AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_mjan_reg_300.orf -o00290_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0627 30 M. jannaschii predicted coding region MJ0627 Input sequences: #1 MJ0161 300 acetolactate synthase small subunit (ilvN) #2 MJ0277 183 acetolactate synthase large subunit (ilvB) #3 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #4 MJ0499 300 3-isopropylmalate dehydratase (leuC) #5 MJ0502 160 3-phosphoshikimate-1-carboxyvinyltransferase (aroA) #6 MJ0503 84 2-isopropylmalate synthase (leuA) #7 MJ0623 300 conserved hypothetical protein #8 MJ0625 49 M. jannaschii predicted coding region MJ0625 #9 MJ0626 92 conserved hypothetical protein #10 MJ0633 137 leucyl-tRNA synthetase (leuS) #11 MJ0663 27 acetolactate synthase large subunit (ilvB) #12 MJ0948 25 M. jannaschii predicted coding region MJ0948 #13 MJ0949 43 conserved hypothetical protein #14 MJ0950 184 conserved hypothetical protein #15 MJ0951 244 conserved hypothetical protein #16 MJ0952 180 conserved hypothetical protein #17 MJ1000 202 histidyl-tRNA synthetase (hisS) #18 MJ1001 36 ribosomal protein S6 modification protein 2 (rimK) #19 MJ1002 87 conserved hypothetical protein #20 MJ1003 101 3-isopropylmalate dehydratase (leuC) #21 MJ1004 90 conserved hypothetical protein #22 MJ1007 101 valyl-tRNA synthetase (valS) #23 MJ1008 100 branched-chain amino acid aminotransferase (ilvE) #24 MJ1009 51 phosphate transport system regulatory protein (phoU) #25 MJ1010 300 M. jannaschii predicted coding region MJ1010 #26 MJ1195 135 2-isopropylmalate synthase (leuA) #27 MJ1196 85 asoB protein #28 MJ1266 189 high-affinity branched-chain amino acid transport protein (braC) #29 MJ1267 96 high-affinity branched-chain amino acid transport ATP-binding protein (braF) #30 MJ1268 158 high-affinity branched-chain amino acid transport ATP-binding protein (braG) #31 MJ1269 32 high-affinity branched-chain amino acid transport protein (braD) #32 MJ1270 21 high-affinity branched-chain amino acid transport protein (braE) #33 MJ1271 205 3-isopropylmalate dehydratase (leuD) #34 MJ1276 217 dihydroxy-acid dehydratase (ilvD) #35 MJ1277 123 3-isopropylmalate dehydratase (leuD) #36 MJ1279 181 M. jannaschii predicted coding region MJ1279 #37 MJ1392 300 2-isopropylmalate synthase (leuA) #38 MJ1543 193 ketol-acid reductoisomerase (ilvC) Motif number 1 TTAATCTTAACTTAATTTTTGGTTTCCTA 1 10 0 CTTAATTTTT 0.70617 -291 TATGACAAGGCTTAATTTTTCTTTTGTTAA 1 175 0 CTTAATTTTT 0.70617 -126 ATATCTATTTTATTATTTTTAAATCTTACT 1 271 1 TATTATTTTT 0.936519 -30 TAATTCTATTTTTTATTTTTAGTCTTTAAG 2 21 1 TTTTATTTTT 0.964443 -163 AGTGTTGGTATTTAATATTTAATTACTAAT 2 51 0 TTTAATATTT 0.789354 -133 TTATATATGATTTCAATTTTATCATTACTT 2 138 1 TTTCAATTTT 0.881339 -46 AGTTTTTTGTTATTATTTTTTATGGACAAA 3 21 0 TATTATTTTT 0.936519 -62 ATAATAAGTTTATTAATTTTGAAAGGCACT 4 235 1 TATTAATTTT 0.899233 -66 TAAATTTTTTTATTATTTTTTAATCAAAAT 6 46 0 TATTATTTTT 0.936519 -39 TTATTACCTGTATAAATTTTTTTATTATTT 6 58 0 TATAAATTTT 0.859628 -27 ATCCTTTCATTTTTAATGTTCAAT 10 124 0 TTTCATTTTT 0.924691 -14 TAATATTAATTTTAAATTTTC 13 2 0 TTTAAATTTT 0.918429 -42 AGGATAAAAATTTTAATTTTACATTT 