AlignACE version 2.2 July 7, 1998 AlignACE -jTIF.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 YDR429C 300 bp YDR429C TIF35 1-825 Translation initiation factor 3 p33 subunit #2 YGL049C 464 bp YGL049C TIF4632 1-2745 mRNA cap-binding protein (eIF-4F), 130K subunit #3 YGR162W 503 bp YGR162W TIF4631 1-2859 mRNA cap-binding protein (eIF-4F), 150K subunit , highly homologous to Tif4632p, homologs of mammalian p220 #4 YJL138C 300 bp YJL138C tif2 1-1188 translation initiation factor eIF4A #5 YKR059W 366 bp YKR059W tif1 1-1188 translation initiation factor eIF4A #6 YMR146C 600 bp YMR146C TIF34 1-1044 p39 subunit of translation initiation factor eIF3 #7 YMR260C 365 bp YMR260C TIF11 1-462 Translation initiation factor eIF1A #8 YPR041W 328 bp YPR041W TIF5 1-1218 Translation initiation factor eIF-5 #9 YPR163C 600 bp YPR163C TIF3 1-1311 Translation initiation factor eIF-4B Motif number 1 AAGTTAAAATTTTTTTCTTTCACTGAGTGT 1 182 1 TTTTTTCTTT 0.979252 -119 TATAACAACCGTTTGTCTTTTCGAGAACAG 2 117 1 GTTTGTCTTT 0.851786 -348 ACTTATTATCTTTTTTTTTTCAGTCCTTTT 2 253 0 TTTTTTTTTT 0.978859 -212 TGGAACAACAGTTTTTTTTTACTTACTAAT 3 52 1 GTTTTTTTTT 0.946162 -452 AAACGATTTTTTTTTTCTTTTTCACCGTAT 3 184 1 TTTTTTCTTT 0.979252 -320 TTCAATTATAGCTTTTTTTTTATTTTTTTT 3 229 1 GCTTTTTTTT 0.869629 -275 TTTTTTTTTATTTTTTTTTTTTCTCGTACT 3 241 1 TTTTTTTTTT 0.978859 -263 ACTGACAAAAGTTTTTTTTTCAAGAAAAAT 3 276 1 GTTTTTTTTT 0.946162 -228 TTGCGTACCTTTTTCTTTTTTTCGAAATTT 4 133 1 TTTTCTTTTT 0.885893 -168 AATTTTTTTATTTTTTTTTCAGCATCATAT 4 158 1 TTTTTTTTTC 0.93141 -143 TTAGCGAACCTTTTTTTTTCCTACTATGTG 4 235 0 TTTTTTTTTC 0.93141 -66 CATTTGTAGATTTTTTATTTGGTCTCTAGT 5 287 1 TTTTTTATTT 0.788087 -80 TGGTCTCTAGTCTTTTCTTTTCTTATTTTA 5 306 1 TCTTTTCTTT 0.94713 -61 TCAGATTTTCTTTTTTTTTTATCCATCGTA 6 18 1 TTTTTTTTTT 0.978859 -583 ATCTTGGTTCTTTTGTTTTTCTTTTTTTTT 6 53 1 TTTTGTTTTT 0.936924 -548 TTTGTTTTTCTTTTTTTTTTTTTACATATA 6 64 1 TTTTTTTTTT 0.978859 -537 CCTTCCACAATCTTCTCTTTATTAATAAAT 6 128 0 TCTTCTCTTT 0.750238 -473 GTTTCGCATATTTTTTTTTTTTTGTGAAAT 6 430 1 TTTTTTTTTT 0.978859 -171 TGCTATTTCTTTTTGTCTTCTCTCCTGGCC 6 569 0 TTTTGTCTTC 0.816198 -32 TTTTTTTTCATTTTTGTTTTCGCCGCAAGA 7 233 1 TTTTTGTTTT 0.867316 -133 CTATTTTCTTTTTTTTTTTTCGTTCATACT 8 146 0 TTTTTTTTTT 0.978859 -183 CGTGTGTTCTTCTTTTTTTTCCAAAAAAAA 8 267 1 TCTTTTTTTT 0.946162 -62 ATAATAGGAGTTTTTTTTTTTGGAAAAAAA 