AlignACE version 2.2 July 7, 1998 AlignACE -jRPP.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 YDL130W 474 bp YDL130W RPP1B 1-114, 416-622 Ribosomal protein P1B (L44') (YP1beta) (Ax) #2 YDL081C 519 bp YDL081C RPP1A 1-321 Acidic ribosomal protein P1A (YP1alpha) (A1) #3 YDR382W 600 bp YDR382W RPP2B 1-333 Ribosomal protein P2B (YP2beta) (L45) #4 YHR062C 300 bp YHR062C RPP1 1-882 Protein subunit of nuclear ribonuclease P (RNase P) #5 YLR340W 600 bp YLR340W RPP0 1-939 60S ribosomal protein P0 (A0) (L10E) #6 YOL039W 600 bp YOL039W RPP2A 1-321 60S acidic ribosomal protein P2A (L44) (A2) (YP2alpha) Motif number 1 AAATTTTATTTTTTTTTGCGTTTCATATAATCCT 1 249 0 TTTTTTCTTC 0.835932 -226 CTGTAAGCCCCTTCGTGATATTTCAAGGTTAAAT 1 391 1 CTTCGTTTTC 0.739105 -84 TTTCTTCTTAGTTGTTTGATTTCTTTG 1 458 0 CTTCTTTTTT 0.949868 -17 TACCACGCAACTTTGTAATGATTTTTTTTTTTTC 2 326 1 CTTTGTTTTT 0.926825 -194 TAATGATTTTTTTTTTTTCATTTTTTAAAGAATG 2 341 1 TTTTTTCTTT 0.952112 -179 AAGCGGACTATTTCTTTATTCTTTTGATTTCTTT 2 447 0 TTTCTTTTTT 0.915071 -73 TTCTTCTTGTTATTTTAGAGATAATC 2 504 0 CTTCTTTTTT 0.949868 -16 GTGTCGCTTCCTTCTTCGCCTTTTAGTTGAAGAC 3 88 0 CTTCTTCTTT 0.96827 -513 TGCTCTTATTTATCTTGTCTATTCGAACCCAACA 3 194 1 TATCTTCTTC 0.563251 -407 TAATAATTTTCTTTTTCCAAATTTTCTCGGTATC 3 407 1 CTTTTTATTT 0.925271 -194 ATCGCACATACATTTTTCATGTTTTCTGGTAGTA 4 170 0 CATTTTATTT 0.78217 -131 CACTTTTGTTTTTTGTGTCTGTTTAGGTTAAGTA 4 257 0 TTTTGTCTTT 0.920635 -44 ATATTTGCGACTTTTTCCATCTTTTGTGAGCTAA 5 140 1 CTTTTTATTT 0.925271 -461 GAACATTTCACATTTTGATTATTTCGAGAAAAAA 5 353 1 CATTTTTTTT 0.862932 -248 CTTTGAGAAATTTTTTGACTTTTTTCTCGAAATA 5 372 0 TTTTTTCTTT 0.952112 -229 TTCGGCATTACTTCTTTTTTCTTTGAGAAATTTT 5 392 0 CTTCTTTTTT 0.949868 -209 CTTGAAGTCATTTTTTACCAGTTTTTCGCAACGA 5 446 0 TTTTTTCTTT 0.952112 -155 GAGAATTAGATATTGTTAATCTTTCATTTACTTA 5 483 0 TATTGTATTT 0.543659 -118 ATTCTCGATTCTTTTTTCAAGTTTCAGCCATAAG 5 511 1 CTTTTTATTT 0.925271 -90 CAATTTATTCCTTTTTAATCTTTTGTGCAGAGTT 6 21 0 CTTTTTTTTT 0.955964 -580 TAGAACCGATTTTCGTTTCTCTTTGGAAGGTCTC 6 155 0 TTTCGTCTTT 0.910109 -446 ATTAAAAAAGTTTTGTACCTGTTTTGAGGCTGTA 6 301 1 TTTTGTCTTT 0.920635 -300 CTTTTTCTATTATTTTAGTGATTTTTTTCTCATT 6 539 1 TATTTTTTTT 0.781662 -62 ****** * *** Masking position 6 Map Score: 22.3958 Number of sites scoring better than the average of aligned sites = 10363 Number in coding regions = 3154 Number in noncoding regions = 7209 Number of orfs with sites within 600 bp upstream = 2312 Fraction of orfs with sites within 600 bp upstream = 0.371346 Motif number 2 AAAAAAAAATAAAATTTTCATTTCTGCGTG 1 266 1 AAAATTTTCA 0.90769 -209 TTGGACTAACAAAGAAATCAAACAACTAAG 