AlignACE version 2.2 July 7, 1998 AlignACE -jVPS.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 YAL002W 600 bp YAL002W VPS8 1-3531 Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif. #2 YBR097W 300 bp YBR097W vps15 1-4365 Myristoylated Serine\/threonine protein kinase involved in vacuolar protein sorting #3 YDR080W 600 bp YDR080W vps41 1-2979 vacuolar protein sorting #4 YDR495C 300 bp YDR495C vps3 1-3036 Vacuolar sorting protein #5 YGL095C 510 bp YGL095C VPS45 1-1734 cytosolic and peripheral membrane protein #6 YHR012W 360 bp YHR012W VPS29 1-48, 168-968 Vacuolar protein sorting #7 YJL154C 396 bp YJL154C vps35 1-2835 Protein involved in vacuolar sorting #8 YKL041W 575 bp YKL041W VPS24 1-675 #9 YKR001C 509 bp YKR001C VPS1 1-2115 putative GTP-binding protein\; similar to mammalian Mx proteins #10 YLL040C 416 bp YLL040C VPS13 1-9435 #11 YLR240W 300 bp YLR240W vps34 1-2628 phosphatidylinositol 3-kinase #12 YLR360W 372 bp YLR360W VPS38 1-1320 #13 YLR396C 300 bp YLR396C vps33 1-2076 Vacuolar sorting protein essential for vacuolar morphogenesis and function #14 YLR417W 300 bp YLR417W VPS36 1-1701 defective in vacuolar protein sorting #15 YML097C 300 bp YML097C VPS9 1-1356 required for Golgi to vacuole trafficking, shares similarity to mammalian ras inhibitors #16 YNR006W 600 bp YNR006W VPS27 1-1869 hydrophilic protein\; has cysteine rich putative zinc finger esential for function #17 YOR069W 600 bp YOR069W VPS5 1-939 Sorting nexin I homologue #18 YOR089C 300 bp YOR089C vps21 1-633 small GTP-binding protein\; geranylgeranylated\; geranylgeranylation required for membrane association\; also involved in endocytosis post vesicle internalization #19 YOR132W 336 bp YOR132W vps17 1-1656 Peripheral membrane protein required for vacuolar protein sorting #20 YPL120W 440 bp YPL120W VPS30 1-1674 Required for sorting and delivery of soluble hydrolases to the vacuole. #21 YPL065W 300 bp YPL065W VPS28 1-729 soluble, hydrophilic protein involved in transport of precursors for soluble vauolar hydrolases from the late endosome to the vacuole #22 YPL045W 316 bp YPL045W vps16 1-2397 Vacuolar sorting protein #23 YPR173C 300 bp YPR173C VPS4 1-1314 defective in vacuolar protein sorting Motif number 1 AATAATGAAATTTTCCTTTTCTTCTAATCGT 1 97 0 TTTTCTTTTC 0.938674 -504 TTATATGTCTTTCTCGTTTTTGCCATGTTAA 1 134 0 TTCTCTTTTT 0.892929 -467 GAGGTTCCCTTTTTTTTTTTTCCACAGGAAA 1 177 0 TTTTTTTTTT 0.958081 -424 ATATATCTGTTTTTCATTTTTATGATGTTGA 2 196 0 TTTTCTTTTT 0.949248 -105 TAATTACTGATTTTCTTCTTCATCCATAGGA 3 193 1 TTTTCTCTTC 0.849858 -408 CCCTTTTAATTTTTCTTTTGTATCGTATTAT 3 501 0 TTTTCTTTGT 0.81352 -100 AACGACTCTCTTTTTCTTTTTCCGCCTACCT 7 20 1 TTTTTTTTTT 0.958081 -377 AGTCTTTATATTTTTTTTTTTTCTTTTGAAC 7 141 1 TTTTTTTTTT 0.958081 -256 