15 7 0 TTTTAATTTT 0.942552 -238 TCCTTTTTTATCTTATTTTTTGTACTCAGA 15 33 1 TCTTATTTTT 0.842909 -212 CTTTATAAATTTTTATTTTTGGG 18 24 1 TTTTATTTTT 0.964443 -13 TAGACTCTATTTTTATTTTTTGCAAATAGA 23 20 1 TTTTATTTTT 0.964443 -81 TAAATATTCATTTTATTTTTATTTTGACAA 23 63 1 TTTTATTTTT 0.964443 -38 CTATACTTTATTTTACTTTTATATTGCCAA 24 11 1 TTTTACTTTT 0.847972 -41 TTTCCCTCCATATAATTTTTTGGCAATATA 24 30 0 TATAATTTTT 0.910103 -22 GCGTTCAAATTTTTATTTTTAATTTTAATA 25 80 0 TTTTATTTTT 0.964443 -221 ATATATTTCATATCATTTTTTTGCCAGTAA 25 266 0 TATCATTTTT 0.869764 -35 CACCAAAACTTTTTAATTTTCTGTTATTTA 26 111 0 TTTTAATTTT 0.942552 -25 ACAATATTATCATTATTTTTAATAACTTCC 28 78 0 CATTATTTTT 0.655746 -112 ATGAGCAATATTTAAATTTTTCGAGATAGA 28 116 0 TTTAAATTTT 0.918429 -74 GTTATGGCAATTTCATTTTTTATATATGAG 28 141 0 TTTCATTTTT 0.924691 -49 ATAACTCTTTTTTAAATTTTTAAGATATGC 29 30 1 TTTAAATTTT 0.918429 -67 GTTCTAAGATTATAAATTTTATTCTTTAAA 29 62 1 TATAAATTTT 0.859628 -35 TTAAACTTTTTATCATTTTT 29 87 1 TATCATTTTT 0.869764 -10 CGTTTAGATTTTTTACTTTTATCATATTAA 30 27 0 TTTTACTTTT 0.847972 -132 GGTATAATTTTTATAAAACCTA 31 3 1 TATAATTTTT 0.910103 -30 GGGAGAATTCTATTATATTTAG 33 3 0 TATTATATTT 0.748113 -203 TCTTTTGAAATTTAATTTTTAAAATTAAGA 33 161 1 TTTAATTTTT 0.949015 -45 AAATATTTTATCTTAATTTTAAAAATTAAA 33 171 0 TCTTAATTTT 0.764469 -35 TTTTATTTTTTGGTGGTAAT 34 1 1 TTTTATTTTT 0.964443 -217 AGACGATAACTTTAACTTTTGAAATTCCAG 34 42 1 TTTAACTTTT 0.79286 -176 TCACATTCTTTTTCAATTTTTTCAACATCT 34 168 0 TTTCAATTTT 0.881339 -50 ATTTCTATTTTCTTATATTTAGATTTTCAT 35 15 1 TCTTATATTT 0.519286 -109 ATATACAAATTTTTATATTTAAAACTAATA 36 31 1 TTTTATATTT 0.845216 -151 AATATAAAATTTTAAATTTTTAAGCAATAT 36 57 1 TTTAAATTTT 0.918429 -125 ATAAAATTTTTATTATTTTTGAAAGATACT 37 49 0 TATTATTTTT 0.936519 -252 TAATAATCTTTATAAAATTTTTATTATTTT 37 60 0 TATAAAATTT 0.552147 -241 ATATTGTATATTTAAAATTTATGTGGGAAA 37 194 0 TTTAAAATTT 0.693884 -107 AACATTTATGTTTTAAATTTATTTCACTAT 38 67 1 TTTTAAATTT 0.767611 -127 ********** Masking position 5 Map Score: 61.6481 Number of sites scoring better than the average of aligned sites = 1515 Number in coding regions = 979 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 366 Fraction of orfs with sites within 600 bp upstream = 0.0587857 Motif number 2 TACGAAAAACTATGAAAATTTTCTTTTAATCT 1 33 0 TATGAAATTT 0.579566 -268 TTTGAAGAACTTTAAAAAGTTTGATATAAAAA 2 81 0 TTTAAAATTT 0.922671 -103 TGAAATCATATATAAAAATTTTTATACTAAGG 2 121 0 TATAAAATTT 0.841879 -63 GTGAAGGGTATATAAATAGTTTTTTGTTATTA 3 36 0 TATAAAATTT 0.841879 -47 TGAAAGATTTTTTATAAACTTTTTTATATCAC 4 112 1 TTTATAATTT 0.904665 -189 AAGAATCGGGTATATAGAATTATCATAATTTC 5 59 1 TATATAATTA 0.668094 -102 TACTCTGTTGATTAAAAAATTAGTGGTG 5 143 1 ATTAAAATTA 0.679353 -18 TTATTACCTGTATAAATTTTTTTATTATTTTT 6 56 0 TATAAATTTT 0.705144 -29 TAGGACTTTTTATATATAGTTTGTGGTGGTGC 7 16 0 TATATAATTT 0.808955 -285 AAAAAGTCCTATTATATTATTAATTGGTGTGC 7 37 1 ATTATATTTA 0.430806 -264 CCAAAAAAGATATATAATGTTTGTTTAAAATC 8 21 0 TATATATTTT 0.655413 -29 AATAGCATTTATATTGTTTTGAGTATTTT 9 74 0 TTTATATTTT 0.809975 -19 GAAATTTATATCTAAAAAGTTTCGCTTTCTAT 14 148 0 TCTAAAATTT 0.644132 -37 AAATGTAAAATTAAAATTTTTATCCTTTTTT 15 10 1 ATTAAATTTT 0.666888 -235 