AlignACE version 2.2 July 7, 1998 AlignACE -jRPB.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 YBR154C 600 bp YBR154C rpb5 1-648 25-kDa RNA polymerase subunit (common to polymerases I, II and III) #2 YDR404C 476 bp YDR404C rpb7 1-516 dissociable subunit of RNA polymerase II #3 YGL070C 300 bp YGL070C rpb9 1-369 RNA polymerase II subunit #4 YHR143W-A 600 bp YHR143W-A RPB12 1-213 subunit of RNA polymerase II #5 YIL021W 444 bp YIL021W RPB3 1-957 45 kDa subunit of RNA polymerase II #6 YJL140W 570 bp YJL140W RPB4 1-666 fourth-largest subunit of RNA polymerase II #7 YOL005C 600 bp YOL005C RPB11 1-363 RNA polymerase II subunit, homologous to S. pombe Rpb11p subunit #8 YOR151C 600 bp YOR151C RPB2 1-3675 second largest subunit of RNA polymerase II #9 YOR210W 593 bp YOR210W RPB10 1-213 RNA polymerase II subunit #10 YOR224C 300 bp YOR224C rpb8 1-441 16-kDa RNA polymerase subunit (common to polymerases I, II and III) Motif number 1 AGCGTATGCGTTCGTATCTCTGTTTAGGCACCTTG 1 99 0 TTCTTCTTTT 0.732722 -502 ACTTTTTATTTTTATTTTATTTTTTTTTCTGTTGG 2 31 1 TTTTTTTTTT 0.965286 -446 TTCTAATACCATCGTTTTCCCTTTTTCATCGAGAA 2 138 1 ATCTTTCTTT 0.52124 -339 CGCATTTATTTTCCTTGTATTTTTCAAAATAGCCG 2 221 0 TTCTGTTTTC 0.797481 -256 TATCATAGCCTTTCTTTTTCCGTTTCTCCTCCTAC 2 366 1 TTTTTTCTTT 0.920332 -111 TCTTGTTCCATTTGACTTACTCTTTAACGCTATTC 3 205 0 TTTATTTTTT 0.861069 -96 TTAAGGGGAGTTTAACTTGCTCTTTTGGCTAGATT 3 269 0 TTTATTTTTT 0.861069 -32 TTTATTTTGTTTTTTTCTCATGATC 4 1 1 TTTTTTTTTT 0.965286 -600 TCATGATCTTTTCATTTTGTAGTTTCAACTATTAT 4 28 1 TTCTTTATTT 0.814641 -573 CTACGGCAATATTTTGTTCTTATTTAGTGTCTCTT 4 264 0 ATTTTTTTTT 0.74617 -337 TGAATTTTAATTTTTTTTTTTTTTTTTTTCATTTC 4 459 1 TTTTTTTTTT 0.965286 -142 TTGGTTTCGATGTACTCTTTTGTTTTCTTT 5 6 1 TTCAGTTTTT 0.671407 -439 ACTCTTTTGTTTTCTTTTCCTTTTCCTTCCTATTC 5 24 1 TTTTTTTTTC 0.922747 -421 CTTCAATTAGTTTATTTTTCATTTTTTTCCACTTT 5 288 0 TTTTTTATTT 0.831364 -157 TTTTCAATATTGTTTTAGTTTTTCAACGCTGGT 5 422 0 ATTTTTTTTT 0.74617 -23 GGAACATAATTTCGTTATCTTTTTTTCACATGCTA 6 23 0 TTCTATTTTT 0.543187 -548 GCCTTTTATATTTTTTTTAGTTTTTTTCTCCAAAT 6 307 1 TTTTTTTTTT 0.965286 -264 CCTAAATCCTTTTTAGGTGTCATTTACGTGCAACG 6 342 1 TTTAGTCTTT 0.487758 -229 CCCTATTACATTTGTCTTCCCTTTTTCGCACCAGC 7 47 0 TTTTTTCTTT 0.920332 -554 AAAAGTCGCCTTCATTTTGCAGTTCTTCAGCAAAC 7 112 0 TTCTTTATTC 0.653722 -489 GATATCGGATTTTCTAGTGATTTTTTTCCATTCGC 7 149 0 TTTTGTTTTT 0.911372 -452 TTTGGACAACTTTATTTCATTCTTT 8 1 0 TTTTTCTTTT 0.754609 -600 ATTTTTCACTTTTCTATTTTTTTTCATCCTCTCAC 8 