AlignACE version 2.2 July 7, 1998 AlignACE -jCLB.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 YDL155W 300 bp YDL155W CLB3 1-1284 G(sub)2-specific B-type cyclin #2 YGR108W 519 bp YGR108W CLB1 1-1416 G(sub)2-specific B-type cyclin #3 YGR109C 600 bp YGR109C CLB6 1-1143 B-type cyclin #4 YLR210W 300 bp YLR210W CLB4 1-1383 G(sub)2-specific B-type cyclin #5 YPR119W 600 bp YPR119W CLB2 1-1476 G(sub)2-specific B-type cyclin #6 YPR120C 582 bp YPR120C CLB5 1-1308 B-type cyclin Motif number 1 CCGCACTGCCTTTTTTCTCTCCCGCTTTTCAG 1 40 1 TTTTTCTCTC 0.771025 -261 TTTGTTTTCTTTTGTTTTGTTTTGTTCCTTCG 1 89 0 TTTTTTTGTT 0.936503 -212 CATTTCAATATTTTTGTTTTCTTTTGTTTTGT 1 101 0 TTTTGTTTTT 0.824636 -200 TCTCTGCAATTTTCTTTTCTTTTCTTCTAAGC 1 203 0 TTTTTTTCTT 0.918225 -98 GAAAAAGCTATTTATTGTTTCTGTCCTTCGCT 1 233 1 TTTTTGTTTT 0.896416 -68 ATAGAGATATTTTGTCCTTTTTATCATTGCTT 1 272 1 TTTTCCTTTT 0.95881 -29 GTCTGCCCAATTTGTTTTGTTTGTGATTTCCT 2 115 1 TTTTTTTGTT 0.936503 -405 TCCATGAAAGTTTTTTTTTTTTGAAGATGTTC 3 26 1 TTTTTTTTTT 0.97531 -575 GAAGATGTTCTTTTTTTTTTTTTGGGCCTCAT 3 48 1 TTTTTTTTTT 0.97531 -553 ATTCTTCGCGTTTTTTTTTTGCGACGGTAAAC 3 240 1 TTTTTTTTTC 0.942758 -361 AGAGGGCCCTTTTTTTGTTTACCGTCGCAAAA 3 256 0 TTTTTGTTTC 0.782993 -345 GGGTTAAGTTTTTGCCTTTTTCTTATTAACAT 3 430 1 TTTCCTTTTC 0.861886 -171 ACAAGTGACTTTTATCTTTTATTAAATAATAA 3 484 1 TTTTCTTTTT 0.970027 -117 TGCTTCGAGATTTTCCTTTTCTTTGCGCTTTG 4 119 1 TTTCCTTTTT 0.937372 -182 TTTCCATTGTTTTTGTTTTTGTTTCAGTGTTT 4 152 0 TTTGTTTTTT 0.885173 -149 AAAGGATCTATTTCTCTTTTCCCCAAAGAGGT 5 70 0 TTTTCTTTTC 0.931003 -531 ATTTTGATTTTTTTTCCTTTCTAAATTTTTGA 5 103 0 TTTTCCTTTT 0.95881 -498 ATACTGGTTATTTATTCTTTCTTTTTTTCTTT 5 309 1 TTTTTCTTTT 0.966 -292 TATTCTTTCTTTTTTTCTTTCTTTTTGATTGA 5 321 1 TTTTTCTTTT 0.966 -280 TGAGCATCTGTTTTCCTTTTGTATTTTTGTCC 5 429 1 TTTCCTTTTT 0.937372 -172 TTGCTAGTCATTTTTTTTTTATACTCAAAAAG 6 37 1 TTTTTTTTTT 0.97531 -546 TCAAGAAAAGTTTTTTTTCTGTCTATCTATTG 6 411 1 TTTTTTTCTT 0.918225 -172 ATTGAAGTCTTTTTGTCTTTGTACTTCAAGAG 6 439 1 TTTGTCTTTT 0.847201 -144 TTAAGCTTATTTTGCTTTGTGTGAGACAACTA 6 502 0 TTTCTTTGTT 0.872137 -81 AGTAACGCGCTTTTCCCTGTATTTAAAGCCGC 6 542 1 TTTCCCTGTT 0.800773 -41 *** ****** * Masking position 8 Map Score: 33.1422 Number of sites scoring better than the average of aligned sites = 11849 Number in coding regions = 2309 Number in noncoding regions = 9540 Number of orfs with sites within 600 bp upstream = 2433 Fraction of orfs with sites within 600 bp upstream = 0.390781 Motif number 2 