AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_bbur_reg_100.orf -o03010_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: BB0394 23 transcription antitermination factor (nusG) BB0488 21 ribosomal protein L14 (rplN) BB0481 21 ribosomal protein L2 (rplB) BB0694 53 signal recognition particle protein (ffh) Input sequences: #1 BB0115 139 ribosomal protein S6 (rpsF) #2 BB0123 214 ribosomal protein S2 (rpsB) #3 BB0132 37 transcription elongation factor (greA) #4 BB0133 162 B. burgdorferi predicted coding region BB0133 #5 BB0189 22 ribosomal protein L35 (rpmI) #6 BB0190 89 translation initiation factor 3 (infC) #7 BB0229 60 ribosomal protein L31 (rpmE) #8 BB0230 79 transcription termination factor Rho (rho) #9 BB0235 32 conserved hypothetical protein #10 BB0236 148 B. burgdorferi predicted coding region BB0236 #11 BB0254 275 single-stranded-DNA-specific exonuclease (recJ) #12 BB0339 49 ribosomal protein L13 (rplM) #13 BB0346 183 B. burgdorferi predicted coding region BB0346 #14 BB0351 106 B. burgdorferi predicted coding region BB0351 #15 BB0386 24 ribosomal protein S7 (rpsG) #16 BB0387 67 ribosomal protein S12 (rpsL) #17 BB0389 82 DNA-directed RNA polymerase (rpoB) #18 BB0390 70 ribosomal protein L7/L12 (rplL) #19 BB0393 51 ribosomal protein L11 (rplK) #20 BB0395 108 preprotein translocase subunit (secE) #21 BB0396 173 ribosomal protein L33 (rpmG) #22 BB0438 240 DNA polymerase III, subunit beta (dnaN) #23 BB0439 90 conserved hypothetical protein #24 BB0440 91 ribosomal protein L34 (rpmH) #25 BB0476 300 translation elongation factor TU (tuf) #26 BB0477 50 ribosomal protein S10 (rpsJ) #27 BB0478 35 ribosomal protein L3 (rplC) #28 BB0503 21 ribosomal protein L17 (rplQ) #29 BB0615 165 ribosomal protein S4 (rpsD) #30 BB0693 158 xylose operon regulatory protein (xylR-1) #31 BB0701 179 B. burgdorferi predicted coding region BB0701 #32 BB0703 63 ribosomal protein L32 (rpmF) #33 BB0776 178 B. burgdorferi predicted coding region BB0776 #34 BB0777 61 adenine phosphoribosyltransferase (apt) #35 BB0778 56 ribosomal protein L21 (rplU) #36 BB0804 198 ribosomal protein S15 (rpsO) Motif number 1 TACATTTTGTATATTATAAAAATTTTTATT 1 32 1 ATATTATAAA 0.858044 -108 TTTTAATATTTTTTTATTAATATAATTTGT 2 48 1 TTTTTATTAA 0.89608 -167 TTTGTTGATAATTTTATTAAAGAGAATTAC 2 73 1 ATTTTATTAA 0.846353 -142 AGAATTACGTTTATTTTTAATGAGGTGGAC 2 95 1 TTATTTTTAA 0.949047 -120 TTTCTTTTTAATATTATAATATAAGATTTT 4 14 1 ATATTATAAT 0.689159 -149 ATATAAGATTTTATTTTAAAAGAATAATAA 4 32 1 TTATTTTAAA 0.901193 -131 TTAATAATTAATTTTATTATACATTCACTA 6 31 0 ATTTTATTAT 0.668926 -59 ATAATAAAATTAATTATTAATGTTAATTAT 6 41 1 TAATTATTAA 0.912201 -49 TTATTAATGTTAATTATTAATTGATTTAGG 6 54 1 TAATTATTAA 0.912201 -36 GGTCAGTGTTTTTTATTAATTAATAATAA 8 10 1 TTTTTATTAA 0.89608 -70 AAAAATCTACTTATTATTAATTAATAAAAA 8 20 0 TTATTATTAA 0.950238 -60 AATAAGTAGATTTTTATAAAATCCTTTCTT 8 35 1 TTTTTATAAA 0.80893 -45 TCTACGAATTAAATTTTTAAGAAAGGATTT 8 53 0 AAATTTTTAA 0.864092 -27 CTATCATATAAAATTATTAATGATAATGTT 10 59 0 