AlignACE version 2.2 July 7, 1998 AlignACE -jMAK.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 YAL025C 419 bp YAL025C mak16 1-921 putative nuclear protein #2 YBR142W 300 bp YBR142W mak5 1-2322 Probable pre-mRNA splicing RNA-helicase #3 YCR019W 600 bp YCR019W MAK32 1-1092 MAK32 sugar kinase #4 YCR020C-A 300 bp YCR020C-A MAK31 1-267 MAK31 snRNP #5 YEL053C 468 bp YEL053C mak10 1-2202 glucose-repressible protein #6 YKL021C 300 bp YKL021C mak11 1-1407 contains four beta-transducin repeats #7 YPR051W 300 bp YPR051W mak3 1-531 N-acetyltransferase Motif number 1 ATGTTTTTAAAAAAAAAAAAACATGTATGTA 1 102 0 AAAAAAAAAA 0.951947 -318 CATGGACTCGAACAGAATAAAAGAATTTATA 1 130 1 AACAAATAAA 0.896358 -290 CAAAAAAAAAAAAAAAAAAAAAAAAGGTTTA 1 264 0 AAAAAAAAAA 0.951947 -156 GAGCTTTTGAAAAAAAATGAAAAAGTGATTG 1 309 1 AAAAAATGAA 0.914664 -111 GAACACTGTCAAAAGAAAGAACTAAGCAATG 1 358 0 AAAAAAAGAA 0.822173 -62 TGTGAGGTGAAAAAAAATATAACAATTATAA 2 102 0 AAAAAATATA 0.873885 -199 AAGCGGAACCAAGACAATATACGGTGTGCTT 3 36 0 AAGAAATATA 0.871594 -565 ATGTCATATCAAGACAATAAACGGTAGTGCT 3 445 1 AAGAAATAAA 0.978255 -156 TTACTGTTCTAAGAAAATAAAGAACGTGATA 3 580 1 AAGAAATAAA 0.978255 -21 TATTTTTTGAAAAAAAAAAAATTAATCCGCC 4 178 0 AAAAAAAAAA 0.951947 -123 TCCGAAAGAACAAAGAATAAATAGGTAAAGC 5 41 0 CAAAAATAAA 0.84537 -428 TCGAAGTTTCAAAACAATAACATTCTAAACG 6 182 1 AAAAAATAAC 0.853461 -119 TCAAAAATGCAAAATAATAAAAAATGAATCT 6 266 0 AAAAAATAAA 0.97869 -35 AAAGAAGATAAAATTCAAAAAT 6 289 0 AAGAGATAAA 0.842654 -12 TGATGTATAAAAGAAAATAAAAGAAGTACTT 7 24 1 AAGAAATAAA 0.978255 -277 AGCCTTATTAAAAATAATAATCATGAAGAAC 7 216 1 AAAAAATAAT 0.797143 -85 AAGAGATTACAAGATAAAAAAGCCACTACTA 7 257 1 AAGAAAAAAA 0.950994 -44 **** ****** Masking position 7 Map Score: 19.6554 Number of sites scoring better than the average of aligned sites = 9260 Number in coding regions = 1473 Number in noncoding regions = 7787 Number of orfs with sites within 600 bp upstream = 1953 Fraction of orfs with sites within 600 bp upstream = 0.313685 Motif number 2 TTATATGCAAAGTTTTTTACAAGAGGAATTTG 1 38 0 ATTTTTTAAA 0.853623 -382 GCTCCATCTGTATATTTTATATGCAAAGTTTT 1 54 0 TTATTTTAAT 0.831328 -366 ACATGTTTTTTTTTTTTTAAAAACATGGACTC 1 107 1 TTTTTTTAAA 0.953854 -313 CTCATCGGAAAATTTTTCAAAAAAAAAAAAAA 1 280 0 ATTTTTCAAA 0.903774 -140 ACTTTTTCATTTTTTTTCAAAAGCTCATCGGA 1 303 0 TTTTTTCAAA 0.970886 -117 ATTGTTATATTTTTTTTCACCTCACAAACCCG 2 107 1 TTTTTTCACT 0.722174 -194 GGCGAATATAACTTTTTTAGATGGAAATTCTT 2 203 0 ATTTTTTAAT 0.810778 -98 GACAGATTTGTACTTTTCATATT 3 2 0 TCTTTTCAAT 0.886654 -599 TTGGTTCCGCTTTTATTCAGAAGAATTACTGA 3 55 1 TTTATTCAAA 0.816564 -546 AGCTTAATAATGTATTTTAAAACTTGCATGTT 3 319 1 TTATTTTAAA 0.870264 -282 CTAGGGAACTTCCTTTTTACATTTAAAGTTTC 3 390 1 TCTTTTTAAT 0.829266 -211 GAAAGGATTGTGTTATTTAGAACAGAGTATCA 