AlignACE version 2.2 July 7, 1998 AlignACE -jSRP.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 YDL092W 600 bp YDL092W SRP14 1-441 Signal recognition particle subunit #2 YDR292C 600 bp YDR292C SRP101 1-1866 signal recognition particle receptor - alpha subunit #3 YKL122C 600 bp YKL122C SRP21 1-504 component of signal recognition particle #4 YKR092C 600 bp YKR092C SRP40 1-1221 nucleolar protein that is immunologically and structurally related to rat Nopp140, a nonribosomal protein of the nucleolus and coiled bodies. #5 YNL189W 600 bp YNL189W srp1 1-1629 karyopherin alpha homolog of 60 kDa #6 YPL243W 483 bp YPL243W SRP68 1-1800 component of signal recognition particle #7 YPL210C 300 bp YPL210C SRP72 1-1941 component of signal recognition particle #8 YPR088C 300 bp YPR088C SRP54 1-1626 Signal recognition particle subunit (homolog of mammalian SRP54) Motif number 1 GGAGGCTTCTACAAAACAACTAATTACATAT 1 435 1 ACAAAACAAT 0.743381 -166 GAACGAAAGTGAAAAACAAGAAAA 2 4 0 GAAAAACAAA 0.959271 -597 ACGAGGTCGAATAAAAAAATTTGGATGATGC 2 145 0 ATAAAAAAAT 0.604844 -456 CCAAAAATACATAAAACAATAATGCAGCCTT 2 194 1 ATAAAACAAA 0.873597 -407 TATAAATAACAAAAGACAATATAAATTGAAA 2 244 0 AAAAGACAAA 0.94147 -357 ATTCTCCTTGGCAAAACAAAAT 4 2 0 GCAAAACAAA 0.928976 -599 AAGGGGAGGAGTAAGAAAAAAGTGTGTCGAA 4 79 0 GTAAGAAAAA 0.874032 -522 TATTGGAGTGAAAAAACAAGATTATGTAGAC 4 227 0 AAAAAACAAA 0.941253 -374 ACCTTCTGTAATAAAACAAATTCACTATAAC 4 263 0 ATAAAACAAT 0.692314 -338 TGTACAAACTACAAAACAAGAGTAAAATAAC 4 309 0 ACAAAACAAA 0.898967 -292 AGCCTGCATTGAAAAAAAAAAAATTGTATGC 4 486 0 GAAAAAAAAA 0.941253 -115 AATGCAGGCTGAAAAAAAAAAATTCACTTGA 4 507 1 GAAAAAAAAA 0.941253 -94 TCTTGAAGAAAAAAGAAAAGAAGAAAATTCG 5 289 0 AAAAGAAAAA 0.916265 -312 TCAAGTGAACAAAAAACAAAATAGAAAGATC 5 546 0 AAAAAACAAA 0.941253 -55 AATATGGAAAAAAAGAAAATTACACTGTAAT 6 431 0 AAAAGAAAAT 0.780821 -53 GAAAAAATGAACAAGAAAATTTAATCAAATA 7 169 0 ACAAGAAAAT 0.664251 -132 CGACAAAGGCGAAAGAAAAGAGGAAAAAATG 7 191 0 GAAAGAAAAA 0.94147 -110 CGCCTTTGTCGAAAGAAAAGAGGAAAACAAG 7 211 1 GAAAGAAAAA 0.94147 -90 TCAACAAAGTGAAAAAAAATAGTGGTAAAAC 8 202 1 GAAAAAAAAA 0.941253 -99 AAAAATAGTGGTAAAACAAGATAATGAAAAG 8 216 1 GTAAAACAAA 0.910391 -85 GAAGAGAAGGGAAAGAAAACACAGCATCGAG 8 268 1 GAAAGAAAAA 0.94147 -33 ********* * Masking position 6 Map Score: 21.1838 Number of sites scoring better than the average of aligned sites = 12375 Number in coding regions = 2430 Number in noncoding regions = 9945 Number of orfs with sites within 600 bp upstream = 2426 Fraction of orfs with sites