8 280 0 TTTTTTTTTT 0.978859 -49 AAATCGATATTTTTTGCTTTTTCCTTTTTT 9 163 1 TTTTTGCTTT 0.869508 -438 CGCCCAACCTTTTTGTCTTCTTGTCTTTTT 9 355 1 TTTTGTCTTC 0.816198 -246 CTTCTTGTCTTTTTTTCTTTTTGGCTTTAT 9 371 1 TTTTTTCTTT 0.979252 -230 TTCTATTTCTGCTTTTCTTTAGCGATGCTG 9 448 0 GCTTTTCTTT 0.871787 -153 ********** Masking position 4 Map Score: 48.2891 Number of sites scoring better than the average of aligned sites = 9316 Number in coding regions = 1000 Number in noncoding regions = 8316 Number of orfs with sites within 600 bp upstream = 1755 Fraction of orfs with sites within 600 bp upstream = 0.281882 Motif number 2 ATCGTGATAATTTTTCACTTTCCACACTCAGTGAAA 1 199 0 TTTTTCACCA 0.758205 -102 GTACCTACTATTTTTCAAAATACACTAAAGGAACGG 2 207 0 TTTTTCACCT 0.905941 -258 TTATCTTTTTTTTTTCAGTCCTTTTTGCAAAGCAGG 2 242 0 TTTTTCATTT 0.974633 -223 TAATAAGGCTTTTTTCAATATCTCTGGAACAACAGT 3 28 1 TTTTTCATTG 0.893812 -476 TTTTTTTTTCTTTTTCACCGTATTTTTGTGCGTCCT 3 191 1 TTTTTCATTT 0.974633 -313 TTGTGCGTCCTTTTTCAATTATAGCTTTTTTTTTAT 3 216 1 TTTTTCAACT 0.957265 -288 TTATTTTTTTTTTTTCTCGTACTGTTTCACTGACAA 3 248 1 TTTTTCTTTT 0.844761 -256 CAAAAGTTTTTTTTTCAAGAAAAATTTTCGATGCCG 3 281 1 TTTTTCAATT 0.959981 -223 AAAGCGTTGATTTTGCGTACCTTTTTCTTTTTTTCG 4 121 1 TTTTGCGTTT 0.758571 -180 CCTTTTTCTTTTTTTCGAAATTTTTTTATTTTTTTT 4 140 1 TTTTTCGTTT 0.92459 -161 TTTTTATTTTTTTTTCAGCATCATATATAAAAGAAA 4 162 1 TTTTTCAAAT 0.687107 -139 CGAACCTTTTTTTTTCCTACTATGTGTATTGGGATC 4 225 0 TTTTTCCTTG 0.648387 -76 AATGCAAAAATTTTTCAGTCACTATAAACGTTGTGA 5 172 0 TTTTTCATTA 0.925974 -195 ACTGAAAAATTTTTGCATTCTCACCTCGTCTATTGA 5 189 1 TTTTGCAACT 0.85164 -178 GGTTCTTTTGTTTTTCTTTTTTTTTTTTTACATATA 6 58 1 TTTTTCTTTT 0.844761 -543 CTCAAGCGAGTTTTTCAACCCTTCCACAATCTTCTC 6 141 0 TTTTTCATCA 0.92114 -460 CAAGAAGTACTTTTTCATCACAACTATGGTTATAGA 6 271 1 TTTTTCAATA 0.886489 -330 ACGAACGCTATTTTTCACTTTTTTTTCATTTTTGTT 7 215 1 TTTTTCATTT 0.974633 -151 CTTTTTTCAATTTTTCACTATTACTTCTTGCGGCGA 7 252 0 TTTTTCAATT 0.959981 -114 ACACTAGTGCTTTTGCAAGTACACCTTCTACATAAG 7 320 0 TTTTGCAACT 0.85164 -46 GCGATGAAAATTTTTCACTATTTACAGAACGGGTAA 8 108 0 TTTTTCATCA 0.92114 -221 TTCTTTTTTTTTTTTCGTTCATACTTCGCGATGAAA 8 135 0 TTTTTCGATT 0.884459 -194 TATTTTTTGCTTTTTCCTTTTTTCCTAAATCTTCTT 9 170 1 TTTTTCCTCT 0.887134 -431 ******* * ** Masking position 4 Map Score: 18.3905 Number of sites scoring better than the average of