4 97 0 TTTATTTAAA 0.734338 -204 ATTAATTTTTTTTTTTTCAAAAAATATCTCGC 4 183 1 TTTTTTCAAA 0.970886 -118 GAGTTCTGACTATTTTTTAAATGCGATGATAT 4 224 1 TTTTTTTAAT 0.938349 -77 ACATAATACGATTATTTCACATTGTTATGTTT 5 299 1 ATATTTCAAT 0.690845 -170 GTACTCTTATTATGTTTCACATTATCGAATTT 6 29 1 TTGTTTCAAT 0.868087 -272 AAGATGATGATATGTTTCATAATTTATCCAAA 6 66 1 TTGTTTCAAA 0.899563 -235 CTTCGATAACTGCATTTTAAAAGAGGTTTTCA 6 156 0 TCATTTTAAA 0.681589 -145 TCATGATTATTATTTTTAATAAGGCTTGCCAT 7 210 0 TTTTTTAAAA 0.74456 -91 * ******* ** Masking position 6 Map Score: 10.2735 Number of sites scoring better than the average of aligned sites = 3254 Number in coding regions = 1816 Number in noncoding regions = 1438 Number of orfs with sites within 600 bp upstream = 982 Fraction of orfs with sites within 600 bp upstream = 0.157726 Motif number 3 TCATCGCTGGAAAAGTTTTTCAGAGAAAAAGAAAAGT 2 160 0 AAATTAGGAA 0.987236 -141 AACCTCAGGTAGAAATTCTTTAGTCAAATACCGGCAT 2 258 1 AAATTAGCAA 0.975526 -43 ACATTTAATTACAATTATCTCAGAGAAGATCTTCTTG 3 245 0 AAATTAGGAA 0.987236 -356 TGATAATGCTACGATTACTCTAGGGAACTTCCTTTTT 3 371 1 AGATCAGGAA 0.948666 -230 AAAGATGTGTAAAATTACGTAAGACAAAGGAACTCGG 5 168 1 AAATTAGCAA 0.975526 -301 AGGTGCCTAAATAAATGAATAAGAGTACTGTATTATC 5 235 1 AAATTAGGTA 0.975946 -234 GAGATTGAAAACAACTGTGCTAGTGTAGAGCAACTTT 5 417 1 AAATCAGGTA 0.951998 -52 GGAATATTTAAGAATTGGTTTAGCCAAGGTACTACTA 6 106 1 AAATTAGCAA 0.975526 -195 CCTTTGAACAACGATTATTTTAGTGTACTGTTGTTGT 7 60 0 AGATTAGGTA 0.951998 -241 * ** * * ** *** Masking position 6 Map Score: 5.06342 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 166 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TTTTTTTCAAAAGCTCATCGGAAAATTTTT 1 295 0 AAGCTCATCG 0.995524 -125 GATTGCCATCAAGGTCATGGCTAGCTCATC 2 68 1 AAGGTCATGG 0.963842 -233 AGGTCATGGCTAGCTCATCGATATTATAAT 2 79 1 TAGCTCATCG 0.982103 -222 AAATTCTTATAAGCTCATCGCTGGAAAAGT 2 181 0 AAGCTCATCG 0.995524 -120 AATCTGTCAAAAGCACACCGTATATTGTCT 3 26 1 AAGCACACCG 0.96112 -575 GTACTCAAATAAGGGCATCGCTATTATATA 7 128 1 AAGGGCATCG 0.981264 -173 ********** Masking position 7 Map Score: 4.75828 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 98 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 5 ACTCGAACAGAATAAAAGAATTTATAATGATA 1 135 1 AAAAAGAATT 0.698547 -285 AACACTGTCAAAAGAAAGAACTAAGCAATGCA 1 356 0 AAGAAGAACT 0.858796 -64 TTCAGAGAAAAAGAAAAGTACGGACTAACTAA 2 147 0 AAAAAGTACG 0.893307 -154 CGCAAATCAGAAGAAAGGAACTTCTCCCTCCC 5 77 1 AAAAGGAACT 0.973966 -392 AATTACGTAAGACAAAGGAACTCGGCACACCT 5 180 1 GAAAGGAACT 0.928396 -289 TAAATAAATGAATAAGAGTACTGTATTATCTA 5 242 1 AAAAAGTACT 0.977983 -227 TGTGAAACATAATAAGAGTACTAAAGTTAAGG 6 18 0 AAAAAGTACT 0.977983 -283 GAATTGGTTTAGCCAAGGTACTACTAGGCAAC 6 117 1 AGCAGGTACT 0.770714 -184 AAAAGAAAATAAAAGAAGTACTTTCCGAACAA 