1 449 1 AAAGAAATCA 0.846579 -26 AACTGGCTTGAAAATATTTATTCGCTGAAC 2 82 1 AAAATATTTA 0.541425 -438 CCTAGCTTATAAAAATTTCATTTAATTAAT 2 117 1 AAAAATTTCA 0.965445 -403 TTCTGTTTCTAAAATTGTCACAGCAAGAAA 2 169 1 AAAATTGTCA 0.82808 -351 AAATGAAAAAAAAAAAATCATTACAAAGTT 2 334 0 AAAAAAATCA 0.956706 -186 GGTATTTGAAAAAAATATCTTTATAAAGTT 2 384 1 AAAAATATCT 0.819368 -136 ATTTTTAGTAAAAGAAATCAAAAGAATAAA 2 437 1 AAAGAAATCA 0.846579 -83 GCTTGCATATAAAAAAATCAAGGCAGATGA 3 19 0 AAAAAAATCA 0.956706 -582 TTGGAAAAAGAAAATTATTACAATTTTTCT 3 397 0 AAAATTATTA 0.602351 -204 CTCTTAAATGAAAAATTTCAGATACCGAGA 3 431 0 AAAAATTTCA 0.965445 -170 GCATAAATGAAAAAATTTCATTTTACCAGT 4 221 1 AAAAATTTCA 0.965445 -80 AGGGCAAGATAAAAATTTTAGCTCACAAAA 5 161 0 AAAAATTTTA 0.801865 -440 TTATTTCGAGAAAAAAGTCAAAAAATTTCT 5 371 1 AAAAAAGTCA 0.915267 -230 AAAAAAGTCAAAAAATTTCTCAAAGAAAAA 5 381 1 AAAAATTTCT 0.809029 -220 TTCCAATGAGAAAAAAATCACTAAAATAAT 6 547 0 AAAAAAATCA 0.956706 -54 ********** Masking position 3 Map Score: 13.862 Number of sites scoring better than the average of aligned sites = 2990 Number in coding regions = 1835 Number in noncoding regions = 1155 Number of orfs with sites within 600 bp upstream = 924 Fraction of orfs with sites within 600 bp upstream = 0.14841 Motif number 3 TTTTTTTGCGTTTCATATAATCCTTCTGAT 1 243 0 TTTCATATAA 0.914733 -232 AAAATAAAATTTTCATTTCTGCGTGTCGCG 1 271 1 TTTCATTTCT 0.853096 -204 TAGCCGGAAGTTTCAATTCTAAGATTTCTC 1 306 0 TTTCAATTCT 0.673697 -169 CGAATTGCAGTTTCAGTTAATCTTGGACTA 1 427 1 TTTCAGTTAA 0.853096 -48 CTTATAAAAATTTCATTTAATTAATGTAAT 2 122 1 TTTCATTTAA 0.938005 -398 GCATGTGAGTTTTCATATTACATTAATTAA 2 138 0 TTTCATATTA 0.879097 -382 ATTTTTTTTTTTTCATTTTTTAAAGAATGC 2 346 1 TTTCATTTTT 0.911152 -174 AAGATATTTTTTTCAAATACCATGTAAAGG 2 375 0 TTTCAAATAC 0.730872 -145 AAATGAAAAATTTCAGATACCGAGAAAATT 3 426 0 TTTCAGATAC 0.745651 -175 ATCTGAAATTTTTCATTTAAGAGATGATAT 3 438 1 TTTCATTTAA 0.938005 -163 AAACTGATTATTTCAAATATAGAAAGTAAT 3 560 1 TTTCAAATAT 0.79228 -41 AATGAAATTTTTTCATTTATGCGAGGTAAA 4 213 0 TTTCATTTAT 0.938007 -88 AATGAAAAAATTTCATTTTACCAGTAGAAA 4 226 1 TTTCATTTTA 0.911152 -75 TCTATAATGCTTTCACTTTTGTTTTTTGTG 4 274 0 TTTCACTTTT 0.851481 -27 CATCCGAACATTTCACATTTTGATTATTTC 5 348 1 TTTCACATTT 0.802563 -253 ATTGTTAATCTTTCATTTACTTATAACTTG 5 476 0 TTTCATTTAC 0.915061 -125 TTGTGCAGAGTTTCACATTATG 6 3 0 TTTCACATTA 0.802563 -598 ********** Masking position 5 Map Score: 12.4013 Number of sites scoring better than the average of aligned sites = 2332 Number in coding regions = 1263 Number in noncoding regions = 1069 Number of orfs with sites within 600 bp upstream = 753 Fraction of