AlignACE version 2.2 July 7, 1998 AlignACE -jLYS.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YBR115C 300 bp YBR115C lys2 1-4179 alpha aminoadipate reductase #2 YDL182W 600 bp YDL182W LYS20 1-1287 homocitrate synthase, highly homologous to YDL131W #3 YDL131W 600 bp YDL131W LYS21 1-1323 homocitrate synthase, highly homologous to YDL182W #4 YDR034C 600 bp YDR034C lys14 1-2373 Transcriptional activator of lysine pathway genes with 2-aminoadipate semialdehyde as co-inducer\; saccharopine reductase synthesis #5 YDR234W 600 bp YDR234W lys4 1-2082 homoaconitase #6 YGL154C 300 bp YGL154C lys5 1-819 aminoadipate-semialdehyde dehydrogenase small subunit (alpha-aminoadipate reductase) #7 YIL094C 357 bp YIL094C LYS12 1-1116 Homo-isocitrate dehydrogenase #8 YIR034C 300 bp YIR034C lys1 1-1122 saccharopine dehydrogenase #9 YMR038C 383 bp YMR038C lys7 1-750 Homocitrate #10 YNR050C 600 bp YNR050C lys9 1-1341 Saccharopine dehydrogenase (NADP+, L-glutamate forming) (saccharopine reductase) (EC 1.5.1.10) Motif number 1 GCCAGCGGAATTCCACTTGCAATTACATAAAAAA 1 63 1 TTCCTTAATT 0.698357 -238 ACATAAAAAATTCCGGCGGTTTTTCGCGTGTGAC 1 87 1 TTCCCGTTTT 0.983331 -214 CTACGCAATATTCCGGCGGAATTTGACGCAGACG 2 23 0 TTCCCGATTT 0.996094 -578 TGCAGAGAGTTCCCGTCGGAATTTGTTTTTTTCT 2 65 0 TCCCCGATTT 0.968112 -536 GAAGAGAAAATTCCCCAGCAATTTTGGTCATATT 2 303 0 TTCCAGATTT 0.97518 -298 TGGTGACGATTTCCAGCGGAATTTCAACTCTGCC 3 267 0 TTCCCGATTT 0.996094 -334 GAGGAAATTTTTCCACTGTCATTTCTTCCAATTG 4 366 0 TTCCTGATTT 0.990769 -235 GTGGAAAAATTTCCTCAGGAATTTCAAAATCATA 4 384 1 TTCCAGATTT 0.97518 -217 GTGAAAAATTTTCCTATGACTTTTTTCACTGCTT 5 171 1 TTCCTGTTTT 0.961279 -430 TTATTGTTTTTTCCCCCGGGATTTTGCTCGAGAT 5 309 1 TTCCCGATTT 0.996094 -292 CGTTCTCAAATTCCACCTCGATTTTTTCAACTGC 7 101 1 TTCCCTATTT 0.973306 -257 GCACTGAAAATTCCCACTCTTTTTTTTTTTTTTT 7 133 1 TTCCCTTTTT 0.893999 -225 TATTTTTTTTTTCCAGCGGAATTTGGAATTCCGC 8 104 1 TTCCCGATTT 0.996094 -197 ACCGCCAAAATTCCCCTGCGATTTCAGCGACAAA 8 143 1 TTCCTGATTT 0.990769 -158 AAGCGAATTTTTCCAACGGAATTTCGATTCCAGA 10 372 0 TTCCCGATTT 0.996094 -229 TTGCTGATAATTCCATTGGAAATTCTCAATACCC 10 434 0 TTCCTGAATT 0.941839 -167 CTAAGGATCCTTCCCATGTAATTTTACCAGGACC 10 519 0 TTCCTGATTT 0.990769 -82 **** ** **** Masking position 13 Map Score: 38.832 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 129 