AlignACE version 2.2 July 7, 1998 AlignACE -jUBP.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 YBL067C 600 bp YBL067C UBP13 1-2067 ubiquitin carboxyl-terminal hydrolase #2 YBR058C 600 bp YBR058C UBP14 1-2412 Ubiquitin-specific protease #3 YDL122W 600 bp YDL122W UBP1 1-2430 Ubiquitin-specific protease #4 YER098W 460 bp YER098W UBP9 1-2265 ubiquitin carboxyl-terminal hydrolase #5 YER144C 302 bp YER144C UBP5 1-2418 Putative Ubiquitin-specific protease #6 YER151C 300 bp YER151C UBP3 1-2739 Ubiquitin-specific protease #7 YFR010W 319 bp YFR010W UBP6 1-1500 encodes putative deubiquitinating enzyme #8 YIL156W 548 bp YIL156W UBP7 1-3216 Ubiquitin-specific protease #9 YJL197W 315 bp YJL197W UBP12 1-3765 ubiquitin carboxyl-terminal hydrolase #10 YKR098C 600 bp YKR098C UBP11 1-2154 Ubiquitin-specific protease #11 YMR223W 405 bp YMR223W UBP8 1-1416 encodes putative deubiquitinating enzyme #12 YMR304W 600 bp YMR304W UBP15 1-3693 encodes putative deubiquitinating enzyme #13 YNL186W 430 bp YNL186W UBP10 1-2379 predicted to encode a ubiquitin-processing protease #14 YOR124C 387 bp YOR124C UBP2 1-3819 Ubiquitin-specific protease #15 YPL072W 484 bp YPL072W UBP16 1-1500 encodes putative deubiquitinating enzyme Motif number 1 GCGTTGGAGAAAAAAAAAAAGTTACCGGAAT 1 184 0 AAAAAAAAAG 0.971882 -417 GAATAGGGATAAAGAAGCAAGGACTGAGCGT 1 211 0 AAGAAGCAAG 0.676655 -390 AAAATGAACAGGTGAAAAAAAATCAATTTGA 1 420 0 GGGAAAAAAA 0.698615 -181 ATCCAAATGGAAAAAAAAAAAATGAACAGGT 1 438 0 AAAAAAAAAA 0.901464 -163 TGGCCCCTTCAACAAATAAAGCTTGATGAGT 1 513 0 AAAAATAAAG 0.813032 -88 TGAAAATTGTGAGAAAAAAAACATGGAGGAA 2 299 0 GAAAAAAAAA 0.828927 -302 GTTTTCCAATGATGGAAAAAGAAACTTGCCT 3 244 0 GAGGAAAAAG 0.685762 -357 TTTTTTCCTGAGAAAAAAAAGGACGCAGATC 3 421 0 AGAAAAAAAG 0.954633 -180 TTTTTTTCTCAGGAAAAAAAAATTTTATACA 3 433 1 AGAAAAAAAA 0.84778 -168 ACGTTATAATGGAAAAGAAAGGAGAAGCGAA 3 493 0 GGAAAGAAAG 0.849859 -108 GTCCTTCAGCAAAAGAAAAAGCAGTTGGGCT 4 91 1 AAAGAAAAAG 0.83983 -370 AGTGAGGCGCAAGGAAAAAAGAAAAAAAATC 5 178 0 AAGAAAAAAG 0.96449 -125 GTAGAGAGATAATAAAGAAAGGACTCCACAT 5 263 0 AAAAAGAAAG 0.946107 -40 GCAAGGAAGAAAAAGAAAAAGAAGGAAAAAA 6 135 1 AAAGAAAAAG 0.83983 -166 AAAGAAAAAGAAGGAAAAAAATATAATGTGA 6 146 1 AAGAAAAAAA 0.877886 -155 AAGTGTTTCTAGAGAAGAAAGTCATTTTAAT 6 214 1 AGGAAGAAAG 0.893596 -87 ACAAGTAGTCAAAAAAAAAAGTATCATGGGG 7 74 0 AAAAAAAAAG 0.971882 -246 