******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/240/240.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10095 1.0000 500 10612 1.0000 500 20597 1.0000 500 21742 1.0000 500 21804 1.0000 500 22315 1.0000 500 22991 1.0000 500 23018 1.0000 500 23393 1.0000 500 23403 1.0000 500 24850 1.0000 500 25027 1.0000 500 260959 1.0000 500 260991 1.0000 500 262598 1.0000 500 262630 1.0000 500 262914 1.0000 500 269240 1.0000 500 269710 1.0000 500 269901 1.0000 500 29782 1.0000 500 3416 1.0000 500 354 1.0000 500 39110 1.0000 500 42652 1.0000 500 4487 1.0000 500 6285 1.0000 500 8437 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/240/240.seqs.fa -oc motifs/240 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 28 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.235 G 0.247 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.235 G 0.248 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 23 llr = 267 E-value = 6.4e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :713:4322629374235132 pos.-specific C 7325a277346:72186:762 probability G 1:11:1::2::1:13::2::: matrix T 1:6::3::3:2:::1:132:5 bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.3 * ** * Entropy 1.0 ** * ** * ** * (16.7 bits) 0.8 ** * ** * ** * * 0.6 ** ** ** ***** ** ** 0.4 ***** ** ***** ****** 0.2 ******** ************ 0.0 --------------------- Multilevel CATCCACCCACACAACCACCT consensus CCA TAATCT ACGAAT AA sequence C A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 4487 200 2.38e-09 AAAGCCCCTC CCTCCTCCCCTACCGCCACCT CGACCCCCTC 260991 412 2.35e-08 AATCTTTCGT CATCCTCAGACAAAGCCACAT AGATATCCAC 3416 118 2.72e-08 TCTTTCAACC CATCCGCCCATACAGCCGCCC TCCAATCAGG 269710 377 2.72e-08 GATCTTTCAA CCTCCAACTCCACAAACACCC CTCCTCCACT 22991 454 7.17e-08 GACATCTAAA TATCCCCAGACACAGCCTCCT TCATTCACTT 269901 353 2.21e-07 TCGAGAACTC GATGCACATCCACAACCTCCT TTTGCCATCA 262630 479 2.79e-07 CCGATCAAAT CATACACCCAAAACACCTTCT C 262598 467 3.13e-07 CATAACCCGC CAACCACCCAAACAACAGCAC TTAAATCGCA 24850 325 6.06e-07 CCAACCAAAC TAGACACCAACACAGCCGCAT TATCCACCCA 21742 468 6.06e-07 TCGCACTGCA CACACTACCAAACATCAACCA TCCAAACGAA 21804 63 9.17e-07 TGAACTCACT CATACTTCTCAACACCCTCCT CGACGGTCTC 23403 434 2.17e-06 CTATTCTAAC CACCCCACCACAAATCTTCAT CCCCATCCAT 262914 70 2.38e-06 GAACTTATTA GACCCTCCAATACATCAACAA ATCAACGCAA 260959 385 2.84e-06 ATTCGGAAGG CAACCTCCACCGCAGAAATCT CGGCCAGTCA 354 129 5.13e-06 AGGTGATGTG TCCGCTCCTCCACCGCCATCA GCTGCCGAGA 23393 307 5.13e-06 AACACCATTT CCTACAAATCCACAACTGACT CCTTCCGTTC 6285 469 5.56e-06 GATATTGCCA