AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_mjan_reg_100.orf -o00620_mjan_100.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: MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) MJ1425 25 malate dehydrogenase Input sequences: #1 MJ0102 300 Phenylacrylic acid decarboxylase #2 MJ0107 167 dihydropteroate synthase #3 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #4 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #5 MJ0487 282 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #6 MJ0490 47 L-lactate dehydrogenase EGAD|7256|705 #7 MJ0502 160 3-phosphoshikimate-1-carboxyvinyltransferase (aroA) #8 MJ0503 84 2-isopropylmalate synthase (leuA) #9 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #10 MJ0542 127 phosphoenolpyruvate synthase #11 MJ0636 239 dihydrolipoamide dehydrogenase #12 MJ1195 135 2-isopropylmalate synthase (leuA) #13 MJ1230 22 M. jannaschii predicted coding region MJ1230 #14 MJ1231 255 oxaloacetate decarboxylase alpha chain (oadA) #15 MJ1392 300 2-isopropylmalate synthase (leuA) #16 MJ1424 202 tRNA intron endonuclease (endA) #17 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 CGGCACCATTTTATTATTTTATTTTAGGTT 1 189 1 TTATTATTTT 0.936912 -112 TAGGTTGTTATATTTATTTTTTTAGATTTA 1 213 1 TATTTATTTT 0.956104 -88 TTTTAAATAGTATTTATTTTTTAAATCTTA 1 255 1 TATTTATTTT 0.956104 -46 TATAAATTATGTTTTAATTTAATTACATTT 2 22 1 GTTTTAATTT 0.814986 -146 ACATTTATAGTTTTCATTTTAAGACTTTCG 2 46 1 TTTTCATTTT 0.824409 -122 AATGATGTTGTATTTATTTTTGAGAATGAC 3 117 0 TATTTATTTT 0.956104 -167 ATGTAAATTAATTTTATTTTTTCTTATGCC 3 170 1 ATTTTATTTT 0.898503 -114 TGCTTCTATTTTTTTAAATTGTTATTTTCT 4 24 1 TTTTTAAATT 0.695903 -96 AATTAATAAAAATTTATTTTAGTAGTTAAT 5 18 0 AATTTATTTT 0.837247 -265 TTCGTCCATATTCTTATTTTAAAAATTTTC 5 154 0 TTCTTATTTT 0.945065 -129 TCTTTTTATAGTATTATTTTCTTTAATAAA 5 232 0 GTATTATTTT 0.776017 -51 TTCCTCTTTTTAATTTAATTTTAAAA 6 7 1 TTTTTAATTT 0.949694 -41 ACTTACTTAATTTATAAATGTTA 7 4 1 TACTTAATTT 0.836366 -157 ATAAATTTTTTTATTATTTTTTAATCAAAA 8 47 0 TTATTATTTT 0.936912 -38 CCTCAAATAATTTTTAATTTATAATGGATA 9 250 0 TTTTTAATTT 0.949694 -27 TATGAAACTTTTTTTAATTTTTTATAACAT 10 12 1 TTTTTAATTT 0.949694 -116 CAAATATTTAAATTTATTTTAAAATAAAAG 10 87 1 AATTTATTTT 0.837247 -41 ATCTATTTTCTTTTTATTTTCTTTTTAAGA 11 30 1 TTTTTATTTT 0.973821 -210 GAGAAAGTTATTCTCATTTTTGCAGAAAAA 11 58 1 TTCTCATTTT 0.684676 -182 