CTTTAGCATCAATAAAAATTTAACTCATCATA 15 213 1 AATAAAATTA 0.485971 -32 TAACTCATCATATATAAAGTTT 15 233 1 TATATAATTT 0.808955 -12 CCGAAAGGTTTATATAGAATTTCATTAACATA 17 47 0 TATATAATTT 0.808955 -156 GATATAAGTATTTATATATTTACAGTTATTGA 17 102 0 TTTATAATTA 0.818542 -101 AATTTAAATCTTTATAAATTTTTATTTTTGGG 18 15 1 TTTATAATTT 0.904665 -22 ATGTTTTGTAAATAAAGTATTTAGGTGATAAA 20 80 1 AATAAATTTT 0.471833 -22 GATTTATAAATTTACAAATATGTA 22 3 1 TTTATAATTA 0.818543 -99 CGTCAAATCTTTTGAAGAGTTTTTAATTTAAT 22 70 0 TTTGAAATTT 0.755455 -32 GAATATTTAATATATAAAATTGTCTATTTGCA 23 40 0 TATATAATTG 0.306028 -61 TTATGAAGAGTTTCAAAGATACT 25 2 1 TATGAAATTT 0.579566 -299 TGAAGATGTGTTTATAGTTTTTGCAAAAGTTA 25 50 1 TTTATATTTT 0.809975 -251 CAATAGCAACATTATAGTTTTTGCAAAACATT 25 150 0 ATTATATTTT 0.614223 -151 TTCGCATCTTTCTAAATATTTTCCTATATTGG 25 194 0 TCTAAAATTT 0.644132 -107 GATGGGATGTTATAAAAATTTTACCTAATCAG 26 78 0 TATAAAATTT 0.841879 -58 ATAACAGAAAATTAAAAAGTTTTGGTGGGATT 26 114 1 ATTAAAATTT 0.816746 -22 AAAAAGATATATTAAATATTTTTGCTTTGTTT 27 41 1 ATTAAAATTT 0.816746 -45 CGCTTTTGATATTATATAATTACTATTATTAT 28 19 1 ATTATAATTA 0.627558 -171 ATCAAAAAGCTTTAAAGTATTAGTAATAATAA 28 44 0 TTTAAATTTA 0.718137 -146 AAAAGAGTTATTTAAAGTTTTAGGAATTTT 29 9 0 TTTAAATTTA 0.718137 -88 ATAACTCTTTTTTAAATTTTTAAGATATGCAA 29 30 1 TTTAAATTTA 0.718136 -67 AAGTTCTAAGATTATAAATTTTATTCTTTAAA 29 60 1 ATTATAATTT 0.779956 -37 AATTTTATTCTTTAAACTTTTTATCATTTTT 29 76 1 TTTAAATTTT 0.842758 -21 TATAGGAGTTTCTATATATTTACTTCAGAATG 33 51 0 TCTATAATTA 0.406281 -155 AATATTTTTATTTGAACATTTTCAGCTCTTTT 33 135 1 TTTGAAATTT 0.755455 -71 TTTCCATAAGTTTATAGAATTTCTCTCCCAAG 34 130 0 TTTATAATTT 0.904665 -88 TTTCTGAATTTGAATTTTTTTCTAAATTCT 34 198 0 TTTGAATTTT 0.581177 -20 AATATAAAAATTTGTATATTTAAATATATAGG 36 18 0 TTTGTAATTA 0.538726 -164 AATATAAAATTTTAAATTTTTAAGCAATATAC 36 57 1 TTTAAATTTA 0.718136 -125 AGTAGAAATTTTTATATAGTTGAATGGATACC 36 97 1 TTTATAATTG 0.497044 -85 TAGAAATAATTTTAAAGTATTTATTAGGTATC 36 123 0 TTTAAATTTT 0.842758 -59 AAATTATTTCTATAAATAGTTTAAAGTATTAA 36 143 1 TATAAAATTT 0.841879 -39 AGTTTAAAGTATTAAAAATTTTATTATGGCAA 36 160 1 ATTAAAATTT 0.816746 -22 AAATACTCGCATTAAAGATTTAAT 37 3 0 ATTAAAATTA 0.679353 -298 ATTAATAATCTTTATAAAATTTTTATTATTTT 37 60 0 TTTATAATTT 0.904665 -241 TAAGATTTCTTTTAAAGATTTTATTCCTGCGA 37 108 0 TTTAAAATTT 0.922671 -193 GAAATCTTAATTTATAAATTTAAATTTAAAGA 37 131 1 TTTATAATTA 0.818543 -170 GATATTTGATATTGTATATTTAAAATTTATGT 37 200 0 ATTGTAATTA 0.303743 -101 TTTAAATTTCATTAAATTATTTTTTATGAGGG 37 273 1 ATTAAATTTT 0.666888 -28 ****** * *** Masking position 6 Map Score: 56.8426 Number of sites scoring better than the average of aligned sites = 1672 Number in coding regions = 1121 Number in noncoding regions = 551 Number of orfs with sites within 600 bp upstream = 443 Fraction of orfs with sites within 600 bp upstream = 0.0711532 Motif number 3 AATTATTGGTTTTTGCAAATATTCTAAAGAT 1 130 0 TTTTGAAATA 0.956233 -171 TAATGTAATGTTTTGTAAAAACTAAGTATTG 10 97 1 TTTTGAAAAA 0.877198 -41 ACGTTTTGTTTTTTGTAAATAAATAGCAAAG 17 174 0 TTTTGAAATA 0.956233 -29 TGGTTATATTTTTTGCAAAAAAGTTATTAGG 20 14 1 TTTTGAAAAA 0.877198 -88 CTTTGGGATGTTTTGTAAATAAAGTATTTAG 20 73 1 TTTTGAAATA 0.956233 -29 