229 1 TTTTTTTTTC 0.922747 -372 TCCTCTCACTTTCGTAGTAGCTTTTGAAAAAGTGG 8 255 1 TTCTGTCTTT 0.792034 -346 TCTATACTTGTTTGTGTTCTTTTTCTGGTCCTAAT 8 561 0 TTTTTTTTTC 0.922747 -40 CCCATCAGTTTTTTTGTTTCAATTCGTCACTGTAA 9 89 0 TTTTTTATTC 0.679247 -505 GCAGCAGCCATTTTTGTTGATATTTTGACGAATTT 9 249 1 TTTTTTTTTT 0.965286 -345 ATATGAACCCTTCATCTTACTTTTTTACGTTGTAA 9 282 0 TTCTTTTTTT 0.961224 -312 TTACTTTTCGTTCAACGTGATCTTTGTGTTCTCAA 9 422 0 TTCAGTTTTT 0.671407 -172 TTATTCAATGTTTCTTTTTTTTTTTCTTATGAAAT 9 486 0 TTTTTTTTTT 0.965286 -108 TTTGTATTATTATTTTGCTTATTGA 9 579 0 TTTTTTTTTT 0.965286 -15 TGTATCAAATTTTGACTTAGTTTTTTCATGTTCGT 10 114 1 TTTATTTTTT 0.861069 -187 ATTTTCATCTTTCATTTTCACATTTTTTTTTTTCT 10 177 1 TTCTTTCTTT 0.911493 -124 TCTGAAATTTTTCATCTTAGTTTTCGCTTTAGAAA 10 207 0 TTCTTTTTTC 0.91415 -94 *** * ** * *** Masking position 13 Map Score: 37.4555 Number of sites scoring better than the average of aligned sites = 10506 Number in coding regions = 3343 Number in noncoding regions = 7163 Number of orfs with sites within 600 bp upstream = 2220 Fraction of orfs with sites within 600 bp upstream = 0.356569 Motif number 2 GAAGGAAAAATTTTTCTTTTCTCTTGAAAAAT 1 417 1 TTTTTTTTCT 0.957003 -184 TTATTTTTATTTTATTTTTTTTTCTGTTGGAG 2 36 1 TTTTTTTTTT 0.964477 -441 GAATACCGCATTTATTTTCCTTGTATTTTTCA 2 230 0 TTTTTTCCTT 0.780016 -247 TTTATTTTGTTTTTTTCTCATG 4 1 1 TTTTTTGTTT 0.786499 -600 GAATATGATTTTTCTGAATTTTAATTTTTTTT 4 445 1 TTTTAATTTT 0.701017 -156 TGAATTTTAATTTTTTTTTTTTTTTTTTTCAT 4 459 1 TTTTTTTTTT 0.964477 -142 TTTTTTTTTTTTTTTCATTTCTTTAACATCTA 4 473 1 TTTTATTTCT 0.84714 -128 GATGTACTCTTTTGTTTTCTTTTCCTTTTCCT 5 19 1 TTTTTTCTTT 0.950402 -426 AATTAGTTTATTTTTCATTTTTTTCCACTTTG 5 287 0 TTTTATTTTT 0.871138 -158 TATTAGGCCTTTTATATTTTTTTTAGTTTTTT 6 301 1 TTTTTTTTTT 0.964477 -270 TTCAAGTCTCTTTCTTTACTTTTGTCTCACCG 6 458 0 TTTTTACTTT 0.869213 -113 CGGATGAATATTTGTGTACTTTCGCCCTCAAA 6 517 0 TTTTTACTTT 0.869213 -54 TTTTCTATATTCTTATATATATA 6 558 0 TTTTTATTCT 0.885317 -13 CCCTATTACATTTGTCTTCCCTTTTTCGCACC 7 50 0 TTTTTTCCCT 0.744033 -551 AAGTAGCATTTTTTTAAATTCTTCACCATTTG 8 32 0 TTTTAATTCT 0.657782 -569 ATAATTGAGGTTTCTCTGTTTTAAAAGCATAA 8 123 1 TTTTTGTTTT 0.774937 -478 ATTTTTCACTTTTCTATTTTTTTTCATCCTCT 8 229 1 TTTTTTTTTT 0.964477 -372 TCTATACTTGTTTGTGTTCTTTTTCTGGTCCT 8 564 0 TTTTTTCTTT 0.950402 -37 TTATTCAATGTTTCTTTTTTTTTTTCTTATGA 9 489 0 TTTTTTTTTT 0.964477 -105 CCGGTTTTTTTTTTCTGGTTGTTTTA 10 5 1 TTTTTTTTCT 0.957003 -296 ATTTTCACATTTTTTTTTTTCTAAAGCGAAAA 10 190 1 TTTTTTTTCT 0.957003 -111 *** * ****** Masking position 5 Map Score: 21.3245 Number of sites scoring better than the average of aligned sites = 8258 Number in coding regions = 1378 Number in noncoding regions = 6880 Number of orfs with sites within 600 bp upstream = 1868 Fraction of orfs with sites within 600 bp upstream = 0.300032 Motif number 3 CGACGCAATTCGGTGAGGAAGATTACAAACGTT 1 474 1 CGGGAGGAAT 0.948778 -127 ACTGTCTAATCGCAAAGGAGAATGGTGTAGGAG 2 394 0 CGCAAGGAAT 0.94386 -83 AACGTTACATCGGTGAGGCTAATTGTAGCCTTA 4 393 0 CGGGAGGCAT 0.952535 -208 GTTTGGCTTTCGGGAAGCAAAGTGGAAAAAAAT 5 270 1 CGGAAGCAGT 0.992712 -175 AGAGGGATCACGGTAAGCCTCGTCGGTAAGCCT 7 327 1 CGGAAGCCGT 0.993269 -274 TAAGCCTCGTCGGTAAGCCTCGTCGGTAAGCCT 7 340 1 CGGAAGCCGT 0.993269 -261 TAAGCCTCGTCGGTAAGCCTCGTCGGTAGATCC 7 353 1 CGGAAGCCGT 0.993269 -248 TTTTTGAACTCGGATAGCAGCATTATCCATGAC 7 393 0 CGGTAGCAAT 0.938674 -208 TCATTTTGAACGCCAAGCAGGGTAACAAATTAT 8 197 0 CGCAAGCAGT 0.983722 -404 TACCTATTTTCGCCAAGCAAGATAACC 9 5 0 CGCAAGCAAT 0.974289 -589 *** ***** ** Masking position 6 Map Score: 9.40323 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 97 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GAGAAAAGAAAAATTTTTCCTTCCGCGGTC 1 410 0 AAATTTTTCC 0.835072 -191 ATATGATTGAAAATTTTTCAAGAGAAAAGA 1 431 0 AAATTTTTCA 0.960441 -170 CACCAAAACAAAATTTTTCAACTTACCCGC 3 176 0 AAATTTTTCA 0.960441 -125 AATGGAGAACAAATTTGACACACATGATTG 4 310 0 AAATTTGACA 0.769701 -291 CTCTTCACCAAAATTCTTCTTTCGATATAT 6 76 1 AAATTCTTCT 0.820933 -495 GGTATTACACAAATTTCTCACTATTAGATT 6 111 0 AAATTTCTCA 0.881943 -460 GCATTTTTTTAAATTCTTCACCATTTGGAC 8 29 0 AAATTCTTCA 0.970222 -572 TTTTTTGTTTCAATTCGTCACTGTAAGGAA 9 85 0 CAATTCGTCA 0.869239 -509 CCTGGGTGAAAAATTCGTCAGATCCGTTCT 9 218 0 AAATTCGTCA 0.972451 -376 TTTACGTTGTAAATTCGTCAAAATATCAAC 9 264 0 AAATTCGTCA 0.972451 -330 AAATATTCTGAAATTTTTCATCTTAGTTTT 10 218 0 AAATTTTTCA 0.960441 -83 ********** Masking position 3 Map Score: 7.28548 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 522 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 356 Fraction of orfs with sites within 600 bp upstream = 0.0571796 Motif number 5 CTCTACATATAAAGTGCCAGATATCTTGGT 1 192 1 AAAGTGCCAG 0.779111 -409 ATTTAAAATTAAAGTGGCAATGTATTGTTG 1 333 1 AAAGTGGCAA 0.933888 -268 TCTCGATGAAAAAGGGAAAACGATGGTATT 2 142 0 AAAGGGAAAA 0.834382 -335 TATCCCAGTGAAAATGCCAATAACGTAGAC 2 265 1 AAAATGCCAA 0.636058 -212 TTGAAACTACAAAATGAAAAGATCATGAGA 4 26 0 AAAATGAAAA 0.870846 -575 TAGAATCAGAAAAGTGAAGAGTATTCCACA 4 515 1 