AlignACE version 2.2 July 7, 1998 AlignACE -jERP.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 YAL007C 485 bp YAL007C ERP2 1-648 p24 protein involved in membrane trafficking #2 YAR002C-A 300 bp YAR002C-A ERP1 1-660 p24 protein involved in membrane trafficking #3 YDL018C 600 bp YDL018C ERP3 1-678 p24 protein involved in membrane trafficking #4 YGL002W 342 bp YGL002W ERP6 1-651 p24 protein involved in membrane trafficking #5 YHR110W 300 bp YHR110W ERP5 1-639 p24 protein involved in membrane trafficking #6 YOR016C 327 bp YOR016C ERP4 1-624 p24 protein involved in membrane trafficking Motif number 1 TTCATAACGAAAAGAACCAGCTGATATACA 2 26 1 AAAGAACCAG 0.885532 -275 ATTCACGTACAAAAATAGAGAATATATAAA 2 126 0 AAAAATAGAG 0.848088 -175 GTTACCGTAAAAAAAAAACGAATCGCGTAA 2 170 1 AAAAAAAACG 0.858251 -131 AAGTTGAAAAAAAAAAACACATCAGCAGAA 2 201 1 AAAAAAACAC 0.686984 -100 ACTACAGAGGGAAGATAGAGTAAGTTTTGT 2 241 0 GAAGATAGAG 0.86922 -60 ACCATTAACAAAAAAAACCGCTCAGCAGGC 3 11 0 AAAAAAACCG 0.947142 -590 AGAGGTTTAAAAAAAAAGCGTCGTTCGTTG 3 317 1 AAAAAAAGCG 0.977567 -284 AGAGGATTATGAAGAACGCGTTCTGTTTTA 3 475 0 GAAGAACGCG 0.966456 -126 TTTCTTACCCGAAGAACGAGTTTCTAATTC 4 191 0 GAAGAACGAG 0.958098 -152 AGGCGATAAGGAAGAAAGCGCCAACAATCT 4 297 0 GAAGAAAGCG 0.981089 -46 AGTCATCCTGAAAGAAAGCCGCATATTGGC 5 65 0 AAAGAAAGCC 0.868217 -236 AGAGACAGTGGAAAAACGCGTCAGATTGTT 5 170 0 GAAAAACGCG 0.967118 -131 CGTTTGAGACAAAAAAAGAGGAGCTTTGTA 5 221 1 AAAAAAAGAG 0.971898 -80 TGAGAGAGCACAAAAAAGAGCCAAACGCTA 6 35 0 CAAAAAAGAG 0.936991 -293 AGGAAACAGTGAAAAAAAAGTAGTCCATAA 6 139 0 GAAAAAAAAG 0.853799 -189 TATATCACGTCAAAAAACAGGAAACAGTGA 6 157 0 CAAAAAACAG 0.859444 -171 ********** Masking position 5 Map Score: 14.778 Number of sites scoring better than the average of aligned sites = 3174 Number in coding regions = 1909 Number in noncoding regions = 1265 Number of orfs with sites within 600 bp upstream = 1043 Fraction of orfs with sites within 600 bp upstream = 0.167523 Motif number 2 TTCAAGAAAATGTTCATAAACTTTCATAAAGCAATCCTC 1 203 1 TTCAAACCAA 0.96465 -283 TTCAGCGACGTGTCCCGAAACACGAAAAAGTACATTCTG 1 306 1 TTCAAACAAA 0.987459 -180 AAAAGTACATTCTGCCAAAACTTGAACTAGTTAAAATGA 1 331 1 TTCAAACAAA 0.987459 -155 TCTGCATCAGGTGACCCAAACTAGAATAAGATAAACAGT 1 430 1 GGCAAACAAA 0.944986 -56 AACCAGCTGATATACACAAACTAAAAGGACTCGGTCTCG 2 40 1 TTCAAACAAA 0.987459 -261 TCGTTTTTTTTTTACGGTAACAGAATACAGAATAAATTC 2 152 0 TTCTAACATA 0.838424 -149 CCCTGGGGCGTCTTCTTGAACGGCATCAATTTAGTGAGT 3 81 0 TTCGAACATA 0.884935 -520 AAGGCGTTTATCGAGCTAAACGGGAAGTAATTTTACTCT 3 179 1 TGGAAACAAA 0.906542 -422 CATACTGATACGTTCGTAAACTTTATCAACGAACGACGC 3 334 0 CTCAAACATA 0.884935 -267 TTCTTCCTTATCGCCTCAATCTGAAAGGATCTAGATTTG 4 311 1 TGCAATCAAA 0.913531 -32 TCCTCTTTTTTTGTCTCAAACGGAAAAGAATAAAACGCG 5 204 0 TGCAAACAAA 0.989155 -97 ACCAACGGCATTGACGGAAACGCGCTTTATTATGGACTA 6 110 1 TGCAAACCTA 0.942514 -218 * * * **** ** * Masking position 9 Map Score: 4.75478 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 