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 TTCAATAGTTTTGCCAGCGGAATTCCACTTGCA 1 51 1 TTGCCGGAAT 0.713381 -250 TCTGCGTCAAATTCCGCCGGAATATTGCGTAGT 2 25 1 ATTCCGGAAT 0.499927 -576 AAAAAAACAAATTCCGACGGGAACTCTCTGCAA 2 67 1 ATTCCGGGAA 0.523684 -534 CGAAGAGAAAATTCCCCAGCAATTTTGGTCATA 2 305 0 ATTCCGCAAT 0.61779 -296 CTGGTGACGATTTCCAGCGGAATTTCAACTCTG 3 269 0 TTTCCGGAAT 0.512936 -332 AGTGGAAAAATTTCCTCAGGAATTTCAAAATCA 4 383 1 TTTCCGGAAT 0.512936 -218 CAGTGCCCCCTTTCCAGTGGGCTTCTCC 5 6 0 TTTCCGGGCT 0.944308 -595 TTTATTGTTTTTTCCCCCGGGATTTTGCTCGAG 5 308 1 TTTCCGGGAT 0.765831 -293 TAAGAATATTTTTCCACGGGAAAAAAGTGAAAA 7 174 0 TTTCCGGAAA 0.499638 -184 TTATTTTTTTTTTCCAGCGGAATTTGGAATTCC 8 103 1 TTTCCGGAAT 0.512936 -198 AACCGCCAAAATTCCCCTGCGATTTCAGCGACA 8 142 1 ATTCCGCGAT 0.895923 -159 AAAGCGAATTTTTCCAACGGAATTTCGATTCCA 10 374 0 TTTCCGGAAT 0.512936 -227 GTATTGAGAATTTCCAATGGAATTATCAGCAAT 10 436 1 TTTCCGGAAT 0.512936 -165 ***** ***** Masking position 2 Map Score: 25.287 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 107 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 ACCCGATGATGATATATATAAATGATATTG 2 478 1 GATATATATA 0.678615 -123 AGCGTATACATATATATATATATATATATA 3 26 1 TATATATATA 0.499412 -575 TATATATATATATATATATATATATATATA 3 36 1 TATATATATA 0.499412 -565 TATATATATATATATATATATATGTATATA 3 46 1 TATATATATA 0.499412 -555 TATATATATGTATATATATATATGTGTGTG 3 60 1 TATATATATA 0.499412 -541 CTTATATACTAATATATATATGCAACAGAT 3 483 1 AATATATATA 0.674102 -118 ACAACCCAAGTAATTGTATACTTTAACAAA 3 579 1 TAATTGTATA 0.60102 -22 CAGACACGCACATATATATATATATATATA 5 436 1 CATATATATA 0.633961 -165 CATATATATATATATATATATATCCCCATA 5 446 1 TATATATATA 0.499412 -155 TCCCCATAGGTATTTATATATACAAAAGAA 5 468 1 TATTTATATA 0.679195 -133 CGTTTGTTTTTAATTATATACAGGTTGGTT 7 41 0 TAATTATATA 0.849329 -317 TAGTGCGACATATTTATATAACTAAGATAG 7 322 1 TATTTATATA 0.679195 -36 GCAAAATGTATAAATGTATAAGAGTCTTTT 8 69 0 TAAATGTATA 0.803409 -232 AAACCACGATGAAATATATAAAAAGCCCAT 8 199 1 GAAATATATA 0.848094 -102 AAAAGAAATAAAAATATATACTTTTCTGTT 9 84 1 AAAATATATA 0.838537 -300 ATTAAAATATATAATACGTTAAT 10 588 0 AAAATATATA 0.838537 -13 ********** Masking position 5 Map Score: 15.5642 Number of sites scoring better than the average of aligned sites = 4620 Number in coding regions = 332 Number in noncoding regions = 4288 Number of orfs with sites within 600 bp upstream = 560 Fraction