aligned sites = 2549 Number in coding regions = 1514 Number in noncoding regions = 1035 Number of orfs with sites within 600 bp upstream = 849 Fraction of orfs with sites within 600 bp upstream = 0.136364 Motif number 3 CCAATGACCGTACTCACCCCTTCTTTGTTTAGTA 1 23 0 TCTCACCTCT 0.99157 -278 TGCCGATCTATACTCATCGCTTGTAACGAAGTTA 1 154 1 TCTCACCTGT 0.907957 -147 AAAGCAGCAATGCTCTGCCCCTCTGTTCTCGAAA 2 135 0 TCTCTCCTCT 0.976294 -330 ATGGGCGCTATCCTCATCGCGACTCGATAACGAC 3 145 1 TCTCACCACT 0.963443 -359 TTATGATTCTTCCTCTTCCCTTCAATTTCTTAAA 3 408 1 TCTCTCCTCA 0.970003 -96 TAGTTTCTTGTACACACCAGTCCTTTGTTTAGCG 4 259 0 TCACACGCCT 0.755819 -42 TGTTTATCTTTTCTCACCTCACAACGTTTATAGT 5 154 1 TCTCACCCAA 0.776043 -213 AATTTTTGCATTCTCACCTCGTCTATTGAATGAT 5 196 1 TCTCACCTCT 0.99157 -171 TTAGCTCAAGTTCTTAGCACATCATTCAATAGAC 5 216 0 TCTTACCTCA 0.938915 -151 TGAGAAACCTTATTCAGCGGGTCTCTGTTGTGTT 6 214 1 TTTCACGTCT 0.844801 -387 AAGAAGTACTTTTTCATCACAACTATGGTTATAG 6 272 1 TTTCACCACT 0.724484 -329 TCTTTTTGTCTTCTCTCCTGGCCAGTTATCTAAC 6 558 0 TCTCTCGCCA 0.908632 -43 GCTATTCTCTTTCTTTGCACATCTAACTTGAAGT 9 59 1 TCTTTCCTCT 0.872676 -542 CTCAATCTGGTACTAATCACTTCAAGTTAGATGT 9 77 0 TCTAACCTCA 0.858822 -524 ATCCTGGCGCTACTTAGCCGCCCAACCTTTTTGT 9 337 1 TCTTACGCCA 0.825391 -264 TTGGCTTTATTTCTCATCAGATCACGCACCACGG 9 391 1 TCTCACGTCA 0.977184 -210 * **** * * *** Masking position 1 Map Score: 11.8546 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 701 Number in noncoding regions = 311 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 4 GTATAGATCGGCAAGAAACTTTGAAGCAGTAT 1 135 0 GCAAGAAATT 0.963157 -166 CTCAGTGAAAGAAAAAAATTTTAACTTCGTTA 1 177 0 GAAAAAAATT 0.710791 -124 TACCTGCTTTGCAAAAAGGACTGAAAAAAAAA 2 240 1 GCAAAAAGAT 0.967974 -225 TACTGTTCCTGAAAGAAAGAATTTATTACAAA 2 418 1 GAAAGAAAAT 0.872682 -47 CGGTGAAAAAGAAAAAAAAAATCGTTTCTCAC 3 179 0 GAAAAAAAAT 0.763967 -325 AGTTTTTTTTTCAAGAAAAATTTTCGATGCCG 3 285 1 TCAAGAAAAT 0.813295 -219 AAGGAGTAAAGTAAGAAGCTTTAAGAAATTGA 3 429 0 GTAAGAAGTT 0.79294 -75 TTATTTATGAGCAAGAAGGAGTAAAGTAAGAA 3 444 0 GCAAGAAGAT 0.984617 -60 AGGTGAGAATGCAAAAATTTTTCAGTCACTAT 5 183 0 GCAAAAATTT 0.719327 -184 GAATTTTCGCGCAAGAAGTACTTTTTCATCAC 6 260 1 GCAAGAAGAT 0.984617 -341 AGGAGAGAAGACAAAAAGAAATAGCACAGACA 6 573 1 ACAAAAAGAT 0.684412 -28 TGTTTTCGCCGCAAGAAGTAATAGTGAAAAAT 7 247 1 GCAAGAAGAT 0.984617 -119 TTGCAAGCAGTCAAGAAGATTTAGGAAAAAAG 