CAACCCCCGACAACAACAACA ACAACAACAA 10095 456 6.02e-06 CAGCAAAAAT CATACCCCAACACACAAAAGT TGACAACTAG 22315 420 8.85e-06 ACGCCGAACA CCGACCACCCCACGACCACAG AAAGCGAAAG 42652 123 9.53e-06 TTGGTAGAAC CCTCCACTGACGCCACATCCA TCACCTCCTC 8437 279 2.17e-05 TCCATATCTG CCTCCGCCAATAAGACCAGAC AAAATGGCTG 29782 409 2.79e-05 AATCCATCAC CATGCAACCATTCGCCATCAT TCCATCCGTC 269240 456 3.15e-05 ACTGTCGACA GCCACACATCCAAAGAAATCC AGCCACCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4487 2.4e-09 199_[+1]_280 260991 2.3e-08 411_[+1]_68 3416 2.7e-08 117_[+1]_362 269710 2.7e-08 376_[+1]_103 22991 7.2e-08 453_[+1]_26 269901 2.2e-07 352_[+1]_127 262630 2.8e-07 478_[+1]_1 262598 3.1e-07 466_[+1]_13 24850 6.1e-07 324_[+1]_155 21742 6.1e-07 467_[+1]_12 21804 9.2e-07 62_[+1]_417 23403 2.2e-06 433_[+1]_46 262914 2.4e-06 69_[+1]_410 260959 2.8e-06 384_[+1]_95 354 5.1e-06 128_[+1]_351 23393 5.1e-06 306_[+1]_173 6285 5.6e-06 468_[+1]_11 10095 6e-06 455_[+1]_24 22315 8.8e-06 419_[+1]_60 42652 9.5e-06 122_[+1]_357 8437 2.2e-05 278_[+1]_201 29782 2.8e-05 408_[+1]_71 269240 3.1e-05 455_[+1]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=23 4487 ( 200) CCTCCTCCCCTACCGCCACCT 1 260991 ( 412) CATCCTCAGACAAAGCCACAT 1 3416 ( 118) CATCCGCCCATACAGCCGCCC 1 269710 ( 377) CCTCCAACTCCACAAACACCC 1 22991 ( 454) TATCCCCAGACACAGCCTCCT 1 269901 ( 353) GATGCACATCCACAACCTCCT 1 262630 ( 479) CATACACCCAAAACACCTTCT 1 262598 ( 467) CAACCACCCAAACAACAGCAC 1 24850 ( 325) TAGACACCAACACAGCCGCAT 1 21742 ( 468) CACACTACCAAACATCAACCA 1 21804 ( 63) CATACTTCTCAACACCCTCCT 1 23403 ( 434) CACCCCACCACAAATCTTCAT 1 262914 ( 70) GACCCTCCAATACATCAACAA 1 260959 ( 385) CAACCTCCACCGCAGAAATCT 1 354 ( 129) TCCGCTCCTCCACCGCCATCA 1 23393 ( 307) CCTACAAATCCACAACTGACT 1 6285 ( 469) CAACCCCCGACAACAACAACA 1 10095 ( 456) CATACCCCAACACACAAAAGT 1 22315 ( 420) CCGACCACCCCACGACCACAG 1 42652 ( 123) CCTCCACTGACGCCACATCCA 1 8437 ( 279) CCTCCGCCAATAAGACCAGAC 1 29782 ( 409) CATGCAACCATTCGCCATCAT 1 269240 ( 456) GCCACACATCCAAAGAAATCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 10.2536 E= 6.4e-008 -1117 165 -92 -96 130 57 -1117 -1117 -102 -11 -151 116 39 115 -92 -1117 -1117 209 -1117 -1117 56 -11 -151 27 -2 157 -1117 -254 -28 165 -1117 -254 -28 57 -51 4 120 74 -1117 -1117 -60 137 -1117 -22 172 -1117 -151 -254 -2 165 -1117 -1117 130 -11 -92 -1117 56 -85 49 -96 -28 174 -1117 -1117 39 127 -1117 -154 98 -1117 -51 27 -102 147 -251 -54 39 137 -251 -1117 -28 -11 -251 104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 6.4e-008 0.000000 0.739130 0.130435 0.130435 0.652174 