AlignACE version 2.2 July 7, 1998 AlignACE -jAPG.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 YBR128C 300 bp YBR128C APG14 1-1035 required for autophagy #2 YBR217W 300 bp YBR217W APG12 1-561 autophagy #3 YGL180W 600 bp YGL180W APG1 1-2694 Protein kinase #4 YHR171W 327 bp YHR171W APG7 1-1893 autophagy #5 YPL149W 416 bp YPL149W APG5 1-885 involved in autophagy #6 YPR185W 563 bp YPR185W APG13 1-2217 Autophagy Motif number 1 CGGCCTTTAATTTTTTTCTTATCAAAATTCCA 1 31 0 TTTTTTTTAT 0.96665 -270 TCATTGGCATTGCTTATATATTTTCGGCCTTT 1 55 0 TGTTATTATT 0.539862 -246 GAATATGTATTGACTTTTTTTTTCTTTGTACT 1 88 1 TGCTTTTTTT 0.881086 -213 ATGTCTAGGGTGATTTTCTTTTTCAGTGTTTA 2 102 1 TGTTTTTTTT 0.963053 -199 TTCAAGCATCTGTTTTTCTTTTTAACCGCTCG 3 106 1 TGTTTTTTTT 0.963053 -495 CCTGATCGTACTATTTTTTTTTAGCTTTTTAT 3 288 1 CTTTTTTTTT 0.954494 -313 TTTTTTTAGCTTTTTATTTTTTAGGCCGAGGT 3 303 1 TTTTATTTTT 0.851808 -298 ATATTATATGTTATTTTATTATGGGTACTATT 3 461 0 TTTTTTTTAT 0.96665 -140 CTTTGCCTTATGTTTTTATTATATTATATGTT 3 481 0 TGTTTTTTAT 0.959614 -120 TTTAAACTTCCGCTTTTTTAATCCATGAGATT 4 185 1 CGTTTTTAAT 0.796034 -143 GTTCCCTTAATTTTTTTGTTTTGCGTGCCGGA 4 232 0 TTTTTTTTTT 0.969509 -96 TTTATTCTTGATTATCTTATATTTGTTGAA 4 308 0 TGTTATTTAT 0.811159 -20 AATTTTAAAGCTTTTTTATTATACCGCAATAT 5 85 0 CTTTTTTTAT 0.950299 -332 AAAAGTCGGGTTTCTTTATAATTTTAAAGCTT 5 104 0 TTCTTTTAAT 0.672289 -313 ACAGATGCCATTATTTTTTTATAATATAATTA 5 144 0 TTTTTTTTAT 0.96665 -273 ATTAAGCTCACTTTTTTCTAATGATCGAAGTT 5 187 1 CTTTTTTAAT 0.826412 -230 GCGAATGAATTTTTGTTCTTTTGGTTCTAGAA 5 365 1 TTTGTTTTTT 0.854728 -52 CGATTTTTATTTGTTTTATTATCAATAGAGAT 6 123 0 TTTTTTTTAT 0.96665 -441 TTCCCTTTATTTCTTTTATTTTCGTTTTCGCT 6 193 0 TTTTTTTTTT 0.969509 -371 AATTCGATATCTTTGTTGTTTTGTTTAATTCG 6 342 1 CTTGTTTTTT 0.795134 -222 GCTGTATGTTCTGCTTTCTTTTCAAGACTTGA 6 522 0 CTCTTTTTTT 0.856369 -42 ** **** **** Masking position 7 Map Score: 23.9327 Number of sites scoring better than the average of aligned sites = 9932 Number in coding regions = 1731 Number in noncoding regions = 8201 Number of orfs with sites within 600 bp upstream = 2124 Fraction of orfs with sites within 600 bp upstream = 0.34115 Motif number 2 TATTTTCGGCCTTTAATTTTTTTCTTATCAA 1 38 0 CTTAATTTTT 0.785636 -263 ATTGGCATTGCTTATATATTTTCGGCCTTTA 1 54 0 CTATATATTT 0.754939 -247 ATTGACTTTTTTTTTCTTTGTACTATTAAAT 1 96 1 TTTTCTTTGT 0.913231 -205 AAAAACTATTTATTTATTTGTATTTTAATGA 1 160 1 TTTTATTTGT 0.967457 -141 TCTTTTTCAGTGTTTATTTGTTAATAATGTT 2 118 1 TTTTATTTGT 0.967457 -183 CGGCAATTAGTCTTTATTTTTTTCCTTTACA 2 152 1 TTTTATTTTT 0.936945 -149 TAGGGATGTACGTTTATTTCTTCAGCTCAAG 2 244 0 CTTTATTTCT 0.940707 -57 CAAGCATCTGTTTTTCTTTTTAACCGCTCGG 3 108 1 TTTTCTTTTT 0.840271 -493 GAGCTTATATTATTAATATCTTCCTGATCGT 3 266 1 TTTAATATCT 0.565075 -335 TTTTTTTAGCTTTTTATTTTTTAGGCCGAGG 3 303 1 TTTTATTTTT 0.936945 -298 ACGATTGTATTATATCTTTTTATCTTCTATA 3 427 0 TTATCTTTTT 0.740621 -174 TTTCTTAATTTCTCGTCTGGTGT 3 588 0 TTTAATTTCT 0.780902 -13 ATTTTACATCCATATATATGTATATAGATAA 4 68 0 CTATATATGT 0.860401 -260 CAAGCAAGATTTTTCATTTGTAGAGCTCTTA 4 145 1 TTTCATTTGT 0.759176 -183 TAATGAGTTCCCTTAATTTTTTTGTTTTGCG 4 239 0 CTTAATTTTT 0.785636 -89 TCTTGATTATCTTATATTTGTTGAAATATAA 4 302 0 CTATATTTGT 0.944158 -26 AAGGAAGTTGTCTATATATGTACATATGGAT 5 56 1 TTATATATGT 0.854696 -361 CCCGCTAATACTTTTATTTCTGTTCAACTAT 6 54 1 CTTTATTTCT 0.940707 -510 TATGTAAATATATATATATGTATATATAGTT 6 79 0 TTATATATGT 0.854696 -485 AAATATACGATTTTTATTTGTTTTATTATCA 6 131 0 TTTTATTTGT 0.967457 -433 AAATAAAAATCGTATATTTTTGTATATGTAT 6 143 1 CTATATTTTT 0.894191 -421 ACGTGTGTTCCCTTTATTTCTTTTATTTTCG 6 201 0 CTTTATTTCT 0.940707 -363 GAATTCGTTCTATATCTATGTGAGGTAACGA 6 454 0 TTATCTATGT 0.675583 -110 * ********* Masking position 7 Map Score: 23.3601 Number of sites scoring better than the average of aligned sites = 3286 Number in coding regions = 1540 Number in noncoding regions = 1746 Number of orfs with sites within 600 bp upstream = 1138 Fraction of orfs with sites within 600 bp upstream = 0.182782 Motif number 3 GATAATAAGCACTTTTTTCCTCGCTGAAAA 1 189 1 ACTTTTTTCC 0.937752 -112 CTAGGATTCTAGTTTTTAACTTTTACTTCC 1 275 0 AGTTTTTAAC 0.946956 -26 CCTCCTTCTGAGTTTTGAACGCATCAGTAA 2 19 1 AGTTTTGAAC 0.927065 -282 ATTAGTCTTTATTTTTTTCCTTTACATTGT 2 157 1 ATTTTTTTCC 0.791305 -144 TTGCCTATCTAGTTTTCAACATGTGGTGGC 4 118 0 AGTTTTCAAC 0.825835 -210 TATTTTTTGCCGTTTTTACCAGTTACTCTG 5 22 0 CGTTTTTACC 0.96947 -395 TAATGATCGAAGTTTTGTCCGGTTATCCAA 5 205 1 AGTTTTGTCC 0.960279 -212 ATTATCATCACCTTTTTTACACTAAATAAT 5 315 1 CCTTTTTTAC 0.881056 -102 TTGAACGGTCCCTTTTTGCCACCCGCTAAT 6 33 1 CCTTTTTGCC 0.837435 -531 TGCTCTGACGCGTTTTGTCCCCCTTGGTTG 6 250 0 CGTTTTGTCC 0.957643 -314 CTAAGATCTAAGTTTTTAACTAAGTGAGCA 6 374 1 AGTTTTTAAC 0.946956 -190 ********** Masking position 5 Map Score: 6.29235 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 620 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 4 ACCAAATACAAAAGTGATTAGAAGGATAACGAGT 1 231 1 AGTGATGAAG 0.839895 -70 GATTAGAAGGATAACGAGTAGAGAAAAAGGGAAG 1 246 1 AACGAGGAGA 0.910941 -55 AAAAAAAAATAGTACGATCAGGAAGATATTAATA 3 276 0 AACGATGGAA 0.898269 -325 ACATAAGGCAAAGGAGATAGGAGAATAATCATTG 3 500 1 AGAGATGAGA 0.966967 -101 TGGTGTTGTAAAAGAGATTTGAAAATATGGGGTA 3 560 0 AGAGATGAAA 0.98126 -41 TGGCAAGAACATCGCGAGGCGGAGCTAAACACAG 5 238 1 AGCGAGGGAG 0.946606 -179 GAATTTTTGTAGCGCGATGAGAAACATAACGCCT 5 271 1 AGCGATGAAA 0.979988 -146 TTCTAGAAGAACGGAGATAGGAAACCTATGATGT 5 389 1 AGAGATGAAA 0.98126 -28 TTTATTATCAATAGAGATAGGGAGGTAAAAATAT 6 107 0 AGAGATGGAG 0.942413 -457 CGTTTTGAGGAGCGAGAGCGAAAACGAAAATAAA 6 177 1 AGAGAGAAAA 0.813161 -387 AACGCGTCAGAGCAAGAGGTGAAAGGGTTGCCAC 6 266 1 AAAGAGGAAA 0.951372 -298 