AlignACE version 2.2 July 7, 1998 AlignACE -jPEX.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 YDL065C 300 bp YDL065C PEX19 1-1053 40 kDa farnesylated protein associated with peroxisomes #2 YDR142C 441 bp YDR142C PEX7 1-1128 Member of beta-transducin-related (WD-40) protein family #3 YDR244W 300 bp YDR244W PEX5 1-1839 69-kDa protein containing tetratricopeptide repeat (TPR) #4 YDR265W 540 bp YDR265W PEX10 1-1014 C3HC4 zinc-binding integral peroxisomal membrane protein #5 YDR329C 300 bp YDR329C PEX3 1-1326 48-kDa peroxisomal integral membrane protein #6 YGL153W 300 bp YGL153W PEX14 1-1026 Peroxisomal peripheral membrane protein (peroxin) involved in import of peroxisomal matrix proteins #7 YGR077C 300 bp YGR077C PEX8 1-1770 peroxisome associated protein containing a PTS1 signal #8 YGR133W 443 bp YGR133W PEX4 1-552 Member of ubiquitin-conjugating protein family #9 YJL210W 600 bp YJL210W PEX2 1-816 CH3HC4 zinc-binding integral peroxisomal membrane protein #10 YKL197C 370 bp YKL197C PEX1 1-3132 member of the AAA-protein family #11 YLR191W 582 bp YLR191W PEX13 1-1161 Peroxisomal membrane protein that contains Src homology 3 (SH3) domain #12 YMR026C 441 bp YMR026C PEX12 1-1200 C3HC4 zinc-binding integral peroxisomal membrane protein #13 YNL329C 300 bp YNL329C PEX6 1-3093 Member of the AAA-protein family that includes NSFp and PEX1p #14 YNL214W 300 bp YNL214W PEX17 1-600 23 kDa peroxisome associated protein, binds Pex14p #15 YOL147C 300 bp YOL147C PEX11 1-711 Peroxisomal membrane protein #16 YOL044W 347 bp YOL044W PEX15 1-1152 44 kDa phosphorylated integral peroxisomal membrane protein Motif number 1 CAAACATTTAAAAAAAGAAGAGAAATTTAGC 1 166 0 AAAAAAGAAA 0.978899 -135 ATGCAGATAAAAAAAAGGTAAAAGGAGTAGA 2 84 0 AAAAAAGGTA 0.729428 -358 AAGTAGAAGTAAAGAAAAATAAGTATATGAT 2 129 0 AAAGAAAAAA 0.813389 -313 TTTCGTCTAGATAAAAAAACACTTCTTTGTT 4 26 0 ATAAAAAAAA 0.810795 -515 ATTTAAATCCAAAGAAAAATAAAGGGCACTA 7 64 1 AAAGAAAAAA 0.813389 -237 AGAAAAAAAAAAAAAAAAAAAAAAAGAGAGC 7 122 0 AAAAAAAAAA 0.954783 -179 GAGAAAAAACAAAAAAGAAAAAAAAAAAAAA 7 137 0 AAAAAAGAAA 0.978899 -164 TAACAATGCAAAAAATGAAGAAAATTGAGAA 7 163 0 AAAAATGAAA 0.768472 -138 AAAGAAGAGGAAAAAAAATAAATCGGTAAAC 8 67 0 AAAAAAAATA 0.855999 -377 AAATTTGAAAAAAAAAGAAAAATGATGGGCA 9 67 1 AAAAAAGAAA 0.978899 -534 AAATAGTGGAAAAAAAGAAAATTAATGCGAT 9 313 1 AAAAAAGAAA 0.978899 -288 TGCGACCCTGATAAAAAAAAATGGCTGATCA 10 120 1 ATAAAAAAAA 0.810795 -251 CGGCGTGGACAAAAAAAAACATCGATTTCTA 10 153 1 AAAAAAAAAA 0.954783 -218 