AlignACE version 2.2 July 7, 1998 AlignACE -jAPL.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 YBL037W 323 bp YBL037W APL3 1-3078 clathrin Associated Protein complex Large subunit #2 YGR261C 300 bp YGR261C APL6 1-2430 putative beta adaptin component of the membrane-associate clathrin assembly complex #3 YJR005W 600 bp YJR005W APL1 1-2103 beta-adaptin, large subunit of the clathrin-associated protein complex #4 YKL135C 483 bp YKL135C APL2 1-2181 Beta-adaptin, large subunit of the clathrin-associated protein (AP-1) complex #5 YPL195W 358 bp YPL195W APL5 1-2799 delta-like subunit of the yeast AP-3 adaptin component of the membrane-associated clathrin assembly complex #6 YPR029C 600 bp YPR029C APL4 1-2499 Gamma-adaptin, large subunit of the clathrin-associated protein (AP) complex Motif number 1 CACATGACGACGTGAAAAAACACTTGTTTG 1 173 1 CGTGAAAAAA 0.740108 -151 AAATATATAAAGAAAAGAAAGGTAAACCAA 2 247 1 AGAAAAGAAA 0.983824 -54 AAATATAAAAAATAAAGAAAGTTTATCCAT 3 30 0 AATAAAGAAA 0.880877 -571 CTTTTCACCAAGAAAAAAAAATTGCATAAT 4 77 1 AGAAAAAAAA 0.95104 -407 AGCTCTTTTCAGTGAAGAAAGCCTACGATA 4 318 1 AGTGAAGAAA 0.962585 -166 GAAGCTGAGCAAAAAAAAAAACTAAGCTGC 4 436 0 AAAAAAAAAA 0.820968 -48 GAAATAAATAGGAAAAGAAAAATATTTTAA 5 162 1 GGAAAAGAAA 0.968457 -197 ACAATGATTTAATGAAGAAAATGAAAAAGA 5 217 0 AATGAAGAAA 0.858626 -142 ATGCAGGCTGGGAAAAACAACCTTGCAATC 5 247 1 GGAAAAACAA 0.724709 -112 AATGTGAAAAAAAAAAGAAAATGAAGATAC 5 281 1 AAAAAAGAAA 0.934886 -78 ACATGTATATAGAGAAGAAAGCTTCGGCGG 6 79 0 AGAGAAGAAA 0.980374 -522 TGAGAAATATCGTAAAGAAAGTTAGTTGTT 6 316 0 CGTAAAGAAA 0.915655 -285 ATAACACCAAAGAAAAGCAATCAGTAGCAA 6 376 0 AGAAAAGCAA 0.942288 -225 CTACCTTAAGAGAAAAAAAATTCAAATGAA 6 406 1 AGAAAAAAAA 0.95104 -195 TGCTAATATTGGAGAAGAAATATTGACCAT 6 546 1 GGAGAAGAAA 0.961857 -55 ********** Masking position 5 Map Score: 15.4895 Number of sites scoring better than the average of aligned sites = 4523 Number in coding regions = 2298 Number in noncoding regions = 2225 Number of orfs with sites within 600 bp upstream = 1513 Fraction of orfs with sites within 600 bp upstream = 0.243013 Motif number 2 ATTTTTCAATAGTTATATACATGTATACATGGTGTGTTCAA 1 16 0 ATTATATAAG 0.922357 -308 GGCTTATAAGATTAGTACTATAATAAAGGTTGCGAAATT 1 295 0 AATAAATAAG 0.939872 -29 TCGTAAGAGAAGTATGCTAGGATAATATAAATGCTAGCGTA 2 63 1 ATTAAATAAA 0.965609 -238 CATACCTAAAAGTTATGTACGTTAATATAAATTATAGATAC 2 131 0 ATTAAATAAA 0.965608 -170 TTGAAGAACCATATATATAAATATATAAAGAAAAGAAAGGT 2 229 1 AATATATAAA 0.907434 -72 ATTTAGGTTAATTAAATTATAAAAAAATATAAAAAATAAAG 3 43 0 ATTAAAAAAA 0.719884 -558 TCAAAAGCTAAATATGGTATTACTATTCATAGTGGTCTTGG 