AlignACE version 2.2 July 7, 1998 AlignACE -jPRP.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 YBR055C 301 bp YBR055C prp6 1-2700 RNA splicing factor #2 YBR237W 300 bp YBR237W PRP5 1-2550 RNA helicase homolog #3 YDL043C 300 bp YDL043C prp11 1-801 snRNA-associated protein #4 YDL030W 332 bp YDL030W PRP9 1-1593 RNA splicing factor #5 YDR235W 300 bp YDR235W PRP42 1-1635 U1 snRNP protein that shares 50\% sequence similarity with Prp39p U1 snRNP protein and has multiple copies of the crn-like TPR motif #6 YDR243C 300 bp YDR243C prp28 1-1767 Required for the first step of splicing in vitro #7 YDR473C 600 bp YDR473C prp3 1-1410 #8 YER013W 409 bp YER013W prp22 1-3438 helicase-like protein #9 YGL120C 504 bp YGL120C PRP43 1-2304 pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA #10 YGR006W 300 bp YGR006W PRP18 1-660 RNA splicing factor associated with U5 snRNP #11 YGR075C 300 bp YGR075C PRP38 1-729 RNA splicing factor #12 YGR091W 300 bp YGR091W PRP31 1-1485 pre-mRNA splicing protein #13 YHR165C 300 bp YHR165C PRP8 1-7242 RNA splicing factor #14 YJL203W 300 bp YJL203W PRP21 1-843 RNA splicing factor #15 YKL012W 300 bp YKL012W PRP40 1-1752 Splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle #16 YKR086W 300 bp YKR086W PRP16 1-3216 putative ATP-binding protein #17 YLL036C 323 bp YLL036C PRP19 1-1512 RNA splicing factor #18 YML046W 398 bp YML046W PRP39 1-1890 RNA splicing factor associated with U1 snRNP #19 YMR268C 441 bp YMR268C PRP24 1-1335 U4\/U6 snRNA-associated splicing factor #20 YMR302C 600 bp YMR302C prp12 1-2553 Integral membrane mitochondrial protein #21 YNR011C 481 bp YNR011C prp2 1-2631 putative RNA-dependent ATPase #22 YPR178W 300 bp YPR178W prp4 1-1398 associated with the U4\/U6 snRNP Motif number 1 ATTATTTATTAAAAGAAGAAACGCCATCATT 1 106 0 AAAAGAGAAA 0.869704 -196 TTCTTTTAATAAATAATGTAACGAAAGTATT 1 120 1 AAATAAGTAA 0.831187 -182 ATTAAGCAAAAAAAAACGAAAAATTTCAGAA 1 227 1 AAAAAAGAAA 0.946196 -75 CATCTCACTAAAAAAATGAAAAAAAAAAATC 3 187 1 AAAAAAGAAA 0.946196 -114 TACCATAGCAAGAAAACAAAAATAGATAGCG 4 56 1 AGAAAAAAAA 0.792424 -277 TAAACTTAATAAATAAAGAAAAGGGTGCGAT 5 39 0 AAATAAGAAA 0.919622 -262 CCCGTGGGAAAAACAACGTAAATTTCTACAT 5 206 1 AAACAAGTAA 0.783337 -95 TGGGGAGTGAAGAAAAAGTAATTATCAGCAT 7 215 0 AGAAAAGTAA 0.839669 -386 TTAGAATGCCAGATGACGTAAAACAATCAAA 7 533 1 AGATGAGTAA 0.563935 -68 TTAGTTTGGAAAATGATGAAATTTGTCCATA 9 193 0 AAATGAGAAA 0.812825 -312 GAGGCACCGAAAAAAAAGAAAAAGAAATAAA 9 344 0 AAAAAAGAAA 0.946196 -161 AAGAGAGTAGAAAAAATGAAAAAAAACCAAA 11 35 1 AAAAAAGAAA 0.946196 -266 AATTATGATAAAAAAAAGTAAAATCTAAAGC 11 203 1 AAAAAAGTAA 0.883287 -98 AGATTAGAATAAACAACAAAATCATAACTTT 12 35 1 AAACAAAAAA 0.724931 -266 AAAAACCAAAAGAAAACAAAAGCTTTTGAGG 14 133 0 AGAAAAAAAA 0.792424 -168 ATACAGGAAGAAATAAGGTAAAGCGTAAAAC 14 253 1 AAATAAGTAA 0.831187 -48 TCACTTTGACAAAAGATAAAAGAGGAAGCAA 15 38 0 AAAAGAAAAA 0.676779 -263 GGAAAATTAAAGACAAAGTAAAATAGCACAA 16 138 0 AGACAAGTAA 0.714443 -163 CTATTTTCTCAAATAATAAAAGCGGTGAAAG 16 208 1 AAATAAAAAA 0.782091 -93 AGATGACTGCAGATGATAAAACACAAGAAGG 16 253 1 AGATGAAAAA 0.485249 -48 TTCCCTTCTGAAATAAGGAAAGACTGCAGTT 17 60 0 AAATAAGAAA 0.919622 -264 GAATGATCTGAAACAATAAAAAAAGATATTT 18 144 0 AAACAAAAAA 0.724931 -255 AAAATGGTAAAGAAAAAGAAAATGAATGATA 18 193 0 AGAAAAGAAA 0.924067 -206 TGTTATATTGAGAAAATGAAAGATGAACTCA 20 512 1 AGAAAAGAAA 0.924067 -89 AATAAATAAAATAAATGCGAGTTC 21 4 1 AAATAAATAA 0.607002 -478 CAGCCTTACGAAAAAAAAAAAAAATCACATC 21 104 1 AAAAAAAAAA 0.846546 -378 CTTCGAGATGAAAAAAGGAAACTGAAAAATT 21 153 0 AAAAAAGAAA 0.946196 -329 ****** **** Masking position 6 Map Score: 24.0177 Number of sites scoring better than the average of aligned sites = 4086 Number in coding regions = 1768 Number in noncoding regions = 2318 Number of orfs with sites within 600 bp upstream = 1574 Fraction of orfs with sites within 600 bp upstream = 0.252811 Motif number 2 TATCCGTCTTAGAAAAGTAGAATGTCAACCAAACCAGAGAAGC 2 14 0 AAAAGCAAAA 0.977272 -287 ACAGCGCCAAATAATTCGAGAAGGGAAATCATAACGCTGTTGC 2 250 1 AAAAGAAAAA 0.960445 -51 AGGCAATTTAATAATTTAAAAGTGCCAAATTAATATCAATTTA 3 40 1 AAAAGCAATA 0.914568 -261 ATATTTGACTACAATAATTGAAAGGAAAACAAAATTGTTTGCC 3 91 0 AAAAGAAAAA 0.960445 -210 CGGTACAATGAAAATAGCAGAATGTAAATAATATTTGACTACA 3 121 0 AAAAGAAAAA 0.960445 -180 TGTATGCTAAAAAAATTAACATAGTCAAGAAACTTTCTTTGAG 7 410 0 AAAAGCAAAC 0.904029 -191 TAAAACAATCAAAAAGACTCACAGAAAACATCAGGCGATCTAT 7 551 1 AAAAGAAATA 0.858069 -50 CTCGCATTTGAAAATTTTTCAGAGGCACCGAAAAAAAAGAAAA 9 353 0 AAAAGCACAA 0.804323 -152 CACATCTAAAAAAAAGAATTAAAGAAAAATATTCTTTATGTAA 12 110 0 AAAAGAAAAT 0.831299 -191 CTTCCTTCCAAAAAAAAAATAGCGTCAAAGAAAG 13 277 1 AAAAGCAAAA 0.977272 -24 GACAAACAATAGAAAAACCAAAAGAAAACAAAAGCTTTTGAGG 14 133 0 AAAAGAAAAA 0.960445 -168 