ATTGTTGTTGTTCTTATTTTTTATTTGATT 11 151 1 TTCTTATTTT 0.945065 -89 CCACCAAAACTTTTTAATTTTCTGTTATTT 12 112 0 TTTTTAATTT 0.949694 -24 ATTTTTGTATTAATTAATTTAAACTCAATT 14 79 1 TAATTAATTT 0.806788 -177 CCCTCACAAATATTTATTTTGATTTAAAAA 14 230 0 TATTTATTTT 0.956104 -26 TATAAAATTTTTATTATTTTTGAAAGATAC 15 50 0 TTATTATTTT 0.936912 -251 TTTAAAAGAAATCTTAATTTATAAATTTAA 15 124 1 ATCTTAATTT 0.675089 -177 TCATTATGAGTATTTAAATTTCATTAAATT 15 261 1 TATTTAAATT 0.570887 -40 AAATTTCATTAAATTATTTTTTATGAGGGA 15 276 1 AAATTATTTT 0.66724 -25 AACTTCGCAGTTTTTATATTAAAAAGGTAT 16 85 0 TTTTTATATT 0.818463 -118 AACCATATGTTATTTATTTTATTATCCACA 16 153 1 TATTTATTTT 0.956104 -50 TTTTATTTGTGTATTATTTTAGACACTTTT 17 42 1 GTATTATTTT 0.776017 -259 ********** Masking position 6 Map Score: 39.7769 Number of sites scoring better than the average of aligned sites = 1597 Number in coding regions = 1014 Number in noncoding regions = 583 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 2 CCCTTAAGCATAAATTTTCTTTAAAAAATT 2 106 1 TAAATTTTCT 0.934832 -62 TTCGTAGAAATAAATTTTTTAAAGAAAATT 2 118 0 TAAATTTTTT 0.936024 -50 TCCATGTAAATTAATTTTATTTTTTCTTAT 3 167 1 TTAATTTTAT 0.776149 -117 AGATTGCCATTAAAATTTCTAATATCAAAG 5 100 1 TAAAATTTCT 0.95343 -183 AAAGAAGGACGAAAATTTTTAAAATAAGAA 5 144 1 GAAAATTTTT 0.653316 -139 ACAGAACTGCTAAATTTTATTCTTTTTATA 5 252 0 TAAATTTTAT 0.899605 -31 AATTTAATTTTAAAATCTCTTTTGTGAGGG 6 22 1 TAAAATCTCT 0.884488 -26 ATTACCTGTATAAATTTTTTTATTATTTTT 8 56 0 TAAATTTTTT 0.936024 -29 GAAACTTTTTTTAATTTTTTATAACATTTT 10 15 1 TTAATTTTTT 0.849944 -113 ATTCAAATATTTAAATTTATTTTAAAATAA 10 84 1 TTAAATTTAT 0.831305 -44 TTAAAATTTTTTAAATAATAT 11 2 1 TAAAATTTTT 0.950409 -238 CAATTACAATTAAATTTTTTAATCAAATAA 11 171 0 TAAATTTTTT 0.936024 -69 TCTGATTAGGTAAAATTTTTATAACATCCC 12 77 1 TAAAATTTTT 0.950409 -59 CCAAAACTTTTTAATTTTCTGTTATTTATG 12 109 0 TTAATTTTCT 0.847324 -27 TCCTAAATCTTAAATTTTCTTAATCAATTT 14 114 1 TAAATTTTCT 0.934832 -142 ATTAAATCTTTAATGCGAGTA 15 2 1 TTAAATCTTT 0.751474 -299 ATAATCTTTATAAAATTTTTATTATTTTTG 15 58 0 TAAAATTTTT 0.950409 -243 TTCGCAGGAATAAAATCTTTAAAAGAAATC 15 107 1 TAAAATCTTT 0.886528 -194 ATCTTTAAATTTAAATTTATAAATTAAGAT 15 134 0 TTAAATTTAT 0.831305 -167 ATTGTATATTTAAAATTTATGTGGGAAATA 15 192 0 TAAAATTTAT 0.926093 -109 TATAAAATCTTAAAATTTATTGTGGATAAT 16 173 0 TAAAATTTAT 0.926093 -30 TTGGGAACTTTAAAATCTCTTTTTTAACAG 17 150 0 TAAAATCTCT 0.884488 -151 ********** Masking