AlignACE version 2.2 July 7, 1998 AlignACE -jRPT.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 YDL007W 300 bp YDL007W RPT2 1-1314 Probable 26S protease subunit and member of CDC48\/PAS1\/SEC18 family of ATPases #2 YDR394W 409 bp YDR394W RPT3 1-1287 probable 26S protease subunit and member of the CDC48\/PAS1\/SEC18 family of ATPases #3 YGL048C 300 bp YGL048C RPT6 1-1218 ATPase #4 YKL145W 351 bp YKL145W RPT1 1-1404 putative ATPase, 26S protease subunit component #5 YOR117W 600 bp YOR117W RPT5 1-1305 Probable 26S protease subunit and member of the CDC48\/PAS1\/SEC18 family of ATPases #6 YOR259C 300 bp YOR259C RPT4 1-1314 ATPase\; component of the 26S proteasome cap subunit Motif number 1 GAAAAGAGACATTTGCCACCGGAGAAAAAC 1 170 0 ATTTGCCACC 0.997071 -131 AGATTTACTATTTTGCCACCTTACTTTCAG 2 234 0 TTTTGCCACC 0.998176 -176 TTTAACCTCTTTTTGCGACTGAAAACTTGT 3 77 1 TTTTGCGACT 0.953962 -224 ATATTACAACTTTTGCCACCTCGCTCGCAT 3 217 0 TTTTGCCACC 0.998176 -84 GATTACCGAATTTTGCCACCCGAAAACTAA 4 196 1 TTTTGCCACC 0.998176 -156 GTTTCACGAAATTTGCCATTTTTTTTGCAA 5 53 0 ATTTGCCATT 0.897017 -548 ATTAATTCATTTTTGCCACCACATATTGGC 5 437 0 TTTTGCCACC 0.998176 -164 AAATAGTGGAATTTGCCACCGAAGGGAAAG 6 188 1 ATTTGCCACC 0.997071 -113 ********** Masking position 8 Map Score: 21.595 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 120 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 AACCTGCGCGGGCAAAGCCCAAAAGATTTC 1 70 0 GGCAAAGCCC 0.959884 -231 TTTCTCCGGTGGCAAATGTCTCTTTTCTTT 1 173 1 GGCAAATGTC 0.960599 -128 AAACAAACGAGTCAGAAGCCAGCTCTTTCA 3 50 0 GTCAGAAGCC 0.862351 -251 CGAGCGAGGTGGCAAAAGTTGTAATATCAG 3 220 1 GGCAAAAGTT 0.856969 -81 GTTTTCGGGTGGCAAAATTCGGTAATCCTA 4 193 0 GGCAAAATTC 0.981251 -159 AGGCTCTTCTGGCAGAACTCATCACCAGAT 5 12 0 GGCAGAACTC 0.924304 -589 CAAAAAAAATGGCAAATTTCGTGAAACACG 5 56 1 GGCAAATTTC 0.972445 -545 ATTTAAAAAAGACGAAAGCCCAAAAGAGAC 5 249 1 GACGAAAGCC 0.940062 -352 CGGCAGCCTTGGCGAATTCCTTTTATTAGC 5 382 1 GGCGAATTCC 0.964127 -219 AAACGTTTTAGACAAACTCCTGATGTGCCC 5 514 0 GACAAACTCC 0.897934 -87 AAAAGACAAAAGCCTGAATTGACA 6 5 1 GACAAAAGCC 0.977319 -296 TCCCTTCGGTGGCAAATTCCACTATTTGAA 6 185 0 GGCAAATTCC 0.986039 -116 ********** Masking position 6 Map Score: 9.46071 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 865 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 3 CCCGGAGTGATAAAAATATTGGGAATATAAAAATGACGAC 1 114 0 TAATATATAA 0.578856 -187 ATATACTGCGCAAGAATATCGTTAAAAAAACACGCATGCA 2 15 1 CAATATAAAA 0.98439 -395 TAGGTAAGGTTAAGGATATTGAAACCAAAACGTGCTATTT 2 104 0 TAATATAAAA 0.879804 -306 TGGGTATAGCCATGAATATAGGAAGTAATAGGGCTCAGAT 2 272 1 CAATATAATA 0.972568 -138 GGATAAAATTCAAGTATTTATAAAGTAAAAACCACAACAA 