GAGTTTTTAATTTAATAAAAATAGTTGAGGT 22 55 0 TTTAAAAAAA 0.613697 -47 TATTTTTATTTTTTGCAAATAGACAATTTTA 23 27 1 TTTTGAAATA 0.956233 -74 CCATATAATTTTTTGGCAATATAAAAGTAAA 24 22 0 TTTTGCAATA 0.751558 -30 TTTTAATAACTTTTGCAAAAACTATAAACAC 25 57 0 TTTTGAAAAA 0.877198 -244 TTTCAAAATGTTTTGCAAAAACTATAATGTT 25 144 1 TTTTGAAAAA 0.877198 -157 TATGATGGGATGTTATAAAAATTTTACCTAA 26 82 0 TGTTAAAAAA 0.614571 -54 GTTCATTAGGTTTTATAAAAATTATACC 31 8 0 TTTTAAAAAA 0.856276 -25 AAAAATATTCTTTAGGAAATATGGTATCTTT 33 113 0 TTTAGAAATA 0.852007 -93 TTGAATTTATTTTTATCAATAAATTCTGGAA 34 66 0 TTTTACAATA 0.548747 -152 AAGGTGTAGATGTTGAAAAAATTGAAAAAGA 34 161 1 TGTTGAAAAA 0.877108 -57 ATGTGAAGAATTTAGAAAAAAATTCAAATTC 34 192 1 TTTAGAAAAA 0.878107 -26 ***** ***** Masking position 8 Map Score: 19.5372 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 133 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 AAAATTAAGTTAAGATTAAAAGAAAATTTTC 1 21 1 TAGATTAAAA 0.53303 -280 TTAAAAATAATAAAATAGATATTTAGTAGAA 1 262 0 TAAATAGATA 0.489231 -39 CTTTTTATAGTAAGATTTAAAAATAATAAAA 1 278 0 TAGATTTAAA 0.624529 -23 AAAGTAATGATAAAATTGAAATCATATATAA 2 138 0 TAAATTGAAA 0.564805 -46 TGAGAAAAATTAACATTTATAAATTAAGTAA 5 13 0 TACATTTATA 0.558804 -148 CCTTAATATATCACATTTAAATTATACTCTG 5 119 1 TACATTTAAA 0.465063 -42 TGCAAAAGGGTTAAATTAATAAATGGAGTTT 10 32 1 TAAATTAATA 0.890163 -106 ATCTCACCGTTTAAATCAATATTTTT 11 12 1 TAAATCAATA 0.392948 -16 GAAAATTTAAAATTAATATTAAAAAACA 13 8 1 TAAATTAATA 0.890161 -36 TTCAAAGCATTAAGATTTATAAGCAACTATA 14 92 0 TAGATTTATA 0.707927 -93 TCGCTTTCTATTAAATGAAAATTATAGGATT 14 128 0 TAAATGAAAA 0.449791 -57 TAGTTTCTATTGAAATTTATATCTAAAAAGT 14 160 0 TAAATTTATA 0.921881 -25 AAATGTAAAATTAAAATTTTTATCCT 15 6 1 TAAATTAAAA 0.847597 -239 GTACAAAAAATAAGATAAAAAAGGATAAAAA 15 27 0 TAGATAAAAA 0.366291 -218 TGTTTATGTCTAAAATAAAAATAGTGGGCCC 15 110 1 TAAATAAAAA 0.73797 -135 ATATGATGAGTTAAATTTTTATTGATGCTAA 15 215 0 TAAATTTTTA 0.687958 -30 ATTAAGGCATTAAAATATATATCTCTTACTA 16 52 1 TAAATATATA 0.856739 -129 TAGTTGAGGTTTAAATAAATAACTCTCTAAT 22 34 0 TAAATAAATA 0.804077 -68 ACTATTTTTATTAAATTAAAAACTCTTCAAA 22 61 1 TAAATTAAAA 0.847599 -41 AAAATAAAAATAAAATGAATATTTAATATAT 23 57 0 TAAATGAATA 0.543642 -44 CAAAAGTTATTAAAATTAAAAATAAAAATTT 25 73 1 TAAATTAAAA 0.847597 -228 GTGGGGGCGTTCAAATTTTTATTTTTAATTT 25 85 0 TAAATTTTTA 0.721994 -216 CAAAACATTTTGAAATATATAGGATATATAT 25 128 0 TAAATATATA 0.856743 -173 AAAAATGATATGAAATATATAGTAAATTTGA 25 276 1 TAAATATATA 0.856743 -25 TCTGATTAGGTAAAATTTTTATAACATCCCA 26 77 1 TAAATTTTTA 0.673037 -59 TAACTCTTTTTTAAATTTTTAAGATATGCAA 29 31 1 TAAATTTTTA 0.687958 -66 GTTTAAAGAATAAAATTTATAATCTTAGAAC 29 62 0 TAAATTTATA 0.921275 -35 TTAGGTTTTATAAAAATTATACC 31 3 0 TAAAATTATA 0.282135 -30 CTGAAAATGTTCAAATAAAAATATTCTTTAG 33 129 0 TAAATAAAAA 0.73797 -77 ATTTAATTTTTAAAATTAAGATAAAATATTT 33 170 1 TAAATTAAGA 0.413602 -36 AGATTATAACTAAAATAAAAAGTAAGTGAAT 35 75 0 TAAATAAAAA 0.73797 -49 ATTTGTATATTTAAATATATAGGTGAAAAT 36 10 0 TAAATATATA 0.85674 -172 TATATTAGTTTTAAATATAAAAATTTGTATA 36 32 0 TAAATATAAA 0.804074 -150 AAAACTAATATAAAATTTTAAATTTTTAAGC 36 51 1 TAAATTTTAA 0.599131 -131 TTGCCATAATAAAATTTTTAATACTTTAAA 36 162 0 TAAATTTTTA 0.673037 -20 