position 6 Map Score: 34.7535 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 368 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 AATATAACAACCTAAAATAAAATAATAAAATG 1 195 0 CCAAAATAAA 0.665697 -106 AATAGTTAATCCATAAATCTAAAAAAATAAAT 1 224 0 CCTAAATTAA 0.576671 -77 AGTATTTATTTTTTAAATCTTAACTTAACAGT 1 263 1 TTTAAATTTA 0.809198 -38 AAAATGAAAACTATAAATGTAATTAAATTAAA 2 34 0 CTTAAATTAA 0.624708 -134 CTGCGAAAGTCTTAAAATGAAAACTATAAATG 2 47 0 CTAAAATAAA 0.708736 -121 TTTCGCAGTATTATATATTAAAAGGCATTTAG 2 71 1 TTTATATAAA 0.525241 -97 TCTACGAAAGTCCTAAATCTTATATTGACTAT 2 140 1 TCTAAATTTA 0.776326 -28 TGAATTACTGTCATAAATCTTAATCTCCCAGC 3 17 0 TCTAAATTTA 0.776326 -267 ATAAAGCTGTTTAAAAATCAAATCGGCTATTA 3 52 1 TTAAAATAAA 0.867816 -232 TTTTAACTCCTTCAATATAATAGCCGATTTGA 3 69 0 TTAATATATA 0.732224 -215 ATCTCCAAAACTTTATATATTACTTTTAATAA 3 225 1 CTTATATTTA 0.409376 -59 TCTAAGCTACTTTTATATAATATAACCTTGTG 4 85 0 TTTATATATA 0.749026 -35 CATTAAAATTTCTAATATCAAAGTTTTACAAA 5 107 1 TCAATATAAA 0.703496 -176 CAAAAGAGATTTTAAAATTAAATTAAAAAGAG 6 14 0 TTAAAATAAA 0.845857 -34 CTTACTTAATTTATAAATGTTAATTTTTCTCA 7 12 1 TTTAAATTTA 0.809201 -149 GGGGTATCCATTATAAATTAAAAATTATTTGA 9 246 1 TTTAAATAAA 0.886784 -31 AATGATAATATTATAAATAAAATAGTAGAGTT 10 55 0 TTTAAATAAA 0.882751 -73 ATATTATCATTCAAATATTTAAATTTATTTTA 10 76 1 TCAATATTAA 0.533528 -52 TTAAATTTATTTTAAAATAAAAGCTATATATA 10 94 1 TTAAAATAAA 0.838661 -34 TTAAAATTTTTTAAATAATATCTATTTTCT 11 9 1 TTTAAATATA 0.89278 -231 AACTTAACCTTTCAAAATGATAGATTAAAGTT 12 26 0 TTAAAATATA 0.861109 -110 CAATTTTATCTCCTAAATCTTAAATTTTCTTA 14 104 1 TCTAAATTTA 0.776326 -152 GCTGTGCCTTTTTTAAATCAAAATAAATATTT 14 221 1 TTTAAATAAA 0.89825 -35 ATAGTATCTTTCAAAAATAATAAAAATTTTAT 15 47 1 TCAAAATATA 0.835351 -254 AAATCTTAATTTATAAATTTAAATTTAAAGAT 15 132 1 TTTAAATTAA 0.807321 -169 ATATTTGATATTGTATATTTAAAATTTATGTG 15 199 0 TTTATATTAA 0.641208 -102 AGATTCACCTCAATATTATAGAACTTTCGC 16 9 1 CTAATATATA 0.503496 -194 ACTTCGCAGTTTTTATATTAAAAAGGTATTTA 16 82 0 TTTATATAAA 0.490282 -121 TTTTAAGATTTTATAAATAATAACT 16 188 1 TTTAAATATA 0.893003 -15 TCTAAAAGTGTCTAAAATAATACACAAATAAA 17 43 0 TCAAAATATA 0.835348 -258 GAGATAGTTCTTCAATATCAAAACCAAAGCTT 17 86 0 TTAATATAAA 0.743617 -215 TAAAACAATCTCTTAAATAATAAGTTAATGAT 17 199 0 TCTAAATATA 0.872546 -102 AACATAGTCCTCTAAAATTATAAAACAATCTC 17 219 0 TCAAAATATA 0.83535 -82 ** ***** *** Masking position 7 Map Score: 