376 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 GACCAGCAGAAGGGAACCAATATCACGAC 1 1 0 AGCAATTCAC 0.993785 -485 AGATCCGCCAAGGAAGCCACTCTGTGAACTTTAAATAAT 1 109 1 AGCACTTGAC 0.976997 -377 AAGTATTTAAAGGTAACCAATCTCTCTACTAATC 2 277 1 AGCAATTCAC 0.993785 -24 GAAAGAATTTGGGGGGACAATATCTTGACAGAAACTGGT 3 512 1 GGCAATTCAC 0.993528 -89 TTCTTCGGGTAAGAAACCAATATCGACACAACAAGATAT 4 205 1 AGCAATTCAC 0.993785 -138 AAGGAAGAAAGCGCCAACAATCTGTTCACAACCTCACCA 4 281 0 GGCAATTGAC 0.993401 -62 GCTTTCTTTCAGGATGACTAGATGAGTACCACTTACGAT 5 76 1 AGCTAGTGAC 0.939572 -225 TTGACGATCTGAGAATTCTATTTGGGAACTCTTCTCTGC 6 202 1 GGCTATTGAC 0.982871 -126 * * **** ** ** Masking position 18 Map Score: 4.49949 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 114 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AGCAGAAGGGAACCAATATCACGAC 1 6 0 AACCAATATC 0.972103 -480 ATTGAAATATAACCAAACGCCATCATGTAA 1 272 0 AACCAAACGC 0.988625 -214 GTAAAAAAAAAACGAATCGCGTAATAAGTT 2 176 1 AACGAATCGC 0.973809 -125 ATTTAAAGGTAACCAATCTCTCTACTAATC 2 281 1 AACCAATCTC 0.990396 -20 TCGGGTAAGAAACCAATATCGACACAACAA 4 209 1 AACCAATATC 0.972103 -134 CACAAAAAAGAGCCAAACGCTACCTGATAC 6 27 0 AGCCAAACGC 0.969493 -301 ********** Masking position 5 Map Score: 3.66833 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 141 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 CTGTGAACTTTAAATAATATTACAAATTGCTACAGC 1 130 1 TAAAATCAAA 0.934597 -356 TTGAATTAAATAAATAAGTCTGAAAACACTTGAATT 1 172 0 TAAATTAAAA 0.974809 -314 AACCAGCTGATATACACAAACTAAAAGGACTCGGTC 2 40 1 TAAAACAAAA 0.826333 -261 CGTACAAAAATAGAGAATATATAAAATAATAGGTTG 2 115 0 TAAAAAAAAA 0.762492 -186 TGGTTACCTTTAAATACTTTTCCAAACTACAGAGGG 2 260 0 TAAATTCAAA 0.960375 -41 CAGGGCAAAGAAGACATAATTTAAAAGCTGACCGGG 3 115 1 AAAAATAAAA 0.900871 -486 GCCTTAGGCCTACATAAATCTTAAACATTTGTCCCC 3 148 0 TAAATTAAAC 0.879335 -453 AACATGCTTATATAGAGGTTTAAAAAAAAAGCGTCG 3 304 1 TAAATTAAAA 0.974808 -297 TTAATAAAGAAACAAATATGTAAAAATATAATATAA 6 75 0 AAAATTAAAA 0.939075 -253 GCAGCTGGGAAATAAATGTCTTCAAAGCAGAGAAGA 6 231 0 AAAATTCAAA 0.906137 -97 TGATTGGGAATATATATTTATGAAAAAACTTCACTA 6 290 0 TAAATTAAAA 0.974792 -38 ** * * * * **** Masking position 6 Map Score: 2.16881 Number of sites scoring better than the average of aligned sites = 1262 Number in coding regions = 604 Number in noncoding regions = 658 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 6 TCCCTTCTGCTGGTCTTCGAGGAAAATTTCTG 1 25 1 TGGTTCGAGG 0.961561 -461 CACAGAGTGGCTTCCTTGGCGGATCTGAAAAA 1 103 0 CTTTTGGCGG 0.613645 -383 CTGAAAACACTTGAATTCGAGATGCTGTAGCA 1 157 0 TTGTTCGAGA 0.929601 -329 GACTTATTTATTTAATTCAAGAAAATGTTCAT 1 188 1 TTTTTCAAGA 0.852945 -298 GATCTTCCCCTGGGGTTCAAGAGTCGAGACCG 2 71 0 TGGTTCAAGA 0.970957 -230 ACTAAATTGATGCCGTTCAAGAAGACGCCCCA 3 85 1 TGCTTCAAGA 0.829284 -516 GGTGTAGCCCTGGTTTTGAAGATAATTAAGAA 3 254 0 TGGTTGAAGA 0.965554 -347 AGAACGCGTTCTGTTTTAAAGAGAGAAAAATT 3 461 0 CTGTTAAAGA 0.850359 -140 TGATAGTTACCGTACTTGAAGGGACACTGTGA 3 559 1 CGTTTGAAGG 0.92716 -42 