GCGTTTTTTATTTTTTTTTTTTTTTTTCAGT 7 203 1 TTTTTTTTTT 0.958081 -194 TTTCTCTCTTTTCTTCTCTTTACTGAGGTGG 7 272 0 TTCTTTCTTT 0.790297 -125 CACCACCTTCTTTTTTTTTTTCTCTCTTTTC 7 290 0 TTTTTTTTTT 0.958081 -107 TTACTCTCCTTTTTTCTTTTTGGTTTTTTTT 10 52 1 TTTTTTTTTT 0.958081 -365 TTCTTTTTGGTTTTTTTTTTTTTTTGATAAA 10 65 1 TTTTTTTTTT 0.958081 -352 CTGTTCTTAATTTTCCTTTTTTCTGCCTTTT 10 392 0 TTTTCTTTTT 0.949248 -25 TGGGATATATTTTTCATCTTCTTCCTTCATA 12 141 1 TTTTCTCTTC 0.849858 -232 CCTTTCATTTTTCTTGTTTTTTTGGCTTACG 12 174 1 TTCTTTTTTT 0.910641 -199 TAGTCAATTCTTTTCCTTTGTGTGCTCAATA 13 81 1 TTTTCTTTGT 0.81352 -220 GTGAAACCCTTTTTCCTCTTCGTTGATCCTA 14 151 0 TTTTCTCTTC 0.849858 -150 TTTCTCTGCTTTTTTGTTTTTCAGTCTCCAT 14 200 0 TTTTTTTTTT 0.958081 -101 TTGAAAGTCATTCTTTTTTTTTCAAAAG 14 283 1 TTCTTTTTTT 0.910641 -18 ATTATCAAGATTTTTTTTTGCTAAGGTGAAT 16 552 1 TTTTTTTTGC 0.81352 -49 AACAAATTCATTCTCTTTTTCAGCTTTCTTT 17 109 0 TTCTCTTTTC 0.8722 -492 CTCATACGTGTTTTTTTTTTTTTTGGTTTTC 18 102 1 TTTTTTTTTT 0.958081 -199 ACGATCTTGCTTTTTATTTTTAAAATCGTTG 18 233 0 TTTTTTTTTT 0.958081 -68 TTTTCTGGTTTTTTCGTTTTCTTTACACTTT 19 137 1 TTTTCTTTTC 0.938674 -200 GCTGATCTAATTTTTTTTTGCCGTACTGTAC 19 287 1 TTTTTTTTGC 0.81352 -50 AAGTTCAAGTTTCTTGTTTTCTTTCCTATTT 20 76 1 TTCTTTTTTC 0.892929 -365 CTATAGTCTTTTTTTCTCTTCATGTAGAAAA 21 179 0 TTTTTTCTTC 0.873687 -122 AACCATAACTTTTTTTTTTTTGCCGGACGCT 21 208 0 TTTTTTTTTT 0.958081 -93 ttgtgcttcctttttttttttacttcttgat 22 96 1 tttttttttt 0.958081 -221 gattttccacttctttttttttgattttggg 22 124 1 ttcttttttt 0.910641 -193 GAAGTTCTTATTTTTTTTTTTTTTTCACCCA 23 194 0 TTTTTTTTTT 0.958081 -107 TGCTGCTTTATTTTTGTCTTCCATGTCCTCA 23 252 0 TTTTTTCTTC 0.873687 -49 ***** ***** Masking position 7 Map Score: 54.0562 Number of sites scoring better than the average of aligned sites = 10805 Number in coding regions = 1821 Number in noncoding regions = 8984 Number of orfs with sites within 600 bp upstream = 2222 Fraction of orfs with sites within 600 bp upstream = 0.35689 Motif number 2 TAACCAGAGGTTCCCTTTTTTTTTTTTCCACAG 1 181 0 TTCCCTTTTT 0.809175 -420 CAAGGTAAATTTCCCTTATTTTTCAACATCATA 2 174 1 TTCCCTTTTT 0.809175 -127 ATTTTATAATTTTTTTGAATTTTTTGTATACTT 5 68 0 TTTTTTTTTT 0.928137 -443 TTTATATTTTTTTTTTTTCTTTTGAACTATTGC 7 145 1 TTTTTTTTTT 0.928137 -252 TTTTTATTTTTTTTTTTTTTTTTCAGTTGAGGT 7 207 1 TTTTTTTTTT 0.928137 -190 TTCTTTTTTTTTTTCTCTCTTTTCTTCTCTTTA 7 281 0 TTTTCTTTTT 0.965872 -116 ATTGTTACTTTTCTTTCAGTTTTCATTAACTAC 8 201 1 TTCTTTTTTT 0.929406 -375 TTGGAATGTATTTTCTAAGGTTTAAAGTAGTTA 8 227 0 TTTTCTGTTT 0.82595 -349 TATATATGTTTACTCTCCTTTTTTCTTTTTGGT 10 43 1 TACTCTTTTT 0.59891 -374 TCTTTTTGGTTTTTTTTTTTTTTTGATAAATAC 10 66 1 TTTTTTTTTT 0.928137 -351 AATTTTCCTTTTTTCTGCCTTTTCCCTTTTGGT 10 382 0 TTTTCTTTTT 0.965872 -35 CTCCTTTCATTTTTCTTGTTTTTTTGGCTTACG 12 172 1 TTTTCTTTTT 