42.304 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 692 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 4 ATGCATCCTATTTTGATGAAATGGAAAGCT 1 40 1 TTTTGATGAA 0.831317 -261 ACCACTAATTTTTTAATCAACAGAGTATAA 7 140 0 TTTTAATCAA 0.976201 -21 TTTTATTATTTTTTAATCAAAATATCAATA 8 39 0 TTTTAATCAA 0.976201 -46 AATGCATCTGTTTTGATCAACGCACCATAG 9 45 1 TTTTGATCAA 0.958213 -232 TTTAACTAAGTTTTGATCAACCTTTTCTAA 9 97 1 TTTTGATCAA 0.958213 -180 TTAAGCCCTATTTTAATCAAACGAACTCAT 9 202 0 TTTTAATCAA 0.976201 -75 CAATTAAATTTTTTAATCAAATAAAAAATA 11 165 0 TTTTAATCAA 0.976201 -75 AGTTATAGCGTTTTAATGATATATCTGATT 12 54 1 TTTTAATGAT 0.663883 -82 ATATATATCATTTCAATCAATACTACACTA 14 28 1 TTTCAATCAA 0.940273 -228 TCTTAAATTTTCTTAATCAATTTTTGATGA 14 121 1 TCTTAATCAA 0.875646 -135 AGTCTTATAATTTCAATCATAGTTACCCCT 14 150 0 TTTCAATCAT 0.779114 -106 CTGTGCCTTTTTTAAATCAAAATAAATATT 14 222 1 TTTAAATCAA 0.852323 -34 ********** Masking position 6 Map Score: 17.2391 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 29 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 AAACGAAACTTTTAGAAAAAGTTAAACAAAATC 1 144 0 TTTAGAAGTT 0.951852 -157 ATAAATACTATTTAAAAATAGTTAATCCATAAA 1 239 0 TTTAAAAGTT 0.94057 -62 AAATTCACCATTAAAAACTGTTAAGTTAAGAT 1 279 0 ATTAAAAGTT 0.460289 -22 TATGTTTTAATTTAATTACATTTATAGTTTTCA 2 29 1 TTTAATATTT 0.719182 -139 GTATTATATATTAAAAGGCATTTAGATGCCCTT 2 78 1 TTAAAAGTTT 0.523143 -90 AAATAAATTTTTTAAAGAAAATTTATGCTTAAG 2 108 0 TTTAAAAATT 0.510385 -60 CGATTTGATTTTTAAACAGCTTTATTGTTGAAT 3 44 0 TTTAAAATTT 0.907369 -240 ATATATTACTTTTAATAATTGTTAATGATTGAT 3 239 1 TTTAATAGTT 0.805364 -45 TCGTTAAATATTAACACAAGGTTATATTATATA 4 71 1 TTAACAAGTT 0.525688 -49 GAATTGTAGATTTAAACATGGGTTGATAAACAT 5 190 1 TTTAAAAGGT 0.786879 -93 CGAACAACCTTTTAGAAAAGGTTGATCAAAACT 9 105 0 TTTAGAAGTT 0.951852 -172 CTCCCAACCTTTTAGTAAAAGGTTACTCGAACA 9 132 0 TTTAGTAGGT 0.546648 -145 TTATAAAAAATTAAAAAAAGTTTCATAA 10 6 0 TTAAAAATTT 0.82464 -122 AGCTTTTATTTTAAAATAAATTTAAATATTTGA 10 86 0 TTAAAAATTT 0.82464 -42 ATAGATATTATTTAAAAAATTTTAA 11 3 0 TTTAAAATTT 0.907369 -237 TATTTTCTTTTTAAGAGAAAGTTATTCTCATTT 11 44 1 TTAAGAAGTT 0.904676 -196 TATCGAAAGTTTTAGATAAGTTTTTGCATGGTT 11 104 1 TTTAGAATTT 0.924448 -136 TTGATGAATTAAATGAACTTTAATCTATCAT 12 9 1 TTAAATATTT 0.551463 -127 ATTAATAATCTTTATAAAATTTTTATTATTTTT 15 59 0 TTTATAATTT 0.490862 -242 TAAAAAATAATTTAATGAAATTTAAATACTCAT 15 266 0 TTTAATATTT 