ATTTTATCAAAAAATGGTCAACAGACAAACAATAGAAAAACCA 14 156 0 AAAAGCAAAT 0.897184 -145 ATAGAACAAAAAAAGCCTGTAAAGCCAAGCAAATAGAGGCTTT 15 84 0 AAAAGCAAAA 0.977272 -217 GTGGTAAACGATATGAAATTATCGACAATAATAATGTACTTGG 15 157 1 AATAGCAAAA 0.734985 -144 TTTGGATTTCCCAAAACACAAGTGACAACGATTTACAACAAGA 16 33 0 CAAAGCAAAT 0.712681 -268 GATACTTTCAACAAGTTAAAATGGAAAATTAAAGACAAAGTAA 16 148 0 AAAAGAAAAA 0.960445 -153 AGCAGCGGTGAAAAATTCGTAAGGGCAATTTTAGAAAGATGCA 17 234 1 AAAAGCAATA 0.914573 -90 ACCACATTGTCTAAGAGGGAAAGGAAAATGACAACAAAGCGCT 18 16 0 CAAAGAAAAA 0.87345 -383 AAAGAAAAAGAAAATGAATGATAGTAAATCATACTGAAAACGA 18 173 0 AAAAGAAAAA 0.960445 -226 AACGAAAGACGGATTGCCAAGTATCCAATAGCAGT 18 374 0 CAAAGCAAAC 0.728087 -25 CTTCGAGATGAAAAAAGGAAACTGAAAAATTTAGATCGATAAG 21 141 0 AAAAGAAATA 0.858069 -341 * ** * * *** * * Masking position 11 Map Score: 19.7106 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 438 Number in noncoding regions = 539 Number of orfs with sites within 600 bp upstream = 442 Fraction of orfs with sites within 600 bp upstream = 0.0709926 Motif number 3 AAAAAAAAACGAAAAATTTCAGAAAATATAC 1 234 1 GAAAATTTCA 0.879633 -68 TGTACCGGGTGAAATATTACATGTACCGCCC 3 157 1 GAATATTACA 0.848625 -144 TCCTATTAAAGCAAAATTAAATGAATGTATA 4 293 0 GAAAATTAAA 0.924183 -40 AAAAGAAGTAGAAAAATTACAAATAAGAACT 5 121 0 GAAAATTACA 0.922724 -180 TTATTCAATTGTAATATTTAACACGTTTACG 9 413 1 GAATATTTAA 0.777906 -92 AACGCATAACGCAATATTAAGAGTAAAATAG 10 118 0 GAATATTAAG 0.810779 -183 AAGGGAAGATGAAAAAGTTAAGAAGAGAATC 10 211 1 GAAAAGTTAA 0.805564 -90 AACTTTTGCCGAAATATTTCGTTGAAGGAAG 14 205 0 GAATATTTCG 0.7198 -96 AAATATTTCGGCAAAAGTTAGCCTTGAAACA 14 217 1 GAAAAGTTAG 0.756214 -84 AAGTTAAAATGGAAAATTAAAGACAAAGTAA 16 148 0 GAAAATTAAA 0.924182 -153 GCTGCTACCCGAAAAAGTACGAAATTTATCA 17 209 0 GAAAAGTACG 0.832351 -115 AACTTTCCAAGAAATATTAAAGACCAAAACA 17 277 1 GAATATTAAA 0.851256 -47 GACGAAAAGTGAAAAATTACATCCGTATAGA 20 342 0 GAAAATTACA 0.922724 -259 AGTAGTATTTGTAAAAGTAAACC 20 588 1 GAAAAGTAAA 0.871291 -13 AAAGGAAACTGAAAAATTTAGATCGATAAGA 21 140 0 GAAAATTTAG 0.848153 -342 AGAACAAGTGGGAAAATTAAAGACTAATCAT 21 245 1 GAAAATTAAA 0.924182 -237 * ********* Masking position 6 Map Score: 8.27708 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 508 Number in noncoding regions = 402 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 4 TGTATTAATTGCAGCACTCTTTCTTTAGTAGC 1 54 1 