AlignACE version 2.2 July 7, 1998 AlignACE -jSEC.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 YBL050W 365 bp YBL050W SEC17 1-30, 147-995 peripheral membrane protein required for vesicular transport between ER and Golgi #2 YBR080C 362 bp YBR080C SEC18 1-2277 cytoplasmic protein involved in protein transport between ER and Golgi\; ATPase #3 YBR171W 300 bp YBR171W SEC66 1-621 glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins #4 YDL195W 300 bp YDL195W SEC31 1-3822 involved in protein transport from endoplasmic reticulum to Golgi #5 YDR164C 600 bp YDR164C sec1 1-2175 Hydrophilic protein involved at the late stage of secretion #6 YDR166C 300 bp YDR166C sec5 1-2916 107 kDa component of the Exocyst complex\; required for exocytosis. #7 YDR170C 508 bp YDR170C sec7 1-6030 Guanine nucleotide exchange protein for ARF #8 YDR238C 300 bp YDR238C sec26 1-2922 encodes a subunit of yeast coatomer #9 YDR498C 600 bp YDR498C SEC20 1-1152 membrane glycoprotein, sorted by HDEL retrieval system #10 YER008C 300 bp YER008C sec3 1-4011 SEC3 encodes the 144 kD and 91 kD components of the Exocyst complex\; the 91 kD component is a C-terminal proteolytic breakdown product of full length Sec3p #11 YFL045C 300 bp YFL045C SEC53 1-765 phosphomannomutase #12 YFL005W 423 bp YFL005W sec4 1-648 Ras-like small GTP-binding protein #13 YGL233W 300 bp YGL233W SEC15 1-2733 113kD component of the Exocyst complex, which contains the gene products encoded by SEC3, SEC5, SEC6, SEC8, SEC10, SEC15 and EXO70. #14 YGL137W 337 bp YGL137W sec27 1-18, 219-2870 encodes beta'-subunit of yeast coatomer #15 YGR009C 542 bp YGR009C SEC9 1-1956 Putative t-SNARE of the plasma membrane #16 YIL109C 600 bp YIL109C SEC24 1-2781 The Sec23p-Sec24p complex is one of three cytoplamic COPII factors involved in ER to Golgi transport #17 YIL076W 515 bp YIL076W SEC28 1-1080 epsilon-COP coatomer subunit Sec28p #18 YIL068C 300 bp YIL068C SEC6 1-2418 88 kD component of the Exocyst complex, which contains the gene products encoded by SEC3, SEC5, SEC6, SEC8, SEC10, SEC15 and EXO70 #19 YIR022W 347 bp YIR022W sec11 1-504 signal peptidase subunit #20 YLR166C 600 bp YLR166C SEC10 1-2616 100 kD component of the Exocyst complex\; required for exocytosis. The Exocyst complex contains the gene products encoded by SEC3, SEC5, SEC6, SEC8, SEC10, SEC15 and EXO70. #21 YLR208W 300 bp YLR208W SEC13 1-894 cytoplasmic protein involved in release of transport vesicles from the ER #22 YLR268W 300 bp YLR268W SEC22 1-645 Synaptobrevin (v-SNARE) homolog present on ER to Golgi vesicles #23 YLR292C 400 bp YLR292C SEC72 1-582 protein involved in membrane protein insertion into the ER #24 YLR378C 600 bp YLR378C SEC61 1-1443 membrane component of ER protein translocation apparatus #25 YML105C 300 bp YML105C SEC65 1-822 signal recognition particle subunit, homologue of mammalian SRP19 #26 YMR013C 600 bp YMR013C sec59 1-1560 membrane protein required for core glycosylation #27 YMR079W 300 bp YMR079W SEC14 1-9, 166-1071 phosphatidylinositol transfer protein #28 YNL287W 