AAATTATTAA 0.868755 -90 ATAAAAAAAATTATTATTAAATGAATTTCC 11 58 0 TTATTATTAA 0.950238 -218 ATAATTTTTTTTATTATAAAATAATAAAAT 11 74 1 TTATTATAAA 0.904417 -202 TAAAATTCTCATTTTATTATTTTATAATAA 11 84 0 ATTTTATTAT 0.668926 -192 TTTATGCATAAAATTATAAAGGGTATAGCG 12 25 1 AAATTATAAA 0.764215 -25 TCTAAGCTTTAAATTTTTATTTTATGTATT 13 37 1 AAATTTTTAT 0.699753 -147 CTATGAACTCTTATTATTAAGCTTAAGCTA 13 163 0 TTATTATTAA 0.950238 -21 AAATTATGTATAATTTTTATAGTTATATTA 14 33 1 TAATTTTTAT 0.785326 -74 ATTTGCTACCATTTTATTAATAGTTTCAAG 16 29 1 ATTTTATTAA 0.846353 -39 CAACTTTGATATATTTTTAATTTT 17 5 0 ATATTTTTAA 0.922282 -78 GAATCAAAAATTATTTTAAACAATTGAACC 22 22 1 TTATTTTAAA 0.901193 -219 TTTGTATTTTTATTTTTTATAGATATATAG 22 169 0 TATTTTTTAT 0.620117 -72 CTAGAAAAGCTTATTTTAATATTCAAAATA 23 27 0 TTATTTTAAT 0.769765 -64 ATCAATTTTTTATACCACAATGC 23 78 0 AATTTTTTAT 0.509797 -13 AGCTTTATTTTTTAATATTTTGTGC 25 6 1 TATTTTTTAA 0.816622 -295 AAGTTTATATTAATTTTTAATGCTATTATA 25 54 1 TAATTTTTAA 0.908923 -247 TTTTTCTAAAAAATTTTAATAGCTTTAAAA 25 146 0 AAATTTTAAT 0.532963 -155 TAAAAAATTGATTTTTTTATTTTTTTGATT 25 197 1 ATTTTTTTAT 0.659997 -104 AGCTATTTTCTTATTTTAATAAGAATAAAT 25 233 1 TTATTTTAAT 0.769765 -68 TCTCTTTAAAAAATTTTTAACAAATTTATT 25 256 0 AAATTTTTAA 0.864092 -45 AATTATTTGTTTATTATTAATTTAA 29 6 0 TTATTATTAA 0.950238 -160 CTGCTATGCTTTATTTTTAATATGTGAGGA 29 145 1 TTATTTTTAA 0.949047 -21 AATAAAAAAAATATTATAAAATATCATATC 30 117 0 ATATTATAAA 0.858044 -42 TACACCTCCTTTATTTTTAAAATAAAAAAA 30 137 0 TTATTTTTAA 0.949047 -22 AGTAAATATTTATTTTTTATAGTTAAGGAG 31 152 1 TATTTTTTAT 0.620117 -28 GTTAATATATATATTATTAAGATAATTTAA 32 15 1 ATATTATTAA 0.924865 -49 TTTATAATTTTAATTATTAAGATAAAAACC 33 65 0 TAATTATTAA 0.912201 -114 TTAATAATTAAAATTATAAAATAAGTTGTA 33 75 1 AAATTATAAA 0.764215 -104 TGTTTGTGGCTAATTTTTAAATTAGCTGCC 33 111 1 TAATTTTTAA 0.908923 -68 ATTATAGCTCTTTTTTTAAATTACTCATGT 33 143 0 TTTTTTTAAA 0.80276 -36 TGACTTTTCTTTTTTATTAAATTTACAATG 35 20 1 TTTTTATTAA 0.89608 -37 TTTATATTTGTTTTTTTAAACAATTTAATA 36 37 1 TTTTTTTAAA 0.80276 -162 ATTTAATAATTTATTATTAAAAATAACCCG 36 59 1 TTATTATTAA 0.950238 -140 ATTGCTTTTGTTATTTTTAAGAAAAAATAT 36 99 1 TTATTTTTAA 0.949047 -100 TTAAGAAAAAATATTATAATCTATCGTAGT 36 115 1 ATATTATAAT 0.689159 -84 ATCGTAGTAGTTATTTTAAATTATGGCAAG 36 137 1 TTATTTTAAA 0.901193 -62 ********** Masking position 5 Map Score: 65.8571 Number of sites scoring better than the average of aligned sites = 2218 Number in coding regions = 1352 Number in noncoding regions = 866 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 TTATATTAATAAAAAAATATTAAAAGCTAA 2 43 0 AAAAAAATAT 0.852304 -172 AAATTAGGGCAAAATAACAATATTTCATTT 4 60 0 AAAATAACAA 0.885298 -103 AAATAATACAAAAAAATTAATACTATCATA 10 81 0 AAAAAATTAA 0.91694 -68 ATAACTTTTCCAAAAAATAATACAAAAAAA 10 95 0 CAAAAAATAA 0.769332 -54 AATTATAACAAAACAAATATTTTATGGAAA 11 33 1 AAACAAATAT 0.735778 -243 TTTATAATAAAAAAAATTATTATTAAATGA 11 64 0 AAAAAATTAT 0.860089 -212 TTTTTATTATAAAATAATAAAATGAGAATT 11 81 1 AAAATAATAA 0.852304 -195 TCATGGAAATAAACTATTATTAATAGTACT 13 72 0 AAACTATTAT 0.622921 -112 CCTTTTCTTGAAACTATTAATAAAATGGTA 16 35 0 AAACTATTAA 0.747893 -33 AGCATGCACTCAAAAATTAAGACTAACACT 18 17 0 CAAAAATTAA 0.780369 -54 GATTGTTTAGAAAAAAACAAGTACTAAATT 21 19 0 AAAAAAACAA 0.932706 -155 GTTTTTTTCTAAACAATCAACTAAGATAAT 21 31 1 AAACAATCAA 0.876926 -143 ATTGAAGAATCAAAAATTATTTTAAACAAT 22 16 1 CAAAAATTAT 0.664272 -225 AAAATACAACAAAAAAACAACCTACAATTT 22 65 1 AAAAAAACAA 0.932706 -176 AAATACAATTAAACAATCAAACAGTAGCTT 22 126 1 AAACAATCAA 0.876926 -115 TACCACAATGCAAAAAACAATATTGAATAA 23 59 0 CAAAAAACAA 0.816879 -32 AGAAAAGCACAAAATATTAAAAAATAAAGC 25 12 0 AAAATATTAA 0.860089 -289 CAAAAAAATAAAAAAATCAATTTTTTAGAA 25 194 0 AAAAAATCAA 0.93657 -107 TCATATACTTAAAATATCAT 27 1 0 AAAATATCAT 0.820747 -35 AATTAATAATAAACAAATAATTGACACTCA 29 14 1 AAACAAATAA 0.833351 -152 TCACATTCATAAAATATCAAAAAC 30 5 0 AAAATATCAA 0.891568 -154 AAAATATTATAAAATATCATATCAAAAAAA 30 110 0 AAAATATCAT 0.820747 -49 TTTTAAAATAAAAAAAATATTATAAAATAT 30 123 0 AAAAAAATAT 0.852304 -36 AAAGTTTTTCAAAAAATCAAAACTTTAAAT 31 70 0 AAAAAATCAA 0.93657 -110 AAAAAAATAAAAACAAATATTTAAGAACAA 31 118 0 AAACAAATAT 0.735778 -62 TTTACTCTTCAAAAAAATAAAAACAAATAT 31 128 0 AAAAAAATAA 0.911993 -52 AAACCTAGACAAAAAAATATAAAATTAAGC 33 40 0 AAAAAAATAT 0.852304 -139 ATATATTTTTCAAATATCAAGACCAAAAGC 34 16 0 CAAATATCAA 0.725755 -46 TAAATTGTTTAAAAAAACAAATATAAAATT 36 34 0 AAAAAAACAA 0.932706 -165 TTTTTTCTTAAAAATAACAAAAGCAATTTA 36 96 0 AAAATAACAA 0.885298 -103 TTTTTAAGAAAAAATATTATAATCTATCGT 36 112 1 AAAATATTAT 0.773669 -87 ********** Masking position 6 Map Score: 41.8405 Number of sites scoring better than the average of aligned sites = 1517 Number in coding regions = 992 Number in noncoding regions = 525 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 3 GTTAGTATATAAAAGAGACTAATTTTTTTCA 1 64 0 AAAAGAGATA 0.591783 -76 CGATAGACCATAAGGAGTTTTAGTA 1 125 1 TAAGGAGTTT 0.965278 -15 ATAATTTTATTAAAGAGAATTACGTTTATTT 2 80 1 TAAAGAGATT 0.914997 -135 AAAATCGATATTAGGAGAGTTTA 3 25 1 TTAGGAGATT 0.930723 -13 ATTAATTGATTTAGGAGTATATATTTTTTAG 6 69 1 TTAGGAGTTA 0.914556 -21 TAATTAATAATAAGTAGATTTTTATAAAATC 8 27 1 TAAGTAGATT 0.743783 -53 AATAGGTATTTAAAGAGTAAAGGGGATT 10 131 1 TAAAGAGTAA 0.564074 -18 TATAATTAGCTTAGGAGATTTCAAGTTTT 11 9 0 TTAGGAGATT 0.930723 -267 TTATTGACAATAAATAGTTTAAATGTAGTTT 13 126 1 TAAATAGTTA 0.444232 -58 ATGTCTTAAAAAAGGAGTCTTTTA 17 69 1 AAAGGAGTTT 0.807489 -14 TGAAAATATATAAGGAGTTAAT 18 59 1 TAAGGAGTAA 0.789206 -12 GTTACTACCATAAGGAGATTAT 19 40 1 TAAGGAGATA 0.965278 -12 ACTAAGATAATAAAGAGTTTTATAGGGAATT 21 50 1 TAAAGAGTTT 0.905729 -124 TTATTGGTAGTTAGGAGTTTTGTTAT 21 158 1 TTAGGAGTTT 0.923028 -16 AAAAATTTTTTAAAGAGATTAAATGTAAGTA 25 268 1 TAAAGAGATA 0.905731 -33 TCTCTAAAGTTTAGGAGAATAAA 26 38 1 TTAGGAGATA 0.923028 -13 TTTTTATAGTTAAGGAGAGTTAATT 31 165 1 TAAGGAGATT 0.968891 -15 ******** ** Masking position 6 Map Score: 18.2436 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 85 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TTTTAATATTTTTTTATTAATATAATTTGTTGA 2 48 1 TTTTAAATAT 0.840636 -167 TATCCCCCCTTTTATAAGAATATAATAAAACAA 