CGGCAGTTACAGAAAGAGGCGAGAAGTAGAAACA 6 405 1 AAAGAGGAGA 0.916229 -159 * ***** **** Masking position 7 Map Score: 5.40465 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 662 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 317 Fraction of orfs with sites within 600 bp upstream = 0.0509155 Motif number 5 TTCTAATCACTTTTGTATTTGGTCCTTTCCCTTAATTT 1 216 0 TTATGTCCTT 0.960783 -85 AAAAAGTATGTCATCAATTGGTTCCATTAGTGTCTGAG 2 53 1 TAATGTCCTT 0.979269 -248 CGGGCATCCTTCATAAGTACGATTCTTTAAATTTGACA 2 184 0 TAGTGTTCTT 0.975372 -117 AGTAATAGTTACTCCGATAAGATTCATTACAGATACAC 3 28 0 ATATGTTCTT 0.844768 -573 TGAATACGAATGATATGCTTGCTTCTTTAACGGTATGG 3 72 0 TAGCGTTCTT 0.961246 -529 AGCTCCTTTATGAGATGCTCGATTCCTTTTGTTGCCAA 3 233 0 TAGCGTTCTT 0.961248 -368 GGAAGATATTAATAATATAAGCTCCTTTATGAGATGCT 3 252 0 ATATGTCCTT 0.896967 -349 TCCGCTTTTTTAATCCATGAGATTCCTTTGGACACCCT 4 193 1 TAATGTTCTT 0.967226 -135 GTAGCATCGTAAAATAATGAGTTCCCTTAATTTTTTTG 4 246 0 AAATGTCCTT 0.943798 -82 TTATATGTGATAAAAGTCGGGTTTCTTTATAATTTTAA 5 109 0 TATCGTTCTT 0.793228 -308 AAAGCATAAATTAATTGAACGGTCCCTTTTTGCCACCC 6 19 1 TAGAGTCCTT 0.909032 -545 TGTCCTTCACTTTCACGTGTGTTCCCTTTATTTCTTTT 6 208 0 TTGTGTCCTT 0.970482 -356 * * ** * *** ** Masking position 13 Map Score: 5.66839 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 385 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 6 AAAAAAGTCAATACATATTCATCATTGGCA 1 78 0 ATACATATTC 0.877694 -223 CTTTTTGAGGTTACTGATGCGTTCAAAACT 2 29 0 TTACTGATGC 0.880239 -272 ATAAGATTCATTACAGATACACGAAACGAA 3 20 0 TTACAGATAC 0.936158 -581 TTAAAAAGAAAAACAGATGCTTGAATACGA 3 101 0 AAACAGATGC 0.958778 -500 TACAAATCACAAACTGATGCTGATGGGGGA 3 159 0 AAACTGATGC 0.880239 -442 GTTTATCTATATACATATATATGGATGTAA 4 66 1 ATACATATAT 0.820417 -262 TCGCGAGTTCATACAGATGCCATTATTTTT 5 158 0 ATACAGATGC 0.986595 -259 TCAACTATATATACATATATATATATTTAC 6 77 1 ATACATATAT 0.820417 -487 CAAAACGATAATACATATACAAAAATATAC 6 154 0 ATACATATAC 0.95925 -410 ********** Masking position 7 Map Score: 2.56152 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 587 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 7 GTTTGACAGAAAGCTACTTGAGCTGAAGAAATAAA 2 228 1 AATATGAGCG 0.981421 -73 CATATATATGTATATAGATAAACTGAAATGCTAGT 4 54 0 TATATAAACG 0.964848 -274 TAATGAACTTTAGTTATCTAAGTAGCATCGTAAAA 4 270 0 TATATAAGTG 0.811299 -58 GCTAAAGCATAAATTAATTGAACGGTCCCTTTTTG 6 16 1 AATATGAACG 0.977663 -548 TATATATGTATATATAGTTGAACAGAAATAAAAGT 6 63 0 TATATGAACG 0.990159 -501 GGTTGCCACGTACGTATTTGAACCGGAGTGAGCCG 6 291 1 TATATGAACG 0.990159 -273 TCTAAGTTTTTAACTAAGTGAGCAGCGGCAGTTAC 6 380 1 TATATGAGCG 0.991836 -184 ** ** ***** * Masking position 6 Map Score: 1.75054 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 69 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TATATAAGCAATGCCAATGATGAATATGTA 1 67 1 ATGCCAATGA 