3 131 1 ATTATATTAA 0.795465 -470 TATTTAATTGAGAATAGTAGCTTAATTGAAACCTTACTAAA 3 232 0 AATAAATTAA 0.836541 -369 AAGAAAAAAAAATTGCATAATCTTATAAATACTAAGACCCA 4 86 1 ATTATATAAA 0.935333 -398 TGAAAAACGAACATGCATATGTTAATTAACGCTTTACAAAC 4 165 1 AATAAATTAG 0.807823 -319 ATAAATACATAGTATGATATTTAAATAGATGACA 5 4 0 ATTAAATAAG 0.958447 -355 AAATAGGAAAAGAAAAATATTTTAATACAAACTATCATTTA 5 167 1 AATAAATAAA 0.950083 -192 CCGGAATTATATACATTTACATGTATATAGAGAAGAAAGCT 6 86 0 AATATATAAA 0.907434 -515 CCTAAAATAGATTTAAATAATCGAATAAACGGTTTGTTCTT 6 247 0 ATTAAATAAG 0.958435 -354 GGCCAAGCCCACTAAATTCAGTGAATACAAACAGCTAAGGA 6 461 0 ATTCAATAAA 0.791621 -140 * * ** **** * * Masking position 15 Map Score: 6.97462 Number of sites scoring better than the average of aligned sites = 1158 Number in coding regions = 316 Number in noncoding regions = 842 Number of orfs with sites within 600 bp upstream = 472 Fraction of orfs with sites within 600 bp upstream = 0.0758111 Motif number 3 GTTTCCAATTTCGCAACCTTTATTATAGTA 1 289 1 TCGCAACCTT 0.986896 -35 TCTTACGACCACGCAACCTGACCTCTTCGA 2 41 0 ACGCAACCTG 0.986634 -260 TATCAAAGTATCGCAGCCTGGAAACAGAAT 3 515 1 TCGCAGCCTG 0.995985 -86 AGGTTGTTTTTCCCAGCCTGCATACAATGA 5 240 0 TCCCAGCCTG 0.992346 -119 GTATTACTTGTCCCAACCTCATTCCTCTTT 6 174 0 TCCCAACCTC 0.990772 -427 TTGTTTTCACTCGCAACCTCTCTACCTTCG 6 291 0 TCGCAACCTC 0.995155 -310 ********** Masking position 5 Map Score: 7.59674 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 23 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 CTAGAATTAATAAACTCATAGCCATGGCTA 1 81 0 TAAACTCATA 0.891001 -243 ACTCCGGGGAAAAACTCCTATTCTTCCGCA 1 129 0 AAAACTCCTA 0.8772 -195 GAGCGCTGAAGAAACACATGACGACGTGAA 1 159 1 GAAACACATG 0.97776 -165 ACGACGTGAAAAAACACTTGTTTGATCCAG 1 179 1 AAAACACTTG 0.832418 -145 TTTAGCTTTTGAAACTCATGTTTTCTATTG 3 113 0 GAAACTCATG 0.988209 -488 TACAAGATTTGAAACTCATAATATCATTCT 4 274 0 GAAACTCATA 0.977095 -210 TTATGAATGAGAACCTCATGATTGTAAACG 5 41 1 GAACCTCATG 0.951414 -318 CGTCACTCATAAAACACATGCAAGTATTAG 5 133 0 AAAACACATG 0.965179 -226 TAAGGACGTCAAAACTCAGAGTCGGGTAAT 6 437 0 AAAACTCAGA 0.862708 -164 ********** Masking position 3 Map Score: 3.93783 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 341 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 CGCAGAGAGTATACAGTGCATACTAGAATTA 1 102 0 ATACAGGCAT 0.840271 -222 ATAAGGCGTTAAGAAGAGTATACATATGCAT 3 181 0 AAGAAGGTAT 0.966778 -420 AACCTTACTAAAAAAGTGTATGGTTACATAA 3 213 0 AAAAAGGTAT 0.964069 -388 TCTACTGCACAAGAAGGGAATACAGCAAGAA 3 548 1 AAGAAGGAAT 0.953075 -53 CGTCCTATTAATGAAGTGAATGTTCTTGCTG 3 570 0 ATGAAGGAAT 0.849382 -31 ACCAAGAAAAAAAAATTGCATAATCTTATAA 