AlignACE version 2.2 July 7, 1998 AlignACE -jGCN.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 YDR283C 500 bp YDR283C gcn2 1-4980 eukaryotic initiation factor 2 alpha (eIF2-alpha) kinase #2 YEL009C 600 bp YEL009C GCN4 1-846 transcriptional activator of amino acid biosynthetic genes #3 YFR009W 300 bp YFR009W GCN20 1-2259 Member of ATP-binding cassette (ABC) family of proteins #4 YGL195W 478 bp YGL195W GCN1 1-8019 translational activator of GCN4 through activation of GCN2 in response to starvation #5 YGR252W 600 bp YGR252W GCN5 1-1320 histone acetyltransferase #6 YKR026C 600 bp YKR026C gcn3 1-918 34 KD alpha subunit of eIF2B Motif number 1 GAGTATATATTCTTTTTTATTC 1 2 0 TTTTTTTATT 0.818549 -499 TAGAAGTTTATTATTTGTTTTAAGTTGGACT 1 191 1 TATTTGTTTT 0.97656 -310 TTATAAGCATTGATTTTTTTTTTCAATAATT 1 449 1 TATTTTTTTT 0.975709 -52 GTTTTTGTTTTGTTTTGTTTTGTATATCTAT 2 30 0 TTTTTGTTTT 0.94325 -571 CCCTAAATTCAAATTTTTTTTGCCCATCAGT 2 83 1 AATTTTTTTT 0.884801 -518 TAAAATAAAATATTTTGTTTTGATTGCGAAG 2 162 0 TTTTTGTTTT 0.94325 -439 AAACCGATTATATTTTGTTTTTAAAGTAGAT 2 260 1 TTTTTGTTTT 0.94325 -341 TTGAAAGAGAAAATTTATTTTCCCTTATTAA 2 332 1 AATTTATTTT 0.610698 -269 TTAAAGTCCTTTACTTTTTTTGAAAACTGTC 2 363 1 TACTTTTTTT 0.801535 -238 TTTTGAAGAGTTATTTGTTTTGTTACCAATT 2 398 1 TATTTGTTTT 0.97656 -203 TAGTATAGGGAAATTTTTATTGGCGAGTAAA 2 500 0 AATTTTTATT 0.683766 -101 TATTTGTATTTAATTTATTTTCTTGAGCAGA 2 578 0 TATTTATTTT 0.891349 -23 TTTATTTGTATTTAATTTATTT 2 589 0 TATTTGTATT 0.921436 -12 CTTGCGCAGTTTCTTTTTTTTCTGATTTTTA 3 114 1 TCTTTTTTTT 0.915132 -187 CTTTTTTTTCTGATTTTTATTTTTTTGTTCC 3 126 1 TATTTTTATT 0.918749 -175 ACTACATGTCTTATTTTTTTTGTCTTTGCTC 5 252 0 TATTTTTTTT 0.975709 -349 CCCTTACCAATCCTTTGTTTTTATTTATTGC 5 524 0 TCTTTGTTTT 0.917928 -77 GCATAATGTTTTTTTTTTTTTACAATAGATA 6 404 1 TTTTTTTTTT 0.941261 -197 CATTTTTTTTTCATTTTTCTTCCGGATGAAA 6 437 0 TATTTTTCTT 0.8359 -164 ACCAATTTTTTCATTTTTTTTTCATTTTTCT 6 448 0 TATTTTTTTT 0.975709 -153 * ********* Masking position 6 Map Score: 25.0991 Number of sites scoring better than the average of aligned sites = 9602 Number in coding regions = 1454 Number in noncoding regions = 8148 Number of orfs with sites within 600 bp upstream = 1919 Fraction of orfs with sites within 600 bp upstream = 0.308224 Motif number 2 GCACGTCAAGATTAATTTGAATAAAGAAGTAACATGTC 1 97 0 AATTTAAAAA 0.808866 -404 TTTTTGAGATAAGAACCTGGTGTAATCAATCTATAAAC 1 265 1 AACTGTAACA 0.886092 -236 TAAATGTAAAAGTAAATTTGCTTAAAAAGATTCTAGGC 1 304 0 AATTTTAAAA 0.953959 -197 TTGTAATGAAAATAACTTCTTGTAAGAAAGAAGATAGA 1 344 0 AATTGTAAAA 0.977718 -157 ATTTTCTAATAATAATCTACTTTAAAAACAAAATATAA 2 267 0 AACTTTAAAA 0.961806 -334 TAAATTTAACACATAATTCTCTTAATAATTTTCTAATA 2 294 0 AATTTTAAAA 0.953959 -307 AAAAAAAGTAAAGGACTTTAATTAATAAGGGAAAATAA 2 346 0 AATTTTAAAA 0.953959 -255 AAATTGGTAAACAAAACTTTAGTAATAATAATGATTTA 2 539 0 AACTGTAAAA 0.981593 -62 TAATAATACGAAAAATTTTCAGGAACAAAAAAATAAAA 