ATAATCTTTATAAAATTTTTATTATTTTTGA 37 57 0 TAAATTTTTA 0.673037 -244 ATCTTTAAATTTAAATTTATAAATTAAGATT 37 133 0 TAAATTTATA 0.921483 -168 CACATAAATTTTAAATATACAATATCAAATA 37 199 1 TAAATATACA 0.342306 -102 AATAATTTAATGAAATTTAAATACTCATAAT 37 263 0 TAAATTTAAA 0.890111 -38 * ********* Masking position 5 Map Score: 34.3326 Number of sites scoring better than the average of aligned sites = 898 Number in coding regions = 603 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 281 Fraction of orfs with sites within 600 bp upstream = 0.0451333 Motif number 5 ATTTAGTAGAACTCACCATATAATAATTATGAT 1 240 0 ATCACCATAA 0.891362 -61 CCAATCACCAAAAAATGTTAAGGGT 2 169 0 ATCACCAAAA 0.935004 -15 AATCTCACCATTTAATTAGTCTTTA 4 286 0 TTCACCTTAA 0.94713 -15 AACCTTAATATATCACATTTAAATTATACTCTG 5 117 1 TTCACATAAA 0.656585 -44 AATATCACCAAAAAAGATATATAAT 8 35 0 TTCACCAAAA 0.980062 -15 AATCTCACCGTTTAAATCAATATTT 11 3 1 TTCACCTTAA 0.947129 -25 TTTATCACCTAAATACTTTATTTAC 20 87 0 TTCACCAATA 0.909416 -15 TATGAATCACCGTCAAATCTTTTGAAG 22 85 0 ATCACCCAAA 0.770699 -17 CTTTTAATGGTATCACCTCAAAATGTTATGGCA 28 162 0 TTCACCAAAA 0.980062 -28 ATTTTCACCCCATAAGTTAAA 32 7 0 TTCACCATAA 0.965559 -15 TTCTTATCACCACAAAAATATTTTATC 33 189 0 TTCACCAAAA 0.980062 -17 TAGCCATAATTACCACCAAAAAATAAAA 34 6 0 TCCACCAAAA 0.877606 -212 TATTTCACCTTTTGAATATGATTAA 35 109 0 TTCACCTTGA 0.754621 -15 ATTTTCACCTATATATTTAAATATA 36 3 1 TTCACCTATA 0.86514 -179 * ***** **** Masking position 5 Map Score: 12.6936 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 64 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 CTCTATCGAAAGACATTTATTATGTCCTTT 1 100 1 AGACATTTAT 0.541649 -201 TCCTTAGTATAAAAATTTTTATATATGATT 2 120 1 AAAAATTTTT 0.373671 -64 ATTATTCATGAAAGATTTTTTATAAACTTT 4 104 1 AAAGATTTTT 0.878177 -197 AAAATAATAAAAAAATTTATACAGGTAATA 6 57 1 AAAAATTTAT 0.691121 -28 GAGCTAAACAGATTTTAAACAAACA 8 6 1 AAACAGATTT 0.20045 -44 TATCACCAAAAAAGATATATAATGTTTGTT 8 28 0 AAAGATATAT 0.878577 -22 GCTAAACCTAAAAGATTTTTTATTATGTAA 9 26 1 AAAGATTTTT 0.878177 -67 TTCAAAGCATTAAGATTTATAAGCAACTAT 14 93 0 TAAGATTTAT 0.52733 -92 TCCTATAGTAAGAGATATATATTTTAATGC 16 58 0 AGAGATATAT 0.638673 -123 ATATGCAATAAAACATTTATTCCTGCGAAA 16 89 0 AAACATTTAT 0.827409 -92 CACAAAACCGAAAGGTTTATATAGAATTTC 17 56 0 AAAGGTTTAT 0.623159 -147 CTGATGAAACAAAGATTTATAAGATAGCTT 17 147 1 AAAGATTTAT 0.951801 -56 AAAAATTTATAAAGATTTAAATTGGGG 18 8 0 AAAGATTTAA 0.755115 -29 CCCAAAAATAAAAATTTATAAAGATTTAA 18 18 0 AAAAATTTAT 0.691121 -19 AATATGTATTAGAGAGTTATTTATTTAAAC 22 27 1 AGAGAGTTAT 0.620082 -75 ACTTAGCAAGAAAGATTTTTGAAGATGTGT 25 31 1 AAAGATTTTT 0.878177 -270 TGACTTTAGAAAAGAGATATACTTTTTAAT 25 237 1 AAAGAGATAT 0.708963 -64 TATAAAAGAAAAAGATATATTAAATATTTT 27 33 1 AAAGATATAT 0.878577 -53 AAAATTTAAAAAAGAGTTATTTAAAGTTTT 29 20 0 AAAGAGTTAT 0.869832 -77 AGAATGATAAAAACATTTATTCTCGGGAGA 33 27 0 AAACATTTAT 0.827409 -179 TACTCGCATTAAAGATTTAAT 37 2 0 AAAGATTTAA 0.755115 -299 GATTTCTTTTAAAGATTTTATTCCTGCGAA 37 107 0 AAAGATTTTA 0.565082 -194 ATTTAAATTTAAAGATGTATATTACCAACT 37 148 1 AAAGATGTAT 0.689733 -153 GAATCATCTCAAAGATATTTGATATTGTAT 37 215 0 AAAGATATTT 0.752219 -86 ********** Masking position 8 Map Score: 19.0544 