CCTTTTTTCTCTCCCGCTTTTCAGCAGAACGAG 1 48 1 CTGCTTTTCA 0.993816 -253 TGTGTCCATGTTCTTGCATTTCAATATTTTTGT 1 116 0 TTGCATTTCA 0.908066 -185 CAATAAATAGCTTTTTCTCTGCAATTTTCTTTT 1 217 0 CTTCTCTGCA 0.896433 -84 CAAAGGAAGCTTTAATCTTCTCATA 2 505 1 TTTCTTCTCA 0.919257 -15 ATATATATAACTGCTTCATTTCATACAAGTGAC 3 460 1 CTTCATTTCA 0.967441 -141 TAGTAAATTTTTGGATCTTTTCAAAAGTCTAGC 5 178 0 TTTCTTTTCA 0.967389 -423 AGCTATATTTCTTTCGCTTTTCAGAAGTATCAA 5 271 0 CTGCTTTTCA 0.993816 -330 TGATTACCCCCTCTCTCTCTTCATTGATCTTAT 5 576 1 CTTCTCTTCA 0.978706 -25 CGTTCTTTTGCTGGTTCTTTTCACTGAGGGCAC 6 155 0 CTTCTTTTCA 0.991719 -428 GGAACTAATTCTTAAGCTTCTCAAGAAAAGTTT 6 391 1 CTGCTTCTCA 0.984046 -192 ACTCAATCACCTAAAGCTTTTCACGGCCAATTA 6 471 1 CTGCTTTTCA 0.993816 -112 ** ******** Masking position 13 Map Score: 13.5061 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 336 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 GGTAACTGAGATGTTTTCATTCTTCCTGCT 1 7 0 ATTTTCATTT 0.799565 -294 TTTTGTTTTGTTCCTTCGCTTGTCGCCTCGTTCT 1 73 0 TTCTTGCTTC 0.937519 -228 ACGATCAGAAATTTTTAGCTGCTTGCTTAGAAGA 1 179 1 ATTTTGCTTT 0.977189 -122 AGATTAAAGCTTCCTTTGATGGTTGATATAACGG 2 489 0 TTCTTGATTT 0.907034 -31 TAGGGCTTTCTTCATTACCTGCTTGCGTCAATTA 3 119 0 TTATTCCTTT 0.827021 -482 ACCAACGCGTATTCTTCGCGTTTTTTTTTTGCGA 3 230 1 ATCTTGCGTT 0.903879 -371 CTGCGTTTAAATATTTACCGTTTTAGCACATTGA 3 381 1 ATTTTCCGTT 0.823656 -220 TTTTAGCACATTGATTACCTTTTTTGCTAGGGTT 3 401 1 TTATTCCTTT 0.827021 -200 AGATTTTCCTTTTCTTTGCGCTTTGTAAACACTG 4 126 1 TTCTTGCGTT 0.919509 -175 TATCTTTCTGATGTTTCCATTGTTTTTGTTTTTG 4 163 0 ATTTTCATTT 0.799565 -138 TAAAGTTTTAATTCTTTGATAATTAACGTCGTAT 4 216 1 ATCTTGATTT 0.889274 -85 CTATTTTATTATATTTTGATTTTTTTTCCTTTCT 5 113 0 ATTTTGATTT 0.921107 -488 TTTTAGGTTAATTTTTTGCCAATTTAGCTAGACT 5 152 1 ATTTTGCCTT 0.836054 -449 ATTTTAGTAAATTTTTGGATCTTTTCAAAAGTCT 5 181 0 ATTTTGATTT 0.921107 -420 TTAGCTATATTTCTTTCGCTTTTCAGAAGTATCA 5 272 0 TTTTTGCTTC 0.956165 -329 GTATAAAAACTTCATTCGCTCGTTTGTCAGAAGT 5 502 1 TTATTGCTTT 0.933303 -99 ACTACTAATTTTATTTTGCTAGTCATTTTTTTTT 6 22 1 TTTTTGCTTC 0.956165 -561 GAGATGCGCGTTCTTTTGCTGGTTCTTTTCACTG 6 162 0 TTTTTGCTTT 0.981147 -421 TTGGAACTAATTCTTAAGCTTCTCAAGAAAAGTT 6 389 1 TTTTAGCTTC 0.73347 -194 TTACTGCTAATTATTAAGCTTATTTTGCTTTGTG 6 513 0 TTTTAGCTTT 0.867821 -70 ** *** *** ** Masking position 5 Map Score: 13.8342 Number of sites scoring better than the average of aligned sites = 3774 Number in coding regions = 2306 Number in noncoding regions = 1468 Number of orfs with sites within 