2 378 1 CAATTTAAAA 0.927889 -32 CATGTACAGACACATATATATATATTTATATATGACTCGT 4 35 1 CAATATAATA 0.95847 -317 GTTCCAGATGCATATAGATAACGAGTCATATATAAATATA 4 55 0 CAAGATAATA 0.959752 -297 ACTAAACTAGCATGCAGCTTACTATACAAAGAACTGGGTA 4 221 1 CAAGCTAAAA 0.877725 -131 CAGTATTTTCCAAGGAGATGAGAATTCAAAGCAATATTCA 4 265 1 CAAGATAAAA 0.976644 -87 AGAGCCTGTGCAATAATTTTGCAAAAAAAATGGCAAATTT 5 35 1 CAATTTAAAA 0.927957 -566 ACACGATATTCACGTATATAGTGATGATAATAAGCATGCT 5 81 1 CAATATATAA 0.922082 -520 ATGCCGTTGGCATTGAGATTCCAACGAATATACACAGATG 5 167 1 CAAGATAATA 0.959758 -434 TTTCACTTCTCATCACTATATTGAAATATAACAATCAAGC 6 121 0 CACTATAATA 0.839878 -180 ACAGACGAAGCAAAGATATTAATAACTAAGA 6 280 1 CAATATAAAG 0.901508 -21 ** **** * *** Masking position 14 Map Score: 7.21773 Number of sites scoring better than the average of aligned sites = 1323 Number in coding regions = 655 Number in noncoding regions = 668 Number of orfs with sites within 600 bp upstream = 389 Fraction of orfs with sites within 600 bp upstream = 0.0624799 Motif number 4 CTGCAGTTGTCGTCATTTTTATATTCCCAA 1 106 1 CGTCATTTTT 0.957162 -195 GAGTTATTAACGGTTTTTCTCCGGTGGCAA 1 158 1 CGGTTTTTCT 0.778291 -143 CGGTGGCAAATGTCTCTTTTCTTTTACCTA 1 179 1 TGTCTCTTTT 0.947559 -122 TTAAAAACGCTGTCTCTTCTTTAACTTGAA 1 270 0 TGTCTCTTCT 0.901203 -31 AAAATGCATGCGTGTTTTTTTAACGATATT 2 29 0 CGTGTTTTTT 0.920009 -381 ATTGAAGAAAAGGCTCTTTTTGTTAC 3 7 0 AGGCTCTTTT 0.900566 -294 TTTCTTCGGTTGGGTTTTTTAATATGAAAT 3 122 1 TGGGTTTTTT 0.798055 -179 TCCGCCATTTTTGACCGAGTAC 4 3 1 CGCCATTTTT 0.916119 -349 ATTATTGCACAGGCTCTTCTGGCAGAACTC 5 22 0 AGGCTCTTCT 0.820536 -579 TCACGAAATTTGCCATTTTTTTTGCAAAAT 5 50 0 TGCCATTTTT 0.800503 -551 TTTGGGCTTTCGTCTTTTTTAAATTTTTTT 5 243 0 CGTCTTTTTT 0.979701 -358 TAATTGCACTCGTCTCTTTTGGGCTTTCGT 5 260 0 CGTCTCTTTT 0.980072 -341 CCATTACTGACGTTATTTTTTTACGAACAT 5 344 0 CGTTATTTTT 0.774888 -257 ********** Masking position 7 Map Score: 6.35147 Number of sites scoring better than the average of aligned sites = 2362 Number in coding regions = 1473 Number in noncoding regions = 889 Number of orfs with sites within 600 bp upstream = 744 Fraction of orfs with sites within 600 bp upstream = 0.119499 Motif number 5 ACCTTCTTTTAGGTAAAAGAAAAGAGACATT 1 187 0 AGGTAAAAGA 0.882733 -114 ATTATGTACAAGGATAAAGGATGAAAAAAAT 2 54 0 AGGATAAAGA 0.903951 -356 ATAAATACACAGTAAATAGCACGTTTTGGTT 2 91 1 AGTAAATAGA 0.909612 -319 ATAACTTATGAGTGAAAGGAAATAGGCAGAA 2 334 0 AGTGAAAGGA 0.979862 -76 GTATTTATAAAGTAAAAACCACAACAAGA 2 391 1 AGTAAAAACA 0.826885 -19 ACCCAACCGAAGAAAAAGGGAAATAGAAAAA 3 106 0 AGAAAAAGGA 0.903139 -195 CCCGGACGAGAGGAAAAGGTATAGTGAATAG 4 165 1 AGGAAAAGGA 0.979862 -187 GAAAAGGTATAGTGAATAGGATTACCGAATT 4 177 