AlignACE version 2.2 July 7, 1998 AlignACE -jSHE.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 YBL031W 369 bp YBL031W SHE1 1-1017 #2 YBR130C 300 bp YBR130C SHE3 1-1278 cytoplasmic protein involved in mother-specific HO expression #3 YDR393W 300 bp YDR393W SHE9 1-1371 mRNA (identified by a library screen) that causes growth arrest when overexpressed #4 YGL228W 600 bp YGL228W SHE10 1-1734 mRNA (identified by a library screen) that causes growth arrest when overexpressed #5 YKL130C 320 bp YKL130C SHE2 1-741 Required for mother cell-specific HO expression #6 YOR035C 300 bp YOR035C SHE4 1-2370 Required for mother cell-specific HO expression Motif number 1 TTTTTATTAAAGGGAAAAAAATGATTCAATATGTATATATT 1 100 1 AAAAAACAAA 0.966213 -270 TTAATTCAAAATACATATACATGAATAAATATATACATATT 1 127 0 ATAAAAAAAA 0.94788 -243 GAATTTCGATAGTAATAAAGAAAATACAACGGCTTTATTGA 1 189 0 ATAAAACAAG 0.750425 -181 CAGAGAGGGAAGGGGAAAATAACATGAAAAAATCGTAAGTT 1 267 1 AAAAAAAAAA 0.98543 -103 GTTTCTAGGCAATGGTATAAACAAATAAACAATAAACATGC 1 305 1 ATAAAAAAAA 0.94788 -65 TATTATTGTCATCGCAATAAAATAGGCTAAATAGTTACCCG 2 111 1 AAAAAACTAA 0.737846 -190 TGAAGCTCTCGCCCGAACAAAAGACGAAACGAGCGGGTAAC 2 144 0 GAAAAAAAAG 0.770332 -157 GCTGCTACTCATGGCAACAAATCAATAAACAAAATGCAATA 2 196 0 AAAAAAAAAA 0.98543 -105 AGCCAAATGAATTGAAAAATACAAATAAAGATTATGTACGT 3 178 1 AAAAAAAAAA 0.98543 -123 TGGACGGTATAGAAGAAAAGAGAACTTAATAACAAAAGACC 4 20 1 AAAAAATAAA 0.878013 -581 CAATCCAATTAGTAGAACACAACACAACACAACACAACACA 4 143 1 AAAAAAACAA 0.9478 -458 AACACAACACAACACAACACAGCACAACACGCTTACCAAAT 4 168 1 AAAAAAACAG 0.876546 -433 CGGCAACCAAAAACCGACAGAATAAAAAACAGCCATCATAC 4 220 1 AGAAAAAAAA 0.914294 -381 ACTCTCGAGGATAATAACAGACAATAAACCAAGAGTTCATC 4 264 0 AAAAAAAACA 0.895588 -337 ACAAACAAAAAATGAAAAAAAAAAAAAAAAAGGGACTTTAA 5 121 0 AAAAAAAAAA 0.98543 -200 TAAACTACTCACATGAAAAGATTACTAAAAAATTAGAATCA 6 268 1 AAAAAAAAAA 0.98543 -33 * ** * * * *** * Masking position 11 Map Score: 12.9216 Number of sites scoring better than the average of aligned sites = 4982 Number in coding regions = 1241 Number in noncoding regions = 3741 Number of orfs with sites within 600 bp upstream = 1360 Fraction of orfs with sites within 600 bp upstream = 0.218439 Motif number 2 TATGTATATATTTATTCATGTATATGTATT 1 129 1 TTTATTCATG 0.939426 -241 AAACTTACGATTTTTTCATGTTATTTTCCC 1 279 0 TTTTTTCATG 0.956938 -91 GAACACATATTATCTTCATGG 1 359 1 TATCTTCATG 0.986599 -11 GTTCTAAACCAATTATCATGTAAATTTTTG 3 97 1 AATTATCATG 0.901375 -204 TTTTGTATAATTTCATCATGGAGGTGCATG 3 122 1 TTTCATCATG 0.973857 -179 GATACATGATTATCATCATGTACGTAGAAA 4 446 0 TATCATCATG 0.983494 -155 TAAACATCTATATATTCATGTTAA 5 5 0 TATATTCATG 0.961358 -316 CGCGGCTGATAATCATCATGATCGACGATG 6 176 0 AATCATCATG 0.949666 -125 TTTTTAGTAATCTTTTCATGTGAGTAGTTT 6 269 0 TCTTTTCATG 0.928751 -32 ********** Masking position 6 Map Score: 8.2599 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 371 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 CACACAGACAAAACAAACTATCATCTTAACGAA 1 36 1 AAACAAACCA 0.972104 -334 TTTTTCCCTTTAATAAAAATACAGTTTAAACTA 1 86 0 TAATAAAACA 0.762785 -284 TGGTATAAACAAATAAACAATAAACATGCAATT 1 317 1 AAATAAACAA 0.610125 -53 TTTGACGTGGAACCAAAAATACATTCTAAATCG 2 51 0 AACCAAAACA 0.972104 -250 GCTCTCGCCCGAACAAAAGACGAAACGAGCGGG 2 148 0 GAACAAAAGA 0.835073 -153 ACAAATCAATAAACAAAATGCAATAGTAGTTAG 2 188 0 AAACAAAAAA 0.920185 -113 GAGAACTTAATAACAAAAGACCAGATTGTCTAT 4 39 1 TAACAAAACA 0.946628 -562 TTACTACGGCAACCAAAAACCGACAGAATAAAA 4 214 1 AACCAAAAGA 0.956677 -387 ACCGACAGAATAAAAAACAGCCATCATACGTGG 4 232 1 TAAAAAACCA 0.626891 -369 ACAGACAATAAACCAAGAGTTCATCCACGTATG 4 256 0 AACCAAGACA 0.931632 -345 TCAATACCCTAACTAAACCCTGAACTGCCCAAG 4 332 1 AACTAAACGA 0.749842 -269 TGTTACATCTAAACAAGAACGCAGCGTAACGAA 4 578 1 AAACAAGACA 0.947917 -23 CCTCTTAACATACCAAAAGTGCATTACATATAC 5 64 1 TACCAAAACA 0.92997 -257 TGAAAAAAAAAAAAAAAAAGGGACTTTAACTTT 5 117 0 AAAAAAAAGA 0.788662 -204 GGGAAAATACAAACAAAAAATGAAAAAAAAAAA 5 137 0 AAACAAAAGA 0.967207 -184 ACATCGTTCAAAACAAGCTTTAAAGATTTGACA 5 199 1 AAACAAGCAA 0.771449 -122 ******** ** Masking position 6 Map Score: 7.18379 Number of sites scoring better than the average of aligned sites = 3943 Number in coding regions = 2465 Number in noncoding regions = 1478 Number of orfs with sites within 600 bp upstream = 1036 Fraction of orfs with sites within 600 bp upstream = 0.166399 Motif number 4 TGAATCATTTTTTTCCCTTTAATAAAAATA 1 98 0 TTTTCCCTTT 0.979484 -272 TTTCATGTTATTTTCCCCTTCCCTCTCTGT 1 266 0 TTTTCCCCTT 0.95557 -104 ACTTACGATTTTTTCATGTTATTTTCCCCT 1 277 0 TTTTCATGTT 0.873737 -93 AGGCTAAATAGTTACCCGCTCGTTTCGTCT 2 134 1 GTTACCCGCT 0.888675 -167 AGGTGCATGGGTTTCCTTCTGGTATGATAA 3 143 1 GTTTCCTTCT 0.861833 -158 AATCACTGAGTTCACCCGTTACAATTTCAC 3 268 0 TTCACCCGTT 0.844667 -33 CAGGTTGTCCTTTTCCCGCTGGGTGAAGCA 4 94 1 TTTTCCCGCT 0.985248 -507 TTTTTTTTTTTTTTCATTTTTTGTTTGTAT 5 134 1 TTTTCATTTT 0.778865 -187 TTTGTTTGTATTTTCCCGTTTTGAAAAACT 5 153 1 TTTTCCCGTT 0.989452 -168 CCCTCCTTAATTTTCCTTTTGCATAATACC 5 289 1 TTTTCCTTTT 0.953215 -32 ********** Masking position 2 Map Score: 5.67753 Number of sites scoring better than the average of aligned sites = 2276 Number in coding regions = 1340 Number in noncoding regions = 936 Number of orfs with sites within 600 bp upstream = 756 Fraction of orfs with sites within 600 bp upstream = 0.121426 Motif number 5 TCCCCTTCCCTCTCTGTGCCTCTAGCCGGCG 1 252 0 TCTTGTGCCT 0.989631 -118 CCAGGCTTCCTCTATATGCCTT 3 2 0 TCTTATGCCT 0.925262 -299 ATAACGCGTATCTACGTACATAATCTTTATT 3 201 0 TCTCGTACAT 0.978037 -100 AAGGCGGATTTCTACGTACATGATGATAATC 4 438 1 TCTCGTACAT 0.978037 -163 GATGTAACAGCTTTTGTGCATCCAAGATATA 4 556 0 CTTTGTGCAT 0.873394 -45 ATAGAATGGTTCTTCGTGCATGCCTCTTAAC 5 42 1 TCTCGTGCAT 0.993911 -279 TGGATTTAAGCCTTCGTGCCTTATCGCGGCT 6 199 0 CCTCGTGCCT 0.992518 -102 *** ******* Masking position 7 Map Score: 3.45566 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 128 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 AAGAAAATACAACGGCTTTATTGAGTATTT 1 183 0 AACGGCTTTA 0.96836 -187 