0.719182 -35 TGTGTATTATTTTAGACACTTTTAGAGATGAGG 17 49 1 TTTAGAATTT 0.924448 -252 AAAATCAATATTAAGAGATAGTTCTTCAATATC 17 99 0 TTAAGAAGTT 0.904676 -202 AACTTATTATTTAAGAGATTGTTTTATAATTTT 17 205 1 TTAAGAAGTT 0.904676 -96 TTGATGATTATTTAGATGAGGGTGATGAATTCA 17 249 1 TTTAGAGGGT 0.51829 -52 GTAGGGGAGTTTTAGATGCATTTAGGGAG 17 282 1 TTTAGAGTTT 0.740564 -19 ****** * *** Masking position 2 Map Score: 24.2785 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 447 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 6 ATATATAATACTGCGAAAGTCTTAAAATGAA 2 58 0 CTGCGAAGTC 0.994931 -110 AAATTTATTTCTACGAAAGTCCTAAATCTTA 2 131 1 CTACGAAGTC 0.981666 -37 ATATATCAAACTGCGAAGTCCTATTCAAAGA 5 72 1 CTGCGAATCC 0.972995 -211 GAAAGATACTATACGAAAGTCATAAAATACT 15 28 0 ATACGAAGTC 0.874135 -273 GATTTTATTCCTGCGAAAGCCCCATTAACTT 15 93 0 CTGCGAAGCC 0.992485 -208 TCATTTATTCCTGCGAAAGTTCTATAATATT 16 22 0 CTGCGAAGTT 0.962205 -181 AATATAAAAACTGCGAAGTTCTATATTAATT 16 95 1 CTGCGAATTC 0.981666 -108 ******* *** Masking position 6 Map Score: 8.72574 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 6 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AGATTTATGGATTAACTATTTTTAAATAGT 1 236 1 ATTAACTATT 0.761526 -65 AGATTTAAAAAATAAATACTATTTAAAAAT 1 253 0 AATAAATACT 0.641594 -48 AAATTCACCATTAAAAACTGTTAAGTTAA 1 282 0 ATTAAAAACT 0.853862 -19 ATTATCAATCATTAACAATTATTAAAAGTA 3 245 0 ATTAACAATT 0.912792 -39 TAGAGAAGAAAATAACAATTTAAAAAAATA 4 30 0 AATAACAATT 0.91276 -90 ATTAAATATTAACTACTAAAATAAATT 5 8 1 ATTAACTACT 0.724854 -275 AATCTCAATTAATAAAAATTTATTTTAGTA 5 24 0 AATAAAAATT 0.876676 -259 AATGAGAAAAATTAACATTTATAAATTAAG 7 16 0 ATTAACATTT 0.391568 -145 TACTCTGTTGATTAAAAAATTAGTGGTG 7 143 1 ATTAAAAAAT 0.713697 -18 TGATATTTTGATTAAAAAATAATAAAAAAA 8 42 1 ATTAAAAAAT 0.713697 -43 TTATACAGGTAATAACAACTCT 8 73 1 AATAACAACT 0.895714 -12 TCCATTATAAATTAAAAATTATTTGAGGTG 9 252 1 ATTAAAAATT 0.876805 -25 TTTTTTAAATAATATCTATTTTCTTTTTAT 11 17 1 AATATCTATT 0.166936 -223 GAACAACAACAATAACAATTGAAATAAAAC 11 134 0 AATAACAATT 0.91276 -106 TTTTTAATCAAATAAAAAATAAGAACAACA 11 156 0 AATAAAAAAT 0.713592 -84 TTTTTATTTGATTAAAAAATTTAATTGTAA 11 168 1 ATTAAAAAAT 0.713697 -72 GTTAATGGTTAATAACAATTACAATTAAAT 11 186 0 AATAACAATT 0.91276 -54 AATTAAAAATTGGTTTAATGT 11 229 0 ATTAAAAATT 0.876805 -11 TTTAAATCAAAATAAATATTTGTGAGGGAT 14 232 1 AATAAATATT 0.675231 -24 TTTCAAAAATAATAAAAATTTTATAAAGAT 15 55 1 