GCAGACTTTT 0.918031 -248 AAAATAGGAACTAAAACTGTTTGGTGAATCAA 6 71 1 CTAAACTTTT 0.921811 -230 TAATACTTTACTAGGACTATTTCTTGTTATTG 7 504 0 CTAGACTTTT 0.983572 -97 GTAATAGTACCCAGTACTTTTTTAGATGATCT 9 98 0 CCAGACTTTT 0.987193 -407 AGCAGGGGCACCAGCACTTTCTAATAATTCCA 10 55 0 CCAGACTTCT 0.947395 -246 AACGCCTCAACTAGCACTATTTGATAGCATTT 12 252 1 CTAGACTTTT 0.983572 -49 GCAGTAAGGGCCAAAACTTTTTGTTGAACAAA 18 347 0 CCAAACTTTT 0.938189 -52 GTTGTATGGGCTAGTACTGTTTTGGCTACATT 21 314 0 CTAGACTTTT 0.983572 -168 AGGGAAATGACTAGTACTATTACCTTGTTGAA 22 273 1 CTAGACTTTA 0.904198 -28 **** *** *** Masking position 6 Map Score: 4.0638 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 45 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 GAACAGCAAATTCAAATCATTTAACGCATCCA 3 269 1 TTCAATCTTT 0.930482 -32 ACATTGCTTCTTCAAAATATTCTCATGCGGGT 8 262 0 TTCAAATTTC 0.872646 -148 TCTTAATTAGTTAAGATCTTTCTGGTACTGTA 9 69 0 TTAAATCTTC 0.713419 -436 ATGGACAAATTTCATCATTTTCCAAACTAAGG 9 194 1 TTCACATTTC 0.665433 -311 ATAATTCTTGTTCAGAACGTTCGTTATTGATA 11 177 0 TTCAAACTTC 0.974224 -124 AGCAGTACTATTCAAAACTTTTAAAAATACTA 12 183 0 TTCAAACTTT 0.930482 -118 AGTTGAGGCGTTCAAATCGTTTACCTAGCTTT 12 232 0 TTCAATCTTT 0.930482 -69 TTATAAAAATTTCATATCATTTAGTACGAATA 13 111 0 TTCAATCTTT 0.930482 -190 TGTCGATAATTTCATATCGTTTACCACGTCGC 15 152 0 TTCAATCTTT 0.930482 -149 AGGTGTGTGCTGCAGATCGTTCCACACTGCTG 16 93 0 TGCAATCTTC 0.846469 -208 TTTTTATTGTTTCAGATCATTCGTTTTCAGTA 18 153 1 TTCAATCTTC 0.974224 -246 CTTTAGGACTTTGAAAACTTTCTTGCGTAAAT 18 288 0 TTGAAACTTC 0.786763 -111 GTCTTCCACTTTCAGCACGTTCTCGTCATCAG 21 346 0 TTCACACTTC 0.916462 -136 TCCTGACATGTTCACAATTTTCTAGTGGAGAA 22 49 1 TTCAAATTTC 0.872646 -252 **** *** *** Masking position 4 Map Score: 6.36544 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 638 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 6 TTAATTAGTTTCATCTAATCCGGGTAATGG 2 165 0 TCATCTAATC 0.920991 -136 GAGTGAGATATCATCTGATCTATTGCAAAT 8 171 1 TCATCTGATC 0.945286 -239 TCAAATGCTGTCATCTCATGTTGTTAATGC 8 333 1 TCATCTCATG 0.982867 -77 AAGTTTCTTTTCACCTCATCTCGCATTTGA 9 385 0 TCACCTCATC 0.958652 -120 TCATCTGCAGTCATCTCATGAATTTTTCAG 16 239 0 TCATCTCATG 0.982867 -62 TGTCATTTACTCATCTCATCTCATCAAGTT 20 305 1 TCATCTCATC 0.986902 -296 ATCTCGAAGCTCATCGCATGAAAAAAAAAC 21 175 1 TCATCGCATG 0.946385 -307 ********** Masking position 3 Map Score: 2.42541 