ACGTTGTAAGAAAAAAGATTAAATCACACGA 11 192 0 AAAAAAGATA 0.928876 -391 ATTAATTACCAAAAAAAATGATATAATAAAG 11 372 1 AAAAAAAATA 0.855999 -211 CATTAATCAGATAAAAGAAGACTTTATTATA 11 393 0 ATAAAAGAAA 0.903984 -190 TGTAAACGGAAAAAAAGGATATTACGGTAGT 12 30 0 AAAAAAGGAA 0.905449 -412 TTAGAATTAGAACAAAGAACAGTAGTGGAGA 13 227 1 AACAAAGAAA 0.831063 -74 TATATAGCCAAAAAAAGAATAGAACATTTAT 16 76 0 AAAAAAGAAA 0.978899 -272 ********* * Masking position 5 Map Score: 19.0771 Number of sites scoring better than the average of aligned sites = 8860 Number in coding regions = 1160 Number in noncoding regions = 7700 Number of orfs with sites within 600 bp upstream = 1801 Fraction of orfs with sites within 600 bp upstream = 0.289271 Motif number 2 TATGCTAAATTTCTCTTCTTTTTTTAAATGTTT 1 163 1 TCTCTTCTTT 0.905223 -138 TCGTTGGTAATTCTCTCGATTGTAAGCTTCGAA 3 93 1 TCTCTCGTTT 0.840833 -208 TCGTCTACTTTTCCCTCTGACATATAAAAGGTA 5 12 1 TCCCTCTACT 0.757841 -289 GTATGAATATTTCCCTTTTTCCTTAAAAATTCC 5 144 1 TCCCTTTTCT 0.955381 -157 CGCGAGTATATCCTCTTGAATTTCAACAACGAA 6 33 1 TCTCTTGATT 0.716226 -268 CGAATATACCTGCCCATGGTCTTACACCTGCCA 6 62 1 TCCCATGTCT 0.883882 -239 TGCTGAGTGATTCTCTTTCTCCTCATTCTCATT 6 147 1 TCTCTTTTCT 0.821032 -154 TATAAGAAATTGCCCATCAATTTGAAAACTCAA 6 246 1 TCCCATCATT 0.692552 -55 TTCTATGTAGTGCCCTTTATTTTTCTTTGGATT 7 69 0 TCCCTTTTTT 0.959965 -232 TTATTTTTTTTCCTCTTCTTTCTGCTTAATATT 8 77 1 TCTCTTCTTT 0.905223 -367 CATCATGGGGTGCCCATCATTTTTCTTTTTTTT 9 75 0 TCCCATCTTT 0.895005 -526 GGATGCGATTTCCCCTCCATTCTATCGATAAGG 9 474 1 TCCCTCCTTT 0.961023 -127 TCGTTATGCTTTCCCTCCGTCTTCACTCATCCC 9 528 0 TCCCTCCTCT 0.956554 -73 TACTGGCGTATGCCCTTGTTTGTGGTCTTTGTG 10 51 1 TCCCTTGTTT 0.97806 -320 TAGTATAGAATCCCCTTGATATTTATAGATAGT 11 546 0 TCCCTTGTAT 0.928808 -37 AATACAACTATTCCCTTCATATTAAAAGAATAA 12 108 0 TCCCTTCTAT 0.928808 -334 TCCCTGCTTATTCCCTTGCTTCTTCTGGAGCCT 12 383 0 TCCCTTGTTT 0.97806 -59 ATTCTTGTCATACCCTCGCTATTGTAAGGCCTG 14 52 0 TCCCTCGTAT 0.878285 -249 TTGGAGTCACTTCCCTTTTATATCTATAAATGA 15 213 0 TCCCTTTATT 0.863693 -88 AAATTATTCTTTCCCTTTATCTTGGAGAGTACG 16 16 0 TCCCTTTTCT 0.955381 -332 * ****** ** * Masking position 1 Map Score: 17.8887 Number of sites scoring better than the average of aligned sites = 1222 Number in coding regions = 756 Number in noncoding regions = 466 Number of orfs with sites within 600 bp upstream = 386 Fraction of orfs with sites within 600 bp upstream = 0.0619981 Motif number 3 AAAAGTGTTTTCACCTTTTACTGTTTTGCGAAACG 2 260 0 TCCTTCTGTT 0.906874 -182 TATTATCAATTCACGTTTTGCTGCTTATTCCTCCG 