600 bp upstream = 1075 Fraction of orfs with sites within 600 bp upstream = 0.172663 Motif number 4 ACATGGACACATAAAAACATTTTTGATCCG 1 138 1 ATAAAAACAT 0.848182 -163 TCTTCAAAAAAAAAAAACTTTCATGGAAGG 3 23 0 AAAAAAACTT 0.967896 -578 CATGTAACACATAATAACCTCTTACATTGT 3 81 0 ATAATAACCT 0.895097 -520 ATATCAGAGAATAATAATTTTCAACACACT 3 555 0 ATAATAATTT 0.678041 -46 TTATCAAAGAATTAAAACTTTATGCGGCCA 4 208 0 ATTAAAACTT 0.943176 -93 CTTAATGGAAAATATAACCTCTTTGGGGAA 5 54 1 AATATAACCT 0.730349 -547 AATTAACCTAAAAAAAATCTATTTTATTAT 5 135 0 AAAAAAATCT 0.800542 -466 CCAGTGTATAATAAAAACCTACTGCGAGCT 5 354 1 ATAAAAACCT 0.966838 -247 TTATACAATGATTAAAATTTCTCCAATGTC 5 478 0 ATTAAAATTT 0.750574 -123 TAATCATTGTATAAAAACTTCATTCGCTCG 5 494 1 ATAAAAACTT 0.975433 -107 AGCAAGTTATAAAAAAACTTCTGACAAACG 5 522 0 AAAAAAACTT 0.967896 -79 AACTATCTCGATTAAAACTTGTCATACTGT 6 111 1 ATTAAAACTT 0.943176 -472 GATAGACAGAAAAAAAACTTTTCTTGAGAA 6 408 0 AAAAAAACTT 0.967896 -175 GTACAAAGACAAAAAGACTTCAATAGATAG 6 433 0 AAAAAGACTT 0.814744 -150 ********** Masking position 4 Map Score: 11.0577 Number of sites scoring better than the average of aligned sites = 1266 Number in coding regions = 738 Number in noncoding regions = 528 Number of orfs with sites within 600 bp upstream = 395 Fraction of orfs with sites within 600 bp upstream = 0.0634436 Motif number 5 CATCTCAGTTACCCGCACTGCCTTTTTTCTC 1 28 1 ACCCGCCTGC 0.984912 -273 CTTTTTTCTCTCCCGCTTTTCAGCAGAACGA 1 49 1 TCCCGCTTTC 0.960463 -252 CAGCAAAAGAACGCGCATCTCGAGTGAAGAC 6 175 1 ACGCGCTCTC 0.988416 -408 TCGAGTGAAGACGCGCCCTTGATGGTACAAA 6 194 1 ACGCGCCTTG 0.97288 -389 GAACATCACGACGCGCCTTCCCGTTAAATTT 6 223 0 ACGCGCTTCC 0.992059 -360 CGTGATGTTCACGCGCTTTGCCCACATTGGG 6 244 1 ACGCGCTTGC 0.995669 -339 ATTAGCAGTAACGCGCTTTTCCCTGTATTTA 6 536 1 ACGCGCTTTC 0.996407 -47 ****** **** Masking position 6 Map Score: 5.9503 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 28 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TTCTTTTGTTTTGTTTTGTTCCTTCGCTTG 1 85 0 TTGTTTTGTT 0.930291 -216 TATTTTTGTTTTCTTTTGTTTTGTTTTGTT 1 95 0 TTCTTTTGTT 0.946402 -206 CAATTTTCTTTTCTTTTCTTCTAAGCAAGC 1 199 0 TTCTTTTCTT 0.868194 -102 TCTGCCCAATTTGTTTTGTTTGTGATTTCC 2 116 1 TTGTTTTGTT 0.930291 -404 TTTGGTTGTATTGTGTTTTTTACATTCGGC 2 281 1 TTGTGTTTTT 0.894976 -239 TTTTAGTGTCTTCGGTTTTTCCAGCGACAG 2 331 1 TTCGGTTTTT 0.737899 -189 TCCATGAAAGTTTTTTTTTTTTGAAGATGT 3 26 1 TTTTTTTTTT 0.917932 -575 TTTGAAGATGTTCTTTTTTTTTTTTTGGGC 3 45 1 TTCTTTTTTT 0.978334 -556 ATTCTTCGCGTTTTTTTTTTGCGACGGTAA 