0.965872 -201 CTTTCTCGAATTTTCTATCTTTTAACTAATTAA 13 228 0 TTTTCTTTTT 0.965872 -73 GGATGACCTTTTCTCTGCTTTTTTGTTTTTCAG 14 207 0 TTCTCTTTTT 0.966499 -94 TATTTTTCACTTTTCTTTCTTTTTTATTATTTT 15 154 1 TTTTCTTTTT 0.965872 -147 TTGATTCCTGTTCTTTGTTGTTTGATGAAGAGA 15 273 0 TTCTTTGTTT 0.688233 -28 GAAGCAGTTGTTCTCTTCGCTTTCAGAGAATGG 17 40 0 TTCTCTCTTT 0.875718 -561 GCCCTCATTGTTTTCTCTCCTTTCATTCCTATC 17 155 0 TTTTCTCTTT 0.873616 -446 TTTTCCAAACTTTTCTGAGTTTTCCTCGACCTC 17 284 0 TTTTCTTTTT 0.965872 -317 GTGTTTTTTTTTTTTTTGGTTTTCTCGGTTTGC 18 109 1 TTTTTTTTTT 0.928137 -192 TCACTTCTCTTTCTTTGTCTTTTCGGGGATATT 18 165 0 TTCTTTTTTT 0.929406 -136 TATATATGACTTTTCTGGTTTTTTCGTTTTCTT 19 127 1 TTTTCTTTTT 0.965872 -210 TTTTTTCGTTTTCTTTACACTTTTTTCCATAGC 19 145 1 TTCTTTCTTT 0.762782 -192 tccacttctttttttttgattttgggaacgtac 22 129 1 tttttttttt 0.928137 -188 tactattcctttctctccttttttcctctattg 22 255 0 ttctcttttt 0.966499 -62 AGTTCTTATTTTTTTTTTTTTTTCACCCAGCGG 23 190 0 TTTTTTTTTT 0.928137 -111 ****** **** Masking position 6 Map Score: 38.053 Number of sites scoring better than the average of aligned sites = 1333 Number in coding regions = 567 Number in noncoding regions = 766 Number of orfs with sites within 600 bp upstream = 584 Fraction of orfs with sites within 600 bp upstream = 0.0938002 Motif number 3 ATGAAATTTTCCTTTTCTTCTAATCGTGAA 1 94 0 CCTTTTCTTC 0.764939 -507 CCAGAGGTTCCCTTTTTTTTTTTTCCACAG 1 181 0 CCTTTTTTTT 0.795956 -420 GAACTAGATGCCAGTTTTTCACTTAATTGG 1 413 0 CCAGTTTTTC 0.762077 -188 GGGAAATTTACCTTGTTTTCTACCGAAGAT 2 159 0 CCTTGTTTTC 0.928583 -142 TTAAGATATATCTGTTTTTCATTTTTATGA 2 202 0 TCTGTTTTTC 0.751092 -99 TTGCACCTGACCACTTTTTCTTCCTTATAT 3 30 1 CCACTTTTTC 0.839001 -571 CTTGCTCTAGCCATTTTTTCGTTCTTTTAC 3 401 1 CCATTTTTTC 0.914183 -200 GTTAAACTTGCCTTTTTTTCCCATCGGAAC 4 170 0 CCTTTTTTTC 0.976045 -131 AAGGAGACTACCTTTTTTTGGTTGCAACCA 4 266 1 CCTTTTTTTG 0.695881 -35 TCTTGTTAAACCTTTTTGTCATCACACGCC 5 165 1 CCTTTTTGTC 0.904812 -346 AAGGGTAAGACCTTCTTTTCTGGTAATAGA 5 227 0 CCTTCTTTTC 0.961876 -284 TTTCAACGACTCTCTTTTTCTTTTTCCGCC 7 16 1 TCTCTTTTTC 0.830779 -381 TGAACTATTGCCTCTTTGTCACTTCGTCTT 7 167 1 CCTCTTTGTC 0.823009 -230 ACATACACCACCTTCTTTTTTTTTTTCTCT 7 296 0 CCTTCTTTTT 0.707218 -101 TTATGAGTTTCCTTTTTTTCTAAAGTATAA 12 219 0 CCTTTTTTTC 0.976045 -154 GGAAGCTTCGCCTTGTTTTCCAGACGCGCT 14 116 1 CCTTGTTTTC 0.928583 -185 TTTTCAGTCTCCATCTTTTCCAGATGAAAC 14 184 0 CCATCTTTTC 0.868358 -117 TCTTGCTCGGCCTCCTTTTCTGAAAATTTC 16 465 1 CCTCCTTTTC 0.925051 -136 ACAAATTCATTCTCTTTTTCAGCTTTCTTT 17 109 0 TCTCTTTTTC 0.830779 -492 AAAAATTAGATCAGCTTTTCAAAACAAACT 19 272 0 TCAGCTTTTC 0.328192 -65 AGTTCAAGTTTCTTGTTTTCTTTCCTATTT 20 77 1 TCTTGTTTTC 0.76205 -364 ATATTTATATTCTTCTTGTCCCGCACTCTG 21 139 1 TCTTCTTGTC 0.591797 -162 GACGCTATAGTCTTTTTTTCTCTTCATGTA 21 184 0 TCTTTTTTTC 