1 AGTGAATAGA 0.903951 -175 TATTAAACATAGTATAAAGTATCAGCCACTA 5 288 0 AGTATAAAGA 0.909612 -313 AACCATTGCTAATAAAAGGAATTCGCCAAGG 5 388 0 AATAAAAGGA 0.803906 -213 TGTATATTTTACTGAAAAGGACCCCATTAAT 5 466 1 ACTGAAAAGA 0.830662 -135 TTGCCACCGAAGGGAAAGGAAGCTTGAAATA 6 200 1 AGGGAAAGGA 0.978497 -101 ********* * Masking position 6 Map Score: 4.86288 Number of sites scoring better than the average of aligned sites = 2404 Number in coding regions = 1392 Number in noncoding regions = 1012 Number of orfs with sites within 600 bp upstream = 765 Fraction of orfs with sites within 600 bp upstream = 0.122872 Motif number 6 AGCGCGCGATGTGCCCTTTCATATTTTTCC 2 205 1 GTGCCCTTTC 0.994023 -205 CTGAGAATCTGAGCCCTATTACTTCCTATA 2 288 0 GAGCCCTATT 0.968138 -122 GTAACAAAAAGAGCCTTTTCTTCAATAATA 3 11 1 GAGCCTTTTC 0.967864 -290 AACTCCTGATGTGCCCTTTTTACCCAAGAG 5 500 0 GTGCCCTTTT 0.990635 -101 GTTTATACGAGTGACTTATTTGTGCATTAT 5 540 1 GTGACTTATT 0.866185 -61 CGATAGGCGGGTGACCTTTCAAATAGTGGA 6 168 1 GTGACCTTTC 0.982514 -133 ********** Masking position 7 Map Score: 3.28684 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 196 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 CGAAAGATTAGAAATCTTTTGGGCTTTGCCC 1 60 1 GAAATTTTTG 0.90013 -241 CCAAACATTAGAGAAATTTTGATTATAATGG 2 166 0 GAGAATTTTG 0.972045 -244 ATTCTTGTTCGGAAATTTTCGTATTTTAAAA 3 178 1 GGAAATTTCG 0.945232 -123 CAAAAAAAATGGCAAATTTCGTGAAACACGA 5 56 1 GGCAATTTCG 0.963219 -545 AGAACAAATTGGAAAGTTTTGATTTTAGTTT 5 577 1 GGAAATTTTG 0.969484 -24 TATCAACGGTGGGAACTTTTGGTCAGCACAG 6 60 1 GGGAATTTTG 0.986033 -241 GATGAGAAGTGAAAAATTTTGCGATAGGCGG 6 147 1 GAAAATTTTG 0.949495 -154 ***** ***** Masking position 4 Map Score: 4.7231 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 217 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 AATTGGGTATAGCCATGAATATAGGAAGTAATA 2 269 1 ACAGAATATA 0.938916 -141 ATCGGATAAAATTCAAGTATTTATAAAGTAAAA 2 375 1 ACAGTATTTA 0.969135 -35 TCATGTACAGACACATATATATATATTTATATA 4 34 1 ACAATATATA 0.971037 -318 ATAGATAACGAGTCATATATAAATATATATATA 4 49 0 ACAATATAAA 0.857311 -303 TGTGTTCCAGATGCATATAGATAACGAGTCATA 4 65 0 ACAATAGATA 0.949963 -287 GAAACACGATATTCACGTATATAGTGATGATAA 5 78 1 ACAGTATATA 0.988475 -523 TCACTAGGTAAACCAGGTATATATATTAAACAT 5 309 0 ACAGTATATA 0.988475 -292 GCAATGGTTTAATCATGTAGTTACCCGGCCAAT 5 410 1 ACAGTAGTTA 0.946753 -191 * ** ******* Masking position 5 Map Score: 3.2342 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 62 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 GTAAGGCAACTTGGCCGAGTGGTTAAGGCG 1 32 1 TTGGCCGAGT 0.994299 -269 CCCTTTTTCTTCGGTTGGGTTTTTTAATAT 3 117 1 TCGGTTGGGT 0.922396 -184 TCCGCCATTTTTGACCGAGTACATCATGTA 4 11 1 