of orfs with sites within 600 bp upstream = 0.0899454 Motif number 4 ATAAACTCAGATTTTTTTTTATACTATTGG 1 216 0 ATTTTTTTTT 0.880665 -85 CCTCTAAAGAATTCTTTTTCTCAACCTAGC 2 124 0 ATTCTTTTTC 0.887128 -477 AGAGATCTTTTTTTTCTTTTACTACGTGTG 2 156 0 TTTTTCTTTT 0.779032 -445 GATTTCAAAATTTATCTTTCTTCTTGTTGC 3 510 1 TTTATCTTTC 0.86895 -91 CAATAAAAATTTTTTTTTTCCAAATCGCTC 5 285 0 TTTTTTTTTC 0.964384 -316 AAGCGATACAATTTTGTTTCCTTGCAAGTT 5 577 0 ATTTTGTTTC 0.786043 -24 ATGTTTTACAATTATCTTTCGGGCGCTTAT 6 218 1 ATTATCTTTC 0.86895 -83 TTGCTGAGTGATTCTCTTTCTCCTCATTCT 6 270 0 ATTCTCTTTC 0.789684 -31 CCACTCTTTTTTTTTTTTTTTTTTTTTTTT 7 146 1 TTTTTTTTTT 0.880665 -212 TTTTTTTTTTTTTTTTTTTCACTTTTTTCC 7 159 1 TTTTTTTTTC 0.964384 -199 GCATTATTATTTTTTTTTTCCAGCGGAATT 8 97 1 TTTTTTTTTC 0.964384 -204 ACGAAAACGCTTTATTTTTCACACAACCGC 8 277 1 TTTATTTTTC 0.932794 -24 TTTTTATTTCTTTTTTTTTTTTTTTATTCT 9 68 0 TTTTTTTTTT 0.880665 -316 AAAGTATATATTTTTATTTCTTTTTTTTTT 9 78 0 TTTTTATTTC 0.712542 -306 GTAAGCGCAAATTTTTTTTTGATAGTATAT 9 199 0 ATTTTTTTTT 0.880665 -185 CCTTTAATATATTATTTTTCCGAACAATGA 9 283 0 ATTATTTTTC 0.932794 -101 CTTAGTCTAAATTTTTTTTTTTTGGCTTGC 9 312 0 ATTTTTTTTT 0.880665 -72 AAAGCTGGCAATTATTTTTCATTTTTTTTC 10 15 1 ATTATTTTTC 0.932794 -586 ATTATTTTTCATTTTTTTTCATTAGGGCTA 10 25 1 ATTTTTTTTC 0.964384 -576 TATTGACATCTTTATTTTTCACTACAAAGC 10 402 0 TTTATTTTTC 0.932794 -199 ********** Masking position 5 Map Score: 24.1978 Number of sites scoring better than the average of aligned sites = 4838 Number in coding regions = 1546 Number in noncoding regions = 3292 Number of orfs with sites within 600 bp upstream = 2088 Fraction of orfs with sites within 600 bp upstream = 0.335368 Motif number 5 TGCAAGTGGAATTCCGCTGGCAAAACTATTG 1 53 0 ATTCCGCGGC 0.949571 -248 TACATAAAAAATTCCGGCGGTTTTTCGCGTG 1 86 1 ATTCCGGGGT 0.961018 -215 ACTACGCAATATTCCGGCGGAATTTGACGCA 2 27 0 ATTCCGGGGA 0.995324 -574 TTGCAGAGAGTTCCCGTCGGAATTTGTTTTT 2 69 0 TTCCCGTGGA 0.902084 -532 GGCACTTCTCTTTCCGTTGTAACATCCTTTA 3 163 1 TTTCCGTGTA 0.786762 -438 CAGAGTTGAAATTCCGCTGGAAATCGTCACC 3 269 1 ATTCCGCGGA 0.990966 -332 TGATTTTGAAATTCCTGAGGAAATTTTTCCA 4 385 0 ATTCCTGGGA 0.948968 -216 CTCGAGCAAAATCCCGGGGGAAAAAACAATA 5 310 0 ATCCCGGGGA 0.98522 -291 TTTTCACTTTTTTCCCGTGGAAAAATATTCT 7 174 1 TTTCCCGGGA 0.898458 -184 GGAATTCCAAATTCCGCTGGAAAAAAAAAAT 8 105 0 ATTCCGCGGA 0.990966 -196 