AATAAAAATT 0.876676 -246 AAAGATGTATATTACCAACTTTTTAGTCCA 15 158 1 ATTACCAACT 0.45088 -143 AGATTTTATAAATAATAACT 16 193 1 AATAATAACT 0.403575 -10 ********** Masking position 3 Map Score: 23.1244 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 452 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 8 AATTTCCCCTCACAAAAGAGATTTT 6 33 0 CCCCTCACAA 0.984986 -15 ACGAACTCATCTCCTCATAACTACCGCATG 9 182 0 CTCCTCATAA 0.95708 -95 TTTATAACATCCCATCATAAATAACAGAAA 12 94 1 CCCATCATAA 0.915874 -42 ATCATAGTTACCCCTCATCAAAAATTGATT 14 135 0 CCCCTCATCA 0.962818 -121 AGCTATCCCTCACAAATATTTATTT 14 241 0 TCCCTCACAA 0.962468 -15 CAGAACTATTTCCCACATAAATTTTAAATA 15 186 1 TCCCACATAA 0.872275 -115 AACAATCCCTCATAAAAAATAATTT 15 286 0 TCCCTCATAA 0.97443 -15 CCATTAATTCCTCCTCAAAATCAATATTAA 17 118 0 CTCCTCAAAA 0.846183 -183 ********** Masking position 7 Map Score: 7.47098 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 31 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TAAGAGGCATTGCCGAGCGTAGCG 1 4 1 GAGCATTGCC 0.993697 -297 ATCAAAATAGGATGCATTGCCTCGCTACGCT 1 26 0 GAGCATTGCC 0.993697 -275 TCATTTAACCGAAGCGTTAGCTTCGGGCTAC 1 102 1 GAGCGTTAGC 0.950398 -199 TAAAAAAATAGAAGCATGGGCTAATTTAT 4 9 0 GAGCATGGGC 0.967875 -111 CTATGCTAAGAGGCATTACCGAGCGTAGCG 9 10 1 GAGCATTACC 0.990124 -267 GATCAAAACAGATGCATTACCTCGCTACGCT 9 32 0 GAGCATTACC 0.990124 -245 ** ******** Masking position 7 Map Score: 6.72232 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 7 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 AAGTGAATAAATCAATCTCTTCATATTGAT 8 16 1 ATCAATCTCT 0.948753 -69 TAGGGCTTAACTCTATCTCTATTTGGGGTA 9 222 1 CTCTATCTCT 0.77832 -55 AAATGAGAATAACTTTCTCTTAAAAAGAAA 11 47 0 AACTTTCTCT 0.791679 -193 TAATTAATACAAAAATCTCTATCCTTGTTT 14 65 0 AAAAATCTCT 0.744335 -191 AGCTATCCCTCACAAATATT 14 246 0 AGCTATCCCT 0.811617 -10 AACAATCCCTCATAAAAAAT 15 291 0 AACAATCCCT 0.935557 -10 GATATTGAAGAACTATCTCTTAATATTGAT 17 99 1 AACTATCTCT 0.96017 -202 ATGATTCATTATCAACCTCTGTTTTTGGGA 17 174 0 ATCAACCTCT 0.812229 -127 AAAATTATAAAACAATCTCTTAAATAATAA 17 208 0 AACAATCTCT 0.967426 -93 ********** Masking position 10 Map Score: 3.91623 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 255 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 GAAAGATTTTGTTTAACTTTTTCTAAAAGTTT 1 140 1 GTTAACTTTT 0.591155 -161 TAGATTTATGGATTAACTATTTTTAAATAGTA 1 235 1 GATAACTATT 0.881136 -66 