0.909386 -117 acttgtgcttcctttttttttttacttctt 22 94 1 cctttttttt 0.795956 -223 tcctttctctccttttttcctctattgatt 22 252 0 ccttttttcc 0.764939 -65 ********** Masking position 6 Map Score: 20.7222 Number of sites scoring better than the average of aligned sites = 2698 Number in coding regions = 1621 Number in noncoding regions = 1077 Number of orfs with sites within 600 bp upstream = 871 Fraction of orfs with sites within 600 bp upstream = 0.139897 Motif number 4 CCAGAGGTTCCCTTTTTTTTTTTTCCACAGGA 1 179 0 CCTTTTTTTT 0.759318 -422 TTTTTGATAACCTTACAGCTTTTGTATTTCTC 2 262 0 CCTTAACTTT 0.6521 -39 CAAGTATACATCTTTAACCGTT 3 1 0 TCTTTACGTT 0.622719 -600 TCTCAATAGCCCTTTTAATTTTTCTTTTGTAT 3 509 0 CCTTTATTTT 0.933926 -92 AATCGAGTTCTCTTTCATCTTTAGGAAAAATA 6 130 0 TCTTTACTTT 0.899192 -231 TTCCGTAACACCTTTCAGTTTTACTATTCCGC 6 236 1 CCTTTATTTT 0.933926 -125 TCGTCCTCCTCCTTTTATCGTTATATATTAAC 7 352 0 CCTTTACGTT 0.87015 -45 ATATAAAAGGCCTTTACGTTTCCGGCTTCTGT 8 128 0 CCTTTCTTTC 0.459653 -448 TTGTTACTTTTCTTTCAGTTTTCATTAACTAC 8 202 1 TCTTTATTTT 0.776858 -374 TTCATTAACTACTTTAAACCTTAGAAAATACA 8 222 1 ACTTTACCTT 0.412103 -354 TAGTTTAGTGTCTTTAAACTTTTGCTAAAACG 9 116 1 TCTTTACTTT 0.899192 -394 TGTTTACTCTCCTTTTTTCTTTTTGGTTTTTT 10 49 1 CCTTTTCTTT 0.889905 -368 ATTGAGTCAACCTTTTAACTCTATTTAATTTG 10 328 1 CCTTTACTCT 0.935024 -89 CTTTTTTCTGCCTTTTCCCTTTTGGTAGTCAC 10 376 0 CCTTTCCTTT 0.907072 -41 TTTACTTTATCCTTTAATCCTTTTGACTCAAA 11 229 0 CCTTTACCTT 0.940761 -72 CCTTCATACTCCTTTCATTTTTCTTGTTTTTT 12 164 1 CCTTTATTTT 0.933926 -209 CATGTGAAACCCTTTTTCCTCTTCGTTGATCC 14 153 0 CCTTTTCTCT 0.76258 -148 ACGGAGCCTACCTTTTAGCTTTTGCTGCCAAA 16 39 1 CCTTTACTTT 0.973129 -562 CGATTATATATCTTTCAATCTTGGTTTAGTTT 16 68 0 TCTTTATCTT 0.604227 -533 CGCCTGGTGTCCTTTGAGCCTCACTTATATAA 16 361 1 CCTTTACCTC 0.780023 -240 GTTTGGAGTTTCTTTGAGCTCTGGC 17 4 0 TCTTTACTCT 0.779952 -597 TGTTTTCTCTCCTTTCATTCCTATCGTCCAAT 17 148 0 CCTTTATCCT 0.711236 -453 TTTTTCGTTTTCTTTACACTTTTTTCCATAGC 19 146 1 TCTTTCCTTT 0.706247 -191 ATTACATAGTCCTTTTACCTTCATTAGTAGTA 20 285 1 CCTTTACTTC 0.889941 -156 ATAGCACTACCCTTTTACTTCTATGAGAGCAA 20 342 0 CCTTTATTCT 0.848866 -99 acttgtgcttcctttttttttttacttcttga 22 94 1 cctttttttt 0.759318 -223 ***** * **** Masking position 4 Map Score: 18.4824 Number of sites scoring better than the average of aligned sites = 1567 Number in coding regions = 1023 Number in noncoding regions = 544 Number of orfs with sites within 600 bp upstream = 436 Fraction of orfs with sites within 600 bp upstream = 0.0700289 Motif number 5 CGTGAGTTTCCTGTGGAAAAAAAAAAAAGGG 1 171 1 CTTGGAAAAA 0.950277 -430 CACAGAGAAACTTTTGAAAGAAGATAGATTT 2 110 0 CTTTGAAAGA 0.811435 -191 CATTTTTATGATGTTGAAAAATAAGGGAAAT 2 182 0 ATTTGAAAAA 0.707743 -119 TATTCAAATAGTATTGAAAAAGCTGAATGAG 3 159 1 GTTTGAAAAA 0.905112 -442 