TTGACCGAGT 0.97095 -341 TCAATTTGGTATGGCTGAGTTTACCCGGAC 4 142 1 ATGGCTGAGT 0.93565 -210 CCTTTTCCTCTCGTCCGGGTAAACTCAGCC 4 154 0 TCGTCCGGGT 0.977564 -198 CCACCACATATTGGCCGGGTAACTACATGA 5 422 0 TTGGCCGGGT 0.996367 -179 ********** Masking position 10 Map Score: 2.33285 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 128 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 ATCATATTCACTAATATTCACATTAACCTTCTTT 1 209 0 CAATTCCATT 0.9632 -92 GTAAGCTTGACACTGATACGCATCATATTCACTA 1 230 0 CTATACCATC 0.889549 -71 ATAATAAAATCATAAATACACAGTAAATAGCACG 2 80 1 CAATACCAGT 0.993274 -330 AGTAATAGGGCTCAGATTCTCAGTGTGTGGACAA 2 295 1 CAATTCCAGT 0.981838 -115 GCCTTTTCTTCAATAATACCCATTGTTTGAAAGA 3 23 1 CTATACCATT 0.9632 -278 TGGAAAATACTGTATATACCCAGTTCTTTGTATA 4 243 0 TAATACCAGT 0.942824 -109 GAGATTCCAACGAATATACACAGATGCCTGATTT 5 181 1 CAATACCAGA 0.968411 -420 TATTTTTTTACGAACATACTCACTAGGTAAACCA 5 327 0 CAATACCACT 0.976711 -274 * * **** **** Masking position 6 Map Score: 1.4917 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 166 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 AGTGGTTAAGGCGAAAGATTAGAAATCTTTT 1 49 1 GCAAAGATTA 0.970505 -252 GATTACACCAGCTAAACATTAGCTAGGTAAG 2 136 0 GCAAACATTA 0.983754 -274 GCTACGAAGAGCCAAACATTAGAGAAATTTT 2 177 0 GCAAACATTA 0.983754 -233 TTACTTTCAGGAAAAATATGAAAGGGCACAT 2 213 0 GAAAATATGA 0.877956 -197 AAGTAAGGTGGCAAAATAGTAAATCTGCAGT 2 238 1 GCAAATAGTA 0.953511 -172 AGAGAAGTATGCAAAATATGATTTCATATTA 3 141 0 GCAAATATGA 0.978941 -160 ** ******** Masking position 6 Map Score: 0.226787 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 215 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 12 TAAGTCAATAATTCATCATTAGTAAGGCAA 1 6 1 CAATTCATTT 0.95776 -295 GTTAAAAAAACACGCATGCATTTTTTTCATCCTTT 2 35 1 CAATGCATTT 0.980802 -375 GTGGACAAACCAATTCTGCCTATTTCCTTTCACTC 2 321 1 CACTGCCTTT 0.959103 -89 TGTACAGACACATATATATATATTTATATATGACT 4 37 1 CAATATATTT 0.805729 -315 GCATCTGGAACACACATACCTTGTTTTAATTATGA 4 84 1 CAATACCTTT 0.988112 -268 CGGGTAAACTCAGCCATACCAAATTGACAAGGATA 4 134 0 CAATACCATT 0.929093 -218 AACGAATATACACAGATGCCTGATTTGTTTGCGAT 5 189 1 CAATGCCTTT 0.990136 -412 CTATGTTTAATATATATACCTGGTTTACCTAGTGA 5 307 1 TAATACCTTT 0.890693 -294 GTAAAATATACATTAATTCATTTTTGCCACCACAT 5 443 0 CAATTCATTT 0.95776 -158 ** ****** ** Masking position 7 Map Score: 1.97571 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 243 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 13 ********** No masking Map Score: -5.80213e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: -5.80213e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: -5.80213e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0