569 bp YNL287W SEC21 1-2808 non-clathrin coat protein involved in transport between ER and Golgi #29 YNL272C 438 bp YNL272C sec2 1-2280 Protein with coiled-coil domain essential for vesicular transport #30 YNR026C 300 bp YNR026C SEC12 1-1416 Guanine nucleotide exchange factor for Sar1p. #31 YOR254C 300 bp YOR254C SEC63 1-1992 Protein involved in protein import into ER #32 YPL094C 300 bp YPL094C SEC62 1-852 membrane component of ER protein translocation apparatus #33 YPL085W 600 bp YPL085W SEC16 1-6588 multidomain vesicle coat protein that interacts with Sec23p #34 YPR055W 300 bp YPR055W SEC8 1-3198 121 kDa component of the Exocyst complex, which is required for exocytosis, and which also contains the gene products encoded by SEC3, SEC5, SEC6, SEC10, SEC15, and EXO70 #35 YPR181C 526 bp YPR181C SEC23 1-2307 cytoplasmic GTPase-activating protein Motif number 1 TTTTTTCCTGGAAAAGAATAACAATTAAAGGCAGCCTT 1 122 0 GAAAAAAATA 0.670405 -244 CCCGAGAACGAAAAGTGAAAAGAACAAACAAGTCGTGT 4 95 1 AAAAGAAAAA 0.909732 -206 GTTGAAAACAGAAACGAAAAATTAAAGAAGCTGCAGAT 6 149 0 GAAAAAAAAA 0.943387 -152 AATTCGGGGAAAAAATGAGAAAGAAACAGTTTAAGATA 7 437 0 AAAAGAAAAA 0.909732 -72 ACACGGAAAGAAAAAAAAAACGAAGTGATAAGCTGGGT 8 139 0 AAAAAAAATA 0.713196 -162 GCTACACGTAGAAAGAAATCAGAAAACAACAGCTCGAC 8 181 1 GAAAAACAAA 0.655376 -120 ATTTTTTTAAAAAAAAAAGAGTCAGACAGGCTCGCTCT 9 54 0 AAAAAAAAAA 0.953211 -547 GCTAACAATAGAAAAAAATACACACACATTAGATTGGA 9 240 0 GAAAAAAAAA 0.943387 -361 ATTACATAAAGAAAAGAAAAGCAACAAAACAGCTTCGT 9 308 1 GAAAAAAAAA 0.943387 -293 TTGTACACTAAAAACTAAAAAGTACTTACTTATCAGCC 10 57 1 AAAAAAAATA 0.713196 -244 GATTTTGGCCAAAATAGATAATAAAATACGCATTTGGC 11 28 1 AAAAGAAAAA 0.909732 -273 GTCGTTGATGAAAAAAAAATTTGAAATATATTAAAATG 11 121 1 AAAAAATAAA 0.804142 -180 AAAAATAAGTGAAAAGAACACGTAAAAAACGGCACATT 11 155 0 GAAAAAAAAA 0.943387 -146 CTTTTAGAGTAAAACTAATCAGCAGATAGCTCCAGCTA 12 69 0 AAAAAACAAA 0.699244 -355 CGTAAATGGAAAAAACAAGAAAAAAAAAAAGAGAACAG 16 395 0 AAAAAAAAAA 0.953211 -206 ACGGCAGAAGAAAATGAAAACTGGAAGAACGAAAACGA 16 430 1 AAAAAAAGAA 0.661139 -171 TGGAAGAACGAAAACGAAGAAAAACAAAACTATGTAAG 16 451 1 AAAAAAAAAA 0.953211 -150 TTGCCGCATTGAAACAGACATAAATATATAAGTCTGAG 16 561 1 GAAAGAAAAA 0.891816 -40 TACACCCGCGGAAATAAAAACACAGAAAAAGAAGGAAA 17 138 1 GAAAAAAAAA 0.943387 -378 AGATCTGGAAAAAACCAACAGCTACAGAAAGAACCGCC 19 79 0 AAAAAAAAAA 0.953211 -269 TTCCATTGGCAAAAGCGATTTCAAAAAAATAATCTCCA 19 246 1 AAAAGATAAA 0.670085 -102 AATGTCGACAGAAAACAAAATAAAGAACCGTTCATGCA 20 517 1 GAAAAAAAAC 0.704895 -84 CGAGAAGAAAAAAAGCGAAACCGACAGAGAATTACCAC 21 131 1 AAAAGAAAAA 0.909732 -170 AAAAGACCGAAAAATGAAAACAAAAAGCGTTGAGGATT 22 151 0 AAAAAAAAAC 0.744913 -150 TGTCTTTTATAAAACAGATTTAAATATATAACAAATAG 23 158 1 AAAAGATAAA 0.670085 -243 AAAAGTTGCCGAAAGAAAGAATGAGAGAGAACGACAAA 24 292 0 GAAAAAAAAA 0.943387 -309 TTCAGTTGGTGAAAGCAAAAGAAAAAAACATAGTTAAA 24 524 1 GAAAAAAAAA 0.943387 -77 TTTGTAATCTGAAAAAAAAAAAAATATCAATGATATTC 25 204 1 GAAAAAAAAC 0.704895 -97 AGCAACTAACGAAATCAAAAGAAATAAAATAAGCCATA 25 250 1 GAAAAAAAAA 0.943387 -51 CTTGATGACCAAAATAAATTTTTACAAACTAGAGTTTC 26 31 0 AAAAAATAAA 0.804142 -570 ACATATCTGAAAAACTAACTTTGATAAAGAAGAAAAAA 26 99 1 AAAAAATAAA 0.804142 -502 TAAAGAAGAAAAAAAGAACACGGAAAAAAACGTTTTAT 26 123 1 AAAAAAAAAA 0.953211 -478 TCCTAGAAGAAAAAAAAATTTTCAGAAATGAAAAAAGT 26 329 1 AAAAAATAAA 0.804142 -272 ATCAACGTTGAAAAAAAAAATGTGGAAAAAACGAACTA 27 161 0 AAAAAAAGAA 0.661139 -140 ACAATACAGGAAAATAGAAAGAGAAAAACAGTAATATA 28 25 0 AAAAGAAAAA 0.909732 -545 CAGTAATACCAAAACAAACATCCAAACAAGCACTAGTA 29 37 1 AAAAAAAAAA 0.953211 -402 AAAAGTTGAAAAAAAAAAAATCCAAAAAATTCAAAAAC 30 200 1 AAAAAAAAAA 0.953211 -101 gttcagttgaaaaaaaaaaagaaagtgaagatcgtgtg 32 185 1 aaaaaaaata 0.713196 -116 AACACGTTTGAAAAAAGAAAAAAAGATACTTGTTGTGA 35 414 1 AAAAGAAAAA 0.909732 -113 **** ** * * * * Masking position 8 Map Score: 41.7811 Number of sites scoring better than the average of aligned sites = 5315 Number in coding regions = 1126 Number in noncoding regions = 4189 Number of orfs with sites within 600 bp upstream = 1501 Fraction of orfs with sites within 600 bp upstream = 0.241086 Motif number 2 TGGGAAATACCTTTTTTTAGTGACGCTACGC 2 194 0 CTTTTTTTGT 0.849423 -169 TTTTTTTTTTTTTCATCTATCCC 4 3 1 TTTTTTTTTT 0.862877 -298 CATAAACATAGTTTTCTTATTGTATCGTTAC 5 153 0 GTTTTCTTTT 0.853318 -448 GGAGTTGATACTTTTGTTTTTTCAAGTTGAA 6 181 0 CTTTTGTTTT 0.852498 -120 CTTTTTATTTTTACTCTAACAA 7 2 1 TTTTTATTTT 0.621959 -507 TTATCACTTCGTTTTTTTTTTCTTTCCGTGT 8 146 1 GTTTTTTTTT 0.921253 -155 CTGTCTGACTCTTTTTTTTTTAAAAAAATTC 9 63 1 CTTTTTTTTT 0.970459 -538 AAACTAGGAACTTTTTTTTTTGGAAGAATAA 12 321 1 CTTTTTTTTT 0.970459 -103 ACTTTTTCTCCTTTTCTTATTCTTCCAAAAA 12 337 0 CTTTTCTTTT 0.942316 -87 ATTAATTGTCCTTTTATTATTGTATTTTTCT 13 211 0 CTTTTATTTT 0.895713 -90 TTCTCTCGATCTTTTTTTGGTTTGGACGTTT 16 18 0 CTTTTTTTGT 0.849423 -583 TAGCTGTTCTCTTTTTTTTTTTCTTGTTTTT 16 392 1 CTTTTTTTTT 0.970459 -209 TCCTTACATAGTTTTGTTTTTCTTCGTTTTC 16 460 0 GTTTTGTTTT 0.67301 -141 TACAGCTAGCCTTTTTTTCTTAATCTTGCCG 18 142 1 CTTTTTTTTT 0.970459 -159 TTTACAGTATGTTTTCTTATTTTCCGATCCC 18 180 0 GTTTTCTTTT 0.853318 -121 GTCGGTTTCGCTTTTTTTCTTCTCGCTGTTC 21 125 0 CTTTTTTTTT 0.970459 -176 CGAGAACAAGCTTTCTTTTTTCCCTACCCTA 23 19 1 CTTTCTTTTT 0.663765 -382 GTTAGTTTGTGTTTTCTTGTTGCAATTATAA 23 118 0 GTTTTCTTTT 0.853318 -283 ATTTAACTATGTTTTTTTCTTTTGCTTTCAC 24 532 0 GTTTTTTTTT 0.921253 -69 GACAATTACACTTTTTTTTTTAGATTGTTCG 25 81 0 CTTTTTTTTT 0.970459 -220 CATTGATATTTTTTTTTTTTTCAGATTACAA 25 205 0 TTTTTTTTTT 0.862877 -96 TTTCCGTGTTCTTTTTTTCTTCTTTATCAAA 26 118 0 CTTTTTTTTT 0.970459 -483 TTCTGAAAATTTTTTTTTCTTCTAGGATTAC 26 325 0 TTTTTTTTTT 0.862877 -276 TGCTAAACCCGTTTTTTTGTTCTTAGCTTCA 28 440 1 GTTTTTTTTT 0.921253 -130 TTTTTTTCAACTTTTCTTTTTTCCCTCATTC 30 184 0 CTTTTCTTTT 0.942316 -117 TTTTTTGGATTTTTTTTTTTTCAACTTTTCT 30 198 0 TTTTTTTTTT 0.862877 -103 CCAGTCGCATCTTTTATTCGTTCAGTGATCT 31 209 0 CTTTTATTGT 0.595936 -92 tcttcactttctttttttttttcaactgaac 32 185 0 cttttttttt 0.970459 -116 ttttgaccattttttttttttcatgaggaag 33 95 1 tttttttttt 0.862877 -506 atcatttcaccttttattatttactgtcact 33 130 0 cttttatttt 0.895713 -471 GTCCGGGTAACTTTTCTTGTTCCACCTCTTT 35 143 0 CTTTTCTTTT 0.942316 -384 ACGTGTTTTTCTTTTATTCTTGCTAGAACTT 35 