AlignACE version 2.2 July 7, 1998 AlignACE -jPEP.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 YBL017C 600 bp YBL017C pep1 1-4740 carboxypeptidase Y sorting receptor in late Golgi\; Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain #2 YDR323C 405 bp YDR323C pep7 1-1548 cytosolic and peripheral membrane protein with three zinc fingers\; cysteine rich regions of amino acids are essential for function #3 YJL053W 300 bp YJL053W PEP8 1-1140 Vacuolar protein similar to mouse gene H58 #4 YLR148W 300 bp YLR148W pep3 1-2757 vacuolar membrane protein #5 YMR231W 403 bp YMR231W pep5 1-3090 peripheral vaculor membrane protein\; putative Zn-finger protein #6 YOR036W 300 bp YOR036W pep12 1-867 integral membrane protein\; c-terminal TMD\; located in endosome #7 YPL154C 600 bp YPL154C pep4 1-1218 vacuolar proteinase A Motif number 1 ATTTTACTTCAGAAAGATAAAAGAGTATGTGA 1 50 1 AGAAAAAAAA 0.940139 -551 GCACTAAACTAGAGGAAAGAAGGCTTAAAACA 1 285 0 AGAGGAGAAG 0.843626 -316 GAGTACGGCGAAAAGAAGGAAAAACCAAGGTC 1 340 1 AAAAGAGAAA 0.859039 -261 AGACCTCTCAAGAAGCACAAAAAAAGGAGGCG 1 414 1 AGAAGAAAAA 0.966885 -187 AGATCTTAGTAGAATGAAATAGTACCACCTAC 1 447 0 AGAATAATAG 0.862502 -154 GGCAAAATAAAAAAGGAAAAAGAGTACGGTAG 1 511 0 AAAAGAAAAG 0.900546 -90 AATGTATTCCTGAATTACAAAAGTACTGGCGA 2 215 1 TGAATAAAAA 0.71217 -191 GGAAAACAATAGAATAATGAAAACATATGATC 2 296 1 AGAATAGAAA 0.944307 -110 ATGTGATCCTAGAATCACGAAGCATATGTTTG 3 39 1 AGAATAGAAG 0.953817 -262 CAATACGAAGAGAATCAGAAAGCGCTGCGAGG 4 149 0 AGAATAAAAG 0.961822 -152 ATAGAACGAAAGAAATAAGAAGCTGCCATCCC 4 223 1 AGAAAAGAAG 0.940056 -78 TAAGGTACCAAGAAGTAAAAAGAGAAATATAG 4 272 1 AGAAGAAAAG 0.972651 -29 TACACATTGTAAAAGGAAATAAAGTGATAAAA 5 112 0 AAAAGAATAA 0.649241 -292 ATGCTTTTATAGAAGAATATAACGTAAATTAC 6 261 1 AGAAGAATAA 0.879081 -40 AATGAATTTTTGAATCAGAAAAAGAAGTTCTG 7 12 1 TGAATAAAAA 0.71217 -589 AGAAGTTCTGAAAAAAACATAATCCTGCTTGA 7 34 1 AAAAAAATAA 0.498901 -567 TTAAGGGAACAGAGTAAAGAAGTTTGGGTAAT 7 333 1 AGAGTAGAAG 0.792602 -268 GCTTCGCTCAAAAAAGAAGAAGGTGGAATGAA 7 378 0 AAAAAAGAAG 0.79971 -223 CTTCTCAAATAAAAATAGAAAAGACCACTAAA 7 424 0 AAAAAAAAAA 0.799945 -177 ACGTAAGGGAAGAATAACAAAAAGTATATCTC 7 462 1 AGAATAAAAA 0.953881 -139 CTATAAGAAAAGAAAAAAAAAAAGCCTAGTGA 7 533 1 AGAAAAAAAA 0.940139 -68 ***** * **** Masking position 7 Map Score: 18.0311 Number of sites scoring better than the average of aligned sites = 4832 Number in coding regions = 2626 Number in noncoding regions = 2206 Number of orfs with sites within 600 bp upstream = 1455 Fraction of orfs with sites within 600 bp upstream = 0.233697 Motif