TCATTGTGGAGAGAAAGAAAGCGCCTTCTTG 8 97 0 GAAAAGAAAG 0.902893 -452 GGGATTACTGGAAAAATAAAGGGAGGAAAAT 9 250 1 GAAAATAAAG 0.697259 -66 TGAGCCAGACGAAGAAAAAAATAAAAAATGA 10 258 0 GAGAAAAAAA 0.791998 -343 ACCAAAAAAAAAAAAAAAAAGAAAAAAAGAA 10 302 1 AAAAAAAAAG 0.971882 -299 AGAAAAAAAGAAAAAAAAAAATAGTTTCTCC 10 321 1 AAAAAAAAAA 0.901464 -280 AAAAGGTATAAGTGAAGAAAGAATGTGCAAT 11 44 0 AGGAAGAAAG 0.893596 -362 AGAATAGAGAAGAAAAAAAAGGTATAAGTGA 11 60 0 AGAAAAAAAG 0.954633 -346 TTCAAAGAAAAGCAAAAAAAGGAAGAATAGA 11 83 0 AGAAAAAAAG 0.954633 -323 GAATTTTTCAAGTGAAAAAAAATCCTCGATT 11 111 1 AGGAAAAAAA 0.814007 -295 ATTAATAACAAATAAAAAAAGCAGGGTTTCA 11 381 0 AAAAAAAAAG 0.971882 -25 TATTTACCAAGAAGAAACAAGAAGTGATAAA 12 24 1 GAGAAACAAG 0.685762 -577 AAAAAAAAAAAAAAAAAAAAGGCAGAGGAGA 12 173 0 AAAAAAAAAG 0.971882 -428 AGATTGAGAGAATGAAAAAAAAAAAAAAAAA 12 187 0 AAGAAAAAAA 0.877886 -414 CCCCAAAAGAAAAGAAAAAAGTTCTTATTTT 13 162 1 AAGAAAAAAG 0.96449 -269 GCTTCTATGAAACAAATAAAGGACAGAAGCG 13 253 0 AAAAATAAAG 0.813032 -178 ATATAGCTTGAAAAAAACAAGCGGCTTGCCA 14 273 1 AAAAAACAAG 0.83983 -115 GCGTCTTAATGGCAAAGAAAGGTATGAGAAG 15 21 1 GGAAAGAAAG 0.849859 -464 AATTGTAAATAAGAAAGAAAAATATCAAATC 15 148 0 AAAAAGAAAA 0.822898 -337 AAAAAAATGAAATAAAAAAAGAAAACAAAAT 15 239 1 AAAAAAAAAG 0.971882 -246 ACTTGGGTGAAATAAAAAAAATAAATCAATA 15 275 1 AAAAAAAAAA 0.901464 -210 ** ******** Masking position 6 Map Score: 47.2413 Number of sites scoring better than the average of aligned sites = 4928 Number in coding regions = 1800 Number in noncoding regions = 3128 Number of orfs with sites within 600 bp upstream = 2020 Fraction of orfs with sites within 600 bp upstream = 0.324446 Motif number 2 AGCGTTGGAGAAAAAAAAAAAGTTACCGGA 1 186 0 AAAAAAAAAA 0.881895 -415 TTTGAAAACCAAAGAAAAACTCTATTGATT 1 395 0 AAAGAAAAAC 0.859229 -206 CCAAATGGAAAAAAAAAAAATGAACAGGTG 1 437 0 AAAAAAAAAA 0.881895 -164 CCAATGATGGAAAAAGAAACTTGCCTACAT 3 240 0 AAAAAGAAAC 0.753466 -361 GTCCTTCAGCAAAAGAAAAAGCAGTTGGGC 4 91 1 AAAAGAAAAA 0.947229 -370 CGCCCCCCCCACAAGAAAACGTTTCTCTTG 4 244 1 ACAAGAAAAC 0.646524 -217 GCGCAAGGAAAAAAGAAAAAAAATCAATGC 5 173 0 AAAAGAAAAA 0.947229 -130 GCAAGGAAGAAAAAGAAAAAGAAGGAAAAA 6 135 1 AAAAGAAAAA 0.947229 -166 CGAAAAAGCGAAAGGGAAGAGAAGTGTTTC 6 193 1 AAAGGGAAGA 0.606018 -108 ATGATGATGGAAAGGAAAGCGGTACCTGGA 6 273 0 AAAGGAAAGC 0.8595 -28 ACAAGTAGTCAAAAAAAAAAGTATCATGGG 7 75 0 AAAAAAAAAA 0.881895 -245 TGTTCGGACCAAAAAAAAAAAAAAAAAGAA 