within 600 bp upstream = 0.389656 Motif number 2 ATTTGTATTAAAGAAGAGGTATGCCAACCCGTA 1 545 0 AAGAGAGGAG 0.769689 -56 CAATCCAAAGAACGAAAGTGAAAAACAAGAAAA 2 11 0 AACGAAGTAA 0.697674 -590 AATAAAAACAAAGGGAAGGGATACTGAGGGGTG 2 49 0 AAGGAAGGAA 0.987974 -552 CGTGGATTAAAAGGAGAAGTACAAAATTCATGC 2 102 0 AAGGGAAGAA 0.979922 -499 TGACTTGTAAAAGGTAGGGGAAACCGTCAGTCT 3 102 0 AAGGAGGGAA 0.972017 -499 CTTATGGCAGAAGGCAGGGTAAGCCGCACCACT 3 447 1 AAGGAGGGAG 0.903147 -154 TTGTTTTGCCAAGGAGAATTATAATCTTAGTGT 4 14 1 AAGGGAATAA 0.839713 -587 TATCCTTGATAAGGGGAGGAGTAAGAAAAAAGT 4 87 0 AAGGGAGGGA 0.980014 -514 CGCACACCACAAGGTGAAGGGCAAAGGTGAATT 4 156 0 AAGGGAAGGA 0.95378 -445 AAATAACTCGAACGAAGGGTACACCTTCTGTAA 4 283 0 AACGAGGGAA 0.900891 -318 GGAAGCTTTGAACGGGAAGAGGAAAAAACCTTC 4 442 1 AACGGAAGGA 0.843752 -159 AGCGACTTGTAAGGTAAGGAAAACCCGCATTCA 5 391 1 AAGGAAGGAA 0.987974 -210 TGTTATGTAGAAGGGAAGGTATATCAAGTGAAC 5 567 0 AAGGAAGGAA 0.987974 -34 ACAACGTAACAAGAAGAAGTAAACAAGGCAGTA 6 24 0 AAGAGAAGAA 0.839713 -460 TGCAGAAGAGAAGGGAAAGAAAACACAGCATCG 8 264 1 AAGGAAAGAA 0.971889 -37 **** **** * * Masking position 2 Map Score: 12.5878 Number of sites scoring better than the average of aligned sites = 1460 Number in coding regions = 923 Number in noncoding regions = 537 Number of orfs with sites within 600 bp upstream = 459 Fraction of orfs with sites within 600 bp upstream = 0.0737231 Motif number 3 AATTAGGATTGAACCGGTAAAAGGAAAGCTG 1 251 1 GAACCGTAAA 0.863569 -350 ACTCAGTGGTGATCTTGAAAAGCCCGATAAG 1 298 0 GATCTGAAAA 0.871272 -303 CGAAAGTGAAAAACAAGAAAA 2 1 0 AAACAGAAAA 0.8966 -600 ATTAAAAGGAGAAGTACAAAATTCATGCAGT 2 99 0 GAAGTCAAAA 0.900607 -502 TATAAATTGAAAAGTTGTAAATATTGAAAAG 2 225 0 AAAGTGTAAA 0.745799 -376 AGACCTAATTGAACTGGAAAAC 3 589 1 GAACTGAAAA 0.960068 -12 AGAGATGTACAAACTACAAAACAAGAGTAAA 4 314 0 AAACTCAAAA 0.677838 -287 CTTTGAACGGGAAGAGGAAAAAACCTTCCCA 4 447 1 GAAGAGAAAA 0.97392 -154 ATTTTTCCTCGAAGCGCAAAAGAGATTACAT 5 249 1 GAAGCCAAAA 0.894447 -352 AGAAAAAAGAAAAGAAGAAAATTCGTTAATG 5 283 0 AAAGAGAAAA 0.922164 -318 AACGTAACAAGAAGAAGTAAACAAGGCAGTA 6 24 0 GAAGAGTAAA 0.913139 -460 AGATCCCATCGAACATGAAAAAATGACAGCA 6 77 0 GAACAGAAAA 0.964703 -407 TGTTCGATGGGATCTACAAAACAACCTTTAG 6 93 1 GATCTCAAAA 0.651199 -391 CACGAACAACGATGTGGTAAAGACAACGAAA 6 275 0 GATGTGTAAA 0.722479 -209 CGCAATATACGATGCCGAAAAGAGTAATGAA 7 137 0 GATGCGAAAA 0.896355 -164 AGGAAAAAATGAACAAGAAAATTTAATCAAA 7 171 0 GAACAGAAAA 0.964703 -130 AGGCGAAAGAAAAGAGGAAAAAATGAACAAG 7 185 0 AAAGAGAAAA 0.922164 -116 TGTCGAAAGAAAAGAGGAAAACAAGCTGAAA 7 217 1 