number 2 AATGAACACCAAAAGATGTGTGTAAGTTAAAAAGTCCGAACG 1 163 1 AAAATTTAAA 0.929006 -438 GTATATCTGGAAAAGCCCTGAAGTGTCCAGTAGTCATCACAC 1 566 1 AAAACTAAGA 0.915963 -35 TTCAGTTACAAAAAACTCTAATGGCGTTAGTACTTTATAGAA 2 80 1 AAAATTAAGA 0.984494 -326 GTGCATATATAAAAACTATTTCAACATGAGTAAAGGGAAATC 3 187 0 AAAATTTAGA 0.970528 -114 ACATATATATAAAATCTGTAAATATAATAAAATGTGTACATT 3 235 1 AAAATTAAAA 0.961876 -66 GAAATCGTTAAAAAATTCTTATAAGAGCAATACGAAGAGAAT 4 166 0 AAAATTAAAA 0.961876 -135 TTAACGATTTCAAAAATATCAAATCTATAGAACGAAAGAAAT 4 197 1 CAAATTAAGA 0.909208 -104 CTAGAAAAGTAAAAACTATAAGGTACCAAGAAGTAAAAAGAG 4 254 1 AAAATTAAGA 0.984494 -47 TAAAGTGATAAAAACTTATTTGATGCATAAAACCACATATAT 5 83 0 AAAATTTAAA 0.929006 -321 ACATCCTGAAAAAATAGATTACATTGTGAGTATTTTACAATA 5 145 0 AAAAGTAAGA 0.915963 -259 GAGCATGCACAAAACATGTCTGCATCGTAACACATCCTGAAA 5 176 0 AAAATTTAAA 0.929006 -228 TAGTTTAGATAAAACGTCTTCACTATTAAGTAGAAGATTCGT 6 104 1 AAAATTCAGA 0.936847 -197 TCTAATAGAAAAAACTTTTTATGAATACAGTAGGGTGAGATA 7 488 0 AAAATTAAGA 0.984494 -113 **** * * * ** * Masking position 4 Map Score: 9.47654 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 320 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 TACAAGCAATGCATAAGCTCTTGAGTTTT 1 5 0 GACTCTTGAG 0.960597 -596 GTCCGCACAGGCGGATACTTTTTAGTTTGGGAAGA 1 107 0 GACTTTTTAG 0.981484 -494 GGATAAATTCGTTCGGACTTTTTAACTTACACACA 1 179 0 GGCTTTTTAA 0.973713 -422 TTATCCTTATGTATGTTCTTTTGAACGTCAAGTAG 1 208 1 GGCTTTTGAA 0.968227 -393 TGTGCTTCTTGAGAGGTCTTTTGAGCTGTTGCATC 1 398 0 GGCTTTTGAG 0.988087 -203 CTCTAATGGCGTTAGTACTTTATAGAAACTCGCTA 2 95 1 GGCTTTATAG 0.957608 -311 TGATTCCATCGCCAGTACTTTTGTAATTCAGGAAT 2 220 0 GGCTTTTGTA 0.779228 -186 CATGAGATCCGGCTTTGCTCTTTAGGTCGGTCAAT 2 337 0 GTCTCTTTAG 0.879677 -69 GACATGTTTTGTGCATGCTCTTTAGCATTGTTGTG 5 198 1 GACTCTTTAG 0.967357 -206 AAGGGGCGGAGGCGGCCCTTTTTAGGATTTATATA 7 257 1 GGCTTTTTAG 0.990179 -344 TCTTTTTTGAGCGAAGCCTTTATAATCAAATTTTA 7 393 1 GACTTTATAA 0.813557 -208 AATTCTAATAGAAAAAACTTTTTATGAATACAGTA 7 498 0 GACTTTTTAT 0.855446 -103 * * ******** Masking position 9 Map Score: 6.93701 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 343 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TCTTTTGAACGTCAAGTAGTCAATCTCTCCA 1 224 1 GCAAGTAGTC 0.825449 -377 CTCTAGTTTAGTGCAGTCGCTGCTTTTTTCT 1 303 1 GGCAGTCGCT 0.986496 -298 GCCCTGAAGTGTCCAGTAGTCATCACACGTT 1 580 1 GCCAGTAGTC 0.927889 -21 GAAAACATATGATCAGTAGCTAAATTGACCG 2 314 1 GTCAGTAGCT 0.985471 -92 AATAGATAAGTCGCCAGGAAATTCG 2 391 0 GTAAGTCGCC 0.967403 -15 TAATTCTTGGGTCCATTCGCTGTTCT 3 6 0 GCCATTCGCT 0.975059 -295 AGTTTACCACGATAAGTCGCTCCCGTTGTTA 