0.347826 0.000000 0.000000 0.130435 0.217391 0.086957 0.565217 0.347826 0.521739 0.130435 0.000000 0.000000 1.000000 0.000000 0.000000 0.391304 0.217391 0.086957 0.304348 0.260870 0.695652 0.000000 0.043478 0.217391 0.739130 0.000000 0.043478 0.217391 0.347826 0.173913 0.260870 0.608696 0.391304 0.000000 0.000000 0.173913 0.608696 0.000000 0.217391 0.869565 0.000000 0.086957 0.043478 0.260870 0.739130 0.000000 0.000000 0.652174 0.217391 0.130435 0.000000 0.391304 0.130435 0.347826 0.130435 0.217391 0.782609 0.000000 0.000000 0.347826 0.565217 0.000000 0.086957 0.521739 0.000000 0.173913 0.304348 0.130435 0.652174 0.043478 0.173913 0.347826 0.608696 0.043478 0.000000 0.217391 0.217391 0.043478 0.521739 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][TC][CA]C[ATC][CA][CA][CTA][AC][CT]A[CA][AC][AG][CA][CA][AT]C[CA][TAC] -------------------------------------------------------------------------------- Time 6.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 23 llr = 240 E-value = 2.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 22:2::1:::3::2:: pos.-specific C ::2:::23:::2:4:1 probability G 6:8316753a147249 matrix T 28:594:27:64326: bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.3 * * * * * Entropy 1.0 ** ** ** * ** (15.1 bits) 0.8 ** *** ** * ** 0.6 *** *** *** * ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel GTGTTGGGTGTGGCTG consensus A G T CG ATTTG sequence T A T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 39110 195 8.56e-09 AGGAGGCGAC GTGTTGGGTGTTGTTG GTTTGGTTTG 23018 96 2.09e-08 TGTTTTTTGT GTGTTGGCGGTGGCTG GTGGTGGTGG 23403 256 2.64e-08 GTACAACGAA GTGTTGGGTGTGGGGG GTTAAATGCT 42652 457 7.69e-08 AGACCACTTA GTGTTGCCTGTTGCTG TCTCTCCAAC 10095 157 9.75e-07 GCGGAGATGG TTGGTGGCTGTGGAGG AGGAGCAAAG 22991 59 1.42e-06 GGTTAGATGG GAGGTTGGTGTTGATG GGCAGAGAAC 20597 252 2.80e-06 GAGTGAACTG ATGTTTGTTGACGTTG ACATCGTTGC 269901 53 3.13e-06 GTCAACCGAG TTGATGGCGGTGTCTG ATGAAAGGCG 25027 130 4.25e-06 ACGAGGTGAT GTCTTGCGTGATGGTG CAGGTGTAGC 8437 426 6.82e-06 CGGGGGTTTG GTGTTTGGTGTCGGTT TCGGACGGTG 260991 212 7.48e-06 TAGCTGCCGT GAGATTGTGGATGCTG CGTAGAGACT 260959 177 1.05e-05 GCCGCTGTTC ATGTTGGGTGGGTGGG TTGGGGTGGG 21742 223 1.15e-05 GTTGTGAGGT GTGTGTAGTGTTGATG TTGGATTTGC 21804 263 1.25e-05 TTGAGAAAGC TTCATTGTTGTTGATG ACTTGCTGTG 10612 255 1.46e-05 AGGGTTTTCT TTGGTGATGGAGGCGG TACGGAGATT 354 212 1.58e-05 CTTGGATTAC ATGTTTGCTGATTCGC TTCTTGCGAT 3416 475 1.58e-05 TCAAGGTTTG GAGGTGCCGGTGGTGG TTTGGGAGGT 29782 336 1.58e-05 GTGAAATTTT GTGGGGGGGGGGGCGG CGTATCCTCC 269240 