orfs with sites within 600 bp upstream = 0.120944 Motif number 4 CTTCTTTCTACGTACAAAACGTGTCTGCAGA 1 35 0 CGACAAAACG 0.982845 -440 ATTTCTCCTTCGCGCGACACGCAGAAATGAA 1 282 0 CGGCGACACG 0.993806 -193 ATGCTTTATTCGAGCGAACCTTAACAGTCTG 4 101 1 CGGCGAACCT 0.944876 -200 AGCAATGTAGCGGACAAACCGAACATTGAAA 5 217 1 CGACAAACCG 0.970253 -384 GAACCTACTCCGAGTGAAACGGACGGAAGAG 6 127 1 CGGTGAAACG 0.965138 -474 GCGGCAGTTCCGCCCAACACGGGCCTAGACA 6 208 0 CGCCAACACG 0.988563 -393 GCGGAACTGCCGCCCAACACGGTTTCCGGGA 6 226 1 CGCCAACACG 0.988563 -375 ATGCGGAAGACGCGCGAAACGTGAAACATTT 6 384 1 CGGCGAAACG 0.996213 -217 ** ******** Masking position 7 Map Score: 7.37346 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 70 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TGTGCAGGCTTATAAAATACCACTGATGTTCA 1 93 0 TAAAAATACA 0.815715 -382 ATATTTCAAGGTTAAATTACGAATTGCAGTTT 1 408 1 GTAAATTACA 0.961915 -67 TGAAGTATTAGACAAGATACTAGAGTTTAATA 2 220 0 GAAAGATACA 0.884361 -300 TATGGATCGTGTAAAGTTACCAAGCAGAAAAA 3 372 1 GTAAGTTACA 0.975774 -229 GTCGCAAATATTCAAGTTACGAAACATTGACA 5 119 0 TTAAGTTACA 0.973805 -482 CTCTTTTAAGTTCAAATTACAAGGGCAAGATA 5 180 0 TTAAATTACA 0.958452 -421 AAACCGAACATTGAAATTACCATTTTAATTGT 5 232 1 TTAAATTACA 0.957879 -369 ACTCCTTCAAGATAAGTTACAATTAAAATGGT 5 250 0 GAAAGTTACA 0.964926 -351 AAAAAATGACTTCAAGTTATAAGTAAATGAAA 5 464 1 TTAAGTTATA 0.764585 -137 TAAACGGAAGTAGAAATTACCAGAAGTAACAA 6 499 0 TAAAATTACA 0.939939 -102 ** ******* * Masking position 5 Map Score: 5.07218 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 342 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 6 TGTCTGCAGAACCTTTAGCCTTAACAATGA 1 15 0 ACCTTTAGCC 0.948349 -460 AGTTTTAGCAACCGTTAGCCGGAAGTTTCA 1 321 0 ACCGTTAGCC 0.966803 -154 TTATTCGCTGAACAGTAGCCTAGCTTATAA 2 99 1 AACAGTAGCC 0.953797 -421 GAAGCCTTAACCCTGTAGCCTCATCTATGT 2 259 1 CCCTGTAGCC 0.978816 -261 AACAGATTCCCACTGCAGCCTTTTTTGTTG 3 223 0 CACTGCAGCC 0.978761 -378 AGTATTCTTAAACGGTAGCCCTTGGTTGTG 3 266 0 AACGGTAGCC 0.990803 -335 ATGGAATCACAATGTTAGCCTTCAAATCCT 5 85 0 AATGTTAGCC 0.874254 -516 TGTTGGGCGGAACTGCCGCCCAACACGGTT 6 220 1 AACTGCCGCC 0.928939 -381 GGCTGTAACTCATGGCAGCCGAGGGGAATA 6 328 1 CATGGCAGCC 0.935203 -273 ********** Masking position 9 Map Score: 5.00584 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 402 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 ACATATCTTACACAAAACATCCGTACATCA 1 217 1 CACAAAACAT 0.955355 -258 ATTTTAGAAACAGAAGGCATGTGAGTTTTC 2 154 0 CAGAAGGCAT 0.9373 -366 TTATTCAGAACAGAAGAGATCGCAAACTTT 2 408 0 CAGAAGAGAT 0.903056 -112 CATTACTGACCTCAAAGCATCACAAATGTG 3 119 0 CTCAAAGCAT 0.921868 -482 CCTTAACAGTCTGAAGGCAGATTAATTTGT 