AAAGTGAAGA 0.95636 -86 TCCAAAAGAAAAAGTGGGGATCGAAGGTGA 5 84 0 AAAGTGGGGA 0.826467 -361 TTCGGGAAGCAAAGTGGAAAAAAATGAAAA 5 278 1 AAAGTGGAAA 0.940543 -167 AAAGTGGAAAAAAATGAAAAATAAACTAAT 5 288 1 AAAATGAAAA 0.870846 -157 CTGGTGCGAAAAAGGGAAGACAAATGTAAT 7 48 1 AAAGGGAAGA 0.827617 -553 GAAGAACTGCAAAATGAAGGCGACTTTTTT 7 119 1 AAAATGAAGG 0.791768 -482 CGGACTTAATAAAGTGGAAGTGTCCGCGAA 7 453 1 AAAGTGGAAG 0.903482 -148 AAAAAATAGAAAAGTGAAAAATCATTTTGA 8 221 0 AAAGTGAAAA 0.958327 -380 AGCTACTACGAAAGTGAGAGGATGAAAAAA 8 247 0 AAAGTGAGAG 0.811291 -354 AGCTTTTGAAAAAGTGGCGAACAAACAAGA 8 273 1 AAAGTGGCGA 0.930851 -328 TTGTTTCCTTACAGTGACGAATTGAAACAA 9 81 1 ACAGTGACGA 0.674808 -513 TTGACTAACCAAAATGACGAGCCTTTCAAC 9 147 0 AAAATGACGA 0.851585 -447 AAAAAATGTGAAAATGAAAGATGAAAATAA 10 175 0 AAAATGAAAG 0.799598 -126 TTTTTTTTCTAAAGCGAAAACTAAGATGAA 10 202 1 AAAGCGAAAA 0.732444 -99 ********** Masking position 3 Map Score: 9.86034 Number of sites scoring better than the average of aligned sites = 2096 Number in coding regions = 1386 Number in noncoding regions = 710 Number of orfs with sites within 600 bp upstream = 634 Fraction of orfs with sites within 600 bp upstream = 0.101831 Motif number 6 TAGAGAATAAATCGACGAAGTGAGCTTGTC 2 292 0 ATCGACGAAG 0.961801 -185 GACGAGGCTTACCGACGAGGCTTACCGTGA 7 334 0 ACCGACGAGG 0.99749 -267 GACGAGGCTTACCGACGAGGCTTACCGACG 7 347 0 ACCGACGAGG 0.99749 -254 ACACGGATCTACCGACGAGGCTTACCGACG 7 360 0 ACCGACGAGG 0.99749 -241 ********** Masking position 5 Map Score: 4.13897 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 GGTTTCAACGGCTATTTTGAAAAATACAAG 2 213 1 GCTATTTTGA 0.976394 -264 TTTTTCACATGCTAATTTGAGCAATC 6 7 0 GCTAATTTGA 0.926306 -564 AAGCCATCGCGCTATTTTGATATTTTTATT 6 275 1 GCTATTTTGA 0.976394 -296 TTAAAAAAATGCTACTTCGAGCTGCTACTA 8 47 1 GCTACTTCGA 0.96976 -554 ACTTCGAGCTGCTACTATGAGTTTATAGGC 8 60 1 GCTACTATGA 0.971764 -541 TAAGATGGCCGCTATTTTGTCAACTCAGAA 8 165 0 GCTATTTTGT 0.867029 -436 TTTTTCAAAAGCTACTACGAAAGTGAGAGG 8 256 0 GCTACTACGA 0.94389 -345 CATTTTTGTTGATATTTTGACGAATTTACA 9 257 1 GATATTTTGA 0.802174 -337 CCCAAAATAAGCTACTATCAGCACTCCGAT 9 366 1 GCTACTATCA 0.833347 -228 ********** Masking position 6 Map Score: 4.05126 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 221 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 GATAGGTGGACAGACCTGATCGACCCAATG 2 323 0 CAGACCTGAT 0.990246 -154 AGTTCTTCAGCAAACGTGATTTGCAAAACA 7 97 0 CAAACGTGAT 0.968685 -504 ACGTAGCCACCAAACCAGATACATTTGGAC 7 570 1 CAAACCAGAT 0.931953 -31 