390 0 CTTTTATTTT 0.895713 -137 CAACAAGTATCTTTTTTTCTTTTTTCAAACG 35 418 0 CTTTTTTTTT 0.970459 -109 ******** ** Masking position 7 Map Score: 45.3445 Number of sites scoring better than the average of aligned sites = 2427 Number in coding regions = 725 Number in noncoding regions = 1702 Number of orfs with sites within 600 bp upstream = 1232 Fraction of orfs with sites within 600 bp upstream = 0.19788 Motif number 3 GACGTTTTTTGGCGGGTAATAAGATGCGTCT 3 150 0 GCGGGTAATA 0.984966 -151 GAAGTGATAAGCTGGGTAATACTTTTCTAAA 8 125 0 GTGGGTAATA 0.939271 -176 GCCCATTAATACCGGGTGACATAGTCCCACA 10 150 0 ACGGGTGACA 0.825308 -151 ACGGCTGCGTGCCGGGTAATAAATCAATTTT 12 131 1 GCGGGTAATA 0.984966 -293 CTGACGAATGAGCGGGTAATAAACTGTCTTT 14 184 1 ACGGGTAATA 0.948681 -154 CTTTTTGAAAGACGGGTAATAGAAAGTCTCT 15 370 0 GCGGGTAATA 0.984966 -173 CGCCTAGAATGCCGGGTAACAAAAAAGTAAT 16 188 1 GCGGGTAACA 0.97537 -413 TAGTGCTATGTTTGGGTGATAGAATCGTGTC 16 219 1 TTGGGTGATA 0.747474 -382 ATTGAAAACTTTCGGGTAATGCGTGGGTGAT 21 89 0 TCGGGTAATG 0.926137 -212 TTTTGTTGGTTTTGGGTAATAATAGGTTGTA 22 236 0 TTGGGTAATA 0.875013 -65 GCGCTGCCGCGCCGGGTAACAAGTGTGAAGA 24 224 0 GCGGGTAACA 0.97537 -377 TGTATGGGTGTGCGGGTAATGCTAAGATACG 26 373 1 TCGGGTAATG 0.926137 -228 TAGGATGAAAAATGGGTAATAGTAATAGTAC 28 198 0 ATGGGTAATA 0.813571 -372 AGGGGTACATTCCGGGTGATAGGATGAAAAA 28 217 0 TCGGGTGATA 0.926137 -353 TAAACTTTATGGCGGGTAACGCTCAAATAGT 34 150 1 GCGGGTAACG 0.943642 -151 * ********* Masking position 9 Map Score: 14.1198 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 37 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 4 AAAAAACGTCAAAAGTTTTAGGAACACGTCTAAA 3 171 1 AAAAGAGGAA 0.776745 -130 ATAACATGGTGTAAGTGATAGAGAGGTGAATGGC 5 393 1 GTAAGAGAGA 0.917566 -208 AATTATGCGGAAAAGTAAAAGCGAACAAAAAATT 13 172 0 AAAAGAGCGA 0.808785 -129 CTGTTAAGTAGAGAGAGAGAGAGAGTTTAAAGTG 15 43 0 GAGAGAGAGA 0.946668 -500 GATCAAGACGATAAGTTTGAGAGATTGTGAAGCT 15 265 1 ATAAGAGAGA 0.862744 -278 CCAAACCAAAAAAAGATCGAGAGAATTGACTGCG 16 24 1 AAAAGAGAGA 0.950756 -577 TTCCCGAGTGGAAAGGTTCAGAAATGCATCTGGA 24 11 1 GAAAGAGAAA 0.950756 -590 AACAAGTGTGAAGAGAGAGAGAGATGTAAGGAAG 24 204 0 AAGAGAGAGA 0.909287 -397 GAGAACGACAAAGAGAATGAGAGAGAACACGTAA 24 270 0 AAGAGAGAGA 0.909287 -331 GTTGCCGAAAGAAAGAATGAGAGAGAACGACAAA 24 292 0 GAAAGAGAGA 0.971582 -309 TTCAGTTGGTGAAAGCAAAAGAAAAAAACATAGT 24 524 1 GAAAGAGAAA 0.950756 -77 TTCTAATCACAAAAGATTCAGAAACTCTAGTTTG 26 11 1 AAAAGAGAAA 0.915985 -590 TGGGAGCTATGAAAGGCTGAGAGAGAAATTGAAT 26 163 0 GAAAGAGAGA 0.971582 -438 GGGTATAAATAAGAGACGCAGAAATGGTTATTGG 26 288 0 AAGAGAGAAA 0.849861 -313 TTCTTTACAAATAAGTGCAAGGGAGGAATTGTGT 28 373 1 ATAAGAGGGA 0.667315 -197 ATTTCCATCCAAAAGTTGTAGAAAATTTTGACCT 29 360 1 AAAAGAGAAA 0.915985 -79 TGACAATAGAGTAAGAATGAGGGAAAAAAGAAAA 30 170 1 GTAAGAGGGA 0.780318 -131 attaaacaatgaaagcggcagaaaaataaaatca 33 159 1 gaaagagaaa 0.950756 -442 ataagacagtgagagaaggagaaagcacttaaaa 33 252 0 gagagagaaa 0.909287 -349 ACATGAGATGGTAAGAGCAAGAAACAACGGTTCT 35 93 0 GTAAGAGAAA 0.862744 -434 TACAAAGGAGGAAAGTTCTAGCAAGAATAAAAGA 35 378 1 GAAAGAGCAA 0.808785 -149 ***** ***** Masking position 