4 267 0 TCCTTCTGCT 0.992686 -274 TGCCTCCTTGTTTCGTGCTTCTGCTTTTACGATGA 5 263 0 TTCTTCTGCT 0.989923 -38 TTTTTAGTCCCTTCTTGAGCCTGCTTCAA 7 5 0 CTCTGCTGCT 0.907449 -296 TATTTCCCTTTTGCATTTGTCTTCTTCGGTTTTCC 7 223 0 TTCTGCTTCT 0.797024 -78 TATTTTTTTTCCTCTTCTTTCTGCTTAATATTATA 8 78 1 CCCTTCTGCT 0.97721 -366 GTGGTATATATCGCATATTACTGCTTCACAGCATG 8 340 1 TCCTTCTGCT 0.992686 -104 TTTTCAGCAGTTGCTTGTTGCTGCTGCCTGTTAAT 9 187 0 TTCTTCTGCT 0.989923 -414 CTCGGCAATCTCTCCTCGTTATGCTTTCCCTCCGT 9 541 0 TCCTTATGCT 0.89939 -60 TCCTCAGGTGTTTCTTGTTACTGCCGTCCCTTCCA 10 333 0 TTCTTCTGCC 0.939372 -38 CCCTGCTTATTCCCTTGCTTCTTCTGGAGCCTTCA 12 380 0 TCCTTCTTCT 0.94497 -62 ATTGAAATATTTCCATCATTCTGATAAGCAGAACC 14 255 1 TTCTTCTGAT 0.875753 -46 TTAGTCTGCCTTACGTGGTTCTGCTTATCAGAATG 14 271 0 TTCTTCTGCT 0.989923 -30 ** * * * ***** Masking position 6 Map Score: 13.8333 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 336 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 AGGAAAACTACTACTTACCTTTCTTCCTGAAGA 1 70 1 CTACTCCTTC 0.973656 -231 TAGTTTGTGTCTACAGCGTCTTCAGGAAGAAAG 1 88 0 CTACGGTCTC 0.8373 -213 CGGCTAATACCTACTTCGCCCTCTCAGATTATC 4 415 0 CTACTGCCTC 0.989581 -126 TTCGTCTACTTTTCCCTCTGACATATAA 5 6 1 CTACTTCCTC 0.947916 -295 CACAATCAACCTACATAGCTCTCTTTTTTTTTT 7 105 1 CTACTGCTTC 0.949771 -196 TGCATTGTTACTACTCTCCCATTAAGGGAAATT 7 184 1 CTACCCCCTT 0.845869 -117 GCTAAGGCGTTTACAGACCCATCGACTGCCCTT 9 137 1 TTACGCCCTC 0.916375 -464 TCAAACCTCCCTACCTGCCCGTCGCTATCGCAT 9 337 0 CTACTCCCTC 0.994642 -264 TAGACGCATACTACGGACCCCTCAAACCTCCCT 9 358 0 CTACGCCCTC 0.993495 -243 GCTGCGTTGCCTTTAGATTACGTC 9 587 0 CTGCTGCCTT 0.858484 -14 TTTCTTGTTACTGCCGTCCCTTCCAGAAGAAAT 10 325 0 CTGCGCCCTC 0.987196 -46 CACTTGACGACTACCTTCCTTTCCTTTGCTTTA 12 419 0 CTACTCCTTC 0.973656 -23 CATCCTTTCTATGCTTGCCCTTCTATTGTAAAA 15 88 1 ATGCTCCCTC 0.870541 -213 **** * *** ** Masking position 2 Map Score: 10.1948 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 356 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 CAGCGTCTTCAGGAAGAAAGGTAAGTAGTA 1 78 0 AGGAAGAAAG 0.794539 -223 CCAGCAAGTAAATATGAAGGCCGAGAAATT 2 200 1 AATATGAAGG 0.834954 -242 TCGAATTCCAAATCAGAAAGAAAACGATTT 2 352 0 AATCAGAAAG 0.909714 -90 CAAAATTAAGCATAAGAAAGGTTTCTGATT 3 207 1 CATAAGAAAG 0.820738 -94 TAGATCGTTCAATATGAGGGTGTAATAAGA 4 151 1 AATATGAGGG 0.776784 -390 ATGAGGGTGTAATAAGAAAGTACGAAACAA 4 164 1 AATAAGAAAG 0.951497 -377 CCACCGTGATAATCTGAGAGGGCGAAGTAG 4 408 1 AATCTGAGAG 0.830918 -133 AAAAAAAAAAAAAAAGAGAGCTATGTAGGT 7 113 0 AAAAAGAGAG 0.90144 -188 