TATGCAAAAGCAGACCTGATAAATCTTTTC 9 316 1 CAGACCTGAT 0.990246 -278 TCATGTTCGTCAGACGTGATAGGTTTTCTC 10 139 1 CAGACGTGAT 0.985855 -162 ********** Masking position 4 Map Score: 2.22544 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 20 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 TATAATCACACATTACACAGTTTTCTGTGA 1 62 1 CATTACACAG 0.956405 -539 ACCTACCGAGCATTACCAAGATATCTGGCA 1 206 0 CATTACCAAG 0.925144 -395 CGACATTGTACATTACCAGGTAAGGCTACA 4 373 1 CATTACCAGG 0.978394 -228 AATCCGATATCATTACCCGTACTGGTTTAT 7 173 1 CATTACCCGT 0.955645 -428 GTTTATTCTACGTTACACGGGTAACCCCGC 7 197 1 CGTTACACGG 0.961158 -404 TTATCCATGACATGACACGGATCTACCGAC 7 374 0 CATGACACGG 0.961156 -227 TCAATATTATCATTACCCGGACTTAATAAA 7 436 1 CATTACCCGG 0.994015 -165 ********** Masking position 5 Map Score: 2.68361 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 70 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 10 GTTAGTAGCGTTACGTTCTCCACAAGAAATG 2 92 1 TTACGTTCTC 0.977786 -385 ATTTTGTAACTTTCGTTCTACCTAGAATCTG 3 241 0 TTTCGTTCTC 0.981894 -60 TTATTTAGTGTCTCTTTCTCCATATCACTGC 4 249 0 TCTCTTTCTC 0.839223 -352 GATTTCCTTTTTTCTCTCTTCCTATTTGATG 5 120 0 TTTCTCTCTC 0.898044 -325 TAGGTGTCATTTACGTGCAACGCGACAATAG 6 355 1 TTACGTGCAC 0.871781 -216 ACTACTGTTGTTACGCGCTGCCCAGAGTGTG 7 236 0 TTACGCGCTC 0.946659 -365 GGCTCAGTTCTCTCGCTCTTCTTTTAACGGA 7 518 0 TCTCGCTCTC 0.956265 -83 AGAAATTACTTTTCGTTCAACGTGATCTTTG 9 431 0 TTTCGTTCAC 0.944864 -163 TTATTGAGGTTTACGTTCTACACTCTACAGT 9 555 0 TTACGTTCTC 0.977786 -39 ********* * Masking position 1 Map Score: 2.91809 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 236 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 11 CCGCACAAGTAAACTTGAGAACACAGACTCTC 1 163 1 AATTGAGAAC 0.689493 -438 TTTGCGATTAGACAGTGGGAAAGTCCAAGAAT 2 411 1 GAGTGGGAAA 0.852702 -66 AAAATGAAAAGATCATGAGAAAAAAACAAAAT 4 14 0 GAATGAGAAA 0.770737 -587 TATGAGCAGTGATATGGAGAAAGAGACACTAA 4 244 1 GATGGAGAAA 0.95328 -357 ATAGGAAGATGCAATGGAGAACAAATTTGACA 4 320 0 GCTGGAGAAC 0.878184 -281 AGTGGGGATCGAAGGTGAGACATAACGGAGTT 5 70 0 GAGTGAGACA 0.939461 -375 TGTTCTGTGGAAAAGGGAGACACTTTTTATAT 5 372 1 AAGGGAGACA 0.839242 -73 TCCCAAATCTAATAGTGAGAAATTTGTGTAAT 6 106 1 AAGTGAGAAA 0.919297 -465 AAGGATTTAGGATTTGGAGAAAAAAACTAAAA 6 321 0 GATGGAGAAA 0.95328 -250 GTACATGCTTAACGGTGAGACAAAAGTAAAGA 6 446 1 AAGTGAGACA 0.805565 -125 TATTAGCAATGCTGGTGCGAAAAAGGGAAGAC 7 37 1 GCGTGCGAAA 0.799283 -564 ATGTAATAGGGAAGGGGAGTAACCGTTGTTTT 7 71 1 GAGGGAGTAA 0.811962 -530 GTTAAAAGAAGAGCGAGAGAACTGAGCCGTGC 7 