2 137 0 TTTTAAATAT 0.840636 -78 AATTTTCTTTTTAATATTATAATATAAGAT 4 8 1 TTTTAATTAT 0.907473 -155 AATAACAATATTTCATTTATTATTCTTTTAAAA 4 45 0 TTTATATTAT 0.860268 -118 CCCGTTACACTTTATATAATTATATCATTTATC 4 108 0 TTTTAATTAT 0.907473 -55 ATTCCCACCATTTTAAACAATATATACAAACCC 4 140 0 TTTAAAATAT 0.795784 -23 TTCTTCCCCTTTAATTTAATAT 5 1 0 TTTATAATAT 0.768047 -22 ATTTCTTTTTGATTTTATTAGAGGTTTA 9 6 1 TTTTGTTTAT 0.753737 -27 TTTTCCTCTTTTTTACTATTATTAGTAACATA 10 10 1 TTTTAATTAT 0.907473 -139 TAGTATTAATTTTTTTGTATTATTTTTTGGAAA 10 86 1 TTTTTATTAT 0.892864 -63 AAATTCTCATTTTATTATTTTATAATAAAAAAA 11 79 0 TTTTTTTTAT 0.906436 -197 TTAATCGATTTTTCAAGGATTATTCTTTACTAA 11 232 0 TTTAAATTAT 0.878718 -44 CGCTATACCCTTTATAATTTTATGCATAAATCT 12 22 0 TTTTATTTAT 0.919362 -28 ATATCTAAGCTTTAAATTTTTATTTTATGTATT 13 34 1 TTTAATTTAT 0.893869 -150 GTTTTTTCTTTTATTTTACAATAA 14 2 1 TTTTTTTTAT 0.906436 -105 ATGTATAATTTTTATAGTTATATTAATTTCCAT 14 38 1 TTTTATATAT 0.859786 -69 TTGTTGTATTTTTGATAAATTATTTGGTTCAAT 22 44 0 TTTATATTAT 0.860268 -197 TTTAATTGTATTTAATACTATATGATGCAAGTA 22 106 0 TTTATTATAT 0.79378 -135 ATTTTTATTTTTTATAGATATATAGTAGTAATA 22 161 0 TTTTATATAT 0.859786 -80 TTTTGTGGATTTTGTATTTTTATTTTTTATAGA 22 176 0 TTTTATTTAT 0.919362 -65 AAAATAAGCTTTTCTAGGTTTATTCAATATTGT 23 40 1 TTTTATTTAT 0.919362 -51 GATTTTTTTATTTTTTTGATTATTTGTAGCTAT 25 206 1 TTTTTATTAT 0.892864 -95 GTTAAGACTTTAAGGATATATTAATACTCTC 26 9 1 TTTAGTATAT 0.548752 -42 GTTTTTGATATTTTATGAATGTGATA 30 4 1 TTTATTTTAT 0.877403 -155 ATTATGACATTTTAATTTTATATTTGTTTTTTT 36 21 1 TTTATTATAT 0.79378 -178 TTTTAAACAATTTAATAATTTATTATTAAAAAT 36 50 1 TTTATTTTAT 0.877403 -149 *** ** ***** Masking position 3 Map Score: 36.263 Number of sites scoring better than the average of aligned sites = 1092 Number in coding regions = 658 Number in noncoding regions = 434 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 TATCAACAAATTATATTAATAAAAAAATAT 2 53 0 TTATATTAAT 0.95755 -162 TTCTTCCCCTTTAATTTAATAT 5 3 0 TTAATTTAAT 0.627705 -20 GGTCAGTGTTTTTTATTAATTAATAATAAG 8 11 1 TTTTATTAAT 0.796515 -69 ATTTTTATAGTTATATTAATTTCCATGCTT 14 45 1 TTATATTAAT 0.95755 -62 TTTGCTACCATTTTATTAATAGTTTCAAGA 16 30 1 TTTTATTAAT 0.796515 -38 AAACTCTTTATTATCTTAGTTGATTGTTTA 21 40 0 TTATCTTAGT 0.715733 -134 CTATTACATTTTATCTTAATAAGATTTTGT 22 203 0 TTATCTTAAT 0.948867 -38 CTAGAAAAGCTTATTTTAATATTCAAAATA 23 27 0 TTATTTTAAT 0.899849 -64 AATATAAACTTTACATTAATTAAAGAAAAG 25 35 0 TTACATTAAT 0.780597 -266 AATGTAAAGTTTATATTAATTTTTAATGCT 25 48 1 TTATATTAAT 0.95755 -253 AGCTATTTTCTTATTTTAATAAGAATAAAT 25 233 1 TTATTTTAAT 0.899849 -68 GACTTTAAGGATATATTAATACTCTCTAAA 26 16 1 ATATATTAAT 0.673717 -35 TTAAATTAATAATAAACAAA 29 1 1 TTAAATTAAT 0.80888 -165 CTACATTAAATTATCTTAATAATATATATA 32 20 0 TTATCTTAAT 0.948867 -44 GTCTAGGTTTTTATCTTAATAATTAAAATT 33 60 1 TTATCTTAAT 0.948867 -119 ********** Masking position 8 Map Score: 18.3626 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 96 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ACAATAAATAGTTTAAATGTAGTTTTGTTA 13 132 1 GTTTAAATGT 