ATATAATATTAAGCAGAAAGAAGAGGAAAA 8 84 0 AAGCAGAAAG 0.794539 -360 GAGTTATTCAAGTATGAGAGATCAACACTG 8 221 0 AGTATGAGAG 0.830918 -223 TCGTTGTTGAAGAAAGAGAGCTCTTATCAT 9 105 0 AGAAAGAGAG 0.824489 -496 GCCCTGTGCAAATAAGAAAGCCTGAAATGG 10 87 0 AATAAGAAAG 0.951497 -284 TTATTCTTTTAATATGAAGGGAATAGTTGT 12 108 1 AATATGAAGG 0.834954 -334 GCATACCCTCCAAAAGAAAGCGATTATAGT 13 272 1 CAAAAGAAAG 0.756282 -29 GGTCCAAGATAAAATGAAAGCATTGAAATA 14 234 1 AAAATGAAAG 0.904096 -67 GCCCCAAAATAGAATGAAAGAAAATACTGC 16 164 0 AGAATGAAAG 0.828825 -184 ATAGTTAGGTAAACAGAAAGAGGCACTAGC 16 284 1 AAACAGAAAG 0.872272 -64 ********** Masking position 7 Map Score: 6.70704 Number of sites scoring better than the average of aligned sites = 2402 Number in coding regions = 1485 Number in noncoding regions = 917 Number of orfs with sites within 600 bp upstream = 705 Fraction of orfs with sites within 600 bp upstream = 0.113235 Motif number 6 TTTATATATATATATCATATACTTATTTTT 2 116 1 TATATCATAT 0.967163 -326 CAATAAACAATATATCATAACAC 3 288 1 TATATCATAA 0.80561 -13 CGAAGTAGAATATATCATTTCCGTTTCGTC 4 50 0 TATATCATTT 0.95985 -491 AAGACTTTATTATATCATTTTTTTTGGTAA 11 377 0 TATATCATTT 0.95985 -206 TAATATTAATTATATCAGATAGTTGGTGAG 11 474 1 TATATCAGAT 0.85999 -109 AAGAACTTTATATATCATGTAGCCAATTGC 13 111 1 TATATCATGT 0.915034 -190 GTATTTGATGTATATCGTTTGTTTTATTTC 14 143 1 TATATCGTTT 0.832933 -158 AGACCAGGAATATCATATTGAAATTTAC 15 9 1 AATATCATAT 0.891154 -292 AAGCGATGGGTATATCATTTATAGATATAA 15 199 1 TATATCATTT 0.95985 -102 TTACATTTTTAATATCATATCATTGCTCTA 16 111 1 AATATCATAT 0.891154 -237 ********** Masking position 5 Map Score: 4.09649 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 150 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 TAAACGCGGTTTCTGAGAGATATAAAGTGAA 1 233 1 TTCTGAGAAT 0.842313 -68 TAAATATGAAGGCCGAGAAATTAAACCACCG 2 208 1 GGCCGAGAAT 0.919842 -234 GTACCGACTTGTCGGAGGAATTCGGAGTTAA 3 149 0 GTCGGAGGAT 0.971752 -152 CTAAAAGTCGTTCGGAGGAATAAGCAGCAAA 4 255 1 TTCGGAGGAT 0.931835 -286 CTCATGTAGCTGTTGAGACGTTATCATTGTT 4 321 0 TGTTGAGAGT 0.527392 -220 ATGAGTTTACGTTCGAGGCAT 6 1 0 GTTCGAGGAT 0.878045 -300 TGGATGCAACGGTTGAGGTATATAATATTAA 8 102 0 GGTTGAGGAT 0.7876 -342 GCGTCTTGTAGTCGGAGGTGTGGCGGGCCGG 9 280 1 GTCGGAGGGT 0.976641 -321 AGGTAGGGAGGTTTGAGGGGTCCGTAGTATG 9 354 1 GTTTGAGGGT 0.871738 -247 CGATACTAACTTCCGAGACGTTGCATCAAAG 9 427 0 TTCCGAGAGT 0.893139 -174 GTTAGTATCGATCCGAGGAGTGGAACGGATG 9 448 1 ATCCGAGGGT 0.767928 -153 GATGACAATAGTCGGAGAGATATTCCGGACC 10 289 0 GTCGGAGAAT 0.95543 -82 GGGCCTCTATGTCTGAGAGGTGTGTGGGTTA 