TGCCCTTAAGCATAAATTTTCTTTAAAAAATT 2 104 1 CATAATTTTT 0.686795 -64 TTTTCTTATGCCTAAACTATTTTCGTTAATTG 3 188 1 CCTAACTATT 0.928754 -96 GCTTAAATCTCCAAAACTTTATATATTACTTT 3 219 1 CCAAACTTTT 0.906366 -65 ATACAGAACTGCTAAATTTTATTCTTTTTATA 5 252 0 GCTAATTTTT 0.635119 -31 ACTAAGTTTTGATCAACCTTTTCTAAAAGGTT 9 101 1 GATAACCTTT 0.789629 -176 AAGGTTACTCGAACAACCTTTTAGAAAAGGTT 9 115 0 GAAAACCTTT 0.623368 -162 TTAAAATAGGGCTTAACTCTATCTCTATTTGG 9 216 1 GCTAACTCTT 0.699364 -61 GCAAAAATGAGAATAACTTTCTCTTAAAAAGA 11 49 0 GAAAACTTTT 0.846262 -191 TGTTATTAACCATTAACTTTATATTCAATAAC 11 199 1 CATAACTTTT 0.948928 -41 AATCCCACCAAAACTTTTTAATTTTCTGT 12 117 0 CCAAACTTTT 0.906363 -19 GCGAAAGCCCCATTAACTTTATTAATAATCTT 15 80 0 CATAACTTTT 0.948928 -221 ACTTTTTAGTCCAGAACTATTTCCCACATAAA 15 175 1 CCAAACTATT 0.851812 -126 TTAATTCATTCATTAATTTTGTTAAATAACAT 16 120 1 CATAATTTTT 0.686781 -83 TGTTAAATAACATAAACCATATGTTATTTATT 16 139 1 CATAACCATT 0.768387 -64 GAGAAAAATCCTAATCTATATAACAATGGAC 17 10 1 CCTATCTATT 0.621875 -291 TTTTGATATTGAAGAACTATCTCTTAATATTG 17 95 1 GAAAACTATT 0.76574 -206 GATAATGAATCATTAACTTATTATTTAAGAGA 17 191 1 CATAACTTAT 0.700967 -110 AATTCATCACCCTCATCTAAATAATCATCAAC 17 248 0 CCTATCTAAT 0.171834 -53 *** ****** * Masking position 12 Map Score: 11.4694 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 542 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 TCTTTAAAAAATTTATTTCTACGAAAGTCCTA 2 123 1 ATTATTTCTC 0.936566 -45 CAGTTCCTTTTTTAACTCCTTCAATATAATAG 3 78 0 TTTACTCCTC 0.840321 -206 ATATGAAGAGATTGATTTATTCACTTACTTT 8 10 0 ATTATTTATC 0.852316 -75 TTGAGTTTAAATTAATTAATACAAAAATCTCT 14 75 0 ATTATTAATC 0.765964 -181 CTTTTAAAGATTTTATTCCTGCGAAAGCCCCA 15 100 0 TTTATTCCTC 0.951954 -201 TCAATAAATCATTTATTCCTGCGAAAGTTCTA 16 29 0 ATTATTCCTC 0.981859 -174 GAAGTTCTATATTAATTCATTCATTAATTTTG 16 109 1 ATTATTCATC 0.954865 -94 TAACAGCTCCATTAATTCCTCCTCAAAATCAA 17 124 0 ATTATTCCTC 0.981859 -177 *** ****** * Masking position 5 Map Score: 3.37793 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 81 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AGGCATTGCCGAGCGTAGCGAGGCAATGCATCC 1 15 1 GGCGAGCAGG 0.996765 -286 TAATAAAATGGTGCCGAGGGAGGGATACAAACG 1 172 0 GGCCAGGAGG 0.970283 -129 AGGCATTACCGAGCGTAGCGAGGTAATGCATCT 9 21 1 GGCGAGCAGG 0.996765 -256 TATCCCAATAGGGCGAAGCTATGGTGCGTTGAT 9 60 0 GGCGAGCATG 0.992742 -217 AGCAATGTTTGAGCTTAGCCATGCGGTAGTTAT 9 163 1 