7 32 1 AAAGAGTACT 0.884157 -269 CTTTCCGAACAACAACAGTACACTAAAATAAT 7 52 1 AAAAAGTACA 0.849604 -249 TCTGATTTGAGAAAATGGTACTCAAATAAGGG 7 111 1 GAAAGGTACT 0.946947 -190 GTTTCTTGGTAGGAATGGAACTATATAATAGC 7 147 0 AGAAGGAACT 0.928392 -154 ** ** ****** Masking position 10 Map Score: 3.44262 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 697 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 278 Fraction of orfs with sites within 600 bp upstream = 0.0446515 Motif number 6 AACTGGAGGAAAGTGGCACAATACC 1 5 0 AAGGGCACAA 0.973394 -415 TGGTATCGCTAAGCTGATACAAGATTGCCAT 2 46 1 AAGTGATACA 0.80941 -255 TTCTGAATAAAAGCGGAACCAAGACAATATA 3 46 0 AAGGGAACCA 0.969234 -555 CAACCAACAAAAGTTTAAACACACAAAAATC 3 209 0 AAGTTAAACA 0.725753 -392 TCCGCCACATAAGATGCACAAAATGAGCCTA 4 153 0 AAGTGCACAA 0.971243 -148 CAAACTTAGTAAGGGGCACCAAAGCGTC 4 283 1 AAGGGCACCA 0.988472 -18 GCTATTATCAAAGTTGCTCTACACTAGCACA 5 432 0 AAGTGCTCTA 0.858145 -37 TACTAAAGTTAAGGGGATCCA 6 1 0 AAGGGATCCA 0.948914 -300 GCAGTTATCGAAGTTTCAAAACAATAACATT 6 175 1 AAGTTCAAAA 0.754533 -126 AAGCGATAAAAAGGCTCTCCATGGCAAGCCT 7 190 1 AAGCTCTCCA 0.840648 -111 ATGAAGAACAAAGTTTCACAAGAGATTACAA 7 238 1 AAGTTCACAA 0.925423 -63 *** ******* Masking position 2 Map Score: 3.1183 Number of sites scoring better than the average of aligned sites = 1680 Number in coding regions = 1376 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 261 Fraction of orfs with sites within 600 bp upstream = 0.041921 Motif number 7 AGAATTGCTTTCATTAGCTCATTATGTTCA 1 210 1 TCATTAGCTC 0.945642 -210 TCATTTTTTTTCAAAAGCTCATCGGAAAAT 1 299 0 TCAAAAGCTC 0.972631 -121 ATGGAAATTCTTATAAGCTCATCGCTGGAA 2 185 0 TTATAAGCTC 0.983923 -116 ATCATTATCATCATAACCTCAGGTAGAAAT 2 244 1 TCATAACCTC 0.949141 -57 TACAAATCTGTCAAAAGCACACCGTATATT 3 22 1 TCAAAAGCAC 0.86429 -579 CGTTACATTGTTGTAAGCTCTTTCAGGATT 4 28 1 TTGTAAGCTC 0.971955 -273 AAATTCAATGTTATAGGCTCATTTTGTGCA 4 140 1 TTATAGGCTC 0.942048 -161 CTTTTTTATCTTGTAATCTCTTGTGAAACT 7 249 0 TTGTAATCTC 0.818027 -52 ********** Masking position 1 Map Score: 2.18549 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 342 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 8 TACTGCATTTTGATAATCTGAACATAATGAG 1 227 0 TGATATCTGA 0.800451 -193 TTCTAACCGTTGTAGTTATGTACTGAAGAGA 1 387 0 TGTAGTATGT 0.896434 -33 GCGTGCATCGTCAAGTTATGTTTGTAAGTAC 3 175 0 TCAAGTATGT 0.748318 -426 AAAACTTGCATGTTGCTCTGTGAATCTGAAT 3 337 1 TGTTGTCTGT 0.979086 -264 CCGTTTATTGTCTTGATATGACATTTATTTG 3 438 0 TCTTGTATGA 0.921526 -163 GAGCTGATTGTGTTGTTCTGTGACATACGAT 4 62 1 TGTTGTCTGT 0.979086 -239 TACGATATACTGATACTCTGTTCTAAATAAC 4 87 1 TGATATCTGT 0.87238 -214 ACTTTAGTACTCTTATTATGTTTCACATTAT 6 23 1 TCTTATATGT 0.832991 -278 TGGGGAAAGATGATGATATGTTTCATAATTT 6 60 1 TGATGTATGT 0.953614 -241 AGTGTACTGTTGTTGTTCGGAAAGTACTTCT 