3 140 0 AATTGGAAAA 0.882802 -161 TCCAACTATAAAAAATCTTGCGTAAGAATTTCAATAGT 5 369 0 AACTGTAAAA 0.981593 -232 AAACATAACGATAGTAAAAATGAGCGGTAT 6 3 1 AACGGTAAAA 0.939317 -598 AACTGATCTGATCAAATTATTTTAAGAATATTTTACTA 6 68 1 AATTTTAAAA 0.953959 -533 TCCGGATGAAATTTATCTATTGTAAAAAAAAAAAAACA 6 410 0 AACTGTAAAA 0.981593 -191 ATTTCTTCATAGTAATTGATAGAAAGAATTTTAAAAGT 6 544 1 AATGGAAAAA 0.722325 -57 * * ** **** ** Masking position 5 Map Score: 11.3536 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 154 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 TCAAGATTAATTTGAATAAAGAAGTAACATGTCATC 1 94 0 TTATAAAAAA 0.927425 -407 AAGAAGTTATTTTCATTACAAAAGGACATTAAATAC 1 361 1 TTATACAAAA 0.823713 -140 GCTTATAAAATCTTAAAAGACAACGAGGCTTTCCAA 1 421 0 TTAAAGAAAA 0.978178 -80 CGGAAAATTATTGAAAAAAAAAATCAATGCTTATAA 1 449 0 TGAAAAAAAA 0.838896 -52 ATATCTATTATATAAGAAGATAAGTAC 2 2 0 TTAAAGAAAA 0.978178 -599 TGCCCATCAGTTTCACTAGCGAATTATACAACTCAC 2 103 1 TTATAGCAAA 0.844448 -498 ATTATCAGTATCGTATTAAAAAATTAAAGATCATTG 2 210 1 TGATAAAAAA 0.822941 -391 TAAAGTAGATTATTATTAGAAAATTATTAAGAGAAT 2 281 1 TTATAGAAAA 0.975616 -320 CAAGGATAGTTTTCACAAGAAAACAAGCGCAAGTGG 3 25 1 TTAAAGAAAA 0.978178 -276 ATGAAAGACATTTGAAAAGAGAAATATATATTCTGC 3 191 1 TTAAAGAAAA 0.978178 -110 GCTTACCATTTCTGAAAAGGTAACCAAACATCGTTG 4 99 0 TTAAAGGAAA 0.917985 -380 AGTTACTATTTATAAATAGATACACAATTACATAGA 4 179 0 TTATAGAACA 0.82648 -300 TGCGTAAATGTTTGATTAAGCAATAAATAAAAACAA 5 505 1 TTATAAGAAA 0.761386 -96 TTGTATTGCTTTTCAAAATAAAACTAAACATATGTA 6 183 1 TTAAATAAAA 0.779347 -418 TATCTTATGTTGGTAATAGATAACGATTAGTAATAC 6 245 1 TGATAGAAAA 0.935696 -356 ATTTATCTATTGTAAAAAAAAAAAAACATTATGCTA 6 402 0 TTAAAAAAAA 0.934712 -199 AAGTTTATGGTGTAAAATGAGAATCATACTGCTCAA 6 480 1 TTAATGAAAA 0.782627 -121 * * * **** ** * Masking position 5 Map Score: 12.1853 Number of sites scoring better than the average of aligned sites = 1084 Number in coding regions = 670 Number in noncoding regions = 414 Number of orfs with sites within 600 bp upstream = 340 Fraction of orfs with sites within 600 bp upstream = 0.0546097 Motif number 4 TGTAGGTAGTTTCTTAGGAAGCAGTTGAGTA 1 229 1 TTTTAGGAAG 0.632153 -272 AATCTTTACATTGTTGGAAAGCCTCGTTGTC 1 408 1 TTTTGGAAAG 0.9591 -93 GAACGGAAAATTATTGAAAAAAAAAATCAAT 1 457 0 TTTTGAAAAA 0.704256 -44 TCCTTTACTTTTTTTGAAAACTGTCAGTTTT 2 369 1 TTTTGAAAAC 0.769603 -232 AACTGTCAGTTTTTTGAAGAGTTATTTGTTT 2 387 1 TTTTGAAGAG 0.958599 -214 AGGGAAATTTTTATTGGCGAGTAAACCTGGA 2 494 0 TTTTGGCGAG 0.879966 -107 TTAATTTATTTTCTTGAGCAGACAAATTGGT 2 569 0 TTTTGAGCAG 0.957883 -32 GAGCTTACCATTTCTGAAAAGGTAACCAAAC 4 106 0 TTCTGAAAAG 0.842182 -373 CGTAACGACTTTATTGAGAAGCTCAATGACG 4 337 0 TTTTGAGAAG 0.968761 -142 ACGTATTCATTTGTTGACAAGCAAACATCAT 5 40 0 TTTTGACAAG 0.959359 -561 TCCACTAGAATTTTTGACCAGCCACTATTTG 5 192 1 TTTTGACCAG 0.945455 -409 TTGCTCTCGAGTATTGAAAAGGATTGCGAAA 5 227 0 GTTTGAAAAG 0.946935 -374 