GGCTAGCATG 0.971772 -114 * *** *** *** Masking position 7 Map Score: 2.45248 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 2 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 TGCCCTTAAGCATAAATTTTCTTTAAAAAA 2 104 1 CATAAATTTT 0.832229 -64 AATCCATGTAAATTAATTTTATTTTTTCTT 3 165 1 AATTAATTTT 0.60923 -119 CACCACTAATTTTTTAATCAACA 7 148 0 CACTAATTTT 0.8847 -13 TTGATTTATTCACTTACTTT 8 1 0 CACTTACTTT 0.58159 -84 TGTTATTAACCATTAACTTTATATTCAATA 11 199 1 CATTAACTTT 0.958289 -41 GCGAAAGCCCCATTAACTTTATTAATAATC 15 82 0 CATTAACTTT 0.958289 -219 CTATTTCCCACATAAATTTTAAATATACAA 15 191 1 CATAAATTTT 0.832229 -110 ATTTAAATTTCATTAAATTATTTTTTATGA 15 272 1 CATTAAATTA 0.550314 -29 TTAATTCATTCATTAATTTTGTTAAATAAC 16 120 1 CATTAATTTT 0.946935 -83 GATAATGAATCATTAACTTATTATTTAAGA 17 191 1 CATTAACTTA 0.864615 -110 ********** Masking position 6 Map Score: 4.70513 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 186 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 15 GGGCTACAAAATCTGAAAGATTTTGTTTAA 1 126 1 ATCTGAAAGA 0.22643 -175 TTGTTTAACTTTTTCTAAAAGTTTCGTTTG 1 148 1 TTTTCTAAAA 0.591018 -153 TAATCCATAAATCTAAAAAAATAAATATAA 1 220 0 ATCTAAAAAA 0.342038 -81 AGCATAAATTTTCTTTAAAAAATTTATTTC 2 112 1 TTCTTTAAAA 0.623378 -56 TATAGTGTCATTCTCAAAAATAAATACAAC 3 111 1 TTCTCAAAAA 0.910449 -173 TACATAGTCTTTCTCTAAAAATGATGTTGT 3 136 0 TTCTCTAAAA 0.943224 -148 AATTGCTTAAATCTCCAAAACTTTATATAT 3 215 1 ATCTCCAAAA 0.883429 -69 TTGATCAACCTTTTCTAAAAGGTTGTTCGA 9 109 1 TTTTCTAAAA 0.591018 -168 GAGAATAACTTTCTCTTAAAAAGAAAATAA 11 43 0 TTCTCTTAAA 0.771368 -197 TAAGCTATTTTTCTGCAAAAATGAGAATAA 11 65 0 TTCTGCAAAA 0.563299 -175 ATGCAAAAACTTATCTAAAACTTTCGATAC 11 103 0 TTATCTAAAA 0.451876 -137 AATATCACAAAAAAAGAGAAGT 13 10 0 ATCACAAAAA 0.410145 -13 ACTCAATTTTATCTCCTAAATCTTAAATTT 14 101 1 ATCTCCTAAA 0.605992 -155 CAGGAATAAAATCTTTAAAAGAAATCTTAA 15 111 1 ATCTTTAAAA 0.599648 -190 AAATTGAATCATCTCAAAGATATTTGATAT 15 220 0 ATCTCAAAGA 0.654766 -81 TTATAGCCTCATCTCTAAAAGTGTCTAAAA 17 58 0 ATCTCTAAAA 0.937547 -243 GATTTTAAAGTTCCCAAAAACAGAGGTTGA 17 163 1 TTCCCAAAAA 0.532985 -138 TTATAAAACAATCTCTTAAATAATAAGTTA 17 204 0 ATCTCTTAAA 0.752881 -97 ATCAACATAGTCCTCTAAAATTATAAAACA 17 224 0 TCCTCTAAAA 0.638054 -77 ********** Masking position 8 Map Score: 8.27596 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 666 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219