CGGAATTTCGATTCCAGAGTATGAGTAATTC 10 359 0 ATTCCAGGTA 0.805779 -242 TGGAATCGAAATTCCGTTGGAAAAATTCGCT 10 374 1 ATTCCGTGGA 0.98911 -227 ATTGCTGATAATTCCATTGGAAATTCTCAAT 10 438 0 ATTCCATGGA 0.933304 -163 ******* *** Masking position 2 Map Score: 15.8868 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 194 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 GCTAAAACTGTGCGATGCCTCTAGAAGCG 1 9 0 TGGATGCCTC 0.990832 -292 TCTAAACATGTGCTCTGACTCGCTATATTAT 4 56 1 TGTCTGACTC 0.961362 -545 GAATGCTTATTGTTCTGCATCACTTCAGTCT 4 433 1 TGTCTGCATC 0.961362 -168 GTTGGTGATATTTGCTGCCTCTGGTATAGAC 5 366 0 TTGCTGCCTC 0.980909 -235 TAGCTAGTTTTGCGCTGCCTCTTATAGTAGA 5 521 1 TGGCTGCCTC 0.997482 -80 GTGGGCTGCCTCTTTTCTCCAA 7 2 1 TGGCTGCCTC 0.997458 -356 TGTTATCTTATGGTATGCCTCCTAAAATACC 8 246 0 TGTATGCCTC 0.981248 -55 ** ******** Masking position 6 Map Score: 8.24326 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 110 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 AAGAGATCTTTTTTTTCTTTTACTACGTGTG 2 156 0 TTTTTCTTTT 0.799276 -445 GCCACTCCCGGTTTCTCTGTGGATACGGCGT 2 190 1 GTTTCCTGTG 0.69351 -411 AAGTGACTAATTTTCGCTGTTCCACCACTAT 3 353 0 TTTTCCTGTT 0.957143 -248 AAGCTGATCGTTCTCGTTGTGTGTGATTCTA 3 396 1 TTCTCTTGTG 0.918187 -205 AAATTTATCTTTCTTCTTGTTGCGTTTAGGC 3 517 1 TTCTTTTGTT 0.872208 -84 GCCAGACACATTCTCTCTTTTTCAAGAAATT 4 139 1 TTCTCCTTTT 0.926802 -462 TTTGGTCATCGTTTCCTTGTGTTATCAAATA 4 238 0 GTTTCTTGTG 0.685686 -363 GCTAGATAAATTTTCCTTTTTAGTCCTTATC 4 525 1 TTTTCTTTTT 0.924006 -76 TTTAGTCCTTATCTCCCTGTTTCTTCCTTCT 4 543 1 ATCTCCTGTT 0.615999 -58 TTGGCTATTCTTTTCGGTGTTTGGTGCTGTT 5 84 0 TTTTCGTGTT 0.908329 -517 AAAAAAAAAATTTTTATTGTTTTTTCCCCCG 5 296 1 TTTTTTTGTT 0.871768 -305 ACCTTACAACTTCTCTGTTTTACTTGAGTTT 6 144 1 TTCTCGTTTT 0.848887 -157 CTTTTTTTTTTTTTTTTTTTTTTTTTTCACT 7 151 1 TTTTTTTTTT 0.793348 -207 TTTTTTTTTTTTTTCACTTTTTTCCCGTGGA 7 164 1 TTTTCCTTTT 0.926533 -194 CCAGTTTAGTTTCTTGTTGTTCTTTCCTCTA 7 220 0 TTCTTTTGTT 0.872208 -138 AAATAAAGCGTTTTCGTTGTTATCTTATGGT 8 263 0 TTTTCTTGTT 0.955618 -38 ATATTTTTATTTCTTTTTTTTTTTTTTTATT 9 70 0 TTCTTTTTTT 0.793994 -314 AAATATATACTTTTCTGTTTGTCAAATTCAT 9 95 1 TTTTCGTTTG 0.743922 -289 CCCTCTTCCATTCTCACTGTGTACTAGTTGT 9 245 0 TTCTCCTGTG 0.920892 -139 TAGTCTAAATTTTTTTTTTTTGGCTTGCCTT 9 309 0 TTTTTTTTTT 0.793348 -75 TGGCAATTATTTTTCATTTTTTTTCATTAGG 10 20 1 TTTTCTTTTT 0.924006 -581 ***** ***** Masking position 4 Map Score: 15.4182 Number of sites scoring better than the average of aligned sites = 3526 Number in coding regions = 1770 Number in noncoding regions = 1756 Number of orfs with sites within 600 bp upstream = 1345 Fraction of orfs with sites within 600 bp upstream = 0.21603 Motif number 8 TATATATATATGTATACGCTTATGTATTTACTCG 3 12 0 TGTACGTTTG 0.680217 -589 TATATATATATGTGTGTGTGTGTAATTGTGTGTA 3 72 1 TGTGTGGTTA 0.951447 -529 TCTTGGAGCTGGTAGCTGCTGGTGACGATTTCCA 3 286 0 GGTATGTGTG 0.798205 -315 TCGTTCTCGTTGTGTGTGATTCTACGATATTGCG 3 403 1 TGTGTGTTTA 0.914675 -198 TGAGTGGTGTTGAGCATGCGTTTGTTCGCATTTT 3 439 1 TGAGTGGTTG 0.969325 -162 CTTGAAAAAGAGAGAATGTGTCTGGCTTGCAGGA 4 131 0 AGAGTGGTTG 0.785414 -470 CAGGAATTGCTGTGAACGTTGCTAGATAAATTTT 4 505 1 TGTGCGTGTA 0.757391 -96 TATTCTTTTCGGTGTTTGGTGCTGTTGTATCGCT 5 76 0 GGTGTGTGTG 0.94368 -525 TGTGTATACCTGTGTATGTTGGTGATATTTGCTG 5 380 0 TGTGTGTGTG 0.97327 -221 TGTGTGGACATGAGATTGTGTATACCTGTGTATG 5 396 0 TGAGTGGTTA 0.909849 -205 TGTGCGTGTCTGTACGTGTGTGTGGACATGAGAT 5 414 0 TGTATGGTTG 0.935418 -187 AGAATCCTCGTGTGTTTGTGTGTGCAATAGCTAG 5 494 1 TGTGTGGTTG 0.983963 -107 TCCTGGAAGTTGAGCTTGCTTATGTCAACGTCTT 9 14 1 TGAGTGTTTG 0.945316 -370 GTCAAGCTGAGGAAATTGTGGATGATCTCTTGTT 10 242 1 GGAATGGGTG 0.788316 -359 AAGTGAAGAGTGTGATTGCGGTTACTACTGACCA 10 299 1 TGTGTGGGTA 0.955072 -302 **** ** ** ** Masking position 13 Map Score: 8.031 Number of sites scoring better than the average of aligned sites = 2033 Number in coding regions = 1153 Number in noncoding regions = 880 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 9 CTCATCATTTCAGCCTGATCTCTTCTCAAGCAGG 3 210 0 CGCTGATCTT 0.848174 -391 TCCTTGTTGTCAGTCTCATCATTTCAGCCTGATC 3 224 0 CGCTCATCTT 0.98132 -377 AAGCATATGTCACCATCTTCTTTTCCTGCAAGCC 4 108 1 CCATCTTCTT 0.886003 -493 TGTTTCTTCCTTCTCTCATCATTTTGGTATAAGA 4 560 1 TCCTCATCTT 0.977965 -41 CGCTGGCTTGTGGTATCTTCTGTTTCCTATTTAA 5 46 0 TGATCTTCTT 0.898574 -555 GAGGACAGCTTTGGCTATTCTTTTCGGTGTTTGG 5 91 0 TGCTATTCTT 0.761505 -510 GCCTCTGGTATAGACTCATCGATTACAAAATTTC 5 347 0 TGCTCATCTT 0.980971 -254 GCATCTTTAATGGACTCATCCTTTAAAAAGGATA 6 52 1 TGCTCATCTT 0.980971 -249 ACTGAAAATTCCCACTCTTTTTTTTTTTTTTTTT 7 135 1 CCCTCTTTTT 0.719991 -223 AGAGTCTTTTTTGACTCATCGACTTAGTATGTAA 8 45 0 TGCTCATCCT 0.890483 -256 AATGAATTTTTACCCTCTTCCATTCTCACTGTGT 9 254 0 TCCTCTTCTT 