282 2.12e-05 TTTGCTTCGG TTTGTTGCTGTTTCTG GGAAGTTCTC 4487 12 2.28e-05 GCCACAGACG ATGATGGGTGACGTGC ACCGTCATTT 262914 348 3.21e-05 TGATCAAGGC ATCTTTAGTGACGTGG AAAACGATGG 262598 168 4.14e-05 GCTTGAACGT GAGACGGGTGAGTCTG GATGAAGTGG 262630 402 4.40e-05 GCGTCCGTCC GTCGTTCTGGTCTCGG CTCACTCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39110 8.6e-09 194_[+2]_290 23018 2.1e-08 95_[+2]_389 23403 2.6e-08 255_[+2]_229 42652 7.7e-08 456_[+2]_28 10095 9.8e-07 156_[+2]_328 22991 1.4e-06 58_[+2]_426 20597 2.8e-06 251_[+2]_233 269901 3.1e-06 52_[+2]_432 25027 4.3e-06 129_[+2]_355 8437 6.8e-06 425_[+2]_59 260991 7.5e-06 211_[+2]_273 260959 1.1e-05 176_[+2]_308 21742 1.1e-05 222_[+2]_262 21804 1.2e-05 262_[+2]_222 10612 1.5e-05 254_[+2]_230 354 1.6e-05 211_[+2]_273 3416 1.6e-05 474_[+2]_10 29782 1.6e-05 335_[+2]_149 269240 2.1e-05 281_[+2]_203 4487 2.3e-05 11_[+2]_473 262914 3.2e-05 347_[+2]_137 262598 4.1e-05 167_[+2]_317 262630 4.4e-05 401_[+2]_83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=23 39110 ( 195) GTGTTGGGTGTTGTTG 1 23018 ( 96) GTGTTGGCGGTGGCTG 1 23403 ( 256) GTGTTGGGTGTGGGGG 1 42652 ( 457) GTGTTGCCTGTTGCTG 1 10095 ( 157) TTGGTGGCTGTGGAGG 1 22991 ( 59) GAGGTTGGTGTTGATG 1 20597 ( 252) ATGTTTGTTGACGTTG 1 269901 ( 53) TTGATGGCGGTGTCTG 1 25027 ( 130) GTCTTGCGTGATGGTG 1 8437 ( 426) GTGTTTGGTGTCGGTT 1 260991 ( 212) GAGATTGTGGATGCTG 1 260959 ( 177) ATGTTGGGTGGGTGGG 1 21742 ( 223) GTGTGTAGTGTTGATG 1 21804 ( 263) TTCATTGTTGTTGATG 1 10612 ( 255) TTGGTGATGGAGGCGG 1 354 ( 212) ATGTTTGCTGATTCGC 1 3416 ( 475) GAGGTGCCGGTGGTGG 1 29782 ( 336) GTGGGGGGGGGGGCGG 1 269240 ( 282) TTTGTTGCTGTTTCTG 1 4487 ( 12) ATGATGGGTGACGTGC 1 262914 ( 348) ATCTTTAGTGACGTGG 1 262598 ( 168) GAGACGGGTGAGTCTG 1 262630 ( 402) GTCGTTCTGGTCTCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 10.2686 E= 2.1e-005 -28 -1117 119 -22 -60 -1117 -1117 171 -1117 -43 166 -254 -28 -1117 30 92 -1117 -243 -151 178 -1117 -1117 119 78 -102 -43 149 -1117 -1117 37 95 -22 -1117 -1117 30 146 -1117 -1117 201 -1117 39 -1117 -151 116 -1117 -11 66 63 -1117 -1117 158 4 -60 89 -51 -22 -1117 -1117 81 116 -1117 -143 181 -254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 2.1e-005 0.217391 0.000000 0.565217 0.217391 0.173913 0.000000 0.000000 0.826087 0.000000 0.173913 0.782609 0.043478 0.217391 0.000000 0.304348 0.478261 0.000000 0.043478 0.086957 0.869565 0.000000 0.000000 0.565217 0.434783 0.130435 0.173913 0.695652 0.000000 0.000000 0.304348 0.478261 0.217391 0.000000 0.000000 0.304348 0.695652 0.000000 0.000000 1.000000 