4 83 1 AAAAATGCAT 0.857186 -401 AACGCTTTACAAACAGAGCATAATTATTGTT 4 192 1 AAACAGGCAT 0.971019 -292 GAAGAAAATGAAAAAGAGCATTTCAATAAAT 5 203 0 AAAAAGGCAT 0.985656 -156 TTGCCACAACCAGAAGAGCATAACATATTGT 5 337 1 CAGAAGGCAT 0.939494 -22 GAAGGTGGTGAAAGAGGGTATCACATATAAG 6 219 1 AAAGAGGTAT 0.877071 -382 ****** **** Masking position 5 Map Score: 4.36589 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 591 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 6 AACTGTAACGTTCCTAGTGCTTCTTTGACC 1 239 0 TTCCTAGTGC 0.907246 -85 GACTAGCAAATTCCAACTGTAACGTTCCTA 1 253 0 TTCCAACTGT 0.911167 -71 TCAATCGAGTTTCCAATTTCGCAACCTTTA 1 281 1 TTCCAATTTC 0.936968 -43 CCATCTAATCCTCCAACTTCAATAGGCCTT 3 289 0 CTCCAACTTC 0.936578 -312 TTTGAACGATCTCCTATTTCCTCGCACATT 3 464 0 CTCCTATTTC 0.877301 -137 AAAGAACACTTTCCCAATGACTAAGCGTTA 4 349 1 TTCCCAATGA 0.887352 -135 TTTGCTCAGCTTCCCACTGCACTTAAAAAA 4 453 1 TTCCCACTGC 0.986136 -31 TATTTTTCTTTTCCTATTTATTTCGTCACT 5 156 0 TTCCTATTTA 0.789094 -203 ACCTTGCAATCTCCCAATGTGAAAAAAAAA 5 266 1 CTCCCAATGT 0.774934 -93 GCAACTGCCTTTCCCACTTCAGGTATGTTC 5 311 0 TTCCCACTTC 0.973957 -48 ACGCTGTCAGTTCCAATTGAGAAATATCGT 6 333 0 TTCCAATTGA 0.902591 -268 ********** Masking position 6 Map Score: 2.89698 Number of sites scoring better than the average of aligned sites = 1341 Number in coding regions = 1100 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 7 TATAACTATTGAAAAATATCGATATTCACAA 1 40 1 GAAAATATCG 0.977982 -284 ACCAAAGACAGCAAACAATCGAAAAGTGGAC 2 272 1 GCAAAAATCG 0.980172 -29 AGTTTCAAAAGCTAAATATGGTATTACTATT 3 127 1 GCTAATATGG 0.935482 -474 GTATTGGGTATCAAAGTATCGCAGCCTGGAA 3 507 1 TCAAATATCG 0.926949 -94 AACGTCGTTGGCAAATAATGGCCTCGATTAA 4 27 0 GCAAAAATGG 0.968135 -457 AAAAGGGTCTGAAAACCATCGATCATATTGC 4 133 1 GAAAACATCG 0.942 -351 AGTTCCAATTGAGAAATATCGTAAAGAAAGT 6 324 0 GAGAATATCG 0.931822 -277 GCAATCAGTAGCAAAATATGGACTTTAACGC 6 359 0 GCAAATATGG 0.985826 -242 ***** ***** Masking position 5 Map Score: 2.91923 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 259 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 GCTATGAGTTTATTAATTCTAGTATGCACTGT 1 89 1 TATTAATCTG 0.831202 -235 GCTAGGATAATATAAATGCTAGCGTACTGCCT 2 78 1 TATAAATCTG 0.97222 -223 TGTACGTTAATATAAATTATAGATACATATTA 2 125 0 TATAAATATG 0.969971 -176 ATTTAGGTTAATTAAATTATAAAAAAATATAA 3 52 0 ATTAAATATA 0.633307 -549 TGCATAATCTTATAAATACTAAGACCCATTAT 4 99 1 TATAAATCTA 0.858154 -385 TTCAGACCCTTTTAAATAATGGGTCTTAGTAT 4 114 0 TTTAAATATG 0.956643 -370 AGAGCATTTCAATAAATGATAGTTTGTATTAA 5 188 0 AATAAATATG 0.936007 -171 CATTTTCTTCATTAAATCATTGTATGCAGGCT 5 224 1 ATTAAATATG 0.909014 -135 