AAAGAGAAAA 0.922164 -84 AAGAGGAAAACAAGCTGAAAATTGCTATGCA 7 228 1 CAAGCGAAAA 0.749936 -73 ***** ***** Masking position 9 Map Score: 16.2372 Number of sites scoring better than the average of aligned sites = 3801 Number in coding regions = 2751 Number in noncoding regions = 1050 Number of orfs with sites within 600 bp upstream = 841 Fraction of orfs with sites within 600 bp upstream = 0.135079 Motif number 4 ATACATCTGGTTCTTTTCCATATGTACGTAGA 1 50 0 TTCTTCCATA 0.97642 -551 TAATGCAGCCTTCTTTTCAATATTTACAACTT 2 213 1 TTCTTCAATA 0.977913 -388 CATCAAGTAGTTTTTTTCAATAGGAGATTCAC 2 558 1 TTTTTCAATA 0.958762 -43 CGAATTATCGTTTTGATCCAGACATAAAGAGA 4 340 0 TTTTTCCAGA 0.936191 -261 TACAATTTTTTTTTTTTCAATGCAGGCTGAAA 4 489 1 TTTTTCAATG 0.814265 -112 TTCTTTTCTTTTTTCTTCAAGAGTTGATGGGG 5 298 1 TTTTTCAAGA 0.943052 -303 ATTAATCATATTCTGCTCAAGAAGCGACTTGT 5 369 1 TTCTTCAAGA 0.969172 -232 CATCAGCTGTTTCTCTTCCAAAGCTTCCCTGA 6 132 0 TTCTTCCAAA 0.881243 -352 TGTAATTTTCTTTTTTTCCATATTGAATCAAA 6 438 1 TTTTTCCATA 0.956083 -46 GTTGAGTTGGTTCTGATCAATAATAAGAGTA 7 280 1 TTCTTCAATA 0.974868 -21 GGTCTTTTCGTTCATCTCAATATCGAAAAATC 8 151 1 TTCATCAATA 0.849078 -150 **** ****** Masking position 10 Map Score: 7.24708 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 420 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TAAACAACTAACGAATACCAAAAAAATGATCCGTATTAA 1 150 1 AAACAAAAAA 0.980789 -451 ATATATTGTCAAATACAACAAGATATTTAATAAACAAAG 1 204 1 AAACAAATAA 0.951114 -397 AGATGAACGTAGGCAGATCAAAACATTCAGCCGATGATA 1 349 1 AAACAAACAA 0.897588 -252 CTCTTCTTTAATACAAATCAAAAAACGTAGCTTTCTTAC 1 560 1 AAACAAAAAA 0.980789 -41 CTTTTGCTGTACAAATATCATCAAAGAGAAGTACTGAAA 2 311 1 AAACATAAAA 0.926988 -290 CGGAAAAATTACCCAGCGCATAAAAAGTAAGCTTTCAGT 2 343 0 AACCATAAAA 0.83235 -258 CAATAAGTAGATAGAAATAAATAAACCAATTTTTCGTCA 2 457 1 AAAAAAAAAA 0.887038 -144 TGCCGTACACAGGTAAAGAAATGAAAGTACTAATTATCC 3 20 0 AAAAAAGAAA 0.754338 -581 TCGCACTTTTATACAAAGCAAGAAAGAAACCCAAGTCGC 4 550 1 AAACAAAAAA 0.980789 -51 TATCAAGTGAACAAAAAACAAAATAGAAAGATCGTTCTA 5 540 0 AAACAAATAA 0.951114 -61 AACATGAAAAAATGACAGCAATGTAATTAGAACCAGAAT 6 58 0 AAACAAGTAA 0.883829 -426 GCATTCCACAAACTACAACAACGAACCAAACGACATATT 6 170 1 AAACAAGAAA 0.9523 -314 TTGATTCAATATGGAAAAAAAGAAAATTACACTGTAATA 6 430 0 AAAAAAAAAA 0.887038 -54 TCACTCCCGCACATATCACATAATACTAAGTATCCATTT 7 91 1 AACCATATAA 0.654217 -210 TATTGATCAGAACCAACTCAACAAAGTAAATCTGCTACT 7 263 0 AACCAAAAAA 0.9523 -38 CGCTAACGATAAAGACATCAACAAAGTGAAAAAAAATAG 8 185 1 AAACAAAAAA 0.980789 -116 * * * *** *** * Masking position 10 Map