12 178 1 GTCTGAGAGT 0.94232 -264 ACAAGAATTCTGCGGAGATATGAAGAAGACT 14 77 1 TGCGGAGAAT 0.849586 -224 ******** ** Masking position 6 Map Score: 4.51208 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 433 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 8 TGTATGCCTACAGAATGTAAGCATAAAAGGAG 1 40 1 CAGAAGTAGC 0.88724 -261 AATTAACATACAGGACGGATGGCAAGACCAAT 3 19 0 CAGGAGGAGG 0.81716 -282 CTTTATCACCCGGAGTGTAGGGTACGGATGTT 4 202 1 CGGAGGTAGG 0.954143 -339 TTTCGAAATCCTGAACGGAAGCGGAATATATG 8 309 1 CTGAAGGAGC 0.881161 -135 ATCCGAGGAGTGGAACGGATGCGATTTCCCCT 9 458 1 TGGAAGGAGC 0.984915 -143 ACCTTATCGATAGAATGGAGGGGAAATCGCAT 9 476 0 TAGAAGGAGG 0.960725 -125 TGAGTGAAGACGGAGGGAAAGCATAACGAGGA 9 532 1 CGGAGGAAGC 0.844832 -69 GAATTTCTTCTGGAAGGGACGGCAGTAACAAG 10 323 1 TGGAAGGAGG 0.986986 -48 AATAAAGCAAAGGAAAGGAAGGTAGTCGTCAA 12 417 1 AGGAAGGAGG 0.931464 -25 CGCTTTCTTTTGGAGGGTATGCAAACACATAT 13 262 0 TGGAGGTAGC 0.939261 -39 AGGGCAAGCATAGAAAGGATGGGTTACTATGA 15 77 0 TAGAAGGAGG 0.960725 -224 AAAATCGCAATGGAATTGATGCCAACTTTGTT 15 134 0 TGGAATGAGC 0.811338 -167 CCCTTTATCTTGGAGAGTACGGAAAA 16 5 0 TGGAGGTAGG 0.947263 -343 ***** *** ** Masking position 9 Map Score: 5.61129 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 419 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 9 GTAAGCATAAAAGGAGGAAAACTACTACTTA 1 56 1 AAGGAGAAAA 0.930115 -245 AAAAAGGTAAAAGGAGTAGAAAATAATGTCT 2 73 0 AAGGAGAGAA 0.973137 -369 AAAAGGTCAATAGGAGCCGAAGAATTAACAT 3 42 0 TAGGAGCGAA 0.960729 -259 GATAATATTATAGGAGCCAAAGTTCTAACAA 4 295 1 TAGGAGCAAA 0.899882 -246 TCAGAGGGAAAAGTAGACGAA 5 1 0 AAGTAGCGAA 0.895988 -300 AGCACGAAACAAGGAGGCAAACCACTAAAAG 5 279 1 AAGGAGCAAA 0.973137 -22 CTAAAATGAGAATGAGGAGAAAGAGAATCAC 6 153 0 AATGAGAGAA 0.930115 -148 AGGAAAACCGAAGAAGACAAATGCAAAAGGG 7 222 1 AAGAAGCAAA 0.759898 -79 AAAATTGTCCAATGAGAAGGATGGATAACGG 11 129 0 AATGAGAGGA 0.714807 -454 TAAGCATCTGAATGAGACGAAAGGATGACTC 12 300 0 AATGAGCGAA 0.973137 -142 GGCCAAGATAAATGAGGCGAAAGAAGTTCTC 13 50 1 AATGAGCGAA 0.973137 -251 ****** **** Masking position 5 Map Score: 5.59683 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 478 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 10 TTCAGAGGAGGTTATGTCGGTGGTTTAATT 2 226 0 GTTATGTCGG 0.924623 -216 CGTCTTCTCAGTTATCTCGGCAATCTCTCC 9 561 0 GTTATCTCGG 0.981651 -40 TTTCGCCTCATTTATCTTGGCCGCCATGTA 13 42 0 TTTATCTTGG 0.976213 -259 ATGCTTTCATTTTATCTTGGACCCTTATAA 14 227 0 TTTATCTTGG 0.976213 -74 CGCGTCGGCATTTATCTCGGAGAACCCGAA 15 171 1 TTTATCTCGG 0.98474 -130 