3 240 1 TTTTTTTTTT 0.917932 -361 TCCATTGTTTTTGTTTTTGTTTCAGTGTTT 4 152 0 TTGTTTTTGT 0.888455 -149 TTATTATATTTTGATTTTTTTTCCTTTCTA 5 112 0 TTGATTTTTT 0.75753 -489 TATTTATTCTTTCTTTTTTTCTTTCTTTTT 5 317 1 TTCTTTTTTT 0.978334 -284 CTTTTTTTCTTTCTTTTTGATTGAGCCAGT 5 329 1 TTCTTTTTGA 0.61391 -272 TGTTTTCCTTTTGTATTTTTGTCCTTTTAG 5 437 1 TTGTATTTTT 0.75753 -164 TTCTTTTTTAGACTACTAAT 6 1 1 TTCTTTTTTA 0.872008 -582 TTGCTAGTCATTTTTTTTTTATACTCAAAA 6 37 1 TTTTTTTTTT 0.917932 -546 TAGTTTGACGTTCGTTTTTTACTTTGAATA 6 86 0 TTCGTTTTTT 0.918533 -497 ********** Masking position 6 Map Score: 15.9072 Number of sites scoring better than the average of aligned sites = 11383 Number in coding regions = 1924 Number in noncoding regions = 9459 Number of orfs with sites within 600 bp upstream = 2179 Fraction of orfs with sites within 600 bp upstream = 0.349984 Motif number 7 AGTTACCCGCACTGCCTTTTTTCTCTCCCG 1 34 1 ACTGCCTTTT 0.948715 -267 CCTTTTTATCATTGCTTATTATAA 1 287 1 ATTGCTTATT 0.866999 -14 TACGCGTAAAACTGCTATTTGGTATCCTCT 3 185 0 ACTGCTATTT 0.961536 -416 CGAATTGCCAATTGCCAATTGTAGGATACA 3 347 0 ATTGCCAATT 0.911814 -254 TATTTGGGAAACTGCTTACTATACCGGATA 4 247 1 ACTGCTTACT 0.941908 -54 GCTAAAGGATACTGGTTATTTATTCTTTCT 5 301 1 ACTGGTTATT 0.830011 -300 TCTTTTTTAGACTACTAATTTTATTTTGCT 6 12 1 ACTACTAATT 0.828275 -571 GCCGATAGCTACTGCCATCTACCGCGAAGG 6 322 1 ACTGCCATCT 0.920919 -261 AAAGCTTTTCACGGCCAATTAGTTGTCTCA 6 483 1 ACGGCCAATT 0.925781 -100 AAAGCGCGTTACTGCTAATTATTAAGCTTA 6 525 0 ACTGCTAATT 0.982209 -58 ********** Masking position 1 Map Score: 3.72556 Number of sites scoring better than the average of aligned sites = 907 Number in coding regions = 581 Number in noncoding regions = 326 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 8 TTCGACCGGATCAAAAATGTTTTTATGTGT 1 144 0 TCAAAAATGT 0.911868 -157 AAGAAAACGATCAGAAATTTTTAGCTGCTT 1 173 1 TCAGAAATTT 0.977422 -128 TTTAAAAATTTAAAAGGAGGG 3 590 0 TTAAAAATTT 0.767251 -11 GCATAGAGTTTCAGAAATTTTGCTCTTAAT 5 30 1 TCAGAAATTT 0.977422 -571 AGATCCTTTCTCAAAAATTTAGAAAGGAAA 5 93 1 TCAAAAATTT 0.97112 -508 TTGGATCTTTTCAAAAGTCTAGCTAAATTG 5 171 0 TCAAAAGTCT 0.895115 -430 TTGAAAAGATCCAAAAATTTACTAAAATTG 5 187 1 CCAAAAATTT 0.887088 -414 CTTTCGCTTTTCAGAAGTATCAATTCGAGA 5 264 0 TCAGAAGTAT 0.88114 -337 CGCTCGTTTGTCAGAAGTTTTTTTATAACT 5 518 1 TCAGAAGTTT 0.972758 -83 ********** Masking position 5 Map Score: 4.23961 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 573 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 9 