AGCCAAGATACTTTTGTAAAAGAACGAAAAA 3 415 0 CTTTGTAAAA 0.850953 -186 TTGTATCGTATTATTGAAAAAAGACGAGCAA 3 484 0 TTTTGAAAAA 0.808065 -117 GCTATTGAGACTGTTGTAAAATATATATGCA 3 531 1 CTTTGTAAAA 0.851004 -70 TTTCCGGCTTCTGTTGGAAAATAACAATGGA 8 111 0 CTTTGGAAAA 0.827607 -465 TAAAACGTTTCACTTGAAAAATCGTTCTAAT 9 141 1 CATTGAAAAA 0.743826 -369 AAAATCCAAGCTCTTGAAAACCAACATGAAT 10 143 0 CTTTGAAAAC 0.927873 -274 GACTCAAACTTTCTTGAAAAAGTGTTTGATG 11 206 0 TTTTGAAAAA 0.809739 -95 TTATATGTTACTAATGAAAAAAATAACAATT 12 49 1 CTATGAAAAA 0.743825 -324 AATGTTTATACTTTAGAAAAAAAGGAAACTC 12 214 1 CTTAGAAAAA 0.785434 -159 AAAAAAGCGCGTCTGGAAAACAAGGCGAAGC 14 120 0 GTTGGAAAAC 0.563662 -181 CTTTTGAAAAAAAAAGAATGA 14 290 0 CTTTGAAAAA 0.976467 -11 TTCACAGCTTCTGTTGAAAAAAATATCCTTG 17 191 1 CTTTGAAAAA 0.977158 -410 ACTCAGAAAAGTTTGGAAAAACCAAGATTGG 17 297 1 GTTGGAAAAA 0.811016 -304 TGAACGCGTGCTATGGAAAAAAGTGTAAAGA 19 156 0 CTTGGAAAAA 0.950276 -181 AGTTCAATCACTCTTGAAAACGTCCCCTTTC 19 202 0 CTTTGAAAAC 0.927873 -135 ATCTATAAAGCTTTTGAATAATGCTAATGTA 21 104 1 CTTTGAATAA 0.743291 -197 ** ******** Masking position 8 Map Score: 12.5794 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 662 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 6 TGGTCTCGGCAGATATATATTTTACACTTAT 1 269 0 AATATATATT 0.874919 -332 TTATCTAAGAATATATATAATCCTATGGATG 3 213 0 AATATATAAT 0.922262 -388 TTTTTATTTTGCATATATATTTTACAACAGT 3 540 0 GATATATATT 0.903725 -61 GAAAGTGCAGGTATATATAATTGTCTCCTAA 4 102 1 GATATATAAT 0.940901 -199 GTTGATTACAGTATATATAATAGTACACAAA 5 111 0 GATATATAAT 0.940901 -400 AAAATCTTGTAAATATGTAATCTTATGTTAA 6 19 1 AATATGTAAT 0.819925 -342 GTTATGTTAAGTATATGTATTGATGGAAGGG 7 86 0 GATATGTATT 0.782736 -311 TCTCATTATAGGATATATAATAAGAATTTGT 8 169 1 GATATATAAT 0.940901 -407 GAGAGTAAACATATATATATTGACATAATGA 10 29 0 AATATATATT 0.874919 -388 CAAGATTGAAAGATATATAATCGACTATCTT 16 77 1 AATATATAAT 0.922262 -524 AGAAGAATATAAATATATAATACATTAGCAT 21 124 0 AATATATAAT 0.922262 -177 * ********* Masking position 5 Map Score: 4.46772 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 93 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 7 ATTCTAACATGTACATACCTGTATAGTCGTA 3 65 1 GTAATACCTG 0.887474 -536 TTAACGAAGAGTATATACCTACTATTAGACA 3 577 1 GTAATACCTA 0.976679 -24 TTATAAAATAGTAAGTACATATGAATATTTC 4 202 0 GTAGTACATA 0.872764 -99 ACGTTGTATCGTAAATACTTACCATACGCTT 6 187 1 GTAATACTTA 0.844533 -174 AAATCTAAAGGAATATACCTAAGCGTATGGT 6 207 0 GAAATACCTA 0.961078 -154 ATTGTTCGGTGTATATACATATATATGTCAA 8 477 0 GTAATACATA 0.947013 -99 CACTTCACACGAACATACATAAATAAAATAT 13 164 1 GAAATACATA 0.913327 -137 AAAAAATCGGGAAAATACCTAGGTTGGTTAA 16 290 0 GAAATACCTA 0.961078 -311 AAATCCTCTGGTATATACCTACCTCAGCATA 18 28 0 GTAATACCTA 0.976679 -273 TATTTATGCGGAAGGTACATAGAAGTTTGGG 20 102 1 GAAGTACATA 0.801757 -339 