TTACAAACGCGTGTTAAACAGGCATATTTAA 5 313 1 GTTTAAACAG 0.566299 -288 TGTTTGGTCTGTTTTGGAGAGATCACCATGT 6 144 0 GTTTGGAGAG 0.847178 -457 GTTTAGTTTTATTTTGAAAAGCAATACAAGC 6 181 0 ATTTGAAAAG 0.817854 -420 GCTTTGTCACTATTTGAGCAGTATGATTCTC 6 498 0 TATTGAGCAG 0.660863 -103 ** ******** Masking position 5 Map Score: 5.84028 Number of sites scoring better than the average of aligned sites = 2569 Number in coding regions = 2002 Number in noncoding regions = 567 Number of orfs with sites within 600 bp upstream = 469 Fraction of orfs with sites within 600 bp upstream = 0.0753293 Motif number 5 AATATATACTCCACATGACATACGAAATAT 1 22 1 CCACATGACA 0.938975 -479 CGGACAATCCCAACATCACTTTACACGAAA 1 157 1 CAACATCACT 0.894739 -344 AAGAAACTACCTACATCACTATAGTCCAAC 1 214 0 CTACATCACT 0.976158 -287 GCTCACTCATCTACTTCGCAATCAAAACAA 2 149 1 CTACTTCGCA 0.90705 -452 ATCTGCATTGCTACATCTCATTTAATGTTA 5 140 0 CTACATCTCA 0.972377 -461 ATACAGCGCACTACATGTCTTATTTTTTTT 5 262 0 CTACATGTCT 0.943486 -339 AGTATGTTTACTACATGACAATCTGCAGCA 6 105 1 CTACATGACA 0.980393 -496 TTAAAGCTTTCTACATAGCATAATGTTTTT 6 387 1 CTACATAGCA 0.912546 -214 ********** Masking position 3 Map Score: 1.90855 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 149 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GAATAAAAAAGAATATATACTCCACATG 1 9 1 AAGAATATAT 0.90858 -492 TTCCATACAGAACAATAAATACGTATATTT 1 46 0 AACAATAAAT 0.936726 -455 TCGCAATCAAAACAAAATATTTTATTTTAG 2 164 1 AACAAAATAT 0.902172 -437 CTACTTTAAAAACAAAATATAATCGGTTTA 2 259 0 AACAAAATAT 0.902172 -342 ATTTGAAAAGAGAAATATATATTCTGCAGT 3 200 1 AGAAATATAT 0.721774 -101 GAAATTTCATAGCATTATATCAACAAATAA 4 301 0 AGCATTATAT 0.91335 -178 TTGCTAGAATAACATTAAATGAGATGTAGC 5 131 1 AACATTAAAT 0.855005 -470 TTTGGACCTAAACAATATATCGACTATTGA 5 347 1 AACAATATAT 0.973799 -254 AGAGAGTTGTAAGAATATATGAATATCCAA 5 402 0 AAGAATATAT 0.90858 -199 AGCTATATGTATCATTATATACGTTTATGG 5 450 1 ATCATTATAT 0.726252 -151 TGTTTGATTAAGCAATAAATAAAAACAAAG 5 513 1 AGCAATAAAT 0.91335 -88 ********** Masking position 4 Map Score: 4.35147 Number of sites scoring better than the average of aligned sites = 908 Number in coding regions = 555 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 7 AAGAAGTAACATGTCATCTTTATGTAATCGC 1 81 0 ATGTCATCTT 0.845138 -420 TCGGTTTAGCAAGCCATTTTTCAATGATCTT 2 236 0 AAGCCATTTT 0.89905 -365 AAATCCAACGTTGCCATCGTTGGGCCCCCGG 3 71 1 TTGCCATCTT 0.984243 -230 GCAGCAAAATTGCCGTCCTTCCTCAACACG 4 10 1 TTGCCGTCTT 0.928708 -469 TACTTGCAGTATGCAATAATTGCCTTGGCTA 5 85 0 ATGCAATATT 0.801241 -516 TTTGCTTTTTTCGCAATCCTTTTCAATACTC 5 219 1 TCGCAATCTT 0.922239 -382 AAGATATAGCTAGCAATTCTTGTAAGCACAA 6 220 0 TAGCAATTTT 0.715328 -381 TAAGGAGGCAATGCCATCATTTTCGCCACAT 6 297 1 ATGCCATCTT 0.984243 -304 AGCAACATTGTCGCCATATTTAAAGCTTTCT 6 368 1 TCGCCATATT 0.905785 -233 AATAGTGACAAAGCCATCATTAATCATAGAT 6 515 1 AAGCCATCTT 0.974961 -86 ******** ** Masking position 7 Map Score: 1.8179 