0.954056 -52 AAATTATTTGGTTCAATTGTTTAAAATAAT 22 31 0 GTTCAATTGT 0.82911 -210 TAAATATCTTGTTAAATTGTAGGTTGTTTT 22 78 0 GTTAAATTGT 0.929918 -163 CTGTTTGATTGTTTAATTGTATTTAATACT 22 120 0 GTTTAATTGT 0.954056 -121 ATCTTATTAAGATAAAATGTAATAGAATAT 22 208 1 GATAAAATGT 0.847257 -33 AGTGAATTGAGTTTAAAAGTTTAAGCGTAT 25 89 1 GTTTAAAAGT 0.795781 -212 TTATTTTTTTGATTATTTGTAGCTATTTTC 25 213 1 GATTATTTGT 0.460738 -88 TTTTTAAAGAGATTAAATGTAAGTAGCTAT 25 274 1 GATTAAATGT 0.896703 -27 CGTCTTACAATTTAAAATGTTAACACAACT 29 50 0 TTTAAAATGT 0.511123 -116 TTCAATGAGGGTTTAATTGTGCTTTTGTCT 31 26 1 GTTTAATTGT 0.954056 -154 ATTTAATGTAGTTTAAAAGTAGTTAGGAGA 32 39 1 GTTTAAAAGT 0.795781 -25 ACAACAGGCCAATTAATTGTTAT 33 4 0 AATTAATTGT 0.633465 -175 CAAATATAAAATTAAAATGTCATAATATAT 36 17 0 ATTAAAATGT 0.725402 -182 ATAATAAATTATTAAATTGTTTAAAAAAAC 36 46 0 ATTAAATTGT 0.725402 -153 ********** Masking position 5 Map Score: 8.80337 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 64 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 GTAACTGAAAAATAATCTTAAACC 1 4 0 AATAATTTAA 0.898602 -136 ATATTAATAAAAAAATATTAAAAGCTAAATC 2 40 0 AAAAATTTAA 0.283714 -175 ATTATCAACAAATTATATTAATAAAAAAATA 2 54 0 AATTATTTAA 0.50888 -161 AATCTTATATTATAATATTAAAAAGAAAATT 4 11 0 TATAATTTAA 0.603032 -152 GTGAATGTATAATAAAATTAATTATTAATGT 6 33 1 AATAAATTAA 0.437599 -57 AAAATTAATTATTAATGTTAATTATTAATTG 6 46 1 ATTAATTTAA 0.787152 -44 TTACATTAGAAATAATGTCAATTTAT 7 6 0 AATAATTCAA 0.527977 -55 TTATGTTACTAATAATAGTAAAAAAGAGGAA 10 13 0 AATAATGTAA 0.519318 -136 AATTATTAATGATAATGTTAAATATATTACA 10 47 0 GATAATTTAA 0.8598 -102 CATTATCATTAATAATTTTATATGATAGTAT 10 61 1 AATAATTTAT 0.276946 -88 AATTTTATATGATAGTATTAATTTTTTTGTA 10 74 1 GATAGTTTAA 0.882053 -75 AATAAAAAAAATTATTATTAAATGAATTTCC 11 58 0 ATTATTTTAA 0.428742 -218 AATTAATGGTCATAATTTTAACTGTTAAAAT 11 108 0 CATAATTTAA 0.471199 -168 CCATAGATTAATTAATTTTAAGTAGTAGTTA 11 196 0 ATTAATTTAA 0.787148 -80 ATTGACAATAAATAGTTTAAATGTAGTTTTG 13 128 1 AATAGTTAAA 0.333363 -56 TGAAAGGTGGGTTAATATTAAAT 15 12 1 GTTAATTTAA 0.719036 -13 CCATTTTATTAATAGTTTCAAGAAAAGGAGA 16 37 1 AATAGTTCAA 0.576986 -31 CATGACAGTGTTAGTCTTAATTTTTGAGTG 18 10 1 GTTAGTTTAA 0.757324 -61 CAAAGCTCCCATTAGTATTAAATT 19 4 0 ATTAGTTTAA 0.818501 -48 CTGACCTGTTGTTAGAATTAAAGTGAGGCTT 20 84 1 GTTAGATTAA 0.215069 -25 AAGAATCAAAAATTATTTTAAACAATTGAAC 22 20 1 AATTATTTAA 0.50888 -221 ACTTGCATCATATAGTATTAAATACAATTAA 22 107 1 TATAGTTTAA 0.649422 -134 ATATAGTAGTAATAGTAGTAAGCTACTGTTT 22 144 0 AATAGTGTAA 0.568491 -97 TAATATTCAAAATAGCATTAATAACTCACT 23 10 0 AATAGCTTAA 0.68131 -81 CTACACATATAATAGCATTAAAAATTAATAT 25 60 0 AATAGCTTAA 0.68131 -241 AAAAAATTTTAATAGCTTTAAAATTCTACAC 25 138 0 AATAGCTTAA 0.68131 -163 CTAAACTTTAGAGAGTATTAATATATCCTTA 26 21 0 GAGAGTTTAA 0.331278 -30 AACTACATTAAATTATCTTAATAATATATAT 32 21 0 AATTATTTAA 0.50888 -43 CAACTTATTTTATAATTTTAATTATTAAGAT 33 72 0 TATAATTTAA 0.603032 -107 TCCTTTTCGGGTTATTTTTAATAATAAATTA 36 65 0 GTTATTTTAA 0.34183 -134 AATTGCTTTTGTTATTTTTAAGAAAAAATAT 36 98 1 GTTATTTTAA 0.34183 -101 ****** **** Masking