Score: 13.0854 Number of sites scoring better than the average of aligned sites = 1453 Number in coding regions = 818 Number in noncoding regions = 635 Number of orfs with sites within 600 bp upstream = 459 Fraction of orfs with sites within 600 bp upstream = 0.0737231 Motif number 6 ACCGTCAGTCTATCACTAGTGGTGTATCTGATGG 3 79 0 TATCAAGGGG 0.987942 -522 GTTCTTAACTTTTCAAGAGTGGTGCGGCTTACCC 3 463 0 TTTCAAGGGG 0.984509 -138 TAATGTTCTTTATCGCGAGAGGGGGTCTACATAA 4 203 1 TATCGAGGGG 0.996714 -398 GCAGATGTCTTATCGTTAGTGGAGAAAGTAAAGT 5 11 0 TATCGAGGGG 0.996689 -590 AAAGAAGAAAATTCGTTAATGGTGATGTAATCTC 5 270 0 ATTCGAAGGG 0.92952 -331 TCCTCTTTTCTTTCGACAAAGGCGAAAGAAAAGA 7 201 0 TTTCGAAGGG 0.98451 -100 TTGATGTCTTTATCGTTAGCGGTGATTTTTCGAT 8 172 0 TATCGAGGGG 0.996595 -129 ***** ** ** * Masking position 8 Map Score: 5.96658 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 53 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AAATACCCTTTTGCTGTACAAATATCATCA 2 304 1 TTGCTGTACA 0.901592 -297 TTTATATTTTTTGCCGTACACAGGTAAAGA 3 40 0 TTGCCGTACA 0.95292 -561 GACTGACGGTTTCCCCTACCTTTTACAAGT 3 103 1 TTCCCCTACC 0.910857 -498 TACAAGTCACTTCCCGTACACCATTATCAA 3 126 1 TTCCCGTACA 0.959201 -475 ATCTGTATTTGTGCTCATCCGGTTCCATTT 3 366 0 GTGCTCATCC 0.563311 -235 GTTTTCCAGTTCAATTAGGTCTG 3 588 0 TTCCAGTTCA 0.8501 -13 ATTCTACGTCGTCCTCTTCACTTTGGTTAA 4 128 1 GTCCTCTTCA 0.935617 -473 TAATTCACCTTTGCCCTTCACCTTGTGGTG 4 155 1 TTGCCCTTCA 0.97412 -446 TTTTTTCCTCTTCCCGTTCAAAGCTTCCTC 4 440 0 TTCCCGTTCA 0.980689 -161 TTCCTAGTCCTTCCCCATCAACTCTTGAAG 5 312 0 TTCCCCATCA 0.899293 -289 CTTATAGTTGGTCCTGTTCCTTATTCCGTC 5 426 0 GTCCTGTTCC 0.894972 -175 GTGATTAATAGTGCCCTTCAAACGATTCTG 7 65 0 GTGCCCTTCA 0.965083 -236 TTCTGCATCCTTGCTGTTCAACCACTTTTC 8 241 0 TTGCTGTTCA 0.951901 -60 ********** Masking position 2 Map Score: 9.71971 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 612 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 8 ATACCAAAAAAATGATCCGTATTAAGTAAT 1 164 1 AATGATCCGT 0.802771 -437 ATGAATTAGGATTGAACCGGTAAAAGGAAA 1 248 1 ATTGAACCGG 0.97895 -353 GACAATATAAATTGAAAAGTTGTAAATATT 2 231 0 ATTGAAAAGT 0.807265 -370 CAATGCACTTATTGAACCGTGAATCTCCTA 2 578 0 ATTGAACCGT 0.966802 -23 ATACTAGTAAATGGAACCGGATGAGCACAA 3 358 1 ATGGAACCGG 0.970685 -243 AACAGACCTAATTGAACTGGAAAAC 3 586 1 ATTGAACTGG 0.877977 -15 AAGGACTAGGAAGGAAACGGTTCAGATACG 5 330 1 AAGGAAACGG 0.903323 -271 CTGACGGAATAAGGAACAGGACCAACTATA 5 424 1 AAGGAACAGG 0.94399 -177 ATTCGTGAACAATGAACAGTGTTTGGGATG 8 46 0 AATGAACAGT 0.936823 -255 AAAACAAGATAATGAAAAGTGGTTGAACAG 