATAATTATATAATAAAACATGTAGA 19 190 1 TATATAATAA 0.546834 -79 TAAAAATAAGTATTTAAAATACTATATAAT 22 19 1 TATTTAAAAT 0.332707 -71 TTAATTATAATAAAAAATATATGAATATTA 22 48 1 TAAAAAATAT 0.38137 -42 AATATATGAATATTACATATTTAAGGAATA 22 63 1 TATTACATAT 0.522852 -27 CACATTCTTATAAATTATATGATAATAAAT 26 20 1 TAAATTATAT 0.433127 -95 AAAGATTAATTAAATTATATTGATTTATAA 26 72 0 TAAATTATAT 0.433127 -43 ********** Masking position 1 Map Score: 5.76373 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 274 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 13 CTAAGATATGTCTTAAGTAAAATTTTTAAA 7 102 0 TCTTAAGTAA 0.854764 -28 ATCATGGTAATTTTTAGTAAGGTTTGTT 8 9 0 TTTTTAGTAA 0.858036 -188 TTTGTGTACTTATTAAGTATTTTTGTACCA 8 106 0 TATTAAGTAT 0.813599 -91 ATTATATTGGTTTTAAGTATTATTCTCTTT 8 139 0 TTTTAAGTAT 0.922617 -58 TTTGATATTATTTTAAGTAAGGCTAAATTA 13 92 1 TTTTAAGTAA 0.950315 -74 AAACATTAAATTTTTAGTATTCTACATGTT 19 210 0 TTTTTAGTAT 0.790254 -59 TCTAATTTATTATTAAGTACGT 20 3 0 TATTAAGTAC 0.719124 -49 AAATACTTATTTTTAAGTAAAAT 22 4 0 TTTTAAGTAA 0.950315 -86 CACTCATCACTTTTACGTAAAAATACGCAC 24 100 0 TTTTACGTAA 0.817147 -66 ********** Masking position 4 Map Score: 5.10224 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 63 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 TTGAAATTAACTCCTAAAGGATAAAAC 3 8 0 CTCCTAAAGG 0.937212 -107 ATAATAATCACCCCTAAAAAGTAAAGTATA 4 17 1 CCCCTAAAAA 0.848609 -140 ATAACAATTCCTCCTAAAAAAGAATAAATA 6 49 0 CTCCTAAAAA 0.928757 -20 CGCCCACTAGCCCCTCAAGCTAGCGTGTCT 10 51 0 CCCCTCAAGC 0.847644 -152 AAAAATCTCTTCAAAAAAGCTTAATT 11 109 0 CTCTTCAAAA 0.670846 -16 TGAAGAAAAGCTTCTAAAGATCGCAGAAAA 14 166 1 CTTCTAAAGA 0.727429 -78 CACACCGATTCTCATCAAGGAT 17 3 0 CTCATCAAGG 0.700098 -89 TAAGTCTCCTCAAAATTTTGTTTTT 19 254 0 CTCCTCAAAA 0.954106 -15 CTTGATCTTGCTCCTAATGAGGTTTATCTT 23 132 0 CTCCTAATGA 0.811264 -169 CCGTAAGCATGTCCTCAAGAACAAAGGGTG 23 170 0 GTCCTCAAGA 0.863165 -131 ********** Masking position 5 Map Score: 2.16897 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 80 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 ATATAGGTTAATAAGTACAGTGTTTTCACA 2 11 0 ATAAGTACAG 0.838098 -86 AAATATATAAATAAGCACAGTTTGTAATTA 2 53 1 ATAAGCACAG 0.910478 -44 ATTTAATTTAATAATTACAAACTGTGCTTA 2 64 0 ATAATTACAA 0.671748 -33 ATTTTTAAACAAAATTACAAATAATATTAA 7 81 0 AAAATTACAA 0.71601 -49 AAAATACTTAATAAGTACACAAAATTAAAG 8 113 1 ATAAGTACAC 0.882908 -84 TTGTAAAATAAAAAGCACAATGTTTATAAA 9 47 1 AAAAGCACAA 0.937943 -73 ACAGATATGAAAAAGCTCAAGTTCTGGTAA 14 135 1 AAAAGCTCAA 0.704371 -109 TATTTAACAAAAAAGCACACCGATTCTCAT 17 18 0 AAAAGCACAC 0.948057 -74 AAAATCACACTCCTTATAAT 18 1 1 AAAATCACAC 0.856771 -154 ********** Masking position 4 Map Score: 3.13389 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 51 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678