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 42 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 7 TTCTATTAAGCAAAAAAAAACGAAAAATTT 1 223 1 CAAAAAAAAA 0.924948 -79 CTAAAAAAATGAAAAAAAAAAATCTGCTAA 3 194 1 GAAAAAAAAA 0.906033 -107 TCACAAAGAACTACAAAGAATTATGAAGAA 4 93 0 CTACAAAGAA 0.755166 -240 ATAAAATGCGCTACAAAAAAAATATTGAAC 4 150 0 CTACAAAAAA 0.887485 -183 TCCGATGAGGCAACAAAGAAGTGTTAAGTA 4 188 1 CAACAAAGAA 0.898058 -145 AAGAATTTTCCTACAAAAAAAGTTGACTAC 7 51 0 CTACAAAAAA 0.887485 -550 CTCACTCTGCCAACAAAAAATGAGAAATTG 8 148 0 CAACAAAAAA 0.957498 -262 TAGAAAAAATGAAAAAAAACCAAAGTATAG 11 42 1 GAAAAAAAAC 0.706537 -259 AAAAACGCAAGAACAAAAACAAAACGTGGG 11 263 1 GAACAAAAAC 0.814851 -38 AGGACCACATCTAAAAAAAAGAATTAAAGA 12 128 0 CTAAAAAAAA 0.811851 -173 AACTTCCTTCCAAAAAAAAAATAGCGTCAA 13 275 1 CAAAAAAAAA 0.924948 -26 TACAATTATAGAACAAAAAAAGCCTGTAAA 15 104 0 GAACAAAAAA 0.94631 -197 TGATCTGAAACAATAAAAAAAGATATTTGT 18 142 0 CAATAAAAAA 0.688334 -257 ACTTTTTGTTGAACAAAGAAATGGCTGTGG 18 334 0 GAACAAAGAA 0.873294 -65 ACAGCCTTACGAAAAAAAAAAAAAATCACA 21 103 1 GAAAAAAAAA 0.906033 -379 CTCATCGCATGAAAAAAAAACTTCGATATG 21 184 1 GAAAAAAAAA 0.906033 -298 ********** Masking position 5 Map Score: 11.135 Number of sites scoring better than the average of aligned sites = 3268 Number in coding regions = 794 Number in noncoding regions = 2474 Number of orfs with sites within 600 bp upstream = 1739 Fraction of orfs with sites within 600 bp upstream = 0.279313 Motif number 8 ATTATTTACATTCTGCTATTTTCATTGTACCGGG 3 132 1 TTCTTATTCA 0.684019 -169 CTGTGAATTGTTCTTATATGTTCTAAAGTAAAGA 7 369 1 TTCTTATTCT 0.808544 -232 AATAAAGTTATTATAGTTTTTTCATCCGTTATAA 8 91 1 TTATTTTTCA 0.684796 -319 TTGAGATGGTTTATTACTTGTTCAAATGCTGTCA 8 312 1 TTATCTTTCA 0.844385 -98 AAGTCCTTTTTTATTTCTTTTTCTTTTTTTTCGG 9 335 1 TTATCTTTCT 0.913687 -170 AGCCAACAGCATATGTCTTATTCTTCTAATTTCA 10 151 1 ATATCTTTCT 0.808544 -150 TATAGTTATCTTCTCTCTTATTCTTCAGAACCAG 11 73 0 TTCTCTTTCT 0.963555 -228 ACTTCACTACATATGCCTTCTGCACTCCCGAGCC 13 62 0 ATATCTTTCA 0.684019 -239 AGATAATCATTTCTATTATATTCTACCGCT 17 7 0 TTCTTATTCT 0.808544 -317 ATCCCTTCTTATCTCTCTTGTGCTTTACCAGTAT 19 107 1 ATCTCTTTCT 0.913402 -335 AAAGATAATATTCTACTTTTTGCTCCCACCGCGT 20 47 1 TTCTTTTTCT 0.913687 -554 AAACAGTCGGTTATAGTTTGTCCTGCTCCTCTGA 20 188 1 TTATTTTTCT 0.809101 -413 ACGGTAATTCTTCTGTCATTTACTCATCTCATCT 20 292 1 TTCTCATTCT 0.913402 -309 