8 228 1 AATGAAAAGT 0.807265 -73 ********** Masking position 5 Map Score: 4.00707 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 457 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 GACTACAACAGCTATTTGATTGTCTTTGCA 1 390 1 GCTATTTGAT 0.874388 -211 GTTAAGTATGGCTATTTTTTCAAATGAGAG 1 501 0 GCTATTTTTT 0.903983 -100 TGATGGAAGTGCCCTTTTATATTTTTTGCC 3 55 0 GCCCTTTTAT 0.939567 -546 GCGGAGGGAAGCTCTTTTATTTGGGTCAAT 3 547 0 GCTCTTTTAT 0.983203 -54 TGAACTCATCGCACTTTTATACAAAGCAAG 4 542 1 GCACTTTTAT 0.912967 -59 AAGTTACATCGTTATTTTATAGAACGATCT 5 521 1 GTTATTTTAT 0.744948 -80 ATATTGGTCTGCTCGTTTATAAAAGCTTAC 6 232 0 GCTCGTTTAT 0.979709 -252 GTCTCCAGCTGCTCGTTTATGCTAATATTG 6 355 0 GCTCGTTTAT 0.979709 -129 TTCAAGCGTGGCTAGTTTTTGATTCAATAT 6 457 0 GCTAGTTTTT 0.885919 -27 ********** Masking position 6 Map Score: 3.24177 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 357 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 10 GAAGTACTGAAAGCTTACTTTTTATGCGCT 2 338 1 AAGCTTACTT 0.956155 -263 TTCGGTAGAAAAGTTTCCTCACCCCAGTAT 3 248 1 AAGTTTCCTC 0.926899 -353 CCAAATAAAAGAGCTTCCCTCCGCGAGCAA 3 553 1 GAGCTTCCCT 0.944005 -48 TTCCCGTTCAAAGCTTCCTCGGACCAACTC 4 430 0 AAGCTTCCTC 0.989876 -171 GACCAACTATAAGCCTCCTTTTACACTCAC 5 443 1 AAGCCTCCTT 0.961441 -158 TTCTCTTCCAAAGCTTCCCTGAGATCGCTT 6 124 0 AAGCTTCCCT 0.982071 -360 TCGTTTATAAAAGCTTACTCCCAATCAAAT 6 220 0 AAGCTTACTC 0.963825 -264 ********** Masking position 2 Map Score: 2.41686 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 287 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 11 AAAACAATAATGCAGCCTTCTTTTCAATATTTAC 2 206 1 TGCAGCTCTT 0.988134 -395 ATAATAAATGTTCAGGCGTCATTTAATGTTGATA 3 150 0 TTCAGCTCTT 0.981209 -451 GCTGGACGAATTGAGGCTTTCATTAGCTAGTGTG 3 306 0 TTGAGCTTTT 0.809992 -295 TTTACTAGTATGCAGACGTATCTTTTTCAGCTGG 3 335 0 TGCAGCTATT 0.96568 -266 GTTTCAATTGTGCTGTCTTCGATTGACCCAAATA 3 526 1 TGCTGCTCTT 0.982723 -75 GTGCGGGTGTTGCAGTCATTAATGTTCTTTATCG 4 184 1 TGCAGCTTTG 0.916309 -417 CACTCACATCTTCAGGCTTTATTTTGTTAAGACT 5 466 1 TTCAGCTTTT 0.97052 -135 CTAATTACATTGCTGTCATTTTTTCATGTTCGAT 6 67 1 TGCTGCTTTT 0.97287 -417 CTTCAAACGATTCTGTCATACTTTAATTCTATAA 7 46 0 TTCTGCTATT 0.923384 -255 TTGTCCACCGTTCTGTCCTCTATTCTAGCATCAT 8 15 1 TTCTGCTCTT 0.972728 -286 ***** * ** ** Masking position 9 Map Score: 5.95867 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 306 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 12 TTAGCTCAAATGTAGTTTTTAAATCT 1 7 0 TGTAGTTTTT 0.973216 -594 AAATAGCTGTTGTAGTCTTTATCATCGGCT 1 377 0 