taaagtcagcgtaaataccaaacctatatcc 22 191 1 gtaataccaa 0.841805 -126 *** ******* Masking position 7 Map Score: 4.45982 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 60 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 8 AAGGACAGTTATTACCAATACATACAAAGG 1 235 1 ATTACCAATA 0.731882 -366 AGTAATATCTATTACCAGAAAAGAAGGTCT 5 220 1 ATTACCAGAA 0.890921 -291 CTTTCCTGAAATTGGCAGAAACAAAAATGA 5 341 0 ATTGGCAGAA 0.671407 -170 GAGGCCTAGAATTAGCAAAATATTTAACGC 9 33 0 ATTAGCAAAA 0.944358 -477 AGTGAAACGTTTTAGCAAAAGTTTAAAGAC 9 125 0 TTTAGCAAAA 0.866977 -385 GAATATTGTGACTACCAAAAGGGAAAAGGC 10 369 1 ACTACCAAAA 0.801813 -48 AAGTATAAACATTGCCAAAATCCGTAAGCC 12 197 0 ATTGCCAAAA 0.89092 -176 GTTTTGACATATTACCAAAAAATCGGGAAA 16 307 0 ATTACCAAAA 0.959293 -294 TAGCGTATGTATTACCAAAATCCAAAATCT 16 406 0 ATTACCAAAA 0.959293 -195 ACTCATTCACCTTAGCAAAAAAAAATCTTG 16 557 0 CTTAGCAAAA 0.798878 -44 GGGATATTGTTTTAGCAAAAAGCCCCATAA 18 143 0 TTTAGCAAAA 0.866977 -158 TATTTTGGCGTTTACCAAAACCAAAACAGT 19 243 0 TTTACCAAAA 0.903655 -94 ********** Masking position 7 Map Score: 2.6614 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 490 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 9 ATGTGTATTTAAGAATATGAAAAGAGAT 1 8 0 AAGAATATAA 0.377942 -593 TTTCCTGTGGAAAAAAAAAAAAGGGAACCTC 1 177 1 AAAAAAAAAA 0.892699 -424 CGGTATTATAAAATATATAAATCTATCTTCT 2 92 1 AAATATATAA 0.172541 -209 GATACAAAAGAAAAATTAAAAGGGCTATTGA 3 508 1 AAAAATTAAA 0.419271 -93 AATATATATGCAAAATAAAAAAGCATTTTAA 3 550 1 CAAAATAAAA 0.53338 -51 GCATCTGTACAATAATAATAAAAAGCTTGAT 4 65 1 AATAATAAAA 0.435423 -236 AAAATTCAAAAAAATTATAAAATGTTACCGG 5 78 1 AAAATTATAA 0.368169 -433 AGGTAGGCGGAAAAAGAAAAAGAGAGTCGTT 7 20 0 AAAAAGAAAA 0.761509 -377 AAGAAAAAAAAAAAATATAAAGACTGTTGAT 7 135 0 AAAAATATAA 0.832882 -262 AAAAAAAAAAAAAAATAAAAAACGCCCCTTT 7 197 0 AAAAATAAAA 0.945223 -200 ACCTCAACTGAAAAAAAAAAAAAAAAATAAA 7 209 0 AAAAAAAAAA 0.892699 -188 GAAAAGAGAGAAAAAAAAAAAGAAGGTGGTG 7 290 1 AAAAAAAAAA 0.892699 -107 GCTTCTGTTGGAAAATAACAATGGAAAGTAA 8 105 0 GAAAATAAAA 0.53338 -471 AAACTGAAAGAAAAGTAACAATTACAAATTC 8 192 0 AAAAGTAAAA 0.542009 -384 AAAAAAAACCAAAAAGAAAAAAGGAGAGTAA 10 52 0 AAAAAGAAAA 0.761509 -365 AGTATTTATCAAAAAAAAAAAAAAACCAAAA 10 69 0 AAAAAAAAAA 0.892699 -348 AGAAAAAAGGAAAATTAAGAACAGTTAA 10 399 1 AAAATTAAAA 0.668604 -18 TACTAATGAAAAAAATAACAATTCTTTATTT 12 57 1 AAAAATAAAA 0.945223 -316 TATATCCCAGTAAAATAAAAATAGTTAACTT 12 119 0 TAAAATAAAA 0.435423 -254 CGTAAGCCAAAAAAACAAGAAAAATGAAAGG 12 174 0 AAAAACAAAA 0.761509 -199 ATGGAGACTGAAAAACAAAAAAGCAGAGAAA 14 200 1 AAAAACAAAA 0.761509 -101 CTTTTGAAAAAAAAAGAATGACTTTCAA 14 283 0 AAAAAAAAAA 0.892699 -18 AAGAAAAGTGAAAAATATTAAGGCATCGGAA 15 140 0 AAAAATATAA 0.832882 -161 CATTCGCGAAAAAAATAATAAAAAAGAAAGA 15 167 0 AAAAATAAAA 0.945223 -134 TAGAGGGTGTAAAATTATCAAGATTTTTTTT 16 539 1 