0.000000 0.347826 0.000000 0.086957 0.565217 0.000000 0.217391 0.391304 0.391304 0.000000 0.000000 0.739130 0.260870 0.173913 0.434783 0.173913 0.217391 0.000000 0.000000 0.434783 0.565217 0.000000 0.086957 0.869565 0.043478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GAT]TG[TGA]T[GT]G[GCT][TG]G[TA][GTC][GT][CT][TG]G -------------------------------------------------------------------------------- Time 13.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 23 llr = 255 E-value = 7.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 21573165:7:111:34:8:1 pos.-specific C :::12:::::1::2:1::::: probability G 563:2933936435614a:38 matrix T 33123:12::3562352:27: bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * **** Entropy 1.0 * * **** (16.0 bits) 0.8 * ** * **** 0.6 * * * ***** * **** 0.4 **** ******** ******* 0.2 **** **************** 0.0 --------------------- Multilevel GGAAAGAAGAGTTGGTGGATG consensus TTG T GG GTGG TAA G sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24850 249 4.08e-08 AAAAGACAAC GGAACGATGAGTTAGATGATG AGATGGGCAC 25027 371 2.55e-07 GAAGTCGATG GGTACGAAGATTTGATGGATG AATCAATGAA 29782 80 3.62e-07 TTACGACTCA GTTTGGAAGAGATGGAGGATG CCGAGGACAT 3416 418 4.06e-07 GACGCTGCTT TGAAGAAGGGGTTGGCGGATG TCAAGCGCGA 4487 43 5.08e-07 CATTTGCAAA TGAACGAAGTGGTATTAGATG AGCTGAACTC 22991 37 5.08e-07 GCGTTCGCAG ATGTAGGAGAGGGGTTAGATG GGAGGTTGGT 10612 310 5.08e-07 TGAAAGTGAT GGCAAAAGGAGGTTGTGGATG TGCATCGAGT 22315 140 5.68e-07 AGTGGTGGAG AGAAAGAGGAGGTATTGGTGG AGAGGTTGCC 10095 135 7.05e-07 GAGGAAACTT GGGAGGAGGAGAGCGGAGATG GTTGGTGGCT 269240 194 1.07e-06 TGATATGTCA TGAAAGTTGATGGGTTAGAGG CGAAGACATC 39110 43 1.94e-06 GAGTACCATC GTGAAGAGGGGTGTGGTGATG GTTGATGTGT 42652 307 3.09e-06 GAGGGAGGAG GGAAAAAAGGTTTCGTGGATT AGGGCTAAAC 23018 346 3.69e-06 CTCGTTTGTG TGGCTGGAGATTTCGTGGTGG TCGTGGCGAA 262630 2 4.03e-06 T TGATTGTAGACTTGGAAGATA TGGATTTGCA 260991 179 4.03e-06 TGCATTAGAT GAAAGGGAGAGGAGTTGGTGG CGTAGCTGCC 23403 11 4.80e-06 CATTTCTTTG ATGTTGATGGGTTCTTTGATG AGGAGGGAAT 354 40 5.68e-06 TTCGTCTTTG ATGCTGGAGATTGTGAAGATG CGGAAGCAGC 269901 21 5.68e-06 ACATTCGTGC CGAAGGAACAGATGGATGATG TGTCAACCGA 20597 159 6.71e-06 AATCCAACAT TGAAAGCTGACGTGGTGAATG CCGTGCTCAG 23393 69 8.56e-06 CAGTAAGCGA GATACGAGGAGGAGGAAGATA CGAGTGCGGC 8437 53 1.70e-05 AGAAACGTCA TTACTGGTGGCGTGTCAGATG TTGCCAGGAA 21804 343 1.96e-05 AGATCTCGAT GGAATGGATGGTGTGAGGTGG AACGATGTGT 21742 4 3.40e-05 GAC GAGGAGAGGATTGGTTAGAGA TGCTCATTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24850 4.1e-08 248_[+3]_231 25027 2.5e-07 