ACCGTATAGACAATGGGCGCGTCCCTAAAG 3 157 1 CAATGGGCGC 0.973725 -444 TGTTTTACCGCAGAGGGCCCTTTTTTTGTT 3 269 0 CAGAGGGCCC 0.993403 -332 AATCTCGAAGCAGAGGGCAGATAGGGCAGG 4 101 0 CAGAGGGCAG 0.980703 -200 GTTCTTTTCACTGAGGGCACAGAATATGAT 6 145 0 CTGAGGGCAC 0.992059 -438 CACAGATATGCTGTGGGCGCTATCCCAATG 6 268 0 CTGTGGGCGC 0.992644 -315 ********** Masking position 5 Map Score: 1.23367 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 74 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 GCATCATTTATGGGTATCCTGCAAGTTAGG 2 39 1 TGGGTATCCT 0.991712 -481 AAACTGCTATTTGGTATCCTCTTTAGGGAC 3 177 0 TTGGTATCCT 0.97995 -424 CTACTCTCCCTGTGTATCCTACAATTGGCA 3 335 1 TGTGTATCCT 0.980641 -266 TGTCATACTGTGGGTATCATATTCTGTGCC 6 130 1 TGGGTATCAT 0.97995 -453 ********** Masking position 5 Map Score: 1.00586 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TGCATTTTTACAGCATCATTTATGGGTATCC 2 27 1 CAGCTCATTT 0.953591 -493 CGCATACGGTCTGCCCAATTTGTTTTGTTTG 2 107 1 CTGCCAATTT 0.966874 -413 AAATTGCAGCCTGCTCAAGTTTGGCCGAATG 2 303 0 CTGCCAAGTT 0.978676 -217 TCGGTTTTTCCAGCGACAGTTTTACTTGTGG 2 342 1 CAGCACAGTT 0.948247 -178 ATCTAAACAGCTGCACCAGTTAGCAACTTTA 2 399 0 CTGCCCAGTT 0.992691 -121 ATATATATAACTGCTTCATTTCATACAAGTG 3 460 1 CTGCTCATTT 0.974579 -141 **** ****** Masking position 8 Map Score: 0.777391 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 209 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 ATATTTACCGTTTTAGCACATTGATTACCTTTTT 3 391 1 TTTACATTGA 0.981624 -210 GAATAATAATTTTCAACACACTGATTTGTATGTT 3 543 0 TTTACACTGA 0.977808 -58 TTCTTTGCGCTTTGTAAACACTGAAACAAAAACA 4 137 1 TTTACACTGA 0.977807 -164 TTTTCAAAAGTCTAGCTAAATTGGCAAAAAATTA 5 160 0 TCTAAATTGG 0.773008 -441 GATCCAAAAATTTACTAAAATTGAATCTTTCTGG 5 194 1 TTTAAATTGA 0.937781 -407 CAGTAGGTTTTTATTATACACTGGCTCAATCAAA 5 344 0 TTAACACTGG 0.87041 -257 ACTGCGAGCTATTCAATAAATTGACATAGAATAT 5 374 1 ATTAAATTGA 0.679569 -227 TTTAGATTCTTTTAACGACATTGGAGAAATTTTA 5 462 1 TTTACATTGG 0.983014 -139 GCGAATGAAGTTTTTATACAATGATTAAAATTTC 5 487 0 TTTACAATGA 0.917282 -114 GTTCACGCGCTTTGCCCACATTGGGATAGCGCCC 6 250 1 TTTACATTGG 0.983014 -333 *** ******* Masking position 8 Map Score: 2.54834 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 447 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 13 ********** No masking Map Score: 2.74513e-12 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: 2.74513e-12 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: 2.74513e-12 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