position 10 Map Score: 13.6704 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 527 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 8 AATTTTTATAATATACAAAATGTAACTGAAA 1 25 0 ATTACAAAAT 0.855188 -115 TTTGTATATATTGTTTAAAATGGTGGGAAT 4 143 1 TTTTTAAAAT 0.654196 -20 ATAAGTAGATTTTTATAAAATCCTTTCTTAA 8 36 1 TTTATAAAAT 0.853168 -44 TTAAATGAATTTCCATAAAATATTTGTTTTG 11 41 0 TTCATAAAAT 0.847043 -235 TAATTTTTTTTATTATAAAATAATAAAATGA 11 75 1 TATATAAAAT 0.705452 -201 AATGAGATTTATGCATAAAATTATAAAGGGT 12 18 1 ATCATAAAAT 0.915545 -32 TACTAGTTTAATACATAAAATAAAAATTTAA 13 45 0 ATCATAAAAT 0.915545 -139 TCTTGAAACTATTAATAAAATGGTAGCAAAT 16 29 0 ATAATAAAAT 0.547621 -39 TTTGGTTCAATTGTTTAAAATAATTTTTGAT 22 24 0 TTTTTAAAAT 0.654196 -217 AAAATACAAAATCCACAAAATCTTATTAAGA 22 189 1 ATCACAAAAT 0.849132 -52 GCTTATTTTAATATTCAAAATAGCATTAATA 23 18 0 ATTTCAAAAT 0.657194 -73 AATTAAAGAAAAGCACAAAATATTAAAAAAT 25 17 0 AACACAAAAT 0.698769 -284 ATTCTACACATTTTACAAAATATAGTCAATA 25 116 0 TTTACAAAAT 0.751048 -185 TCAAATTCATATACTTAAAATATCAT 27 6 0 ATCTTAAAAT 0.779208 -30 ATAATATCACATTCATAAAATATCAAAAAC 30 10 0 ATCATAAAAT 0.915532 -149 TCTTTTAAGAATAGATAAAATATTGTATTGG 30 79 1 ATGATAAAAT 0.642118 -80 ATAAAAAAAATATTATAAAATATCATATCAA 30 115 0 TATATAAAAT 0.705452 -44 CACCTCCTTTATTTTTAAAATAAAAAAAATA 30 134 0 ATTTTAAAAT 0.739605 -25 CTAGACAAAAAAATATAAAATTAAGCAAAAA 33 35 0 AATATAAAAT 0.824206 -144 TAATAATTAAAATTATAAAATAAGTTGTATA 33 76 1 AATATAAAAT 0.824194 -103 TTAAAAAAACAAATATAAAATTAAAATGTCA 36 25 0 AATATAAAAT 0.824206 -174 ** ******** Masking position 11 Map Score: 20.3532 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 253 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 CCCCCCTTTTATAAGAATATAATAAAACAA 2 137 0 ATAAGAATAT 0.24603 -78 TGAGTAAAAGAGAAGGACAATAGGAGGTTG 2 193 1 AGAAGGACAA 0.332384 -22 ATTTTATTTTAAAAGAATAATAAATGAAAT 4 39 1 AAAAGAATAA 0.920893 -124 AAATTAGGGCAAAATAACAATATTTCATTT 4 60 0 AAAATAACAA 0.6921 -103 AATACCTATTATAAGCATAACTTTTCCAAA 10 111 0 ATAAGCATAA 0.819864 -38 TTTTTATTATAAAATAATAAAATGAGAATT 11 81 1 AAAATAATAA 0.624668 -195 CCATTCGATAATAAGCATAATAACTACTAC 11 176 1 ATAAGCATAA 0.819864 -100 GTGAAGTTAGTAAAGAATAATCCTTGAAAA 11 226 1 TAAAGAATAA 0.722087 -50 TGAATGAGATTTATGCATAAAATTATAAAG 12 16 1 TTATGCATAA 0.0547647 -34 TGTTAATAGCTTAAGCTTAATAATAAGAGT 13 157 1 TTAAGCTTAA 0.0547647 -27 ATTGTAAAATAAAAGAAAAAAC 14 3 0 AAAAGAAAAA 0.553337 -104 GATTGTTTAGAAAAAAACAAGTACTAAATT 21 19 0 AAAAAAACAA 0.810789 -155 AAAATACAACAAAAAAACAACCTACAATTT 22 65 1 AAAAAAACAA 0.810789 -176 TTAATTAAAGAAAAGCACAAAATATTAAAA 25 20 0 AAAAGCACAA 0.928 -281 ACAAATAATCAAAAAAATAAAAAAATCAAT 25 203 0 AAAAAAATAA 0.76035 -98 TCTTATTTTAATAAGAATAAATTTGTTAAA 25 241 1 ATAAGAATAA 0.847496 -60 TTTTAAAGACAAAAGCACAATTAAACCCTC 31 32 0 AAAAGCACAA 0.928 -148 AAACAAATATTTAAGAACAAAATCACTCAC 31 108 0 TTAAGAACAA 0.626241 -72 TTTACTCTTCAAAAAAATAAAAACAAATAT 31 128 0 AAAAAAATAA 0.76035 -52 AAAATTAAGCAAAAACACAACAGGCCAATT 33 20 0 AAAAACACAA 0.77841 -159 TAAATTGTTTAAAAAAACAAATATAAAATT 36 34 0 AAAAAAACAA 0.810789 -165 AAATAACCCGAAAAGGATAAATTGCTTTTG 36 79 1 AAAAGGATAA 0.744034 -120 TTTTTTCTTAAAAATAACAAAAGCAATTTA 36 96 0 AAAATAACAA 0.6921 -103 ********** Masking position 3 Map Score: 9.4358 Number of sites scoring better than the average of aligned sites = 1213 Number in coding regions = 817 Number in noncoding regions = 396 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 10 ATCCGCTAAAACTATACCATTCGATAATAA 11 160 1 ACTATACCAT 0.866612 -116 AATAGCGCTATACCCTTTATAATTTT 12 34 0 GCTATACCCT 0.965823 -16 CCATGGTGGTGCTCTACCAACTGAGCTATA 21 89 0 GCTCTACCAA 0.956639 -85 GCATTTATATGCTATACCATGTTAGTGTTT 24 26 1 GCTATACCAT 0.976742 -66 GCTACCAACTGCTCTACCCTGCGTCTTACA 29 71 0 GCTCTACCCT 0.971531 -95 TTATAGCAAAGCTCTAACAAACCTCTTGCC 36 161 0 GCTCTAACAA 0.741046 -38 AAAGCAACTCCTATACCATTATAGCAAAG 36 180 0 CCTATACCAT 0.90592 -19 ********** Masking position 6 Map Score: 3.0971 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 19 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ATTATAAAAATTTTTATTGTTGAAAAAAATTAG 1 44 1 TTTTATTTTA 0.940355 -96 ACTCTCCTAATATCGATTTTTTAGCATCAAGCA 3 12 0 TATGATTTTA 0.810449 -26 CGGGGGTTTGTATATATTGTTTAAAATGGTGGG 4 137 1 TATTATTTTA 0.948257 -26 GATTTAGGAGTATATATTTTTTAG 6 76 1 TATTATTTTA 0.948237 -14 TATAAAAATCTACTTATTATTAATTAATAAAAA 8 20 0 TACTATTTTA 0.574918 -60 TATTAATTTTTTTGTATTATTTTTTGGAAAAGT 10 89 1 TTTTATTTTT 0.589983 -60 ATAATAATTTTTTTTATTATAAAATAATAAAAT 11 71 1 TTTTATTTAA 0.599583 -205 ATTCATTTTTAATCGATTTTTCAAGGATTATTC 11 240 0 AATGATTTTA 0.29761 -36 ACATTTAAACTATTTATTGTCAATAAACTTTAT 13 119 0 TATTATTTCA 0.594116 -65 TAACAACTTTGATATATTTTTAATTTT 17 5 0 GATTATTTTA 0.73749 -78 TTAAAATAATTTTTGATTCTTCAATTAAGT 22 8 0 TTTGATTTTA 0.786236 -233 TTGTTTTTTTGTTGTATTTTTGATAAATTATTT 22 52 0 GTTTATTTTA 0.707323 -189 GGATTTTGTATTTTTATTTTTTATAGATATATA 22 170 0 TTTTATTTTA 0.940355 -71 GTAAAGTTTATATTAATTTTTAATGCTATTATA 25 51 1 TATAATTTTA 0.654891 -250 AATTGATTTTTTTATTTTTTTGATTATTTGTAG 25 202 1 TTTTTTTTTA 0.744579 -99 GTCAATTATTTGTTTATTATTAATTTAA 29 6 0 TGTTATTTTA 0.71319 -160 TACAATATTTTATCTATTCTTAAAAGACAAACA 30 73 0 TATTATTTTA 0.948259 -86 TATAATATTTTTTTTATTTTAAAAATAAAGGAG 30 129 1 TTTTATTTAA 0.599686 -30 AATATTTGTTTTTATTTTTTTGAAGAGTAAATA 31 127 1 TTTTTTTTTA 0.744579 -53 GAAGAGTAAATATTTATTTTTTATAGTTAAGGA 31 148 1 TATTATTTTA 0.94826 -32 TTGGTTAATATATATATTATTAAGATAATTTAA 32 12 1 TATTATTTTA 0.94807 -52 TTTGCTTAATTTTATATTTTTTTGTCTAGGTTT 33 37 1 TTTTATTTTT 0.589982 -142 TATTTTATAATTTTAATTATTAAGATAAAAACC 33 65 0 TTTAATTTTA 0.620119 -114 TCTATATGTTTATATATTTTTCAAATATCAAGA 34 24 0 TATTATTTTA 0.948257 -38 TAATTTTATATTTGTTTTTTTAAACAATTTAAT 36 33 1 TTTTTTTTTA 0.744579 -166 ACAATTTAATAATTTATTATTAAAAATAACCCG 36 56 1 AATTATTTTA 0.644915 -143 TAGATTATAATATTTTTTCTTAAAAATAACAAA 36 105 0 TATTTTTTTA 0.772143 -94 *** **** ** * Masking position 7 Map Score: 31.4459 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 258 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 ATTCTTATAAAAGGGGGGATAATTTCCGCC 2 149 1 AAGGGGGGAT 0.933919 -66 