AAAATTATAA 0.368169 -62 GAAAACCAAAAAAAAAAAAAACACGTATGAG 18 102 0 AAAAAAAAAA 0.892699 -199 CAACGATTTTAAAAATAAAAAGCAAGATCGT 18 233 1 AAAAATAAAA 0.945223 -68 GCGGGACAAGAAGAATATAAATATATAATAC 21 132 0 AAGAATATAA 0.377942 -169 AGCGTCCGGCAAAAAAAAAAAAGTTATGGTT 21 208 1 AAAAAAAAAA 0.892699 -93 atcaagaagtaaaaaaaaaaaggaagcacaa 22 96 0 aaaaaaaaaa 0.892699 -221 cccaaaatcaaaaaaaaagaagtggaaaatc 22 124 0 aaaaaaaaaa 0.892699 -193 AAAAAAAAAAAAAAATAAGAACTTCATGATA 23 200 1 AAAAATAAAA 0.945223 -101 ******** ** Masking position 2 Map Score: 23.2714 Number of sites scoring better than the average of aligned sites = 9961 Number in coding regions = 1785 Number in noncoding regions = 8176 Number of orfs with sites within 600 bp upstream = 2056 Fraction of orfs with sites within 600 bp upstream = 0.330228 Motif number 10 ATTCCATCCTGGGTGCTTATGGAGGGCCCAC 1 549 1 GGGTGCTATG 0.913861 -52 GAGCAAGAAAGGGTGCACTGGTTCAATGTGA 3 377 0 GGGTGCCTGG 0.808216 -224 GTGGTGCGCTGGTGGCTCTTGAGATTACGTG 5 28 0 GGTGGCCTTG 0.960859 -483 GTTTCAAAATGTTTGCATATGTTGATTACAG 5 131 0 GTTTGCTATG 0.859569 -380 TCTTTACTGAGGTGGCCCTTGAATAAATACA 7 256 0 GGTGGCCTTG 0.960859 -141 GCAATACAAAGTTTACTTTTG 8 565 1 GTTTACTTTG 0.60066 -11 GAGGAAAAAGGGTTTCACATGTTTCATCTGG 14 164 1 GGTTTCCATG 0.706326 -137 GCTCCGAACAGTTTGCTTTTGTCTAGTACAT 16 202 0 GTTTGCTTTG 0.945104 -399 ATAGACGCCTGGTGTCCTTTGAGCCTCACTT 16 356 1 GGTGTCTTTG 0.821338 -245 TTCAGAGAATGGTTGCGTTTGGAGTTTCTTT 17 21 0 GGTTGCTTTG 0.98161 -580 GGGTGCTTTTGAGTGATAAGT 21 290 0 GGGTGCTTTG 0.967575 -11 tcttcctattgtttgcttttgtcagaaattt 22 33 0 gtttgctttg 0.945104 -284 ****** **** Masking position 6 Map Score: 2.72072 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 562 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 11 TCATGGACAACTTTAACACACGTATATTCCA 1 524 1 CTTTAACAAC 0.736232 -77 GGAACGGTATCTTCAACAGATATTATGCGAT 4 144 0 CTTCAACAAT 0.843915 -157 ATAGATATTACTTCATCGCACAAAGAAGTCT 5 201 0 CTTCATCGAC 0.92393 -310 AAATACAGCACTTTCTCGCATCTACCTCAAC 7 232 0 CTTTCTCGAT 0.796646 -165 GGATTGATTTCTTCCCCAAACATTATTAAGT 9 304 1 CTTCCCCAAC 0.890406 -206 CTTTTTCTTCCTTTCTCGAATTTTCTATCTT 13 240 0 CTTTCTCGAT 0.796644 -61 CCATCTCCAACTTTATCAAATCATTTCACG 13 281 1 CTTTATCAAT 0.814063 -20 CAAGGCGAAGCTTCCTCACATGGAAAAGGCT 14 100 0 CTTCCTCAAT 0.955998 -201 TTGAGTTTCTCTTCATCAAACAACAAAGAAC 15 266 1 CTTCATCAAC 0.955997 -35 TCCAATGGCTCTTCAACAAATTCATTCTCTT 17 123 0 CTTCAACAAT 0.843914 -478 TTTATACAATCTTCCTCAGACAGGTGCTAAT 17 238 1 CTTCCTCAAC 0.972046 -363 GTATCCTAAGCTTCCTCAAACGAACATTCTC 23 33 1 CTTCCTCAAC 0.972046 -268 ******** ** Masking position 10 Map Score: 3.387 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 575 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 12 GAACCTCTGGTTACGATGATATACCTGCGTG 1 201 1 TTACGATGAA 0.772365 -400 