10 295 1 AAAAAAAAAA 0.881895 -306 AAAAAAAAAAAAAAGAAAAAAAGAAAAAAA 10 308 1 AAAAGAAAAA 0.947229 -293 AGAAAAAAAGAAAAAAAAAAATAGTTTCTC 10 321 1 AAAAAAAAAA 0.881895 -280 CGATTTAGCGAAAAGAAAACGGAAAGTAAG 10 566 0 AAAAGAAAAC 0.958161 -35 GAAAAGCAAAAAAAGGAAGAATAGAGAAGA 11 78 0 AAAAGGAAGA 0.705954 -328 TGAAAAATTCAAAGAAAAGCAAAAAAAGGA 11 91 0 AAAGAAAAGC 0.717901 -315 AACTGGTCTCAAAAGAAAACCTTTATTATT 11 256 0 AAAAGAAAAC 0.958161 -150 GATCGGATCAAAAGGGAAAACTACAGCTTC 11 333 1 AAAGGGAAAA 0.786749 -73 TGAAAAAAAAAAAAAAAAAAAAGGCAGAGG 12 176 0 AAAAAAAAAA 0.881895 -425 TCCCCAAAAGAAAAGAAAAAAGTTCTTATT 13 161 1 AAAAGAAAAA 0.947229 -270 AGGAGAATTGAAAGGAAAACGGTTTGATAA 14 52 1 AAAGGAAAAC 0.936194 -336 GTGGTAATTAAAAAGAAAGCTTTTGTTCAA 14 348 1 AAAAGAAAGC 0.905197 -40 ATGTATTATCAAAGAAAAACTAACTTCGGT 15 110 1 AAAGAAAAAC 0.859229 -375 ATGAAATAAAAAAAGAAAACAAAATAATAT 15 245 1 AAAAGAAAAC 0.958161 -240 ********** Masking position 7 Map Score: 35.5073 Number of sites scoring better than the average of aligned sites = 3202 Number in coding regions = 1242 Number in noncoding regions = 1960 Number of orfs with sites within 600 bp upstream = 1388 Fraction of orfs with sites within 600 bp upstream = 0.222936 Motif number 3 AAGTACTAGAGATAAAGAGTGTAGAAACCGG 2 62 1 GATAAAGAGG 0.614355 -539 GAAACCGGAAGAACAAAGGTGGAACATATCA 2 85 1 GAACAAAGGG 0.964458 -516 ACGTAAAGAGGAAAAGAAGGGATATAGCAGA 3 195 0 GAAAAGAAGG 0.923538 -406 CACATTCAAAGAATAGAAGCGATTGTCAAAA 3 462 1 GAATAGAAGG 0.893948 -139 ATCTAGTTTCGAACAAGGGAGGGCACTGAAG 3 539 0 GAACAAGGGG 0.908001 -62 AAATTTTGTAGATTAAAAGGGGAGAAGTGTT 3 577 0 GATTAAAAGG 0.753496 -24 GTTTGGAAAGGAACAGAAGTGCAACTTTTTC 4 207 0 GAACAGAAGG 0.985212 -254 AAGCGAAAGGGAAGAGAAGTGTTTCTAGAGA 6 198 1 GAAGAGAAGG 0.876313 -103 TTAGACTACACAACAGAAGTGTTGGATTAAT 9 64 0 CAACAGAAGG 0.905707 -252 TCTAATGTTCGAAAAAAAGGTACGCTTCCCT 9 90 1 GAAAAAAAGT 0.557663 -226 TTATTGATCGGATCAAAAGGGAAAACTACAG 11 328 1 GATCAAAAGG 0.960253 -78 GTGATAAAAACAACAAGAGAGCAGTAGTAAG 12 47 1 CAACAAGAGG 0.796428 -554 CTGATAGTTTGATCAAAGGGGCAAAACGTAG 12 523 0 GATCAAAGGG 0.897824 -78 GGCAAGAAGTGAACAAAAGAGGTGGTGTCTG 13 93 0 GAACAAAAGG 0.986774 -338 AACAAATAAAGGACAGAAGCGGGGATGGAAG 13 243 0 GGACAGAAGG 0.888029 -188 GTGCAGTACAGAACAAAAGAGGCTTCAGACA 13 322 0 GAACAAAAGG 0.986774 -109 TCTTAACCTTGAACAAAAGCTTTCTTTTTAA 14 355 0 GAACAAAAGT 0.874276 -33 ********* * Masking position 5 Map