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 576 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 7 CTTTCGATAGAGGGTGTTCAATTTTTCATA 1 82 0 AGGGTGTTCA 0.946277 -219 CTTCCTTTAGGAGGCGTTCATTAATACCTT 4 191 0 GAGGCGTTCA 0.984749 -110 CTCCTAAAGGAAGGCGTTCAAAGTTTAATA 4 208 1 AAGGCGTTCA 0.981641 -93 GTATATTAATAAGGCGTTTAAAACTCCATT 10 53 0 AAGGCGTTTA 0.873982 -85 ATCCCAAAGAAAGGTGTTCAAATTTTCTAT 20 52 0 AAGGTGTTCA 0.93584 -50 CCCCCAAGTGGGGGCGTTCAAATTTTTATT 25 93 0 GGGGCGTTCA 0.987337 -208 CCCCCACTTGGGGGCGTTCATATATATCCT 25 109 1 GGGGCGTTCA 0.987337 -192 ********** Masking position 10 Map Score: 9.31966 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 4 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 GCTTTTGTCCATAAAAAATAATAACAAAAAACTA 3 18 1 ATAAATAATA 0.861224 -65 TATACCCTTCACAAAAAGTATTTGGAAAGGTTAG 3 56 1 ACAAATATTG 0.54534 -27 ATAGTGCCTTTCAAAACTTATTGAGATAATAAAA 4 159 1 TCAAATATTA 0.660132 -142 TATTGAGATAATAAAAGGTATTAATGAACGCCTC 4 177 1 ATAAATATTA 0.924063 -124 AGGAAGGCGTTCAAAGTTTAATAATAAGTTTATT 4 215 1 TCAAATAATA 0.497624 -86 AGTTATTCTTATAAAGACTAATTAAATGGTGAGA 4 275 1 ATAAATAATA 0.861225 -26 TACTTAATTTATAAATGTTAATTTTTCTCATTAG 5 14 1 ATAAATAATT 0.580741 -147 GATATTTTGATTAAAAAATAATAAAAAAATTTAT 6 43 1 TTAAATAATA 0.502832 -42 ACGCACCACCACAAACTATATATAAAAAGTCCTA 7 14 1 ACAAATATAA 0.552603 -287 CAGATTTTAAACAAACATTATATATCTTTTTTGG 8 19 1 ACAAATATAA 0.552603 -31 TAATGCCTTAATAAAACTTATTGTAAGCATGGTT 16 30 0 ATAAATATTT 0.730769 -151 TTTACAAAAAACAAAACGTATTTAAGG 17 186 1 ACAAATATTA 0.922654 -17 AGTATCACAAAGAATATTTATGATAAAATA 21 71 0 ACAAATATTA 0.922655 -20 AAAAATAAAAATAGAGTCTATTCACTTAT 23 6 0 ATAGATATTA 0.50361 -95 TATAGTTTTTGCAAAAGTTATTAAAATTAAAAAT 25 62 1 GCAAATATTA 0.532792 -239 TACGGAAGTTATTAAAAATAATGATAATATTGTT 28 75 1 ATTAATAATA 0.391197 -115 TTCTAAGATTATAAATTTTATTCTTTAAACTTTT 29 63 1 ATAAATATTT 0.731085 -34 TATAATTTTTATAAAACCTAATGAACACAT 31 13 1 ATAAATAATA 0.861224 -20 TCAGAAATTAATAAAATTTATTAATGGGTATTAT 33 80 0 ATAAATATTA 0.924063 -126 AATACAGAAAACAAAACTTATTTATTCACTTACT 35 52 1 ACAAATATTA 0.922654 -72 TATAATCTACATTAATCATATTCAAAAGGTGAAA 35 98 1 ATTAATATTA 0.55775 -26 TAAAAATTTTATAAAGATTATTAATAAAGTTAAT 37 67 1 ATAAATATTA 0.924128 -234 ACAATCCCTCATAAAAAATAATTTAATGAAATTT 37 276 0 ATAAATAATT 0.580741 -25 AATGTTGGTTATAAACGATATTTAGCAATTACAC 38 39 0 ATAAATATTA 0.924129 -155 ***** **** * Masking position 9 Map Score: 18.1964 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 161 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 CTTGTCATATCCTATCAAAAATATGCAAAT 1 196 1 CCTATCAAAA 0.850454 -105 CTCCTAACCTTTCCAAATACTTTTTGT 3 66 0 CCTTTCCAAA 0.950605 -17 AAGTATAGTGCCTTTCAAAACTTATTGAGA 4 155 1 CCTTTCAAAA 0.978145 -146 ATATATAGTGCCTTTCAAAATTAATAAACT 4 241 0 CCTTTCAAAA 0.978145 -60 TAGTTATAGTCCTTTGCAAAAGGGTTAAAT 10 18 1 CCTTTGCAAA 0.692064 -120 AATACTTATATCTTACAAAATTATGCTGAT 17 122 1 TCTTACAAAA 0.749368 -81 ATATCCTATATATTTCAAAATGTTTTGCAA 25 132 1 TATTTCAAAA 0.64963 -169 AATTTTCGCATCTTTCTAAATATTTTCCTA 25 200 0 TCTTTCTAAA 0.787668 -101 TATAACTTAACCTTTCAAAATGATAGATTA 26 31 0 CCTTTCAAAA 0.978145 -105 AAATATGGTATCTTTCAGAAATTAATAAAA 33 98 0 TCTTTCAGAA 0.81589 -108 