0.974562 -130 TAACCGCAATCACACTCTTCACTTCTGTTGTGGT 10 289 0 CCCTCTTCTT 0.975024 -312 CTGTGCTACTTTCTATCATCTATTGCTGATAATT 10 456 0 TCATCATCTT 0.898333 -145 * * ****** ** Masking position 6 Map Score: 7.80487 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 438 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 10 ACACCACTCATGCGCAATATCGTAGAATCACAC 3 416 0 TGCAATATCT 0.954166 -185 CATGCGTTTGTTCGCATTTTCATGCAGTCTCTT 3 453 1 TGCATTTTCT 0.88778 -148 TTTGTTAAAGTATACAATTACTTGGGTTGTCGT 3 576 0 TACAATTACT 0.786662 -25 AGCACATGTTTAGACAATATCTGATTTAAATTT 4 37 0 TACAATATCG 0.793699 -564 TTATGCAGAATGTACAATCTCGTCTAAGCATAT 4 83 1 TACAATCTCT 0.94425 -518 GTTATTGTAGACAACAATTTCTTGAAAAAGAGA 4 152 0 AACAATTTCT 0.786656 -449 TATCAAGTGATAAACAATTTCGTGTCAAGTGAG 5 245 1 TACAATTTCT 0.971949 -356 TACACAGGTATACACAATCTCATGTCCACACAC 5 398 1 TACAATCTCT 0.94425 -203 CCTCTTATAGTAGACAATATCACTTTTTCAATA 5 538 1 TACAATATCC 0.876241 -63 ATTGTTCGACTCAGCAGTATCCTTTTTAAAGGA 6 70 0 TGCAGTATCT 0.796767 -231 TTCAAATTGATGGGCAATTTCTTATATTTTTAA 6 174 1 TGCAATTTCT 0.972458 -127 TTGCGCTTACTAAGCATTTTCCCCGTACAACTA 9 219 1 TGCATTTTCC 0.732745 -165 CAAGAGATCATCCACAATTTCCTCAGCTTGACT 10 241 0 TACAATTTCT 0.971949 -360 * ******** * Masking position 6 Map Score: 3.34403 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 447 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 11 TATAAGTAACAAGCAGCCAATAGTATAAAA 1 200 1 AAGCAGCCAA 0.987366 -101 CTTTATCGATAAGCAGCCAATATCATTTAT 2 495 0 AAGCAGCCAA 0.987366 -106 TGAGATTCTCAAGAGGTCAAAGACTCTTCA 3 119 0 AAGAGGTCAA 0.869503 -482 TCACTTTGCAAAGATGCCAAGCTGATCGTT 3 378 1 AAGATGCCAA 0.959118 -223 TTTTTCACCGTAGCAGCCAACGCAGTTGCG 5 149 0 TAGCAGCCAA 0.933356 -452 TCGCACGAACAAGCAGTGAAAAAAGTCATA 5 185 0 AAGCAGTGAA 0.86231 -416 GGGAAAAGCTGGCAATTATTTTTCA 10 6 1 AAGCTGGCAA 0.944585 -595 GTGAAAAATAAAGATGTCAATAAAGGGTAT 10 410 1 AAGATGTCAA 0.919088 -191 ********** Masking position 2 Map Score: 2.26026 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 452 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 12 TTTTTTTGCCACTTGCAACGCTAGTAACGC 2 217 0 ACTTGCAACG 0.979918 -384 ATGATGTGCAACTTGAAGCGCGGAATTCAC 4 312 0 ACTTGAAGCG 0.959492 -289 GGAGAAGCCCACTGGAAAGGGGGCACTGAC 5 11 1 ACTGGAAAGG 0.947058 -590 ATTGTTTATCACTTGATACGTGTACATTTT 5 233 0 ACTTGATACG 0.949978 -368 CATTCTGCTCACTTGACACGAAATTGTTTA 5 255 0 