Score: 12.1461 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 850 Number in noncoding regions = 440 Number of orfs with sites within 600 bp upstream = 361 Fraction of orfs with sites within 600 bp upstream = 0.0579827 Motif number 4 TTATTTGTTGAAGGGGCCAAATTCGGCTTT 1 525 1 AAGGGGCCAA 0.94591 -76 ATTGAAGAAGTGGTGGAAAAGCTTTATTGG 2 218 1 TGGTGGAAAA 0.781316 -383 TGTAGATTAAAAGGGGAGAAGTGTTCGAAA 3 572 0 AAGGGGAGAA 0.854079 -29 ATTAAACTTCTAGGGGCGAACTCAACCTTT 4 319 1 TAGGGGCGAA 0.923107 -142 AACAGAAAATAGGTGGAAAACTCCCACCCT 5 25 0 AGGTGGAAAA 0.781316 -278 GTAATTTTTCTACGGGCAAAGGCAAGGAAG 6 114 1 TACGGGCAAA 0.928886 -187 CAATTACTTGCAGTGGCAAAATTCGAAAAG 7 219 0 CAGTGGCAAA 0.843809 -101 GGCACCCAGCCGGGGGCCAAAATTAATAAC 8 484 1 CGGGGGCCAA 0.85003 -65 ATTTCAAGGAAAGTGGAAAAATTTTTAATC 9 161 0 AAGTGGAAAA 0.843462 -155 AAGATGGGATTACTGGAAAAATAAAGGGAG 9 245 1 TACTGGAAAA 0.649377 -71 GTTTCCCGCCTGCGGGCAAAACGTCATAAC 12 298 1 TGCGGGCAAA 0.896491 -303 GGGCAAAACGTAGGGGCAAACAAACGGAAA 12 506 0 TAGGGGCAAA 0.97436 -95 AGTTTGATCAAAGGGGCAAAACGTAGGGGC 12 519 0 AAGGGGCAAA 0.97436 -82 TAGTGCCACCATCGGGAAAAACTTCCCTGT 13 197 1 ATCGGGAAAA 0.587929 -234 AAGAAGTTGAAAGGGGAAAATTCCTTCTCA 15 45 0 AAGGGGAAAA 0.948787 -440 TTTCATTTTTTTGGGGCCAATATAGTAAGC 15 221 0 TTGGGGCCAA 0.796244 -264 ********** Masking position 9 Map Score: 7.41689 Number of sites scoring better than the average of aligned sites = 967 Number in coding regions = 649 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 5 TTTTGATTCATTCTTCCTCCATGTTTTTTTTCTC 2 286 1 TTTCTCATGT 0.937045 -315 CTCCTAAATTTTCTGTCCCCTTGCCTCCAGCTTA 2 407 0 TTTCCCTTGC 0.959757 -194 TACGCTTGTGCCTATTTGTGTAGAGAGAT 5 284 0 TTTCTTTTGT 0.753308 -19 CTTCTTTTTCTTTTTCTTCCTTGCCTTTGCCCGT 6 125 0 TTTTTCTTGC 0.756789 -176 ACATTATATTTTTTTCCTTCTTTTTCTTTTTCTT 6 141 0 TTTCTCTTTT 0.753308 -160 CCCTTTCGCTTTTTCGCTGCTTGTTTGTTTTATC 6 175 0 TTTCTCTTGT 0.978886 -126 ATACTTTTTTTTTTGACTACTTGTATTGGAATCT 7 81 1 TTTCTCTTGT 0.978886 -239 CGAAAAGCACTTCACCCTTCTTGTAGATTTTATG 7 192 0 TTACTCTTGT 0.843012 -128 TACGACTATTCTGTTGCCACTTGTGGCTCCTCGA 8 388 1 CTTCCCTTGT 0.786845 -161 TAATCCCATCTTTTATCTTCATGCACTTCTTCAA 9 223 0 TTTCTCATGC 0.938146 -93 CTTGTTGTTTTTATCACTTCTTGTTTCTTCTTGG 12 30 0 TTTCTCTTGT 0.978886 -571 TTTTGTTCACTTCTTGCCTCATGCCGTCAAAAAA 13 106 1 TTTCCCATGC 0.884482 -325 AATTTTCCCCTTTCAACTTCTTGCTTCTGATCTA 15 53 1 TTCCTCTTGC 0.890231 -432 ** * ** ***** Masking position 12 Map Score: 3.90893 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 291 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 6 TATTGATTCCTTTGCTGTTGTCGACCTTCT 1 373 0 TTTGCTGTTG 0.860355 -228 ACCATCGAGCTTTTATGTTGTGTCATTTCT 2 124 0 TTTTATGTTG 0.705375 -477 TTTCTCACAATTTTCAGTTTGAGTTTCTTC 2 314 1 TTTTCAGTTT 0.599135 -287 CCCAACTGCTTTTTCTTTTGCTGAAGGACA 4 90 0 TTTTCTTTTG 0.92781 -371 AATGTTTTAATTTTCTGTTTATTACTGATA 4 410 0 TTTTCTGTTT 0.954318 -51 TTTCCACCTATTTTCTGTTGATAAAAATAC 5 36 1 TTTTCTGTTG 0.950507 -267 CATTGATTTTTTTTCTTTTTTCCTTGCGCC 5 174 1 TTTTCTTTTT 0.933245 -129 TTTTCCTTCTTTTTCTTTTTCTTCCTTGCC 6 134 0 TTTTCTTTTT 0.933245 -167 TCTCTTCCCTTTCGCTTTTTCGCTGCTTGT 6 185 0 TTCGCTTTTT 0.651554 -116 TTCTTGTAGATTTTATGTTTTATATTAGCC 7 179 0 TTTTATGTTT 0.722549 -141 CTGTTTTATCTTTTACTTTTATGTCGTGGA 8 18 1 TTTTACTTTT 0.490134 -531 GATAATCCGGTTTGCTGATTTGAATCGTTC 10 51 0 TTTGCTGATT 0.636645 -550 AATAAGAAATTTTTCTTATTAGTTTACTAT 10 124 0 TTTTCTTATT 0.78518 -477 CATTCTCATTTTTTATTTTTTTCTTCGTCT 10 253 1 TTTTATTTTT 0.635409 -348 TTTTTTCTTTTTTTCTTTTTTTTTTTTTTT 10 307 0 TTTTCTTTTT 0.933245 -294 AAAAAATAGTTTCTCCGTTGCACATCGTCA 10 336 1 TTCTCCGTTG 0.815383 -265 ATAATAAAGGTTTTCTTTTGAGACCAGTTA 11 257 1 TTTTCTTTTG 0.92781 -149 CAATCTGAAATTCTCTTATTTCTCCAACTT 12 212 1 TTCTCTTATT 0.60379 -389 GTTTCTCAAATTTTCTGATGCCAAGAACTC 12 472 0 TTTTCTGATG 0.833917 -129 GAGAAACGATTTTTCCGTTTGTTTGCCCCT 12 495 1 TTTTCCGTTT 0.920145 -106 CGAATACGGGTTTGCCGTTT 13 1 0 TTTGCCGTTT 0.787076 -430 CCGGCCAGCTTTCTCCGATGAACGCGCACA 13 39 1 TTCTCCGATG 0.535901 -392 AACTTTTTTCTTTTCTTTTGGGGATTTTTT 13 155 0 TTTTCTTTTG 0.92781 -276 TTCCTTTCAATTCTCCTTTTCTGGCATAAC 14 39 0 TTCTCCTTTT 0.762754 -349 TATTATTTTGTTTTCTTTTTTTATTTCATT 15 244 0 TTTTCTTTTT 0.933245 -241 ********** Masking position 2 Map Score: 19.4321 Number of sites scoring better than the average of aligned sites = 4372 Number in coding regions = 2285 Number in noncoding regions = 2087 Number of orfs with sites within 600 bp upstream = 1527 Fraction of orfs with sites within 600 bp upstream = 0.245262 Motif number 7 GGTGTGGTCATCATTTTACAAAGGAGGGAGGT 1 20 0 TCATTTCAAA 0.956849 -581 TTATCCGTGTGCATTTACCAAAATTCATGAGT 1 116 1 GCATTTCAAA 0.854855 -485 CCAAACGATGTCATTTTTCAAAGGCACATCAA 2 528 0 TCATTTCAAA 0.956849 -73 AAATGTATTTTCGTTTTCCAATGATGGAAAAA 3 255 0 TCGTTTCAAT 0.945802 -346 CATCACGCTGTCGTATCTCAATTGTCCTTCAG 4 68 1 TCGTATCAAT 0.91142 -393 GAAAATTAAAACATTTACCAAAGGCAACGAGT 4 425 1 ACATTTCAAA 0.909426 -36 AAAAAGTGATACATATACCAATGACCCAGAAT 7 132 0 ACATATCAAT 0.832826 -188 GAACGAAATCTCGTATTTCAATTGCACCAATT 7 244 0 TCGTATCAAT 0.91142 -76 AACGGAAAAATCGTTTCTCAAATTTTCTGATG 12 482 0 TCGTTTCAAA 0.953997 -119 CGTCCTATTGTCATATCACAATCACAGACT 13 411 1 TCATATCAAT 0.916681 -20 TTTAATTAGGACATTTATCAAACCGTTTTCCT 14 64 0 ACATTTCAAA 0.909426 -324 ****** **** Masking position 10 Map Score: 2.42408 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 314 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 8 CATGATATATAAAATATTAATAAGAATAAAATAAATAGGTAGT 1 70 0 AAAATTTAAA 0.79921 -531 GGAGAAAAAAAAAAAGTTACCGGAATGGGAATAGATAGATACC 1 167 0 AAAAATTTAA 0.819384 -434 ATAGGCAATAATAATATTATCCAAATGGAAAAAAAAAAAATGA 1 444 0 ATAATTTTAA 0.680188 -157 GGCCATCTTGAAAATTTTGTGGTGCTAGTGAAAAATGTATTTT 3 276 0 AAAATTTTAA 0.96564 -325 TTTAAAGCAAAAAATGTTTCTGTTTTTTAAATATATAACCAAT 3 348 0 AAAATTTTAA 0.96564 -253 GAATGTGTATAAAATTTTTTTTTCCTGAGAAAAAAAAGGACGC 3 426 0 AAAATTTTAA 0.96564 -175 GAATGTGTCGAAAACCTTAGCTCGATCCTTAAAAAAGTATTTG 4 364 1 AAAACTTTAA 0.87527 -97 ACGATATTAGAAATTATTGTATATATGTATATAAATGTAGTAT 5 62 0 AAATTTTTAA 0.809171 -241 GCCGTTATACAAAATATTATCAACATATATAGAATATAAACGT 8 444 0 AAAATTTTAA 0.96564 -105 GGAAAGTGGAAAAATTTTTAATCTTTTAGCTTATAAGAATAAC 9 141 0 AAAATTTTTA 0.680188 -175 GGTTCGTGGAAAAATATTATTACGTATTGAAGAAGTGCATGAA 9 197 1 AAAATTTAAA 0.79921 -119 AACTAATAAGAAAAATTTCTTATTATATAAATATAGCTGGTTA 10 130 1 AAAAATTTAA 0.819384 -471 CATCTATTATAAAGTTTTTCCGGAGTGCTTAAAAAAGGGATTG 10 381 1 AAAGTTTTAA 0.780895 -220 TATACAATATAAATTATTGATGCTTTTTACACACTATAATCGA 11 136 0 AAATTTTTAA 0.809171 -270 TAATTCTAAAAAGATATTTTACGGATAATAATAAAGGTTTTCT 11 230 1 AAGATTTTAA 0.860274 -176 TCCCTTAATTAAAACATTAGAATGGTGATTAGAAAGGCAGGAT 12 363 1 AAAACTTTAA 0.87527 -238 ACTATCAGTTAAGATATTAATTTTTTTGAGAAAACGATTCTTT 12 546 1 AAGATTTTAA 0.860274 -55 ATGCCGTCAAAAAATTTTTTTCGCATCGAAAAAAATCCCCAAA 13 126 1 AAAATTTTAA 0.96564 -305 ***** ** * * * Masking position 8 Map Score: 6.80732 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 205 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 9 CTGCCATTAAGAAATGTATTTCATTTTG 3 3 1 GCCTAGAATA 0.960049 -598 ATTTTGTGGTGCTAGTGAAAAATGTATTTTCGTTTT 3 270 0 GCTTGAAATA 0.85437 -331 CCTTGCCTTTGCCCGTAGAAAAATTACCCTCTTATT 6 