10 Map Score: 17.5905 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 425 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 5 GGAATTTTCCTAATCTCAAAACAAGTGGTAAATC 9 366 1 TACCAAACAA 0.839613 -235 TGATTTTTATACAGCTCAATACAAAGCAACAAAA 14 51 0 AACCAAACAA 0.885371 -287 AACAGGCCAAAAATAGCACTACAAAAAGGTTTTA 16 507 1 AAACACACAA 0.916958 -94 ACGCACCTATACAGCAAGACAAAAGATTTTAT 17 494 0 AAACAAACAA 0.9481 -22 TAGTCTATGTATATATCTATACAAACCACATCAT 21 46 0 AAACTAACAA 0.903926 -255 TTAACCCCATTGAGATCAACACAATTTCGAACAG 21 178 1 TAACAAACAA 0.925269 -123 AAATTAGACCTCAAACCACGACAAACTTCTGTCT 22 12 0 TAACACACAA 0.88213 -289 TTTCCATCACAAAGATCAATACAAAAGAAATATT 26 205 0 AAACAAACAA 0.9481 -396 ATGCATATAAATATAACTATACAAAATTAGGAGA 28 102 0 AAACTAACAA 0.903926 -468 GTATAATACAAAATAACTAAACAAATACGGATAG 28 503 1 AAACTAACAA 0.903926 -67 ATGACAACAGTAATACCAAAACAAACATCCAAAC 29 30 1 TAACAAACAA 0.925269 -409 GTCTTTATAGTAACCACTACACAAATAGGTATAT 34 72 1 TACCTAACAA 0.729449 -229 AACAATAAGTATACAACTAAACAAAGTCTGCTAC 34 202 1 AAACTAACAA 0.903926 -99 ACACACTACGTCACAACACAACAAGACA 35 5 0 TAACACACAA 0.88213 -522 CTGAACGTGGAAAGATCACAACAAGTATCTTTTT 35 433 0 AAACACACAA 0.916958 -94 * * * *** **** Masking position 11 Map Score: 8.42072 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 242 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 6 CTTTTCCAGGAAAAAATCGCAAAGTTGCAGCATCC 1 144 1 AAAAAACAGT 0.96218 -222 GTGTAAAGAGAAAAAAATACTAGGTGACATTTTAG 2 157 0 AAAAAACAGT 0.96218 -206 ATGGCGAGGTGAAAAAAATCGATGAGATGAAAAAA 5 44 0 GAAAAACAGA 0.824625 -557 TAATCAGCGAAAAAAATGGCGAGGTGAAAAAAATC 5 59 0 AAAAAACAGT 0.96218 -542 ACACATCAACAAAAAATATCAATGTTGATTTGTTA 7 27 0 AAAAAACAGT 0.96218 -482 AGGCGAGGGAAAAACAAAGCAACGAGAAAGGAAGC 7 228 1 AAAACACAGA 0.771326 -281 AAGAAGATAAGAAACAAGTCTAAGTGCTACTATAT 7 481 1 GAAACACAGT 0.76226 -28 CACGGAAAGAAAAAAAAAACGAAGTGATAAGCTGG 8 141 0 AAAAAACAGT 0.96218 -160 TTTTTTTTTTAAAAAAATTCAAGGTAAAACCTAAC 9 74 1 AAAAAACAGT 0.96218 -527 TCTTCCAAAAAAAAAAGTTCCTAGTTTATTTTCTT 12 313 0 AAAAAACTGT 0.633151 -111 TCGTCTCCAAGAAAAATAACAATGTAAATTGACCC 15 142 0 GAAAAACAGT 0.914262 -401 TGGTATAAGCAAAAAATGGCCAGAAACAGGCGATT 15 209 1 AAAAAACAAA 0.706187 -334 AAAACGAAGAAAAACAAAACTATGTAAGGAGGATG 16 461 1 AAAACACAGT 0.884386 -140 TTCTATGGTAGAAAAAGACCGAAAAATGAAAACAA 22 166 0 GAAAAACAAA 0.501852 -135 CTGAAAAAAAAAAAAATATCAATGATATTCAACAG 25 212 1 AAAAAACAGA 0.918154 -89 TTCAGAAATGAAAAAAGTTCTAGATGTATGGGTGT 26 349 1 AAAAAACAAT 0.84498 -252 TGAAACTAAAACAAAAAGGCAAGGTTAAAACAATA 28 57 0 ACAAAACAGT 0.718944 -513 CTCGTATCCAAAAAAACGCCTATGTATATTTCATT 28 318 0 AAAAAACAGT 0.96218 -252 AGTTGAAAAAAAAAAAATCCAAAAAATTCAAAAAC 30 203 1 AAAAAACAAA 0.706187 -98 AGGTAAAAAAAATGACCAGATTTGGACTTTC 31 7 1 AAAAAACAAT 0.84498 -294 ****** * * ** Masking position 6 Map Score: 16.5809 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 253 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 7 CTATTCAACTAAAGTAACAAAAATAAGCTGCG 6 214 1 AAAGAAAAAA 0.895152 -87 CTGTTGAAATAAAGTAGCGAAAAAAAGTTTGG 6 275 1 AAAGAGGAAA 0.920784 -26 AGGGAAAAACAAAGCAACGAGAAAGGAAGCTC 7 233 1 AAAGAAGAGA 0.849093 -276 GAGTACACGGAAAGAAAAAAAAAACGAAGTGA 8 149 0 AAAGAAAAAA 0.895152 -152 CTACACGTAGAAAGAAATCAGAAAACAACAGC 8 182 1 AAAGAACAGA 0.665627 -119 TATTAGGAGCAAAGCAGTAAAAAGTCTCTGAA 9 11 0 AAAGAGAAAA 0.942758 -590 AAAGAAAAGAAAAGCAACAAAACAGCTTCGTT 9 315 1 AAAGAAAAAA 0.895152 -286 TGGTTCTCAAAAAGCAACGAAAAATTTTCTGA 10 114 0 AAAGAAGAAA 0.857662 -187 GATAGGTAAAAAAGGAGAAAGAAGTACTAAGG 11 259 0 AAAGAGAAGA 0.938948 -42 AAGAATAAGAAAAGGAGAAAAAGTAGACATAC 12 344 1 AAAGAGAAAA 0.942758 -80 CGAGCGTAAAATAGTAGCAAGAGAATACTGTT 13 250 1 ATAGAGAAGA 0.63626 -51 AGCTCAATACAAAGCAACAAAACTAAAAATAG 14 41 0 AAAGAAAAAA 0.895152 -297 CGTCTTTCAAAAAGAAATGAGATACGTTGATC 15 387 1 AAAGAAGAGA 0.849093 -156 AAACACAGAAAAAGAAGGAAATAATGTATAAA 17 155 1 AAAGAGAAAT 0.651959 -361 GGAAGCAGGAAAAGAAGTAAAATTGGGCCGAG 18 246 1 AAAGAGAAAA 0.942758 -55 CCATTTGTTGAAAGGAGAGAAATTAAACTTGG 20 135 0 AAAGAGGAAA 0.920784 -466 AACGAAATCAAAAGAAATAAAATAAGCCATAA 25 257 1 AAAGAAAAAA 0.895152 -44 TAACTTTGATAAAGAAGAAAAAAAGAACACGG 26 114 1 AAAGAGAAAA 0.942758 -487 catcttcggtataggagggagatgtgtttgct 32 21 1 atagaggaga 0.552479 -280 aaagcacttaaaagaagaaagtcttaacttag 33 233 0 aaagagaagt 0.63626 -368 AGTTTACGTCAAAGAAAGAAGAATTGTTACGG 34 124 0 AAAGAAAAGA 0.888547 -177 GTATTATGGCAAAGCAGGCAAAACAACCGCTC 35 178 0 AAAGAGCAAA 0.804399 -349 **** ** **** Masking position 6 Map Score: 19.2817 Number of sites scoring better than the average of aligned sites = 1888 Number in coding regions = 837 Number in noncoding regions = 1051 Number of orfs with sites within 600 bp upstream = 779 Fraction of orfs with sites within 600 bp upstream = 0.12512 Motif number 8 TCCATAAACGTACATATATGACATCTACAA 8 88 0 TACATATATG 0.842845 -213 AAAATGCTGTTCCATAAACGTACATATATG 8 98 0 TCCATAAACG 0.899368 -203 TGTTTAGATGTACATATATGTCTAGATATG 12 37 0 TACATATATG 0.842845 -387 TTATAATAGATTCATATATGCGCGTACATA 13 95 1 TTCATATATG 0.789158 -206 TATTTTACATTCCATATACGAATAGTACGA 15 319 1 TCCATATACG 0.969835 -224 TCTTGTTTTTTCCATTTACGGCAGAAGAAA 16 413 1 TCCATTTACG 0.818969 -188 TCTTCAAACATCCATATACGGCTAGTAACT 20 407 1 TCCATATACG 0.969835 -194 AATAATTAATTACATATACGTACATAAGTA 20 467 0 TACATATACG 0.926294 -134 TTTGAAACGATCCATAAACGATCTAAAAAA 23 258 0 TCCATAAACG 0.899368 -143 CCATCTCATGTTCATATATGTTGGGGAAAA 35 116 1 TTCATATATG 0.789158 -411 ********** Masking position 5 Map Score: 2.52588 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 88 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 AATTAACCCATGGGAAATACCTTTTTTTAGT 2 204 0 TGGAAATACC 0.856526 -159 GCTTGCGTCTTGGGAAAAGCATTCCCAATAA 5 195 1 TGGAAAAGCA 0.971623 -406 AAGAGGATCATGGTAAATACAATTACATAAA 9 287 1 TGGAAATACA 0.846396 -314 GTATGGTAGATGGTATAAGCAAAAAATGGCC 15 199 1 TGGATAAGCA 0.798621 -344 CTGCCGTAAATGGAAAAAACAAGAAAAAAAA 16 406 0 TGGAAAAACA 0.939389 -195 GAACGGAATGTGGCAAAAGCCTGAACCAGGC 18 22 1 TGGAAAAGCC 0.973751 -279 ACATAAGATCTGGAAAAAACCAACAGCTACA 19 91 0 TGGAAAAACC 0.943793 -257 TTTTTTCCATTGGCAAAAGCGATTTCAAAAA 19 242 1 TGGAAAAGCG 0.950955 -106 AAGGTTCAGTTGGTGAAAGCAAAAGAAAAAA 24 520 1 TGGGAAAGCA 0.854609 -81 AAAAAAAATGTGGAAAAAACGAACTAGCCAG 27 156 0 TGGAAAAACG 