GGCTCAAGTTTTCCAATGGTACTGTCTCGTG 2 20 0 TTCCAATGGA 0.922396 -281 GCTCGTCTTTTTTCAATAATACGATACAAAA 3 486 1 TTTCAATAAA 0.678538 -115 ATACCTGCACTTTCAATGAGATCAAGCTTTT 4 85 0 TTTCAATGAA 0.925175 -216 GAAGATACCGTTCCGATGGGAAAAAAAGGCA 4 161 1 TTCCGATGGA 0.947337 -140 TACCATACAATTTCAATCACACAGAACATCA 6 83 0 TTTCAATCAA 0.765512 -278 TGTATGGTATTTTCGATCATACGAGTATTTT 6 105 1 TTTCGATCAA 0.81859 -256 TTAAGTTGCTTTCCGATAGCATTAATCCTTA 8 281 0 TTCCGATAGA 0.73545 -295 CAATCTGCGGTTCCAATGGAATGCGTAAACG 8 383 1 TTCCAATGGA 0.755707 -193 ATGTAGAACTTTTCAATGTTATGTGTCATTA 15 226 0 TTTCAATGTA 0.682695 -75 TTTCTGAAAATTTCGATGATACCTGAAATAA 16 481 1 TTTCGATGAA 0.949674 -120 GAACAACTGCTTCCGATGATACCATCAAAAC 17 60 1 TTCCGATGAA 0.956263 -541 AATCTTCTATTTTCAATGAAATTTTCCTTAA 17 576 0 TTTCAATGAA 0.752963 -25 ********* * Masking position 6 Map Score: 2.28732 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 559 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 13 ATCATTGTGTTGGACGAAATCCTCTGTGAT 6 57 1 TGGACGAAAT 0.896018 -304 AATATCGCTTTTGACGATATAGTACTAGCA 8 355 1 TTGACGATAT 0.968066 -221 TACTATCCTCTGGACGATATTAGAACGATT 9 160 0 TGGACGATAT 0.979627 -350 CGGTCTGTCTTGGAAGATATGTTGTTCTCT 9 388 0 TGGAAGATAT 0.861822 -122 GAAGAGCCATTGGACGATAGGAATGAAAGG 17 140 1 TGGACGATAG 0.927387 -461 TGTTCTGCAATTGACGATATAGCCACCTGA 17 492 0 TTGACGATAT 0.968066 -109 TTATGACGATATAAACTTATGC 18 3 1 ATGACGATAT 0.844538 -298 TTATTCTTGCTTGATGATATTTATTGTATT 23 145 1 TTGATGATAT 0.79725 -156 ********** Masking position 4 Map Score: 1.26892 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 93 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 CTACGAATAATGAAATTTTCCTTTTCTTCT 1 103 0 TGAAATTTTC 0.887697 -498 TTTCTCCAATTCAACTTGTCTGCTTAAGTA 2 238 0 TCAACTTGTC 0.797563 -63 AACATTTCTGGCAACTTTTCGCCATACAGT 5 312 0 GCAACTTTTC 0.812064 -199 GAAACAAAAATGAACATTTCTGGCAACTTT 5 324 0 TGAACATTTC 0.890544 -187 AATAATTCTATGACCTTTTCGCCACTAGTT 6 331 0 TGACCTTTTC 0.92639 -30 CTATCTTGGATGACCTTTTCTCTGCTTTTT 14 217 0 TGACCTTTTC 0.92639 -84 TACTAAATCTGGAACTTTCCGATGCCTTAA 15 124 1 GGAACTTTCC 0.843769 -177 CGTTGGATGTAGAACTTTTCAATGTTATGT 15 233 0 AGAACTTTTC 0.835017 -68 TAGTTACTGGTGAACTTTCCTGGATATGCG 16 173 0 TGAACTTTCC 0.952107 -428 TGTTGTTGAATCAACTTTTCTTAAGGCTCT 16 247 1 TCAACTTTTC 0.925763 -354 CCTCCTTTTCTGAAAATTTCGATGATACCT 16 475 1 TGAAAATTTC 0.618271 -126 ACAGAAGCTGTGAACTTGCCCTCATTGTTT 17 175 0 TGAACTTGCC 0.863995 -426 CTATTTTCAATGAAATTTTCCTTAAAACTG 17 571 0 TGAAATTTTC 0.887697 -30 ********** Masking position 3 Map Score: 1.87707 Number of sites scoring better than the average of aligned sites = 1065 Number in coding regions = 856 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 15 ********** No masking Map Score: 1.27069e-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