AACGTTTGGTAACCCCTTCAGACTGCTGCT 2 231 0 AACCCCTTCA 0.96707 -70 TGGGTGAAGCAACCGTTTCACTTATTCGCA 4 113 1 AACCGTTTCA 0.972176 -488 AGCCGTTTGGAACGGTTCCAGA 6 3 0 AACGGTTCCA 0.960696 -298 AACCGTTCCAAACGGCTTCATTATCACCAC 6 16 1 AACGGCTTCA 0.994971 -285 GTTTAGATAAAACGTCTTCACTATTAAGTA 6 243 0 AACGTCTTCA 0.9743 -58 ********** Masking position 7 Map Score: 2.95333 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 422 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 TTGGGGTCTTTTTCGTTGTGAAATTGTAAC 3 251 1 TTTCGTTGTG 0.95321 -50 GTTCTACTAATTGGATTGTGCGAATAAGTG 4 131 0 TTGGATTGTG 0.946884 -470 TTGTGTTGTGTTGTGTTGTGTTCTACTAAT 4 150 0 TTGTGTTGTG 0.994004 -451 CTGTGTTGTGTTGTGTTGTGTTGTGTTGTG 4 160 0 TTGTGTTGTG 0.994004 -441 GCGTGTTGTGCTGTGTTGTGTTGTGTTGTG 4 170 0 CTGTGTTGTG 0.980773 -431 AGACGAATTTTTTGGTGGTGATAATGAAGC 6 30 0 TTTGGTGGTG 0.92023 -271 ACTACAATAATTGTGTTGAGATGTCGGAAG 6 58 0 TTGTGTTGAG 0.971764 -243 ********** Masking position 6 Map Score: 5.40587 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 197 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 TGTATATGTATTTTGAATTAAAAAAAAACG 1 147 1 TTTTGAATTA 0.851208 -223 ACGACACTACTTTTGTGTAAG 2 290 1 TTTTGTGTAA 0.956634 -11 TCATGTAAATTTTTGTATAATTTCATCATG 3 112 1 TTTTGTATAA 0.929231 -189 TATTTTCCCGTTTTGAAAAACTCCCACTTT 5 161 1 TTTTGAAAAA 0.700558 -160 GAGAAAAATGTCTTGAGTAAAGTGAGGATT 5 236 0 TCTTGAGTAA 0.931092 -85 CTTTCTCTTTTTTTGAGAAAAATGTCTTGA 5 250 0 TTTTGAGAAA 0.932683 -71 TTAATTTTCCTTTTGCATAATACCAGACAC 5 295 1 TTTTGCATAA 0.810794 -26 TGATTCTAATTTTTTAGTAATCTTTTCATG 6 279 0 TTTTTAGTAA 0.848826 -22 ********** Masking position 10 Map Score: 0.94415 Number of sites scoring better than the average of aligned sites = 1153 Number in coding regions = 800 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 9 AGTTTCATTTGACGTGGAACCAAAAATACA 2 61 0 GACGTGGAAC 0.974149 -240 CAAAAGTAGTGTCGTTGAACCTTGGCGTGC 2 275 0 GTCGTTGAAC 0.991698 -26 GCCATCATACGTGGATGAACTCTTGGTTTA 4 251 1 GTGGATGAAC 0.982502 -350 TTCAGAAATGGTGGTTGAAACAGAATGCCC 4 520 0 GTGGTTGAAA 0.940364 -81 CATCATGATCGACGATGAACTACTGCGCCA 6 163 0 GACGATGAAC 0.983137 -138 ********** Masking position 8 Map Score: 0.746309 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 265 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 CTCTCCAGGCTTCCTCTATATGCCTT 3 7 0 TTCCTCTATA 0.972963 -294 AAGTTCTCTTTTCTTCTATACCGTCCAGTT 4 17 0 TTCTTCTATA 0.958135 -584 CCAGCCCTAAATCCCCTAAATAAGAACTCT 4 300 0 ATCCCCTAAA 0.933156 -301 AAAGTAAGAAATGTCCTATACGTTTCTATG 4 377 1 ATGTCCTATA 0.891907 -224 TTACGTTATATTCTTCTATAAAAGCATTCT 6 91 1 TTCTTCTATA 0.958135 -210 CCAGAGTATAATCCCCTATAAAACAGGCCT 6 136 0 ATCCCCTATA 0.982635 -165 ********** Masking position 7 Map Score: 0.734429 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 124 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 11 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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: -1.88842e-14 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