0.897714 -145 aagtttatagtggaaaatgccacatgtacgg 33 371 0 tggaaatgcc 0.929523 -230 GAACATGAGATGGTAAGAGCAAGAAACAACG 35 98 0 TGGAAGAGCA 0.854609 -429 *** ******* Masking position 1 Map Score: 2.9102 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 313 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 10 ATTAAAGATAAAATATTCAACTATTTAGCGCGCTCA 2 11 0 AAATTACATT 0.510888 -352 ATTTGCTTATAAAGGTTGTACTATTTACTTGTAGTT 2 54 1 AAGTTACATT 0.625401 -309 CGTGTTCCTAAAACTTTTGACGTTTTTTGGCGGGTA 3 163 0 AATTTACTTT 0.929794 -138 ATATTATTTCAACTTTTAGACGTGTTCCTAAAACTT 3 183 0 AATTTACTTT 0.929072 -118 ATATTTCATCAATTTTTTCACATATTATTTCAACTT 3 204 0 AATTTACTTT 0.896988 -97 GTGTATATACAGTATGTCTACTTTTTCTCCTTTTCT 12 351 0 AGTGTACTTT 0.520187 -73 TACGTAATAAGTGCACTTTTTCTTGCCTTCT 15 6 1 AAAGTACTTT 0.463513 -537 TCCCTACCCTAAACTGTATACATATTTACATTCATC 23 39 1 AATGTACTTT 0.775245 -362 GTGATTTAAGTATATTTAAACGTATTTGGCTTGTCT 23 213 1 TATTTACTTT 0.625724 -188 ATAGCAAATAAATTGGTACACTTCTTCAGCCGCTTT 25 115 1 AAGGTACTTT 0.564361 -186 GCCGCTTTAAAAATTGTGTACTTCTTCTTAAAACAA 25 143 1 AATGTACTTT 0.62897 -158 ATAGGATTCTAATATTGTAACTTATTAAAGAGAGGA 26 241 1 AATTGACTTT 0.720879 -360 TTTTATTCCTAATGTGTACACTATTTGACCCAAAAG 27 72 0 AATGTACATT 0.762955 -229 CTAAAGGTCAAAATTTTCTACAACTTTTGGATGGAA 29 362 0 AATTTACATT 0.792446 -77 taaatttcaaaattttttgaccattttttttttttc 33 81 1 aatttacatt 0.810268 -520 ttcattgtttaatcatttcaccttttattatttact 33 136 0 aaattacttt 0.753417 -465 taaccaaggaaaccgttgtacctattattttgtata 33 550 1 aagttacttt 0.827516 -51 ATCGGTTTTGAAATTTTTCACTTCTTCAACCAAGTA 34 25 0 AATTTACTTT 0.921786 -276 AGACTTTGTTTAGTTGTATACTTATTGTTATTTGAA 34 195 0 TATGTACTTT 0.587531 -106 TAAACAAGATAAGCTTGCTACTTTTTCAGCACAACC 34 254 1 AATTGACTTT 0.721153 -47 ** *** ** * ** Masking position 15 Map Score: 3.05272 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 387 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 11 GAGTGTGCACATGCTTGGTTTGGCGGAACG 5 581 1 AGCTTTTGGC 0.938782 -20 TGGAAATTTTATGTTTAGTTAGGTTTTACCTTGA 9 92 0 AGTTTTTGGT 0.952446 -509 TAGAGGTAGAATGCTTTGTTTGGTATAACGTTTC 12 205 0 AGCTTTTGGT 0.9779 -219 TTGATTAGTAAAGCTTAGTTCCGTTTTCAATCAC 13 50 0 AGCTTTTCGT 0.957694 -251 AGGAACAGTCAGGCTTTCTTAGGTTTCAGAAGTT 16 70 0 AGCTTTTGGT 0.9779 -531 CACTACAAAAAGGTTTTATCTGGCACTCAGGTCC 16 523 1 AGTTTTCGGC 0.706373 -78 GGAAAAAAGAAAGCTTGTTCTCGTTTGTCCC 23 8 0 AGCTTTCCGT 0.886947 -393 GGTTGAATAAGCTTGCTTTGGTATGCCTTTAA 23 379 0 AGCTTTTGGT 0.9779 -22 AATCCATAAAACGTTTTTTTCCGTGTTCTTTTTT 26 132 0 AGTTTTTCGT 0.911084 -469 ATATGAAATCATGTTTATTTACGTGTTAGATGTT 27 109 1 AGTTTTTCGT 0.911084 -192 GCTTGTTTGGATGTTTGTTTTGGTATTACTGTTG 29 34 0 AGTTTTTGGT 0.952446 -405 TTTGTTGCGAAGGCCTTCTTTGGTCAATTATAAC 31 251 0 AGCCTTTGGT 0.883667 -50 * **** ** *** Masking position 1 Map Score: 5.13872 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 102 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 ACACAGCACGGTGTTTTTCTTTTGCTTAAA 5 466 1 GTGTTTTTCT 0.930847 -135 AAGTACTAAAGTGTATATCTTAAGAGCATC 7 77 0 GTGTATATCT 0.816835 -432 AGAAAATATTTTATATTTCTCCGGAAAATG 7 352 0 TTATATTTCT 0.711611 -157 