9 186 0 TCAAGAAGTT 0.860127 -415 GCTGATTTCCGCAAAAAAATTTTCATTCCGTG 9 420 0 GCAAAAAATT 0.925064 -181 ******** * * Masking position 6 Map Score: 8.1792 Number of sites scoring better than the average of aligned sites = 1653 Number in coding regions = 1186 Number in noncoding regions = 467 Number of orfs with sites within 600 bp upstream = 368 Fraction of orfs with sites within 600 bp upstream = 0.059107 Motif number 5 ATTATACCGCTGGATATACAGGATATAACAAC 2 94 1 TGATATACAG 0.804352 -371 CCTCTGTTCTCGAAAAGACAAACGGTTGTTAT 2 118 0 CGAAAGACAA 0.814505 -347 AAGACCTTTTCGACTATACAAAAATGCATAAC 5 55 1 CGCTATACAA 0.950812 -312 GTCAGGGCTGCGTATATTCATACCTTTGTTCT 5 256 0 CGATATTCAA 0.964684 -111 TTTTTTTTTACATATATACATATTACCCATAC 6 78 1 CAATATACAA 0.957963 -523 ACTTCTTGCGCGAAAATTCAGAGGATAAGACA 6 247 0 CGAAATTCAA 0.919814 -354 ATACGAACAGCGGCTATACAGAAACCCCACTA 6 365 0 CGCTATACAA 0.950812 -236 TTTATCGTGCTGTATATACATATATACGTAAA 7 109 0 TGATATACAA 0.965339 -257 CAATCAAATATACAAAACAATACGTA 8 5 1 CAATATACAA 0.958328 -324 AAACAATACGTACAAATACATACACGTCACAT 8 25 1 TAAAATACAA 0.801797 -304 ACATACACGTCACATATACATAAGCTCCGGAT 8 42 1 CAATATACAA 0.958321 -287 TCCTATTATTTGCATAAACACACGTTCACTGG 8 301 1 TGATAAACAA 0.748892 -28 AAGAGAATAGCATAAATTCAAAACCAAAGGAA 9 38 0 CAAAATTCAA 0.785572 -563 AAAGGAAAGATGAAGATACAAAGATTGCAAGC 9 210 0 TGAGATACAA 0.850891 -391 AAATTTAGCCTGTATATTCATAGAGACTTCTT 9 253 1 TGATATTCAA 0.919221 -348 ** ******* * Masking position 6 Map Score: 7.77077 Number of sites scoring better than the average of aligned sites = 868 Number in coding regions = 424 Number in noncoding regions = 444 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 6 TGACCGTACTCACCCCTTCTTTGTTTAGTA 1 23 0 CACCCCTTCT 0.983514 -278 TGCTGCTTTTTCCCCGTCCTGACCTTATTA 2 160 1 TCCCCGTCCT 0.945555 -305 AAGGAACGGGCCCCCCGGCTTACTATTAAT 2 186 0 CCCCCCGGCT 0.897512 -279 CTTCTTACTTTACTCCTTCTTGCTCATAAA 3 443 1 TACTCCTTCT 0.802284 -61 TCAACGCTTTCACCCGGCCTTTTGTATTCG 4 101 0 CACCCGGCCT 0.985346 -200 TTCTTGTACACACCAGTCCTTTGTTTAGCG 4 259 0 CACCAGTCCT 0.835297 -42 TTTGCATTCTCACCTCGTCTATTGAATGAT 5 200 1 CACCTCGTCT 0.914137 -167 ATATATCAGTTACCCCGCGTGCCACCTTCA 6 400 1 TACCCCGCGT 0.923468 -201 CCTTAAGATATACCTCGCCTCTTGTTCATC 6 526 0 TACCTCGCCT 0.945888 -75 CTTTTGCAAGTACACCTTCTACATAAGTAA 7 317 0 TACACCTTCT 0.802284 -49 ATCATGCTCTTACCCGTTCTGTAAATAGTG 8 99 1 TACCCGTTCT 