CATTACCGTTATCTCCCTTATACTTCTCAAATTC 20 480 0 ATCTCTTTCT 0.913402 -121 TACTGAGTTCATCTTTCATTTTCTCAATATAACA 20 512 0 ATCTCATTCT 0.807987 -89 GTCTTTAATTTTCCCACTTGTTCTCACTATTTCC 21 235 0 TTCCCTTTCT 0.747825 -247 CAGCTATCCGTTATTACTTATACAATTGATTAAT 21 408 0 TTATCTTTCA 0.844385 -74 TTACTAATGATTCTGTTTTCTCCACTAGAAAATT 22 64 0 TTCTTTTTCA 0.844385 -237 **** *** * ** Masking position 9 Map Score: 7.98876 Number of sites scoring better than the average of aligned sites = 1485 Number in coding regions = 993 Number in noncoding regions = 492 Number of orfs with sites within 600 bp upstream = 416 Fraction of orfs with sites within 600 bp upstream = 0.0668166 Motif number 9 GTCAACTCACCCGTATATTTTCTGAAATTTTTC 1 244 0 CCTATATTCT 0.866222 -58 AAATGAGAAATTGTCTTATTTCTGATACATTTG 8 128 0 TTTCTTTTCT 0.901524 -282 TTGTCCATAACTATATACTATCAGTCAGCAAAC 9 169 0 CTTATATTCA 0.597111 -336 TATGTCTTATTCTTCTAATTTCAAGCCTGATAA 10 162 1 TCTCTATTCA 0.918223 -139 TTTTTTCATTTTTTCTACTCTCTTGGCATACTT 11 26 0 TTTCTATTCT 0.921008 -275 TAAACTATAGTTATCTTCTCTCTTATTCTTCAG 11 79 0 TTTCTTTTCT 0.901524 -222 AAGGTCTTTGTATATTTTCTGCAGCCAAAA 12 281 0 TTTATATTCT 0.850395 -20 GAAGGAAGGTTCTTATTTTATCAAAAAATGGTC 14 180 0 TCTATTTTCA 0.811254 -121 ATCAGTTGCTTCCTCTTTTATCTTTTGTCAAAG 15 33 1 TCTCTTTTCT 0.949439 -268 TTTTGCCCTCTTTTCTATTTTCTCAAATAATAA 16 194 1 TTTCTATTCT 0.921008 -107 GAAATGATTATCTTCTTCTCTCTGCCAAACTAA 17 28 1 TCTCTTTTCT 0.949439 -296 AAATATCTTTTTTTATTGTTTCAGATCATTCGT 18 144 1 TTTATTTTCA 0.676943 -255 TTACCCAATCCCTTCTTATCTCTCTTGTGCTTT 19 100 1 CCTCTTTTCT 0.912499 -342 TTGACGTCCACCCTATAATTTCAATTATTGAAC 20 373 1 CCTATATTCA 0.752476 -228 GTACACACCCTCATATAGTTTCTCAGGGCTTGA 20 429 1 TCTATATTCT 0.921008 -172 TCTCACTATTTCCTCTATTGTCTTAATACGCTC 21 215 0 TCTCTATTCT 0.959865 -267 ** **** * *** Masking position 6 Map Score: 6.93234 Number of sites scoring better than the average of aligned sites = 1265 Number in coding regions = 803 Number in noncoding regions = 462 Number of orfs with sites within 600 bp upstream = 405 Fraction of orfs with sites within 600 bp upstream = 0.0650498 Motif number 10 AGCTTACAATCGAGAGAATTACCAACGACAATA 6 223 1 CGAAGATACC 0.98331 -78 GTCCAGAGGCCAAAAGCAGTATCTCTAGCTAAA 7 331 0 CAAAGATATC 0.933623 -270 TAAACCATCTCAAAAGTACTATCGTAGCCCTAC 8 292 0 CAAAGATATC 0.933623 -118 GATTGAGTAACGATAGTATAACCTTATAAACGC 9 451 1 CGAAGAAACC 0.949027 -54 