7 45 0 TGTTGTCGGA 0.913746 -256 CTACCCGGTTTCTTGGTAGGAATGGAACTAT 7 155 0 TCTTGTAGGA 0.821344 -146 ***** ***** Masking position 7 Map Score: 2.61702 Number of sites scoring better than the average of aligned sites = 1481 Number in coding regions = 1149 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 9 TCCATCTATATATGCTCCATCTGTATATTTTATA 1 65 0 TGCTCATTGT 0.990077 -355 AACATGTATGTATGCTCCATCTATATATGCTCCA 1 80 0 TGCTCATTAT 0.928283 -340 ATTGCTTTCATTAGCTCATTATGTTCAGATTATC 1 213 1 TGCTCTTTGT 0.992363 -207 TTGAATGCATTCCGCTGTATTAGTGGTATCGCTA 2 23 1 TGCTGATAGT 0.948236 -278 TACATTGTTGTAAGCTCTTTCAGGATTCATTGAG 4 31 1 TGCTCTTAGG 0.945633 -270 CAGGATTCATTGAGCTGATTGTGTTGTTCTGTGA 4 51 1 TGCTGTTTGT 0.982088 -250 TTCAATGTTATAGGCTCATTTTGTGCATCTTATG 4 143 1 TGCTCTTTGT 0.992363 -158 * **** ** *** Masking position 6 Map Score: 1.44982 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 103 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 ********** No masking Map Score: -3.16659e-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: -3.16659e-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 AAGAATTTATAATGATAGATAATGCATACTTCAATA 1 150 1 AGTAGTATCA 0.98825 -270 TGATTGGTATAGAGGCAGATATTGCATTGCTTAGTT 1 334 1 AGCAGTATCA 0.989146 -86 AACCCGCCTCAAGGTTAGTTAGTCCGTACTTTTCTT 2 133 1 AGTAGTATCG 0.946059 -168 AAATACCGGCATAATCAGTTTTTCCATC 2 283 1 AACAGTTTCA 0.920908 -18 AAGTACTGGGATAGTTAATTACTACATAGGAATATT 3 145 0 AGTAATATCA 0.935654 -456 AAGCTTTTGCAGAGGCAAATTATACATGAACACTCC 3 288 0 AGCAATTTCA 0.877055 -313 GTTTTCATGTATAGCCAGGTTATGCAATAATAGAAG 3 519 0 AGCAGTTTCA 0.97634 -82 AGAACAAAGAATAAATAGGTAAAGCAGTGAAACATA 5 30 0 AATAGTAACA 0.769567 -439 TAATATAACAACTACTAGATAATACAGTACTCTTAT 5 253 0 AATAGTATCA 0.95956 -216 GTATTATGTAAAGGTTAGATAATATAACAACTACTA 5 272 0 AGTAGTATTA 0.880227 -197 * * *** ** * ** Masking position 7 Map Score: 1.25192 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 452 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 13 TGACAGTGTTCTCTTCAGTACATAACTACAA 1 378 1 CTCTTCATAC 0.984854 -42 TACGTCATTCCTCTTCATTTCAGTAATTCTT 3 75 0 CTCTTCATTC 0.941507 -526 TATAATTTGCCTCTGCAAAAGCTTAATAATG 3 300 1 CTCTGCAAAG 0.932392 -301 CCACTATTACCTATTCAATAGGTGTGCCGAG 5 200 0 CTATTCATAG 0.696467 -269 AAAATAGCAGCTCTTCAATAGCAAGAAGAGT 5 380 1 CTCTTCATAG 0.959952 -89 ATCAAAGTTGCTCTACACTAGCACAGTTGTT 5 426 0 CTCTACATAG 0.97424 -43 ******* *** Masking position 7 Map Score: 0.366833 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 275 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 ********** No masking Map Score: -3.16659e-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 15 ********** No masking Map Score: -3.16659e-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