TCGTATAGTATCTTTCAAAAATAATAAAAA 37 43 1 TCTTTCAAAA 0.95923 -258 ********** Masking position 9 Map Score: 8.55431 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 60 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TGACTTAATATGATGAACCTTTC 4 1 0 TGAGACTTTC 0.970097 -300 TAATTTAGGATGATGAACCTTACGGGGGCTGAG 4 72 0 TGAGACTTAC 0.775399 -229 AAAAAGTTTATAAAAAATCTTTCATGAATAATA 4 103 0 TAAAACTTTC 0.648431 -198 ACTCTAAAAGTATAGTGCCTTTCAAAACTTATT 4 148 1 TATGGCTTTC 0.924257 -153 ACTGTAGATATATAGTGCCTTTCAAAATTAATA 4 245 0 TATGGCTTTC 0.924257 -56 TGCATCGTTTTGATGAAACTTTC 14 1 0 TGAGACTTTC 0.970097 -184 CGGATATATTAAAAGGAGCTTTCATCCCCTTAA 19 18 0 AAAGACTTTC 0.748532 -70 TTTGCAGAATTTTCGCATCTTTCTAAATATTTT 25 204 0 TTTGACTTTC 0.81246 -97 GTCCAACAACTGTGGTAATTTTCCCTTTTCTAT 30 101 0 TGTGATTTTC 0.779887 -58 CTTTAGGAAATATGGTATCTTTCAGAAATTAAT 33 102 0 TATGACTTTC 0.960277 -104 ATTTTTTTCTTGATGAAATTTTCAAGCTCCTTT 34 97 0 TGAGATTTTC 0.804099 -121 ATGACTTTCGTATAGTATCTTTCAAAAATAATA 37 36 1 TATGACTTTC 0.96027 -265 TTAATAAAGTTAATGGGGCTTTCGCAGGAATAA 37 87 1 TAAGGCTTTC 0.933933 -214 *** * * ***** Masking position 10 Map Score: 9.04297 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 51 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 ATGAAAAATTGAACACCCTCTATCGAAAGA 1 83 1 GAACACCCTC 0.933702 -218 AGGTATTAATGAACGCCTCCTAAAGGAAGG 4 192 1 GAACGCCTCC 0.988263 -109 ATTAAACTTTGAACGCCTTCCTTTAGGAGG 4 207 0 GAACGCCTTC 0.942189 -94 TTTACCTGCCGAACCCCGCCAGGCCCGGAA 7 244 1 GAACCCCGCC 0.958436 -57 ATAAAAATTTGAACGCCCCCACTTGGGGGC 25 94 1 GAACGCCCCC 0.995353 -207 GGATATATATGAACGCCCCCAAGTGGGGGC 25 108 0 GAACGCCCCC 0.995353 -193 ********** Masking position 3 Map Score: 7.33737 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 2 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 AATAATATAATAGGACTTTTTATATATAGT 7 28 0 TAGGACTTTT 0.961996 -273 AGTTTAAATATAGGAATTACTGTTTTAGTT 15 74 0 TAGGAATTAC 0.848916 -171 TCTCTTACTATAGGACTTTCGCAGGAATAA 16 73 1 TAGGACTTTC 0.984793 -108 ATTATGTAGATAGGACTTTCGCAGCTTATC 16 152 0 TAGGACTTTC 0.984793 -29 TCTATCTCTTTAGGAATTTTAATACCTATT 21 14 0 TAGGAATTTT 0.924562 -77 TTTAAAGTTTTAGGAATTTT 29 1 0 TAGGAATTTT 0.924562 -96 ATGGGTATTATAGGAGTTTCTATATATTTA 33 61 0 TAGGAGTTTC 0.948431 -145 GCGAGTATTTTATGACTTTCGTATAGTATC 37 25 1 TATGACTTTC 0.878514 -276 ********** Masking position 5 Map Score: 6.46639 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 45 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 ATTAACAAAAGAAAAATTAAGCCTTGTCATA 1 174 1 GAAAATTAAG 0.580484 -127 GCTCATCATCGAGGAATTAAAATAATCTCTC 4 44 1 GAGGATTAAA 0.835275 -257 AAAACTTATTGAGATAATAAAAGGTATTAAT 4 171 1 GAGAAATAAA 0.438603 -130 AATTAACATTTATAAATTAAGTAAGT 5 6 0 TATAATTAAG 0.702371 -155 ATTTAAATGTGATATATTAAGGTTGTTATAA 5 110 0 GATAATTAAG 0.915896 -51 TCATCAAAACGATGCATTAAATGGACTTTCA 14 18 1 GATGATTAAA 0.860604 -167 TATATACTAAGAGACATTAAGGGACTGAAAG 14 43 0 GAGAATTAAG 0.89944 -142 AGAGACATTAAGGGGATGAAAG 19 2 1 GAGAATTAAG 0.89944 -86 AACCAAAACGGATATATTAAAAGGAGCTTTC 19 28 0 GATAATTAAA 0.917471 -60 TGGAATAGGTATTAAAATTCCTAAAG 21 6 1 TAGGATTAAA 0.523546 -85 TAGACAATTTTATATATTAAATATTCATTTT 23 46 1 TATAATTAAA 0.706666 -55 