AACAGACAAACAATAGAAAAACCAAAAGAAAAC 14 147 0 CAAAGAAACC 0.957577 -154 GGCCCAAAGACAATACAAATACCTCTGGT 16 282 1 CAAACATACC 0.912116 -19 TCATTCCCGCCAGGAGCATTACCCAATCCCTTC 19 82 1 CAGAGATACC 0.972156 -360 GAGTAAATGACAGAAGAATTACCGTTTCATCAT 20 284 0 CAGAGATACC 0.972156 -317 CTTGTAATAGCGATAGTAATACCAGTAGTAAAG 22 147 0 CGAAGATACC 0.98331 -154 *** ** * **** Masking position 8 Map Score: 3.39385 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 208 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 GTTTCGCGAATATAGCTGCCAAGTATTATCCA 7 250 0 TAGCTGCCAA 0.98286 -351 AGATGATATCTCACTCTGCCAACAAAAAATGA 8 155 0 TCTCTGCCAA 0.979698 -255 CAGGTCCCAATAAGGATGCCAAGGAAGCGTAC 9 33 1 TAGATGCCAA 0.918642 -472 CCTCGGTTCATCCTTCTGCCATGGTCACTTTA 13 164 0 TCTCTGCCAT 0.938458 -137 CTGCAGCACACACCTCTGCCAATCATTCTTGT 16 110 1 CATCTGCCAA 0.931829 -191 ATTATCTTCTTCTCTCTGCCAAACTAAACTGC 17 34 1 TCTCTGCCAA 0.979698 -290 ACATGAAATTTATTCCTGCCAAGTCATCGAGT 17 177 0 TACCTGCCAA 0.95534 -147 AATGTTGTAGTAAATCTGCCATTTTGAATAAG 19 344 0 TATCTGCCAT 0.948685 -98 TTGTTATCTATATAGATGCCAATTAAACATAT 21 444 0 TAGATGCCAA 0.918644 -38 ** ******** Masking position 7 Map Score: 1.73305 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 142 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TAGAATGTCAACCAAACCAGAGAAGCCAA 2 8 0 ACCAAACAAG 0.938091 -293 AGAGCAATGGACCAAACTAAAGGTATTAGAGT 2 203 1 ACCAAATAAG 0.972407 -98 TCTTATATGTTCTAAAGTAAAGAGCCATGACT 7 380 1 TCTAAATAAG 0.911287 -221 TTCATCATTTTCCAAACTAAGGTCGTTTAGTT 9 204 1 TCCAAATAGG 0.833885 -301 ATGAAAAAAAACCAAAGTATAGGCTGGTTCTG 11 50 1 ACCAAATAAG 0.972407 -251 GGTTTACTATTCTAAACTATAGTTATCTTCTC 11 92 0 TCTAAATAAG 0.911287 -209 TCTCTGCCAAACTAAACTGCAGTCTTTCCTTA 17 46 1 ACTAAATGAG 0.866069 -278 AATATTAAAGACCAAAACATAGCCAAGAAAGC 17 289 1 ACCAAACAAG 0.938091 -35 TACCCATTCCTCTAAACTGTAGACATGGTAGC 20 121 1 TCTAAATGAG 0.815394 -480 AGGATCTAAAACCAAAATATAGCGGGCCTATA 20 551 1 ACCAAATAAG 0.972407 -50 ****** ** ** Masking position 6 Map Score: 2.21546 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 175 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 CCGGGTAATGGTAAATCAAGATATTTCAACA 2 145 0 GTAATCAAGA 0.950861 -156 CTATATATCTGTAGATCTAGATGGTTTTAAA 4 15 0 GTAATCTAGA 0.812579 -318 TAGTTATACGGTAGATCAAGAACCTTCGGTG 4 247 1 GTAATCAAGA 0.950861 -86 ACTATAATGTGCATAAATATCTAGAAAAA 5 9 1 GTGATAAATA 0.861904 -292 