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 900 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 8 CTGTTATTCCATACAGAACAATAAATACGT 1 52 0 ATACAGAACA 0.9283 -449 TATAATAGATATACAAAACAAAACAAAACA 2 26 1 ATACAAAACA 0.868244 -575 CTAGCGAATTATACAACTCACCAGCCACAC 2 118 1 ATACAACTCA 0.981714 -483 CTCACCAGCCACACAGCTCACTCATCTACT 2 134 1 ACACAGCTCA 0.961005 -467 GGTTTAATAAGTACAACTCAAAGATCTTTT 4 402 0 GTACAACTCA 0.926163 -77 ATTCTTTTCCATACAGCGCACTACATGTCT 5 272 0 ATACAGCGCA 0.974727 -329 ATGTCATAACATACCGCTCATTTTTACTAT 6 21 0 ATACCGCTCA 0.965536 -580 AGGGAATTTGATACAACACAGCAACATTGT 6 349 1 ATACAACACA 0.970985 -252 AATGAGAATCATACTGCTCAAATAGTGACA 6 495 1 ATACTGCTCA 0.949754 -106 ********** Masking position 3 Map Score: 5.27572 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 182 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 ********** No masking Map Score: 6.92312e-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 10 ********** No masking Map Score: 6.92312e-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 11 TGTTCTGTATGGAATAACAGCGATTACATAAAG 1 62 1 GGAATAAAGA 0.962413 -439 ATTGTCCGATGAAATAACAAGCAGGCCCTTGCA 1 132 0 GAAATAAACA 0.867899 -369 CTTCTTGTAAGAAAGAAGATAGAGATAAATGTA 1 334 0 GAAAGAAAGA 0.988869 -167 TTTAATTAATGATAGTATAGGGAAATTTTTATT 2 510 0 GATAGTAAGA 0.815685 -91 CAAAACTTTAGTAATAATAATGATTTAATTAAT 2 533 0 GTAATAAAGA 0.903729 -68 TGTTTACCACGAAATAATATGGAAATTGTCCCA 4 53 0 GAAATAAAGA 0.978363 -426 TCAAAAAACTGAAAGTAGAGAGAGTTGTAAGAA 5 417 0 GAAAGTAAGA 0.965604 -184 CCTTTTATGAGAAAGAATAAGGAGGCAATGCCA 6 280 1 GAAAGAAAGA 0.988869 -321 AATTTCATCCGGAAGAAAAATGAAAAAAAAATG 6 435 1 GGAAGAAAGA 0.980509 -166 ******* * ** Masking position 7 Map Score: 4.74291 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 326 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 12 ********** No masking Map Score: 6.92312e-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 13 ********** No masking Map Score: 6.92312e-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 ACACGAAAGCCTTAGAAGTTTATTATTTGTT 1 179 1 CTTAGAATTT 0.944598 -322 CTATAAACAGCCTAGAATCTTTTTAAGCAAA 1 295 1 CCTAGAACTT 0.860373 -206 ATCATGTACCCGTAGAATTTTATTCAAGATG 2 432 1 CGTAGAATTT 0.984252 -169 ACGATGGCAACGTTGGATTTTACCACTAAAC 3 60 0 CGTTGGATTT 0.942167 -241 CAATGACGGTAGTTGAAATTTCATAGCATTA 4 314 0 AGTTGAATTT 0.866186 -165 TTAATGCTCCACTAGAATTTTTGACCAGCCA 5 185 1 ACTAGAATTT 0.896304 -416 AAAAGAATTAATTAGAACTTTACAAACGCGT 5 294 1 ATTAGAATTT 0.848208 -307 AAAAATCTTGCGTAAGAATTTCAATAGTCGA 5 366 0 CGTAAGATTT 0.83482 -235 TTCTGGTATACGTAGGACTTTTAAAATTCTT 6 567 0 CGTAGGATTT 0.980972 -34 ******* *** Masking position 7 Map Score: 0.0873264 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 524 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 15 ********** No masking Map Score: 6.92312e-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