4 119 1 CTGAAGGCAG 0.8916 -182 TTACTACTACCAGAAAACATGAAAAATGTA 4 166 1 CAGAAAACAT 0.962295 -135 AATTTTAGCTCACAAAAGATGGAAAAAGTC 5 148 0 CACAAAAGAT 0.925762 -453 TTTAAACATCCTGCAAACAGTCTAATAAAT 5 563 1 CTGCAAACAG 0.843398 -38 TGAAACTCTGCACAAAAGATTAAAAAGGAA 6 18 1 CACAAAAGAT 0.925762 -583 CGCAGCTTCCCAGCAAGGAGTTTCTCAGAG 6 98 1 CAGCAAGGAG 0.833023 -503 GAGTTACAGCCTCAAAACAGGTACAAAACT 6 309 0 CTCAAAACAG 0.921859 -292 ********** Masking position 5 Map Score: 3.54278 Number of sites scoring better than the average of aligned sites = 1042 Number in coding regions = 805 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 8 TTTTGTACGTAGAAAGAAGCAATCATGCCA 1 47 1 AGAAAGAAGC 0.957003 -428 TTTATATGCAAGCAGGACGCTCGGGTTTGT 3 36 1 AGCAGGACGC 0.988644 -565 CGGGTTTGTAAGGAGGAAGATTGAAAAGGA 3 57 1 AGGAGGAAGA 0.958264 -544 TAAAAGGCGAAGAAGGAAGCGACACATTTG 3 97 1 AGAAGGAAGC 0.985046 -504 AATCGGTTCTAGGAGGACGCTCCCTCTAAG 6 178 1 AGGAGGACGC 0.995733 -423 GGACGATATGCGGAAGACGCGCGAAACGTG 6 377 1 CGGAAGACGC 0.96648 -224 ********** Masking position 4 Map Score: 2.66292 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 221 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 GCTCCTCAGATATTCCTTTAAACCCATACA 1 190 1 TATTCCTTTA 0.972268 -285 GCTTATTTGGTATTACATTGGAAACTAGTT 1 347 0 TATTACATTG 0.836385 -128 TGAGTTTTCATATTACATTAATTAAATGAA 2 133 0 TATTACATTA 0.950538 -387 CAAAGCGGACTATTTCTTTATTCTTTTGAT 2 453 0 TATTTCTTTA 0.898212 -67 TATATATATATATTACATTACTGACCTCAA 3 134 0 TATTACATTA 0.950538 -467 TACTCTAAACTATTACTTTACGTATCTTTG 3 475 1 TATTACTTTA 0.977012 -126 ATTCGCGGACTATTCCTTAACGATCTGTAA 3 518 0 TATTCCTTAA 0.831458 -83 GATTAATAGATATTACTTTCTATATTTGAA 3 571 0 TATTACTTTC 0.91863 -30 GCAATCAATTTATTCCTTTTTAATCTTTTG 6 30 0 TATTCCTTTT 0.862693 -571 AAGCTTTTTCTATTATTTTAGTGATTTTTT 6 536 1 TATTATTTTA 0.78781 -65 ********** Masking position 4 Map Score: 4.17162 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 600 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 10 TTTAAATGAAGTATTAGACAAGATACTAGA 2 228 0 GTATTAGACA 0.937555 -292 CTCACGATATGTAGCAGACATAGATGAGGC 2 276 0 GTAGCAGACA 0.98705 -244 TTAAGCTGTTGTATTGGACAAAGCGGACTA 2 471 0 GTATTGGACA 0.971288 -49 ATACAGCAATGTAGCGGACAAACCGAACAT 5 213 1 GTAGCGGACA 0.994211 -388 AGTTAACCTAGTAGCGGAGAGCCGTTATTA 6 454 1 GTAGCGGAGA 0.979909 -147 ********** Masking position 3 Map Score: 1.12938 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 46 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 CAGTAATGTAATATATATATATATATATAT 3 141 1 ATATATATAT 0.498896 -460 ATATATATATATATATATATATATATATTA 3 153 1 ATATATATAT 0.498896 -448 