521 1 GAGAGAGAAC 0.755115 -80 TGGCTGCTGCGCCTGGGTGAAAAATTCGTCAG 9 227 0 GCGGGTGAAA 0.771975 -367 GGAAGTGTCAGCAATTGAGAACACAAAGATCA 9 408 1 GCTTGAGAAC 0.851219 -186 ACCAAATACAACGAGTGAGAAATTACTTTTCG 9 447 0 ACGTGAGAAA 0.886824 -147 ATGAAAATAAGACCTGGAGAAAACCTATCACG 10 153 0 GATGGAGAAA 0.95328 -148 ** ******** Masking position 7 Map Score: 4.20587 Number of sites scoring better than the average of aligned sites = 1828 Number in coding regions = 1292 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 456 Fraction of orfs with sites within 600 bp upstream = 0.0732412 Motif number 12 GTTTTCTGTGAAACTGTACAAGGTGCCTAA 1 81 1 AAACTGTACA 0.956254 -520 ATATCAGGAAAAACTGTAGATTCTGACAAT 4 217 0 AAACTGTAGA 0.987174 -384 GCGGAATAAGACACTGTAGAAGCTCCGTAT 8 524 1 ACACTGTAGA 0.971967 -77 GTAAGGAAACAAACGGTAGATAATATTTTA 9 63 0 AAACGGTAGA 0.971967 -531 AAGTGTATTCAAACTGTAGAGTGTAGAACG 9 543 1 AAACTGTAGA 0.987174 -51 ********** Masking position 7 Map Score: 1.56514 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 30 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 GCAGCCCGTCAGCAGCAAACACAGTCAATT 3 67 0 AGCAGCAAAC 0.901589 -234 TTTTCCACAGAACAGCCAACGCACTTACGA 5 356 0 AACAGCCAAC 0.950656 -89 GGTGAAGAGCAACAGCCATTGTGCAAGGGA 6 55 0 AACAGCCATT 0.922873 -516 TTGACAAAATAGCGGCCATCTTAAAATAAT 8 172 1 AGCGGCCATC 0.983375 -429 ACCCAGGCGCAGCAGCCATTTTTGTTGATA 9 241 1 AGCAGCCATT 0.977878 -353 CTTCCAGTGTAGTAGCCATCGGAGTGCTGA 9 383 0 AGTAGCCATC 0.954626 -211 GGGCTTTTATAGCTGCCATCACAGTTTAAA 10 245 0 AGCTGCCATC 0.975635 -56 ********** Masking position 8 Map Score: 1.39453 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 218 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 14 TATCATAGCCTTTCTTTTTCCGTTTCTCCTCC 2 366 1 TTTCTTTCCG 0.973656 -111 ACGGGCTGCTTGTCCTGTTCCTTCCAGAACTT 3 88 1 TGTCTTTCCT 0.984609 -213 TTGTTCTCCATTGCATCTTCCTATTTGACATT 4 328 1 TTGCTTTCCT 0.945462 -273 TTTGTTTTCTTTTCCTTTTCCTTCCTATTCCG 5 29 1 TTTCTTTCCT 0.98491 -416 CTTATTCCGCTGTCGTGTTCCTTATGTTTGTT 8 502 0 TGTCTTTCCT 0.984609 -99 GCTTCTACAGTGTCTTATTCCGCTGTCGTGTT 8 515 0 TGTCTTTCCG 0.973138 -86 TGATAAATCTTTTCATATTCTTGAGGTTTTTA 9 332 1 TTTCTTTCTT 0.894359 -262 GACTTAGTTTTTTCATGTTCGTCAGACGTGAT 10 127 1 TTTCTTTCGT 0.926186 -174 **** * ***** Masking position 6 Map Score: 4.11614 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 292 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 15 ********** No masking Map Score: 1.28633e-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