TTGATGAATTAAATGAACTTTAA 26 3 1 GATGATTAAA 0.860604 -133 CTTTCAAAATGATAGATTAAAGTTCATTTAA 26 19 0 GATAATTAAA 0.917471 -117 AAAAGAAAAAGATATATTAAATATTTTTGCT 27 36 1 GATAATTAAA 0.917471 -50 AATTTTTCGAGATAGATTTAACCAACAATAT 28 101 0 GATAATTTAA 0.487502 -89 AATTTAAATTTATAAATTAAGATTTCTTTTA 37 126 0 TATAATTAAG 0.702371 -175 **** ****** Masking position 6 Map Score: 14.0194 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 275 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 AAAAATTAAGTTAAGATTAAAAGAAAATTTTC 1 20 1 TTAGATAAAA 0.703313 -281 ACTTTACGAAAAACTATGAAAATTTTCTTTTA 1 37 0 AAATATAAAA 0.659412 -264 GCCTTGTCATATCCTATCAAAAATATGCAAAT 1 194 1 ATCTATAAAA 0.520331 -107 TTTTTAAATCTTACTATAAAAAGGA 1 286 1 TTATATAAAA 0.930801 -15 TTTAAAAAGTTTGATATAAAAAAGTGTTGGTA 2 71 0 TTGTATAAAA 0.683234 -113 TGCTAAATCCTTAGTATAAAAATTTTTATATA 2 113 1 TTATATAAAA 0.930801 -71 TCCATAAAAAATAATAACAAAAAACTATTTAT 3 25 1 ATATAAAAAA 0.552622 -58 ATTAATAAACTTATTATTAAACTTTGAACGCC 4 220 0 TTATATAAAC 0.518389 -81 TGATTAAAAAATAATAAAAAAATTTATACAGG 6 50 1 ATATAAAAAA 0.552621 -35 ACAAAACATTACATTATTAAAATAATTAAGGT 10 81 0 ACATATAAAA 0.531764 -57 AAATTTAAAATTAATATTAAAAAACACGTTTA 13 13 1 TTATATAAAA 0.930866 -31 TTAATGTCTCTTAGTATATAAATAGGTAAATA 14 54 1 TTATATTAAA 0.571766 -131 AGTACAAAAAATAAGATAAAAAAGGATAAAAA 15 27 0 ATAGATAAAA 0.6868 -218 AAATGAATATTTAATATATAAAATTGTCTATT 23 44 0 TTATATTAAA 0.571272 -57 GCAAAAGTTATTAAAATTAAAAATAAAAATTT 25 72 1 TTAAATAAAA 0.465007 -229 CTAATCAGATATATCATTAAAACGCTATAACT 26 54 0 ATACATAAAA 0.686803 -82 TTATGATGGGATGTTATAAAAATTTTACCTAA 26 82 0 ATGTATAAAA 0.66624 -54 TAGTAATTATATAATATCAAAAGCGGGATAGT 28 12 0 ATATATAAAA 0.92573 -178 TTTTGAGGTGATACCATTAAAAGAATAA 28 172 1 ATACATAAAA 0.686808 -18 TCCTTGGTGATTAATATGATAAAAGTAAAAAA 30 17 1 TTATATATAA 0.415603 -142 ATATTTTATCTTAATTTTAAAAATTAAATTTC 33 167 0 TTATTTAAAA 0.420709 -39 TCTGTATTGTTTAATATGAAAATCTAAATATA 35 28 0 TTATATAAAA 0.930763 -96 ATATTAGTTTTAAATATAAAAATTTGTATATT 36 30 0 TAATATAAAA 0.676721 -152 TAAATAGTTTAAAGTATTAAAAATTTTATTAT 36 155 1 AAATATAAAA 0.659412 -27 TCAGAAATCGATACTATAAAAACCATATAATA 38 137 0 ATATATAAAA 0.92573 -57 *** *** **** Masking position 11 Map Score: 13.7372 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 156 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 15 TCGAAAGACATTTATTATGTCCTTTATCTT 1 105 1 TTTATTATGT 0.768728 -196 TTTGTTATTATTTTTTATGGACAAAAGCGT 3 16 0 TTTTTTATGG 0.630315 -67 TAAAAGATTTTTTATTATGTAATGAAACCA 9 34 1 TTTATTATGT 0.768728 -59 AAGCATGGTTTTTATAAGGGGGGAGGTTT 16 10 0 TTTATAAGGG 0.8868 -171 TACAATAAGTTTTATTAAGGCATTAAAATA 16 39 1 TTTATTAAGG 0.768007 -142 TTTTCTGTTATTTATGATGGGATGTTATAA 26 95 0 TTTATGATGG 0.917139 -41 GTTTAATCAATTTATAAGGGTGTAGTT 27 69 1 TTTATAAGGG 0.8868 -17 TTTTAAAGTATTTATTAGGTATCCATTCAA 36 116 0 TTTATTAGGT 0.841287 -66 TATTAAAAATTTTATTATGGCAA 36 169 1 TTTATTATGG 0.930646 -13 ATATTTAAAATTTATGTGGGAAATAGTTCT 37 187 0 TTTATGTGGG 0.691618 -114 TAAATTATTTTTTATGAGGGATTGTT 37 285 1 TTTATGAGGG 0.946383 -16 ********** Masking position 5 Map Score: 6.25253 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 94 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097