ATAAATACTGATATATATACACTCTTAATG 4 74 1 ATATATATAC 0.579201 -227 ********** No masking Map Score: -3.16736 Number of sites scoring better than the average of aligned sites = 3892 Number in coding regions = 234 Number in noncoding regions = 3658 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 12 CAGTAATGTAATATATATATATATATATAT 3 141 1 ATATATATAT 0.498938 -460 ATATATATATATATATATATATATATATTA 3 153 1 ATATATATAT 0.498938 -448 ATAAATACTGATATATATACACTCTTAATG 4 74 1 ATATATATAC 0.578157 -227 ********** No masking Map Score: -3.16736 Number of sites scoring better than the average of aligned sites = 3892 Number in coding regions = 234 Number in noncoding regions = 3658 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 13 CCCTGGTAGTAGGGCGGAGAGATCAGA 2 2 0 AGGCGAGTCG 0.968808 -518 TTACCGCTCGAATGCGACGTTTCCTGCCTCATAAAA 2 48 1 AAGCGTTCCG 0.981774 -472 TTACGCAGGTAATGCGAAAATTACAGTATGGATCGT 3 346 1 AAGCGATACG 0.955582 -255 AAGGACTGAAAATGCGCGGATATCAGCCAGAACATA 4 31 1 AAGCGATTCG 0.96858 -270 ATGAAAAATGTATGTGCGATGCCCAGAATTTTACCT 4 184 1 TAGTGTGCCG 0.960516 -117 AAATAATCAAAATGTGAAATGTTCGGATGTTAAGCA 5 341 0 AAGTGTGTCG 0.932983 -260 ACGCTCCCTCTAAGTGTCTAGGCCCGTGTTGGGCGG 6 194 1 TAGTGAGCCG 0.972688 -407 ATGTTATGTCTGGGCGTATAGTCCCGGAAACCGTGT 6 242 0 TGGCGAGCCG 0.981907 -359 CATTGATTTATACGCGCGGTGTACGGATTAAAAAAG 6 275 1 TAGCGTGACG 0.959216 -326 ATGGAACTCCAAAGCGTTGATACCCGCTTGAAGTTT 6 418 1 AAGCGATCCG 0.987478 -183 ** *** ** ** * Masking position 14 Map Score: 4.14032 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 154 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 14 GTTTCTAAAATTGTCACAGCAAGAAATAACAT 2 173 1 TTGTCAAGAA 0.947617 -347 ATCAAGATACTTCTCAGGGCAATATCTACATT 5 297 1 TTCTCAGGAA 0.977738 -304 GTCAAAAAATTTCTCAAAGAAAAAAGAAGTAA 5 387 1 TTCTCAAGAA 0.987451 -214 TCGGAGTAGGTTCTCTGAGAAACTCCTTGCTG 6 108 0 TTCTCTAGAA 0.976907 -493 CGATTTTCGTTTCTCTTTGGAAGGTCTCTTCC 6 151 0 TTCTCTTGAA 0.965182 -450 AGTGATTTTTTTCTCATTGGAAATTCATACAC 6 555 1 TTCTCATGAA 0.980078 -46 ****** ** ** Masking position 4 Map Score: 0.960281 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 140 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 15 CAGTAATGTAATATATATATATATATATAT 3 141 1 ATATATATAT 0.498938 -460 ATATATATATATATATATATATATATATTA 3 153 1 ATATATATAT 0.498938 -448 ATAAATACTGATATATATACACTCTTAATG 4 74 1 ATATATATAC 0.578157 -227 ********** No masking Map Score: -3.16736 Number of sites scoring better than the average of aligned sites = 3892 Number in coding regions = 234 Number in noncoding regions = 3658 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549