4 36 1 GTAAGTCGCT 0.979338 -265 TTCTTGAAGGGATCATTAGTTAATATTATGA 5 310 0 GTCATTAGTT 0.901534 -94 CTATCGATTGGATCATTCCCTTTCTCACACA 6 30 1 GTCATTCCCT 0.846982 -271 TTATACTCTGGCGCAGTAGTTCATCGTCGAT 6 193 0 GGCAGTAGTT 0.933826 -108 AAGAAGTTTGGGTAATTCGCTGCTATTTATT 7 349 1 GTAATTCGCT 0.945693 -252 * ********* Masking position 5 Map Score: 4.82715 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 504 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 CCAAGCACATACGCAGACATATATATGTAG 2 141 1 ACGCAGACAT 0.985534 -265 GTAATCACGTATGCAGACATTAAATGTGAG 2 170 1 ATGCAGACAT 0.987671 -236 GTTTTTATATATGCACACATATACATATAT 3 213 1 ATGCACACAT 0.984788 -88 TTCTTTTACAATGTACACATTTTATTATAT 3 256 0 ATGTACACAT 0.871996 -45 ATGTGTTACGATGCAGACATGTTTTGTGCA 5 183 1 ATGCAGACAT 0.987671 -221 ********** Masking position 5 Map Score: 4.68026 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 70 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GCGTGATGTTTTAAGCCTTCTTTCCTCTAG 1 279 1 TTAAGCCTTC 0.989309 -322 TTGACCTTGGTTTTTCCTTCTTTTCGCCGT 1 344 0 TTTTTCCTTC 0.903694 -257 ATATTCAAAGTTAAACCTTCCAAAAATCAT 5 356 1 TTAAACCTTC 0.958835 -48 GTAATTGGATTTAAGCCTTCGTGCCTTATC 6 144 1 TTAAGCCTTC 0.989309 -157 GTAACCCGTCTTATGCCTTCCGGGTACTAT 7 201 1 TTATGCCTTC 0.986123 -400 CCTCCGCCCCTTAATCCATCGACACCCGCA 7 239 0 TTAATCCATC 0.924348 -362 TCGCTGCTATTTATTCATTCCACCTTCTTC 7 365 1 TTATTCATTC 0.854285 -236 ********** Masking position 2 Map Score: 4.11149 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 180 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 ACATCACGCGATCCATATAAAGACCCGAGTAGTT 1 254 0 ATCCATAAAC 0.969147 -347 AATGTAAAATAGCCAAGCACATACGCAGACATAT 2 129 1 AGCCAAACAC 0.870217 -277 ATTCGGTGATATCCCTTTAAAAACCATGAGATCC 2 362 0 ATCCCTAAAC 0.951669 -44 ACGAAAAACCACCCAAGGAAGAGCCAGAATCAGA 3 74 1 ACCCAAAAGC 0.870217 -227 CATAATATATATCCAATTAAATATCTGATTCTGG 3 97 0 ATCCAAAAAT 0.951434 -204 TTGTAAAAGAATCCAAGCACAACTATTATTAGCA 3 275 1 ATCCAAACAT 0.941577 -26 AGAAGCTGCCATCCCTAGAAAAGTAAAAACTATA 4 240 1 ATCCCTAAAT 0.89912 -61 TTAACTAATGATCCCTTCAAGAACGCGCCATATA 5 318 1 ATCCCTAAGC 0.941832 -86 GAAGGCTTAAATCCAATTACGAATCTTCTACTTA 6 130 0 ATCCAAACGT 0.92986 -171 CCGCCCCTTAATCCATCGACACCCGCAAATGAAA 7 232 0 ATCCATACAC 0.962775 -369 TTTTATATAAATCCTAAAAAGGGCCGCCTCCGCC 7 261 0 ATCCTAAAGC 0.848592 -340 CTAGTATTTAATCCAAATAAAATTCAAACAAAAA 7 566 1 ATCCAAAAAT 0.951434 -35 ****** *** * Masking position 9 Map Score: 3.47271 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 508 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 8 