GTGAATAACCGTAAATAAATAAATAAACTTA 5 62 0 GTAATAAATA 0.883542 -239 ATAAGAACTTGTGTATCAATAGATTAACAAA 5 99 0 GTGATCAATA 0.950861 -202 AAACTGTTTGGTGAATCAATATTAATCAGAA 6 84 1 GTGATCAATA 0.950861 -217 AATTACTTTAGTATATCATTAGCAATCACCT 8 38 0 GTAATCATTA 0.840515 -372 ATAATCTACAGTAGATAAATATGAGGCAATA 14 53 1 GTAATAAATA 0.883542 -248 AATTTTCTATGTACATCATGACAATGAATTG 19 258 1 GTAATCATGA 0.812579 -184 GAATTGTAGAGTGCATCAATGTCTTTTTTAA 19 283 1 GTGATCAATG 0.76862 -159 AAGAAACTGTGTATATATATATTTCAGATAC 22 106 0 GTAATATATA 0.629609 -195 *** ******* Masking position 5 Map Score: 1.42023 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 100 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 14 AATTATCAGCATTCATTTTCGAGAATTTTA 7 197 0 ATTCATTTTC 0.964063 -404 CTTATTTCTGATACATTTGCTATTATAACG 8 117 0 ATACATTTGC 0.844831 -293 ATTGATTGGGATTCATTTGCAATAGATCAG 8 185 0 ATTCATTTGC 0.971861 -225 TCCGGGTAATATTCATTTGTAAAGCTTTAG 9 134 0 ATTCATTTGT 0.771996 -371 TACGCTCTGTATTCGTTTGCTGTTTCAACT 9 237 1 ATTCGTTTGC 0.944078 -268 GTTTCAGATCATTCGTTTTCAGTATGATTT 18 161 1 ATTCGTTTTC 0.929143 -238 ATTTACTATCATTCATTTTCTTTTTCTTTA 18 187 1 ATTCATTTTC 0.964063 -212 GCACTCTACAATTCATTGTCATGATGTACA 19 267 0 ATTCATTGTC 0.862408 -175 TGAGTTCATCTTTCATTTTCTCAATATAAC 20 513 0 TTTCATTTTC 0.808758 -88 ********** Masking position 6 Map Score: 2.24362 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 256 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 15 GTTATGATTTCCCTTCTCGAATTATTTGGC 2 255 0 CCCTTCTCGA 0.741855 -46 CTGGATCCCGCACTGATCAATAACAAGAAA 7 487 1 CACTGATCAA 0.899712 -114 GAATCCCAATCAATGCTGATACCGCTTCGT 8 201 1 CAATGCTGAT 0.726391 -209 GTGCTGGTGCCCCTGCTGAACCACTGCTCA 10 70 1 CCCTGCTGAA 0.983041 -231 CCTGCTGAACCACTGCTCATGGTGTTAAGT 10 81 1 CACTGCTCAT 0.899863 -220 GATCGTTCCACACTGCTGGATCTGCCTGGA 16 81 0 CACTGCTGGA 0.943111 -220 CCTGATCTTTCCCTTCTGAAATAAGGAAAG 17 69 0 CCCTTCTGAA 0.8993 -255 AATTATTCAGCCATGCTCAAACCTCCAGAT 18 107 0 CCATGCTCAA 0.923309 -292 ACATAACGAACACTGCTGAAGCTACCATGT 20 143 0 CACTGCTGAA 0.977373 -458 GATCGAAGTTCAATGATGAAACGGTAATTC 20 272 1 CAATGATGAA 0.726059 -329 ATCTACGGAACCCTGATCAAGCCCTGAGAA 20 448 0 CCCTGATCAA 0.923309 -153 ********** Masking position 4 Map Score: 2.04501 Number of sites scoring better than the average of aligned sites = 664 Number in coding regions = 527 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497