CTAAAATAGATTTAAATAATCGAATAAACGGT 6 255 0 TTTAAATATG 0.956643 -346 ATATTAGCAGTATAAAATCTCGAAAAAGTATG 6 523 0 TATAAAACTG 0.831206 -78 ******* ** * Masking position 6 Map Score: 1.83842 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 320 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 9 TTTATACCTCAGCTGGATCAAACAAGTGTTTTT 1 188 0 AGCTGGACAC 0.987539 -136 TACTGCTCTGAGCTAGATAAGGCCTATTGAAGT 3 271 1 AGCTAGAAAC 0.979382 -330 AAGGGAATACAGCAAGAACATTCACTTCATTAA 3 561 1 AGCAAGACAC 0.980545 -40 GTTTATTCATAGCTGAAGAATTCTTTTCACCAA 4 55 1 AGCTGAAAAC 0.917248 -429 CAGTAAGAAAAACTAGAAAATACGGTCCTAATA 5 106 1 AACTAGAAAC 0.952988 -253 AAAGAAACTATACCACCCACGCATCCAA 6 6 1 AACTATACAC 0.860351 -595 TGTTGTTCGTAGCAGGACCACACTTCCGGAATT 6 119 0 AGCAGGACAC 0.972888 -482 GATAACACCAAAGAAAAGCAATCAGTAGCAAAA 6 374 0 AAGAAAACAC 0.653373 -227 TTTTCTCTTAAGGTAGATAACACCAAAGAAAAG 6 389 0 AGGTAGAAAC 0.927016 -212 TGAGAATTACAACTAAATCATACTTTTTCGAGA 6 505 1 AACTAAACAC 0.939642 -96 ******* ** * Masking position 7 Map Score: 2.22713 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 572 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 TTCAATAGTTATATACATGTATACATGGTG 1 23 0 ATATACATGT 0.972911 -301 AAGAGTATACATATGCATTATTCATTACCA 3 169 0 ATATGCATTA 0.918172 -432 AAGGTAAGTGATATGCATGAATGGGAATAG 3 355 0 ATATGCATGA 0.966175 -246 GTTAATTAACATATGCATGTTCGTTTTTCA 4 165 0 ATATGCATGT 0.871059 -319 TTTCTTCTCTATATACATGTAAATGTATAT 6 89 1 ATATACATGT 0.972911 -512 TTCCGGAATTATATACATTTACATGTATAT 6 99 0 ATATACATTT 0.931686 -502 ********** Masking position 4 Map Score: 4.63462 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 54 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 GCACTGTATACTCTCTGCGGAAGAATAGGAG 1 114 1 CTCTCTCGGA 0.904432 -210 TTCTTCAGCGCTCACTCCGGGGAAAAACTCC 1 141 0 CTCACTCGGG 0.986479 -183 TAAATGCTAGCGTACTGCCTGTATATCGCTG 2 90 1 CGTACTCCTG 0.875559 -211 CATCGCGATTCTGTCTTCCGGGTATCGCTCC 3 430 1 CTGTCTCCGG 0.975397 -171 TGGGTACGAACTCACTTCCTGCAGCTTAGTT 4 416 1 CTCACTCCTG 0.987747 -68 ATCTATTACCCGCTCGCCCGGTCGTTTGGAT 6 33 0 CGCTCGCCGG 0.973586 -568 GTAGCAGGACCACACTTCCGGAATTATATAC 6 113 0 CACACTCCGG 0.980723 -488 CACTCGCAACCTCTCTACCTTCGTGGCCTAA 6 283 0 CTCTCTCCTT 0.91271 -318 ****** **** Masking position 5 Map Score: 0.22016 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 219 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 12 ********** No masking Map Score: -5.96613e-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: -5.96613e-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: -5.96613e-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