105 0 GCCTAAAATA 0.971224 -196 CTTAATTTAGGCTTCTATGGAAAATATATTCTGAGG 7 25 0 GCTTAGAATA 0.956861 -295 AAAAGTAGTGGCTAATATAAAACATAAAATCTACAA 7 170 1 GCTTAAAATA 0.968898 -150 CCGGCTGGGTGCCGTTATACAAAATATTATCAACAT 8 461 0 GCCTAAAATA 0.971223 -88 GCATGTAACAGCGTATATATAATCTATATGTATTCG 9 28 1 GCGTAAAATA 0.905532 -288 ACCTTTCAGAGCTTATAATCAACCTAATGATTACTC 10 470 0 GCTTATAATA 0.848089 -131 CAGCTTTCTAGCCCATATACAATATAAATTATTGAT 11 158 0 GCCTAAAATA 0.971224 -248 AACGGCTTTCGCTCATAAAAATGTTATGACGTTTTG 12 314 0 GCTTAAATTA 0.885448 -287 TTTCATAGAAGCTATTAAGCATCATATACTGCACAC 13 272 1 GCTTAGATTA 0.846237 -159 *** ** * ** ** Masking position 11 Map Score: 2.62484 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 112 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 AATAATAGTATAAGCTGGAGGCAAGGGGAC 2 397 1 TAAGCTGGAG 0.985954 -204 GGACTCCACATACGTTGGAGAATACCTAGC 5 244 0 TACGTTGGAG 0.966988 -59 GTTTGACGCCTAAACTGGAGACTCTGGACA 8 305 1 TAAACTGGAG 0.930798 -244 CTCCAACTTATAAGTTGGAGAAATAAGAGA 12 223 0 TAAGTTGGAG 0.984854 -378 CTCCAACTTATAAGTTGGAGATGCCCGGTG 12 233 1 TAAGTTGGAG 0.984854 -368 ********** Masking position 6 Map Score: 1.21755 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 35 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 AAGAGTGTAGAAACCGGAAGAACAAAGGTG 2 76 1 AAACCGGAAG 0.956334 -525 ACGTAATGGGAAATCAGAAGGCATACTAAA 2 184 1 AAATCAGAAG 0.97442 -417 AAGTTTAATAAAATCGGAAGTTCCAAATAC 4 298 0 AAATCGGAAG 0.983579 -163 TCTTTTCGCTAAATCGGAAGTCATAAAGAC 10 580 1 AAATCGGAAG 0.983579 -21 TAATAAAATTAGATCAGAAGCAAGAAGTTG 15 66 0 AGATCAGAAG 0.933014 -419 GAAAAATATCAAATCATAAGGGAACCGAAG 15 133 0 AAATCATAAG 0.854926 -352 ********** Masking position 3 Map Score: 1.07626 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 93 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 GATGAGGCAAGATAACTATAAAGATAAAGAACC 1 311 1 GTACATAAAG 0.943046 -290 CAGCAAACCGGATTATCAGAAAGCAAATAATTA 10 64 1 GTATAGAAAG 0.981714 -537 TTTCTTATTAGTTTACTATAAAGGACTAGTGTA 10 110 0 GTACATAAAG 0.939881 -491 ATATTTTACGGATAATAATAAAGGTTTTCTTTT 11 243 1 GTATATAAAG 0.971312 -163 ACATTAGAATGGTGATTAGAAAGGCAGGATTAA 12 376 1 GTATAGAAAG 0.981729 -225 CGGGGCCACTGCTAATAATAAAGTGGTAATTAA 14 326 1 GTATATAAAG 0.971312 -62 ATAATAAAGTGGTAATTAAAAAGAAAGCTTTTG 14 340 1 GTATAAAAAG 0.911477 -48 AAAACTAATTGTAAATAAGAAAGAAAAATATCA 15 152 0 GAATAGAAAG 0.894409 -333 