ATTCTTTCCCTTTATCTTGGAGAGTACGGA 16 14 0 TTTATCTTGG 0.976213 -334 ********** Masking position 5 Map Score: 3.86484 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 60 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 CTTCATATTTACTTGCTGGAGACATGCAAATTT 2 186 0 ATGTGGAGAC 0.989551 -256 ACTATGACTACATAGTTGGAGTCTTAGACCATT 8 257 0 CTGTGGAGTC 0.968285 -187 TTATGCTGCCACTTACTGGAGACAACATAAAAT 8 393 1 ATATGGAGAC 0.942432 -51 CCTTAGCAATCGTTGTTGAAGAAAGAGAGCTCT 9 111 0 CTGTGAAGAA 0.832615 -490 GTCCAGCTAACTTGGTTGGAGAATTCGACAGAT 10 195 0 CTGTGGAGAA 0.966414 -176 CCTCCAATTCAGTCACTGGAGAAGAGAGGTACA 12 257 1 ATATGGAGAA 0.874786 -185 GCAGAATCACATTAGGTAGAGAAACGGTTTTGC 12 346 1 ATGTAGAGAA 0.779289 -96 ACGGTTTTTCAGTTGTTGGAGTCACTTCCCTTT 15 228 0 ATGTGGAGTC 0.977211 -73 TCTTTGAAGTAGTAGATGGAGACAACGGTTTTT 15 252 0 ATGTGGAGAC 0.989551 -49 TTATACTATTACTTGATGAAGTCTTTGAAGTAG 15 273 0 ATGTGAAGTC 0.881133 -28 * * * ******* Masking position 7 Map Score: 3.63884 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 308 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 GAAGTAATGTACAGACACAAGTGCAAGCGA 4 115 0 ACAGACACAA 0.832833 -426 TAGTGTCACTACAAACGCATAGACTACGAC 5 62 0 ACAAACGCAT 0.97496 -239 ATTTAAATTTACAGACACATTATATCTTGA 7 42 0 ACAGACACAT 0.969328 -259 TAAGGCGTTTACAGACCCATCGACTGCCCT 9 139 1 ACAGACCCAT 0.93437 -462 TGTTGCAACGATAGACGCATACTACGGACC 9 372 0 ATAGACGCAT 0.848434 -229 AAGGTTGCTGGGAAACGCATTATAAGGGAT 9 503 1 GGAAACGCAT 0.841658 -98 GACTGGTATCACAAACACATAATTTATATA 11 307 1 ACAAACACAT 0.960857 -276 TAGTTGGTGAGCAAACGCATGTGGAAATGA 11 493 1 GCAAACGCAT 0.969803 -90 TGGAGGGTATGCAAACACATATATGCTCTC 13 254 0 GCAAACACAT 0.952936 -47 ********** Masking position 5 Map Score: 2.73623 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 143 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 CAATTTGTAATTCTTTCTTCACTTTATATCTCTCA 1 246 0 TTCTTTTCTT 0.975464 -55 CTACTTAAAGTTCTATAATCATTGTTAATCAGAAA 2 154 1 TTCTTATCGT 0.952937 -288 AAAAAAACACTTCTTTGTTCAGAGTAGCTAATTG 4 10 0 TTCTTTTCGT 0.977338 -531 TAGTGTCTGTTTCTTTCTTCGATGTGTAGTGTGCT 4 480 0 TTCTTTTCGT 0.977338 -61 ACCTTACAACTTCTCTGTTTTACTTGAGTTTTCAA 6 267 0 TTCTTTTTTT 0.798657 -34 TTTTTTTTTTTTTTTTTTTCTTTTTTGTTTTTTCT 7 132 1 TTTTTTTCTT 0.895999 -169 ATTTGTCTTCTTCGGTTTTCCTGGTAGAATTTCCC 7 209 0 TTCGTTTCGT 0.845424 -92 TCACTGAAGTTTCTCTTTTCGAAATCCTGAACGGA 8 293 1 TTCTTTTCAT 0.848348 -151 ATCATTTTTCTTTTTTTTTCAAATTTTGGGCTATT 9 58 0 TTTTTTTCTT 0.895999 -543 ATCAGCCATTTTTTTTTATCAGGGTCGCAACTGCC 10 114 0 TTTTTATCGT 0.814397 -257 AAACATCGATTTCTATATTCATGGTAATCTGTCGA 10 169 1 TTCTTTTCGT 0.977338 -202 CGTGATTGGATTTTCTATTCAGCTTTTAAAAGCGG 11 268 0 TTTTTTTCTT 0.895999 -315 TAATAAAGTCTTCTTTTATCTGATTAATGACACCT 11 395 1 TTCTTATCTT 0.949149 -188 ATATATAAAGTTCTTTTATCTCTTTCTTAGTAAAA 13 91 0 TTCTTATCTT 0.949149 -210 TCCACTACTGTTCTTTGTTCTAATTCTAATGACTT 13 221 0 TTCTTTTCTT 0.975464 -80 ATGCAGTATTTTCTTTCATTCTATTTTGGGGCAAA 16 162 1 TTCTTATTTT 0.650634 -186 **** * *** ** Masking position 9 Map Score: 16.3997 Number of sites scoring better than the average of aligned sites = 878 Number in coding regions = 501 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 315 Fraction of orfs with sites within 600 bp upstream = 0.0505943 Motif number 14 CGAAACGACTTTTCAGAGGAGGTTATGTCGG 2 236 0 TTCAGAGGAG 0.826851 -206 GCCCATGGTCTTACACCTGCCACCTTTGAAA 6 73 1 TTCACCTGCC 0.927145 -228 AAAACCGCACTTACAGAGGGCATTAGGACAT 7 279 1 TTCAGAGGGC 0.968621 -22 CCTTGGTGCCTTGCAGACGGCTATTGTCCTG 9 222 1 TTCAGACGGC 0.941636 -379 GCTTTCTTATTTGCACAGGGCAGTTGCGACC 10 96 1 TTCACAGGGC 0.9628 -275 ATCACGCACATTGCAGATGCGTAACTCGATA 11 94 0 TTCAGATGCG 0.950876 -489 ATGACACCTTTTTCAGCGGGCCAAATTTTTT 11 421 1 TTCAGCGGGC 0.966519 -162 TGTTGTTCATTTCCACATGCGTTTGCTCACC 11 498 0 TTCACATGCG 0.94196 -85 TACTATCACGTTGCACCTGGGGCCTCTATGT 12 159 1 TTCACCTGGG 0.957306 -283 GGTATTATTGTTACACCCGCGTTGTCAAGTA 14 193 1 TTCACCCGCG 0.910821 -108 GATGATGTCCTAGCAGATGGGACAGAGTTTC 15 42 0 TACAGATGGG 0.784178 -259 ** ******** Masking position 5 Map Score: 1.97538 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 319 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 15 TTTTTCTAATGTAAACGGCTAATACCTACTT 4 432 0 GTAAACGGCA 0.895264 -109 GTTAATACTAGTCATCGTAAAAGCAGAAGCA 5 252 1 GTCATCGTAA 0.962506 -49 AATCGCGATAGTAATCGGATATAAGACAATA 10 230 0 GTAATCGGAA 0.962506 -141 TCCGACTATTGTCATCGTCGAATTTCTTCTG 10 304 1 GTCATCGTCA 0.971791 -67 TGGTCCTTGTGTAAACGGAAAAAAAGGATAT 12 39 0 GTAAACGGAA 0.864306 -403 GCCAGTGACGGTAATCGTCCACATCGATGAT 12 218 0 GTAATCGTCA 0.973571 -224 GGAAAGGAAGGTAGTCGTCAAGTG 12 428 1 GTAGTCGTCA 0.874011 -14 GTATACGGCGATAATCGTCAACACTTCCGGG 13 162 1 ATAATCGTCA 0.743756 -139 GGAAAGTGCGGCCATCGGAGACTTTCAAACA 13 191 1 GCCATCGGAA 0.818878 -110 ACTTCATCAAGTAATAGTATAATCAAT 15 284 1 GTAATAGTAA 0.683831 -17 CCATAGAAAAGTCATCGTAGACTTACATATT 16 241 1 GTCATCGTAA 0.962506 -107 ********* * Masking position 11 Map Score: 2.45736 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 229 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714