370_[+3]_109 29782 3.6e-07 79_[+3]_400 3416 4.1e-07 417_[+3]_62 4487 5.1e-07 42_[+3]_437 22991 5.1e-07 36_[+3]_443 10612 5.1e-07 309_[+3]_170 22315 5.7e-07 139_[+3]_340 10095 7e-07 134_[+3]_345 269240 1.1e-06 193_[+3]_286 39110 1.9e-06 42_[+3]_437 42652 3.1e-06 306_[+3]_173 23018 3.7e-06 345_[+3]_134 262630 4e-06 1_[+3]_478 260991 4e-06 178_[+3]_301 23403 4.8e-06 10_[+3]_469 354 5.7e-06 39_[+3]_440 269901 5.7e-06 20_[+3]_459 20597 6.7e-06 158_[+3]_321 23393 8.6e-06 68_[+3]_411 8437 1.7e-05 52_[+3]_427 21804 2e-05 342_[+3]_137 21742 3.4e-05 3_[+3]_476 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=23 24850 ( 249) GGAACGATGAGTTAGATGATG 1 25027 ( 371) GGTACGAAGATTTGATGGATG 1 29782 ( 80) GTTTGGAAGAGATGGAGGATG 1 3416 ( 418) TGAAGAAGGGGTTGGCGGATG 1 4487 ( 43) TGAACGAAGTGGTATTAGATG 1 22991 ( 37) ATGTAGGAGAGGGGTTAGATG 1 10612 ( 310) GGCAAAAGGAGGTTGTGGATG 1 22315 ( 140) AGAAAGAGGAGGTATTGGTGG 1 10095 ( 135) GGGAGGAGGAGAGCGGAGATG 1 269240 ( 194) TGAAAGTTGATGGGTTAGAGG 1 39110 ( 43) GTGAAGAGGGGTGTGGTGATG 1 42652 ( 307) GGAAAAAAGGTTTCGTGGATT 1 23018 ( 346) TGGCTGGAGATTTCGTGGTGG 1 262630 ( 2) TGATTGTAGACTTGGAAGATA 1 260991 ( 179) GAAAGGGAGAGGAGTTGGTGG 1 23403 ( 11) ATGTTGATGGGTTCTTTGATG 1 354 ( 40) ATGCTGGAGATTGTGAAGATG 1 269901 ( 21) CGAAGGAACAGATGGATGATG 1 20597 ( 159) TGAAAGCTGACGTGGTGAATG 1 23393 ( 69) GATACGAGGAGGAGGAAGATA 1 8437 ( 53) TTACTGGTGGCGTGTCAGATG 1 21804 ( 343) GGAATGGATGGTGTGAGGTGG 1 21742 ( 4) GAGGAGAGGATTGGTTAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 9.59136 E= 7.8e-004 -60 -243 95 27 -102 -1117 130 4 98 -243 30 -96 130 -85 -251 -54 39 -43 -19 4 -102 -1117 181 -1117 120 -243 8 -154 85 -1117 30 -22 -1117 -243 188 -254 139 -1117 8 -254 -1117 -85 130 4 -102 -1117 66 92 -160 -1117 30 127 -102 -43 108 -54 -260 -1117 130 46 20 -143 -151 104 56 -1117 81 -54 -260 -1117 195 -1117 164 -1117 -1117 -54 -1117 -1117 8 155 -102 -1117 174 -254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 7.8e-004 0.173913 0.043478 0.478261 0.304348 0.130435 0.000000 0.608696 0.260870 0.521739 0.043478 0.304348 0.130435 0.652174 0.130435 0.043478 0.173913 0.347826 0.173913 0.217391 0.260870 0.130435 0.000000 0.869565 0.000000 0.608696 0.043478 0.260870 0.086957 0.478261 0.000000 0.304348 0.217391 0.000000 0.043478 0.913043 0.043478 0.695652 0.000000 0.260870 0.043478 0.000000 0.130435 0.608696 0.260870 0.130435 0.000000 0.391304 0.478261 0.086957 0.000000 0.304348 0.608696 0.130435 0.173913 0.521739 0.173913 0.043478 0.000000 0.608696 0.347826 0.304348 0.086957 0.086957 