ACACGTTTGAGTTAATGGGAAAGCAAAGTCCAG 15 356 1 GTATGGAAAG 0.926216 -129 * * ** ****** Masking position 5 Map Score: 2.82362 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 131 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 TTTTCCACCACTTCTTCAATAGTATTTAGT 2 208 0 CTTCTTCAAT 0.982817 -393 ATTTTGACAGCTTCTTCGATCAATACCGCC 3 33 1 CTTCTTCGAT 0.97106 -568 TCTTCATGCACTTCTTCAATACGTAATAAT 9 212 0 CTTCTTCAAT 0.982817 -104 TTCAAAGTTTCTTCTTCAATCTCAATTTAT 15 324 1 CTTCTTCAAT 0.982817 -161 ********** Masking position 5 Map Score: 1.03698 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 178 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 TTGGGTTCTTTATCTTTATAGTTATCTTGCC 1 316 0 TATTTTATAG 0.81138 -285 GTATTGTGTGTATATTTATGTAACTCTATCC 2 452 0 TATTTTATGT 0.899995 -149 ATAAAAATACTACATTTATATACATATATAC 5 56 1 TACTTTATAT 0.938219 -247 CTAATTTCCTTATTTTTATATCCTCTTAGAG 7 275 0 TATTTTATAT 0.948483 -45 TTTTATCTTTTACTTTTATGTCGTGGACTGG 8 21 1 TACTTTATGT 0.881279 -528 AGGAAATAGGTACGTTTATATTCTATATATG 8 433 1 TACTTTATAT 0.938219 -116 ATTAACCAGCTATATTTATATAATAAGAAAT 10 144 0 TATTTTATAT 0.948483 -457 CTACTGGCACTCTATTTATATGTGATAGGCA 12 103 1 TCTTTTATAT 0.81138 -498 AAAAAGTTCTTATTTTTATATAGTGCCACCA 13 177 1 TATTTTATAT 0.948483 -254 *** ******* Masking position 6 Map Score: 1.08735 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 140 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 15 GTAATTGAACTATTGTGTGAAAGAAGGTCGAC 1 352 1 TATGTGTGAA 0.945542 -249 AGAGTTTTTCTTTGGTTTTCAAATTGATTTTT 1 402 1 TTTGTTTTAA 0.769024 -199 TTAGTTTATGTATTGTGTGTATATTTATGTAA 2 460 0 TATGTGTGAT 0.795511 -141 CAGAAACATTTTTTGCTTTAAAAGCACGCCAT 3 369 1 TTTGCTTTAA 0.794102 -232 CACGCCATAGTATTGCTTTTAATATTGTGATC 3 393 1 TATGCTTTAA 0.915598 -208 GGGGGGCGTATATCGTTTGGAAAGGAACAGAA 4 220 0 TATGTTTGAA 0.915598 -241 TAATTTCTAATATCGTTTTTATAAAGTTGGCC 5 89 1 TATGTTTTAT 0.677233 -214 GTCAAACCTGTATTGCGTTTAATCCCCGCGAG 8 280 0 TATGCGTTAA 0.945542 -269 AGTGTACGTTTTTTGTGTTTAATTATTTGCTT 10 84 0 TTTGTGTTAA 0.841996 -517 AATCCTCGATTATAGTGTGTAAAAAGCATCAA 11 131 1 TATGTGTGAA 0.945542 -275 ATATTGGTCATATAGCGTTAAAATGCGTAAGG 14 122 0 TATGCGTTAA 0.945485 -266 CTATAGTACATATAGCTTGAAAAAAACAAGCG 14 264 1 TATGCTTGAA 0.926287 -124 *** ***** ** Masking position 11 Map Score: 1.86285 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 252 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524