AAATCGATATTAGGAGAGTTTA 3 26 1 TAGGAGAGTT 0.742397 -12 TATAAAGTGTAACGGGGGTTTGTATATATT 4 125 1 AACGGGGGTT 0.82125 -38 AAATTAGAGTAAGGTGGCTTAAGAGCTTTT 14 81 1 AAGGTGGCTT 0.899333 -26 CTGAAAGGTGGGTTAATATTAAAT 15 5 1 AAGGTGGGTT 0.958225 -20 TGTCTTAAAAAAGGAGTCTTTTA 17 70 1 AAGGAGTCTT 0.759451 -13 AACAACAGGTCAGGAGGGATTCGAACCCCC 20 67 0 CAGGAGGGAT 0.857749 -42 TAGAATATATAAGGAGGCATC 22 230 1 AAGGAGGCAT 0.918445 -11 AAGGAGAGTTTAGGCTATTT 28 1 1 AAGGAGAGTT 0.953447 -21 ATTAAATTTCAATGAGGGTTTAATTGTGCT 31 19 1 AATGAGGGTT 0.863795 -161 TTTTATAGTTAAGGAGAGTTAATT 31 166 1 AAGGAGAGTT 0.953447 -14 ********** Masking position 2 Map Score: 7.44247 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 30 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 TGACATTATTTCTAATGTAAATTAAACTTTATTGA 7 17 1 TTATGAAATA 0.965496 -44 TAAGAAAGGATTTTATAAAAATCTACTTATTATTA 8 31 0 TTATAAAATA 0.864906 -49 AAAACAAATATTTTATGGAAATTCATTTAATAATA 11 42 1 TTATGAAATA 0.965506 -234 TAATTTTTACTATAATCCAAATTAATGGTCATAAT 11 123 0 TTATCAAATA 0.843279 -153 GTTTAATACATAAAATAAAAATTTAAAGCTTAGAT 13 36 0 TAATAAAATA 0.669211 -148 TAATACTACATATCATGGAAATAAACTATTATTAA 13 79 0 TTATGAAATA 0.965505 -105 TGATATGTAGTATTATGGAAATAAAGTTTATTGAC 13 99 1 TTATGAAATA 0.965505 -85 GCTATCACTGTGAAATGAAAATATATAAGGAGTTA 18 44 1 TAATGAAATA 0.898397 -27 TTTAATACTATATGATGCAAGTAAATATCTTGTTA 22 94 0 TTATGAAGTA 0.867372 -147 * * *** **** * Masking position 9 Map Score: 4.25003 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 23 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 CTAATGTAAATTAAACTTTATTGAAGATTA 7 28 1 TTAAACTTTA 0.772968 -33 GTGTTTATATCTAAGCTTTAAATTTTTATT 13 28 1 CTAAGCTTTA 0.853515 -156 TTTATTGTCAATAAACTTTATTTCCATAAT 13 110 0 ATAAACTTTA 0.857465 -74 CGACAGTCTCCAAAACTGTATGCTGGGGGT 20 43 1 CAAAACTGTA 0.784919 -66 AAAAATTAATATAAACTTTACATTAATTAA 25 42 0 ATAAACTTTA 0.857465 -259 TTTATTCTCCTAAACTTTAGAGAGTATTA 26 32 0 CTAAACTTTA 0.956609 -19 AAAATGTTAACACAACTTTATTATGAGTGT 29 37 0 CACAACTTTA 0.784919 -129 TTCAAAAAATCAAAACTTTAAATCTTCAGC 31 63 0 CAAAACTTTA 0.93174 -117 ********** Masking position 4 Map Score: 2.39499 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 25 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TGTTTTGTTATAATTAGCTTAGGAGATTTC 11 18 0 TAATTAGCTT 0.850184 -258 TTATTGACAATAAATAGTTTAAATGTAGTT 13 126 1 TAAATAGTTT 0.779131 -58 TGTAGTTTTGTTAATAGCTTAAGCTTAATA 13 149 1 TTAATAGCTT 0.953303 -35 GTAAGGTGGCTTAAGAGCTTTTAGGGGG 14 89 1 TTAAGAGCTT 0.809794 -18 TACCATTTTATTAATAGTTTCAAGAAAAGG 16 35 1 TTAATAGTTT 0.779204 -33 ATAAAACTCTTTATTATCTTAGTTGATTGT 21 43 0 TTATTATCTT 0.495208 -131 ATGATGCAAGTAAATATCTTGTTAAATTGT 22 88 0 TAAATATCTT 0.779145 -153 CTAAAAAATTTTAATAGCTTTAAAATTCTA 25 141 0 TTAATAGCTT 0.953303 -160 ATTCTAAATAGCTACTTACATTTA 25 287 0 TAAATAGCTA 0.7417 -14 CCGAAAAGGATAAATTGCTTTTGTTATTTT 36 86 1 TAAATTGCTT 0.741772 -113 ********** Masking position 3 Map Score: 3.22467 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 115 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678