0.521739 0.391304 0.000000 0.434783 0.173913 0.043478 0.000000 0.956522 0.000000 0.826087 0.000000 0.000000 0.173913 0.000000 0.000000 0.260870 0.739130 0.130435 0.000000 0.826087 0.043478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][GT][AG]A[ATG]G[AG][AGT]G[AG][GT][TG][TG]G[GT][TA][GA]GA[TG]G -------------------------------------------------------------------------------- Time 19.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10095 1.17e-07 134_[+3(7.05e-07)]_1_[+2(9.75e-07)]_\ 283_[+1(6.02e-06)]_24 10612 3.78e-05 254_[+2(1.46e-05)]_39_\ [+3(5.08e-07)]_170 20597 3.16e-04 158_[+3(6.71e-06)]_72_\ [+2(2.80e-06)]_233 21742 4.46e-06 3_[+3(3.40e-05)]_198_[+2(1.15e-05)]_\ 229_[+1(6.06e-07)]_12 21804 4.28e-06 62_[+1(9.17e-07)]_179_\ [+2(1.25e-05)]_64_[+3(1.96e-05)]_137 22315 6.57e-05 139_[+3(5.68e-07)]_259_\ [+1(8.85e-06)]_60 22991 2.09e-09 36_[+3(5.08e-07)]_1_[+2(1.42e-06)]_\ 379_[+1(7.17e-08)]_26 23018 2.48e-06 58_[+2(1.05e-05)]_21_[+2(2.09e-08)]_\ 234_[+3(3.69e-06)]_134 23393 3.77e-04 68_[+3(8.56e-06)]_217_\ [+1(5.13e-06)]_173 23403 9.76e-09 10_[+3(4.80e-06)]_87_[+1(5.50e-05)]_\ 116_[+2(2.64e-08)]_162_[+1(2.17e-06)]_46 24850 1.14e-06 248_[+3(4.08e-08)]_55_\ [+1(6.06e-07)]_3_[+1(1.27e-05)]_131 25027 2.20e-05 129_[+2(4.25e-06)]_225_\ [+3(2.55e-07)]_109 260959 9.57e-05 176_[+2(1.05e-05)]_5_[+2(4.40e-05)]_\ 171_[+1(2.84e-06)]_95 260991 2.32e-08 178_[+3(4.03e-06)]_12_\ [+2(7.48e-06)]_184_[+1(2.35e-08)]_46_[+1(9.43e-05)]_1 262598 1.19e-04 167_[+2(4.14e-05)]_283_\ [+1(3.13e-07)]_13 262630 1.10e-06 1_[+3(4.03e-06)]_379_[+2(4.40e-05)]_\ 61_[+1(2.79e-07)]_1 262914 3.29e-04 69_[+1(2.38e-06)]_257_\ [+2(3.21e-05)]_137 269240 1.19e-05 193_[+3(1.07e-06)]_67_\ [+2(2.12e-05)]_158_[+1(3.15e-05)]_24 269710 1.52e-04 376_[+1(2.72e-08)]_103 269901 1.12e-07 20_[+3(5.68e-06)]_11_[+2(3.13e-06)]_\ 284_[+1(2.21e-07)]_48_[+1(1.27e-05)]_58 29782 3.15e-06 79_[+3(3.62e-07)]_235_\ [+2(1.58e-05)]_57_[+1(2.79e-05)]_71 3416 6.39e-09 117_[+1(2.72e-08)]_21_\ [+1(6.42e-05)]_195_[+3(1.47e-05)]_21_[+3(4.06e-07)]_36_[+2(1.58e-05)]_10 354 8.12e-06 39_[+3(5.68e-06)]_68_[+1(5.13e-06)]_\ 62_[+2(1.58e-05)]_273 39110 5.49e-07 42_[+3(1.94e-06)]_131_\ [+2(8.56e-09)]_290 42652 6.73e-08 122_[+1(9.53e-06)]_163_\ [+3(3.09e-06)]_129_[+2(7.69e-08)]_28 4487 1.16e-09 11_[+2(2.28e-05)]_15_[+3(5.08e-07)]_\ 136_[+1(2.38e-09)]_27_[+1(1.56e-05)]_232 6285 4.00e-02 468_[+1(5.56e-06)]_11 8437 3.62e-05 52_[+3(1.70e-05)]_205_\ [+1(2.17e-05)]_126_[+2(6.82e-06)]_59 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************