ACTTGACACG 0.965683 -346 ATAAAATAGAACTTGCAAGGAAACAAAATT 5 568 1 ACTTGCAAGG 0.935709 -33 ACAAACTGTTACTTGAAAGGTTTTCCCACG 10 72 1 ACTTGAAAGG 0.982078 -529 ********** Masking position 1 Map Score: 3.11357 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 88 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 GGGATAGTGGGACAAGGCCAGGCCATTGTGA 2 256 0 GACAAGCCAG 0.976415 -345 AAAGTGCAACGACAACCCAAGTAATTGTATA 3 568 1 GACAACCAAG 0.987776 -33 TCACTTATTTGATAACACAAGGAAACGATGA 4 233 1 GATAACCAAG 0.972874 -368 AGGCGAATAAGAAAAGCCCAGCAGAGGTCAT 4 464 1 GAAAAGCCAG 0.948385 -137 GGAAACAGAAGATACCACAAGCCAGCGATAC 5 53 1 GATACCCAAG 0.916913 -548 CCATCAATTTGAAAACTCAAGTAAAACAGAG 6 156 0 GAAAACCAAG 0.972874 -145 CGCAACTGCAGACAAGTCAAGCTGAGGAAAT 10 227 1 GACAAGCAAG 0.984006 -374 ****** **** Masking position 4 Map Score: 2.65694 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 130 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 14 CAATAATTTAATTTGCGCTTTAGGTTCTTG 2 370 1 ATTTGCGCTT 0.978975 -231 TCTTTCTTCTTGTTGCGTTTAGGCCTTTAT 3 524 1 TGTTGCGTTT 0.939602 -77 CAGCCAACGCAGTTGCGTTTTTTCCAGTTT 5 136 0 AGTTGCGTTT 0.961474 -465 CAATAGCTAGTTTTGCGCTGCCTCTTATAG 5 518 1 TTTTGCGCTG 0.885183 -83 TTTTGCGGTTGTGTGAAAAA 8 291 0 TTTTGCGGTT 0.891818 -10 TAGTCCTGGAAGTTGAGCTTGCTTATGTCA 9 11 1 AGTTGAGCTT 0.891865 -373 TCAAAAAAAAATTTGCGCTTACTAAGCATT 9 207 1 ATTTGCGCTT 0.978975 -177 ACTTGTCTGCAGTTGCGATTAAAATTTGAC 10 214 0 AGTTGCGATT 0.933987 -387 ********** Masking position 4 Map Score: 2.15865 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 150 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 CGACGGGAACTCTCTGCAAGGAAGTTTAAG 2 81 1 TCTCTGCAAG 0.956715 -520 GGCGTTACTAGCGTTGCAAGTGGCAAAAAA 2 216 1 GCGTTGCAAG 0.96641 -385 CCATCTTCTTTTCCTGCAAGCCAGACACAT 4 120 1 TTCCTGCAAG 0.829995 -481 CGTGAATTCCGCGCTTCAAGTTGCACATCA 4 311 1 GCGCTTCAAG 0.94963 -290 ATAAACAATTTCGTGTCAAGTGAGCAGAAT 5 254 1 TCGTGTCAAG 0.857997 -347 CAATTTTGTTTCCTTGCAAGTTCTATTTTA 5 569 0 TCCTTGCAAG 0.9748 -32 CAAAATTGTATCGCTTCAAG 5 591 1 TCGCTTCAAG 0.97084 -10 AATAAAGATATCTTTGCAAGGCAGAAACCC 9 347 1 TCTTTGCAAG 0.944958 -37 ACGTGGGAAAACCTTTCAAGTAACAGTTTG 10 73 0 ACCTTTCAAG 0.803438 -528 ********** Masking position 8 Map Score: 1.60999 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 343 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161