TGACAAAAATCGGAGTTAGAGGATGAACCAAG 4 46 1 CGGTTAGAGG 0.887705 -297 GGTTTACTGATTTTTTTCAAGAAGAGGTAAGC 5 35 1 TTTTTCAAGA 0.852945 -266 TATTAACCAACGGCATTGACGGAAACGCGCTT 6 105 1 CGGTTGACGG 0.925748 -223 GAACTCTTCTCTGCTTTGAAGACATTTATTTC 6 227 1 CTGTTGAAGA 0.954194 -101 *** ******* Masking position 6 Map Score: 1.98404 Number of sites scoring better than the average of aligned sites = 2128 Number in coding regions = 1777 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 7 GTGATATTGGTTCCCTTCTGCTGGTCTTCGAGGAA 1 14 1 TTCCTTGCGT 0.985269 -472 TTTGGCAGAATGTACTTTTTCGTGTTTCGGGACAC 1 315 0 TGTCTTTCGT 0.957627 -171 GTTTTTCATTTTAACTAGTTCAAGTTTTGGCAGAA 1 340 0 TTACTTTCGT 0.975556 -146 ACTCCACTGTTTATCTTATTCTAGTTTGGGTCACC 1 439 0 TTACTTTCGT 0.975556 -47 TTTTTCCACTGTCTCTTTCTCGCGTTTTATTCTTT 5 184 1 GTCCTCTCGT 0.968503 -117 GGCTCTTTTTTGTGCTCTCTCAAGTGCCCTGTTTA 6 43 1 TGTCTCTCGT 0.956807 -285 CTACTTTTTTTTCACTGTTTCCTGTTTTTTGACGT 6 146 1 TTCCTTTCGT 0.991605 -182 ATGAAAAAACTTCACTAGCGCTCGTGAAACTACTT 6 272 0 TTCCTCGCGT 0.984975 -56 *** ** *** ** Masking position 6 Map Score: 2.34989 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 142 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 ATTTCGATTCATTAACCTTAGGGATCGACACCGCCAATTC 1 392 1 ATAATGGAAA 0.965011 -94 CAGAATACAGAATAAATTCACGTACAAAAATAGAGAATAT 2 131 0 AAAATGTAAA 0.895358 -170 GAAGATAATTAAGAATCTAATGGGGCAATGCTTGTGTAGA 3 229 0 AAAATGGGAG 0.963308 -372 TCCTCAATGAAAGAATTTGGGGGGACAATATCTTGACAGA 3 504 1 AAAATGGGAA 0.991179 -97 GCAACTAAATTTAGGATGAAGACTAGAAGGAA 4 3 1 AATATGGAAA 0.932244 -340 TGCGATGAAGAAGAACCTCATGGATTTACAATACCTTAGA 4 93 0 AAAATGGAAA 0.988672 -250 TGTGGGATAAAAAAACGTCGTGGAATTAGAAACTCGTTCT 4 169 1 AAAATGGAAA 0.988672 -174 ATATCGACACAACAAGATATGGGGTGTATAGTTAAAATCT 4 224 1 AAAATGGGAA 0.991179 -119 AAAAAAATCAGTAAACCTGCTGGGTGTATAATAAGAAAGA 5 12 0 GTAATGGGAA 0.892431 -289 ** ** * *** * * Masking position 8 Map Score: 2.40799 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 165 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 ATAAATAAGTCTGAAAACACTTGAATTCGA 1 169 0 CTGAAAACAC 0.879339 -317 AACATTAGCGCTAAGAGGATTGAGGATTGC 1 233 0 CTAAGAGGAT 0.939184 -253 TCCTGTAAAAGGATGTTCATAACG 2 5 1 GTAAAAGGAT 0.917882 -296 TATACACAAACTAAAAGGACTCGGTCTCGA 2 50 1 CTAAAAGGAC 0.970523 -251 ATTTCCCAAGCTAAAAACATGCTTATATAG 3 289 1 CTAAAAACAT 0.957854 -312 TCGCCTCAATCTGAAAGGATCTAGATTTGC 4 321 1 CTGAAAGGAT 0.970523 -22 GAAAGGACAACTAAAAACATTTATATACAA 5 116 0 CTAAAAACAT 0.957854 -185 TTCTTCTACATTAAAAGCATCACAAAGAAC 5 143 1 TTAAAAGCAT 0.882926 -158 ********** Masking position 6 Map Score: 1.11172 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 440 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 10 ********** No masking Map Score: -3.10975e-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 ********** No masking Map Score: -3.10975e-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: -3.10975e-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