TTCTTTTCACTTATTTTTCTGTTTATATCG 11 175 1 TTATTTTTCT 0.792434 -126 TTTTATTATTGTATTTTTCTGGAAGAATTA 13 201 0 GTATTTTTCT 0.843492 -100 ATTTACATTGTTATTTTTCTTGGAGACGAC 15 148 1 TTATTTTTCT 0.792434 -395 TTACATAGTTTTGTTTTTCTTCGTTTTCGT 16 458 0 TTGTTTTTCT 0.90508 -143 TTACTTTCCGGTATATTTCTGTAGTATATT 19 306 0 GTATATTTCT 0.776953 -42 TAAGGTATTTTTGTTTATCTGGGCTACTTA 20 443 1 TTGTTTATCT 0.830153 -158 GATAGTCTATGTATATATCTATACAAACCA 21 52 0 GTATATATCT 0.641003 -249 TGGGCTCTACTTGTTTATCTTCTATGGTAG 22 190 0 TTGTTTATCT 0.830153 -111 AGATATATTACTGTTTTTCTCTTTCTATTT 28 22 1 CTGTTTTTCT 0.856571 -548 TACCCGGAACTTGTATTTCTGCGTTCGCTG 29 235 1 TTGTATTTCT 0.860391 -204 TGTTATATATCTGTATTTCTATCACGTATC 30 257 0 CTGTATTTCT 0.794236 -44 ctgtttgattttatttttctgccgctttca 33 168 0 ttatttttct 0.792434 -433 tgtcttatcgctgtatatctcattgttgaa 33 278 1 ctgtatatct 0.664269 -323 TTTTTCAAACGTGTTTTTCTTTTATTCTTG 35 399 0 GTGTTTTTCT 0.930847 -128 ACTGAAGCCAGTGTTTATCTGTCTGTCGCC 35 482 1 GTGTTTATCT 0.873414 -45 ********** Masking position 6 Map Score: 9.21384 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 457 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 13 GTTGTGCGTACCTCTTTCCTGTACTTGAAT 3 264 0 CCTCTTTCCT 0.960687 -37 CATCTATCCCCTTCCATCCCCTTCTGGTTC 4 24 1 CTTCCATCCC 0.713997 -277 CAGATCCATTCCTCTATTCCTGTAGTCGGG 4 133 1 CCTCTATTCC 0.817036 -168 TCAACAGAAACTTCTTTCCTAGTTTAGCAG 6 252 0 CTTCTTTCCT 0.938529 -49 AAACGTTCACCTTCTTTCCTGTAGAGGGAA 7 160 0 CTTCTTTCCT 0.938529 -349 CAACTTTGAGCTTCCTTTCTCGTTGCTTTG 7 242 0 CTTCCTTTCT 0.842092 -267 CTATTTTTGGCCTGTTTCCTGATGTACCAT 16 493 0 CCTGTTTCCT 0.722125 -108 CCCAATTTTACTTCTTTTCCTGCTTCCCTA 18 243 0 CTTCTTTTCC 0.886973 -58 CACTTTGCACCCTCCATCCTCAATTCCTGC 24 414 1 CCTCCATCCT 0.829266 -187 TGCTCTCATGCTTCTTTTCTATTTTGAGTT 31 55 1 CTTCTTTTCT 0.905115 -246 TCTTGTTCCACCTCTTTTCCCCAACATATA 35 130 0 CCTCTTTTCC 0.926255 -397 GCCTCCCCTTCCTCTTTTCTAGCC 35 513 1 CCTCTTTTCT 0.938529 -14 ********** Masking position 7 Map Score: 2.79945 Number of sites scoring better than the average of aligned sites = 857 Number in coding regions = 521 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 297 Fraction of orfs with sites within 600 bp upstream = 0.0477032 Motif number 14 ********** No masking Map Score: -4.68934e-11 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 TTTTTTTTTTCTTTCCGTGTACTCGCTACAC 8 157 1 CTTCCGTGTA 0.902981 -144 CCTGCACACGCTGTCCGGGTAAATAGAATTG 9 453 1 CGTCCGGGTA 0.981739 -148 ATCACGGCTGCGTGCCGGGTAATAAATCAAT 12 128 1 CTGCCGGGTA 0.987391 -296 TTCCGCCTAGAATGCCGGGTAACAAAAAAGT 16 185 1 ATGCCGGGTA 0.939099 -416 GGAGCGCTGCCGCGCCGGGTAACAAGTGTGA 24 227 0 CCGCCGGGTA 0.960152 -374 CTTAAGTGTCCTTTCCTGGTATATCGCTTGA 27 234 1 CTTCCTGGTA 0.902981 -67 ACAAGGGGTACATTCCGGGTGATAGGATGAA 28 220 0 CTTCCGGGTG 0.956859 -350 CAGAAATACAAGTTCCGGGTAGTCACATGGA 29 225 0 ATTCCGGGTA 0.949225 -214 AACCGCTCTGCCGTCCGGGTAACTTTTCTTG 35 155 0 CGTCCGGGTA 0.981739 -372 * ********* Masking position 10 Map Score: 3.15764 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 22 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392