CGAATTTATCCTTATGTATGTTCTTTTGAA 1 203 1 CTTATGTATG 0.945224 -398 CATACGCAGACATATATATGTAGTAATCAC 2 148 1 CATATATATG 0.494563 -258 AATCACGAAGCATATGTTTGTTTACGAAAA 3 51 1 CATATGTTTG 0.87113 -250 TGAAATAGTTTTTATATATGCACACATATA 3 206 1 TTTATATATG 0.941904 -95 TATATATATGTATATGTGTGCATATATAAA 3 216 0 TATATGTGTG 0.855365 -85 TTACAGATTTTATATATATGTATATGTGTG 3 226 0 TATATATATG 0.81255 -75 TCGTCGTTTGTTTCTGTATGTGGTGTACGG 5 245 1 TTTCTGTATG 0.88209 -159 CTTTGAATATTTTATATATGGCGCGTTCTT 5 336 0 TTTATATATG 0.941904 -68 GTCTTTTCTATTTTTATTTGAGAAGCCTAC 7 431 1 TTTTTATTTG 0.745406 -170 TTAGTTTTGGTTTTTGTTTGAATTTTATTT 7 580 0 TTTTTGTTTG 0.823605 -21 ********** Masking position 5 Map Score: 0.996829 Number of sites scoring better than the average of aligned sites = 1264 Number in coding regions = 385 Number in noncoding regions = 879 Number of orfs with sites within 600 bp upstream = 532 Fraction of orfs with sites within 600 bp upstream = 0.0854481 Motif number 9 TATGTGAAAGTAAACTGCCCTCTCCAGTTAAC 1 75 1 TAAATGCCTC 0.897273 -526 TCGGACTTTTTAACTTACACACATCTTTTGGT 1 170 0 TAACTACCAC 0.947868 -431 CGAGTTTCTATAAAGTACTAACGCCATTAGAG 2 95 0 TAAATACAAC 0.883949 -311 CTCGCTAATGTAAAATAGCCAAGCACATACGC 2 123 1 TAAATAGCAA 0.882253 -283 TTTATACCAATAAATGGCTCACATTTAATGTC 2 185 0 TAAAGGCCAC 0.963887 -221 GTGAAATTATTAAATGAGGCACAGGGACATAT 4 81 0 TAAAGAGCAC 0.919474 -220 TGTATTATTGTAAAATACTCACAATGTAATCT 5 140 1 TAAATACCAC 0.98866 -264 GACGACAATCTAAAATGCACAACAATGCTAAA 5 218 0 TAAATGCCAA 0.94599 -186 GCGCCATATATAAAATATTCAAAGTTAAACCT 5 342 1 TAAATATCAA 0.733116 -62 ACGTTTTATCTAAACTACTCACATGAAAAGAT 6 89 0 TAAATACCAC 0.988659 -212 **** *** *** Masking position 3 Map Score: 3.02694 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 226 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 10 AAGCACTACCGCCCCTTGAATGAACACCAAA 1 145 1 GCCCCTTGAT 0.97932 -456 TTTTTATTTTGCCCTTAGATTGTATTATAAA 1 530 1 GCCCTTAGAT 0.991759 -71 ACTGAAAAATGCCCTTAGAGTATGATAGCCT 2 55 0 GCCCTTAGAT 0.991533 -351 AAGTACTAACGCCATTAGAGTTTTTTGTAAC 2 84 0 GCCATTAGAT 0.949703 -322 ACAGCGAATGGACCCAAGAATTAGTATGTGA 3 14 1 GACCCAAGAT 0.94118 -287 ATTAGTATGTGATCCTAGAATCACGAAGCAT 3 33 1 GATCCTAGAT 0.909358 -268 ********* * Masking position 9 Map Score: 0.299394 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 131 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 ********** No masking Map Score: 2.53907e-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: 2.53907e-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: 2.53907e-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