0.960496 -234 TTAAAGAATCGTACTTATGAAGGATGCCCG 2 192 1 GTACTTATGA 0.867858 -109 ACAGTAGAGTGAACCAATGACAGT 2 287 1 GAACCAATGA 0.961438 -14 AGATGCTTGAATACGAATGATATGCTTGCT 3 87 0 ATACGAATGA 0.947693 -514 TTTTGTGGAGATATCAATGATTATTCTCCT 3 518 0 ATATCAATGA 0.827431 -83 ATGCTCAGAAGTGCGAATGAATTTTTGTTC 5 353 1 GTGCGAATGA 0.942108 -64 CGGAGATAGGAAACCTATGATGTAAGT 5 400 1 AAACCTATGA 0.907393 -17 AATGTATTTGGTACCTATGAATTCGTTCTA 6 473 0 GTACCTATGA 0.976987 -91 ********** Masking position 7 Map Score: 1.53996 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 581 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 CGTGTAATTGTTTTCCTTACGTCTAGTTAAAAA 1 131 1 TTTCTTACTC 0.960357 -170 TATTTGGTCCTTTCCCTTAATTTTCAGCGAGGA 1 206 0 TTTCTTAATT 0.846703 -95 GTTTTTAACTTTTACTTCCCTTTTTCTCTACTC 1 261 0 TTTCTCCCTT 0.974768 -40 TCTTTATTTTTTTCCTTTACATTGTCAAATTTA 2 162 1 TTTCTTACTT 0.98256 -139 AGAACGCCACATTTCATCACCTTTAAGTTAAGT 3 342 1 ATTCTCACTT 0.926698 -259 TCCTATCTCCTTTGCCTTATGTTTTTATTATAT 3 489 0 TTTCTTATTT 0.846703 -112 TTTAGATAAATTATCATCACCTTTTTTACACTA 5 306 1 TTACTCACTT 0.926698 -111 TTTACATATTTTTACCTCCCTATCTCTATTGAT 6 102 1 TTTCTCCCAT 0.844621 -462 TGGTTGGTGCTGTCCTTCACTTTCACGTGTGTT 6 223 0 TGTCTCACTT 0.949334 -341 GGTGTATAGATTTTCGTTACCTCACATAGATAT 6 441 1 TTTCTTACTC 0.960357 -123 *** * **** ** Masking position 7 Map Score: 1.04181 Number of sites scoring better than the average of aligned sites = 1778 Number in coding regions = 1140 Number in noncoding regions = 638 Number of orfs with sites within 600 bp upstream = 473 Fraction of orfs with sites within 600 bp upstream = 0.0759717 Motif number 10 CGATACTCAGACACTAATGGAACCAATTGAT 2 65 0 ACACAATGGA 0.864435 -236 CATTACAGATACACGAAACGAACAAGGAAAA 3 11 0 ACACAAACGA 0.989835 -590 CTTTTGTTGCCAACTAAATGACGCTTAGAAT 3 215 0 CAACAAATGA 0.837654 -386 ATTTAGTTGGCAACAAAAGGAATCGAGCATC 3 227 1 CAACAAAGGA 0.920795 -374 ATTGATATCTCCACAAAACGAATTTGAAGCT 3 530 1 CCACAAACGA 0.989139 -71 CTCTTTTACAACACCAGACGAGAAATTAAGA 3 578 1 ACACAGACGA 0.94829 -23 AAAAACACCAAAGAATGGAGAGTAG 4 5 1 ACACAAAGAA 0.948554 -323 CCTTTCCGGCACGCAAAACAAAAAAATTAAG 4 228 1 ACGCAAACAA 0.881815 -100 CACCTTTTTTACACTAAATAATGAAGTAGCA 5 323 1 ACACAAATAA 0.891106 -94 CGCTCTCGCTCCTCAAAACGATAATACATAT 6 166 0 CCTCAAACGA 0.927612 -398 TTAGCGAATTAAACAAAACAACAAAGATATC 6 347 0 AAACAAACAA 0.898604 -217 **** ****** Masking position 6 Map Score: 5.26033 Number of sites scoring better than the average of aligned sites = 885 Number in coding regions = 638 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 11 ********** No masking Map Score: -2.42052e-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 12 ********** No masking Map Score: -2.42052e-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: -2.42052e-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