0.963433 -230 GGCAAACGCCTACCCCTCCTTCCCACTTTG 8 200 1 TACCCCTCCT 0.989894 -129 ********** Masking position 10 Map Score: 6.43919 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 429 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 7 AAAAATTATCACGATGGCAAAAGAGAGGGAAGAGAAG 1 220 1 ACACAAAAAG 0.958777 -81 TTAATGCTAAACTATGATATTATACACATACACTAAG 2 45 0 ACATATAAAC 0.527568 -420 TCCTGAAAGAAAGAATTTATTACAAAGAACAATAGAT 2 424 1 AAATATAAAG 0.953964 -41 TTTTTTGAAGATTACATTAATAAGGCTTTTTTCA 3 8 1 AAACATATAG 0.752626 -496 CGAGAAAAAAAAAAAATAAAAAAAAAGCTATAATTGA 3 230 0 AAAAAAAAAG 0.853906 -274 CAATCATTCAACTAAACTACTACATAGTATACATTAG 4 43 1 ACATATAAAG 0.934445 -258 AAAAAATAAAAAAATTTCGAAAAAAAGAAAAAGGTAC 4 137 0 AAACGAAAAG 0.894096 -164 TGGTGTGTACAAGAAACTAATAAATAGTAATTGCAAT 4 274 1 AAATATAAAG 0.953964 -27 TGTATAGTCGAAAAGGTCTTTACATAGATATGTCTTT 5 38 0 AAACTTAAAG 0.77617 -329 AACTTGAGCTAACATCACAGAACAAAGGTATGAATAT 5 238 1 AAACAAAAAG 0.971273 -129 TTCAGAGGATAAGACAACACAACAGAGACCCGCTGAA 6 226 0 AAACAAAAAG 0.971273 -375 GAGGCCGGAAAAAATTTCACAAAAAAAAAAAAATATG 6 436 0 AAACAAAAAA 0.641212 -165 CAAAAATGAAAAAAAAGTGAAAAATAGCGTTCGTGTA 7 212 0 AAATGAAAAG 0.822015 -154 TTGCAAAAGCACTAGTGTAATATAGAGCAAAGTTCAT 7 338 1 ACATATAAAG 0.934445 -28 ATGAACGAAAAAAAAAAAAGAAAATAGATGAACTTTT 8 149 1 AAAAAAAAAG 0.853906 -180 TTACAAAGACACCACTACATTAAAGAGTATCTCGTGT 8 235 1 ACACATAAAG 0.963041 -94 TTAGGAAAATAATACCATAATAAAAAGGACACATC 9 576 1 AAATATAAAG 0.953964 -25 ** * ** ** * ** Masking position 12 Map Score: 8.59144 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 633 Number in noncoding regions = 503 Number of orfs with sites within 600 bp upstream = 404 Fraction of orfs with sites within 600 bp upstream = 0.0648892 Motif number 8 CCGAAAAATATCTACTAAACAAAGAAGGGGTG 1 7 1 ATATCTACAA 0.968916 -294 AAAGTGAAAAATTATCACGATGGCAAAAGAGAGGGA 1 214 1 ATATCAGCAA 0.909643 -87 CTGTATTGAAAGGATCAAAAGACCAAAGACCACCAG 1 270 1 AGATCAACAA 0.980198 -31 ATAGTTTAGCATTAACTAAGAGGCAAAATTATACCG 2 67 1 ATAACTGCAA 0.748003 -398 ATTTATTACAAAGAACAATAGATCAATTGTAGGCAC 2 438 1 AGAACAACAA 0.92508 -27 GGCTTTTTTCAATATCTCTGGAACAACAGTTTTTTT 3 34 1 ATATCTACAA 0.968915 -470 AATTAAGTAAATTATCACAATATCAAGATTGGTAAA 3 374 0 ATATCAACAA 0.963011 -130 TGATTATTATAAGATCTCATTAACAATATGAGAAAT 7 173 0 AGATCTACAA 0.983402 -193 CATACAAGAAATGATCTTAAAATCATGCTCTTACCC 8 78 1 AGATCTACAT 