TGTAGTCTTT 0.930003 -224 ATGTTTACGCAGTAGTTTCTGAAGTACGAG 2 416 0 AGTAGTTTCT 0.91947 -185 TACTTCATCAAGTAGTTTTTTTCAATAGGA 2 553 1 AGTAGTTTTT 0.951159 -48 ACTCTTGTTTTGTAGTTTGTACATCTCTTT 4 317 1 TGTAGTTTGT 0.97514 -284 GGTTCGTTGTTGTAGTTTGTGGAATGCCAG 6 167 0 TGTAGTTTGT 0.97514 -317 ********** Masking position 6 Map Score: 1.72376 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 140 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 13 TATACATCTGGTTCTTTTCCATATGTACGT 1 53 0 GTTCTTTTCC 0.867682 -548 TGTGAACATGGTATTTCTCTTATCGGGCTT 1 280 1 GTATTTCTCT 0.844485 -321 ATCTGCCTACGTTCATCTCCTCATGTGCTT 1 337 0 GTTCATCTCC 0.974888 -264 CATGAATTTTGTACTTCTCCTTTTAATCCA 2 103 1 GTACTTCTCC 0.985034 -498 TAAGCTTTCAGTACTTCTCTTTGATGATAT 2 325 0 GTACTTCTCT 0.976671 -276 TTTGTAGTTTGTACATCTCTTTATGTCTGG 4 325 1 GTACATCTCT 0.969834 -276 TGGTCTTTTCGTTCATCTCAATATCGAAAA 8 150 1 GTTCATCTCA 0.907168 -151 ********** Masking position 6 Map Score: 1.88788 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 268 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 14 TCCTTTTGCACGGGCGAGGAAGTAAGAATATG 1 461 0 CGGCGAGAAG 0.986645 -140 TGACTTAACGAGGTCGAATAAAAAAATTTGGA 2 151 0 AGGCGAAAAA 0.919871 -450 TAGTTTCTGAAGTACGAGCAAAATTGCTCGAC 2 402 0 AGTCGAGAAA 0.910958 -199 AGAAAATACTGGGGTGAGGAAACTTTTCTACC 3 251 0 GGGTGAGAAA 0.962535 -350 CCTTGATAAGGGGAGGAGTAAGAAAAAAGTGT 4 85 0 GGGGGAGAAG 0.966643 -516 TCTTTACAACGGGCCGAGAAAAAGTGGAGTTG 4 404 1 GGGCGAGAAA 0.992394 -197 AAGTGGAGTTGGTCCGAGGAAGCTTTGAACGG 4 425 1 GGTCGAGAAG 0.964252 -176 AGCTTTGAACGGGAAGAGGAAAAAACCTTCCC 4 445 1 GGGAGAGAAA 0.935772 -156 TTTTCAATGCAGGCTGAAAAAAAAAAATTCAC 4 502 1 AGGTGAAAAA 0.693301 -99 TGAATTAATTCGGTCGATTAAGTTAACTACTA 5 154 0 CGGCGATAAG 0.878684 -447 TTGATGGGGAAGGACTAGGAAGGAAACGGTTC 5 321 1 AGGCTAGAAG 0.87534 -280 *** **** *** Masking position 7 Map Score: 3.23727 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 349 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 15 GAAAAAAACTACTTGATGAAGTAGCTGAAT 2 546 0 ACTTGATGAA 0.962953 -55 ATCTTTGAATACTTGATAATCATGCTTTGA 3 203 1 ACTTGATAAT 0.969091 -398 AAAAAAATTCACTTGATGATTGAACTCATC 4 522 1 ACTTGATGAT 0.962953 -79 TGATAAAGTAACTTGTTAATAAAAAATTTA 5 122 0 ACTTGTTAAT 0.885517 -479 GTTAACTACTACTTGATAAAGTAACTTGTT 5 135 0 ACTTGATAAA 0.969091 -466 TTTTTTGTTCACTTGATATACCTTCCCTTC 5 561 1 ACTTGATATA 0.885518 -40 ********** Masking position 4 Map Score: 0.891412 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 260 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207