0.787393 -251 AAGTAGCGCCAGGATATAAAAAGCAACATAGATTTC 9 316 0 AGATATACAA 0.823671 -285 AGAGTTAGAGAAGATCAGTAGACCAATAAGCGGGAT 9 501 1 AGATCAACAA 0.980198 -100 * ***** * *** Masking position 4 Map Score: 4.89987 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 430 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 9 AAAAATCGTTTCTCACGTCGTTATCGAGTC 3 165 0 TCTCACGTCG 0.979575 -339 ATAAAAGAAATCTCATCTCAAGGAGAAGGA 4 188 1 TCTCATCTCA 0.985798 -113 GTTTATCTTTTCTCACCTCACAACGTTTAT 5 155 1 TCTCACCTCA 0.993648 -212 ATTTTTGCATTCTCACCTCGTCTATTGAAT 5 197 1 TCTCACCTCG 0.994113 -170 GAATAAGGTTTCTCATCTCAATCAATTACA 6 199 0 TCTCATCTCA 0.985798 -402 ********** Masking position 5 Map Score: 4.11901 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 6 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ACTAAACAAAGAAGGGGTGAGTACGGTCAT 1 24 1 GAAGGGGTGA 0.939166 -277 ACCTGGAATCGAGGGGAAGACTGTTTCACC 1 57 1 GAGGGGAAGA 0.992061 -244 ACCAAATTGGGAGGTGAAGGAACTGTAGAT 1 84 1 GAGGTGAAGG 0.916011 -217 TTCGAGAACAGAGGGGCAGAGCATTGCTGC 2 136 1 GAGGGGCAGA 0.98654 -329 TTAAGAAATTGAAGGGAAGAGGAAGAATCA 3 411 0 GAAGGGAAGA 0.98374 -93 GAAGATTGTGGAAGGGTTGAAAAACTCGCT 6 143 1 GAAGGGTTGA 0.948368 -458 AAGTGGGAAGGAGGGGTAGGCGTTTGCCAC 8 198 0 GAGGGGTAGG 0.983244 -131 ********** Masking position 2 Map Score: 3.58209 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 115 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 GGAAAGTGAAAAATTATCACGATGGCAAAA 1 212 1 AAATTATCAC 0.821099 -89 TTTTCAAGAAAAATTTTCGATGCCGCGTTC 3 292 1 AAATTTTCGA 0.949359 -212 CAAGATTGGTAAAATTTCAAGCAACATATT 3 357 0 AAAATTTCAA 0.943183 -147 ATAATTAAGTAAATTATCACAATATCAAGA 3 382 0 AAATTATCAC 0.821099 -122 AAAAAATAAAAAAATTTCGAAAAAAAGAAA 4 144 0 AAAATTTCGA 0.95704 -157 ACCTTTAAAGTAAATTTCGAGTTTGAATGT 5 97 0 TAAATTTCGA 0.738944 -270 GAGGCCGGAAAAAATTTCACAAAAAAAAAA 6 443 0 AAAATTTCAC 0.931939 -158 CGGCCTCTGAAAAATTTCGAATAGTCGTAA 6 466 1 AAAATTTCGA 0.95704 -135 AAATAGTGAAAAATTTTCATCGCGAAGTAT 8 121 1 AAATTTTCAT 0.836443 -208 GAAAAAGCAAAAAATATCGATTTTTATGAC 9 156 0 AAAATATCGA 0.898718 -445 TTCCGCAAAAAAATTTTCATTCCGTGGTGC 9 416 0 AAATTTTCAT 0.836443 -185 ********** Masking position 3 Map Score: 4.82271 Number of sites scoring better than the average of aligned sites = 1273 Number in coding regions = 835 Number in noncoding regions = 438 Number of orfs with sites within 600 bp upstream = 391 Fraction of orfs with sites within 600 bp upstream = 0.0628012 Motif number 12 TTCACTGAGTGTGGAAAGTGAAAAATTATCACGA 1 200 1 GTGGAATGAA 0.509234 -101 TGGCAAAAGAGAGGGAAGAGAAGCCCTAGTTACT 1 234 1 GAGGAAAGAC 0.986513 -67 CATATACAATGAGCCAAGTGAAACGAATACA 2 8 0 GAGCAATGAC 0.882068 -457 CATTAACTAAGAGGCAAAATTATACCGCTGGATA 2 76 1 GAGGAAATAA 0.956935 -389 AGGTCAGGACGGGGAAAAAGCAGCAATGCTCTGC 2 151 0 GGGGAAAGAC 0.90846 -314 TAAGAAATTGAAGGGAAGAGGAAGAATCATAATT 3 406 0 AAGGAAAGAG 0.915694 -98 ATAAATAAGCAAGGTAAGAGGACAACTGTAATTA 3 468 1 AAGGAAAGAA 0.956935 -36 TCTCAAGGAGAAGGAAACAGCAGATCCCAATACA 4 203 1 AAGGAAAGAA 0.956935 -98 GTTGTGAGGTGAGAAAAGATAAACAGCAAGCATC 5 145 0 GAGAAAATAC 0.832061 -222 CTAAGAACTTGAGCTAACATCACAGAACAAAGGT 5 233 1 GAGCAAATAA 0.90135 -134 GAAAGTACAGGAGGGAAAATGATCGC 7 3 0 GAGGAAATAC 0.972722 -363 GTGTAATATAGAGCAAAGTTCATC 7 352 1 GAGCAATTAC 0.78475 -14 TGTGCAAAGAAAGAGAATAGCATAAATTCAAAAC 9 46 0 AAGAAAAGAA 0.755342 -555 TTTAGGAAAAAAGGAAAAAGCAAAAAATATCGAT 9 165 0 AAGGAAAGAA 0.956935 -436 AAACATGAGAAAGGAAAGATGAAGATACAAAGAT 9 217 0 AAGGAAATAG 0.841149 -384 AGACAGATGAAAGCTAATATAAACTCGAGTTTTA 9 542 0 AAGCAAATAC 0.877276 -59 **** ** ** * * Masking position 7 Map Score: 8.65263 Number of sites scoring better than the average of aligned sites = 1588 Number in coding regions = 1101 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 419 Fraction of orfs with sites within 600 bp upstream = 0.0672984 Motif number 13 TAGAGGTAAACACAGCAAACGACCACTCAGCC 2 290 1 CACAGCACGA 0.971202 -175 ATCCGTTGCACACAGAGAACGCGGCATCGAAA 3 306 0 CACAGAACGC 0.940542 -198 GTACAGTCGTCACATCAGACGAATACAAAAGG 4 82 1 CACATCACGA 0.955081 -219 AATCTCATCTCAAGGAGAAGGAAACAGCAGAT 4 196 1 CAAGGAAGGA 0.854788 -105 GATCCCAATACACATAGTAGGAAAAAAAAAGG 4 225 1 CACATAAGGA 0.983894 -76 ACTTCCACGCACATATTAGGAAAATTAAAAG 5 10 1 CACATAAGGA 0.983894 -357 AAAGAAATAGCACAGACAAGGAAT 6 587 1 CACAGAAGGA 0.989785 -14 TGTGTTTATGCAAATAATAGGAGTTTTTTTTT 8 291 0 CAAATAAGGA 0.933211 -38 ****** **** Masking position 9 Map Score: 1.90612 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 160 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 14 ********** No masking Map Score: 1.02627e-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 ********** No masking Map Score: 1.02627e-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