******************************************************************************** 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/174/174.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42494 1.0000 500 8747 1.0000 500 9312 1.0000 500 32071 1.0000 500 46608 1.0000 500 47575 1.0000 500 38124 1.0000 500 48875 1.0000 500 43587 1.0000 500 54134 1.0000 500 49229 1.0000 500 55046 1.0000 500 49639 1.0000 500 18769 1.0000 500 11048 1.0000 500 10747 1.0000 500 41878 1.0000 500 34536 1.0000 500 45190 1.0000 500 8091 1.0000 500 47006 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/174/174.seqs.fa -oc motifs/174 -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= 21 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= 10500 N= 21 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.252 C 0.256 G 0.234 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.256 G 0.234 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 21 llr = 193 E-value = 2.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1189757:1793335 pos.-specific C 332::12:511521: probability G 66:132:a:1:2552 matrix T :::::2::3:::::2 bits 2.1 * 1.9 * 1.7 * 1.5 * * * Relative 1.3 ** * * Entropy 1.0 ** * * (13.2 bits) 0.8 **** ** ** 0.6 ***** ** ***** 0.4 ***** ********* 0.2 *************** 0.0 --------------- Multilevel GGAAAAAGCAACGGA consensus CCC G C T AAAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 34536 72 6.06e-09 TAGCGTTGAC GGAAGAAGCAACGGA TCCTCTTGAT 47006 263 1.24e-07 CTATGGGATG GGCAAGAGCAACGGA GAGACAACTC 48875 151 7.01e-07 TTGGGTTCAA CCAAAAAGCAACAAA TCAAGAATAG 43587 134 2.52e-06 ATCGAGTCGT GGAAATAGAAACGAT TCCCGCCTTG 18769 127 5.97e-06 AAACAAAGCC GGAAGAAGCCACACA ATCCGTTCAT 8747 131 5.97e-06 ACAAGCTCAC GCCAACAGCAAAGGA CGATGGTGAA 8091 199 7.50e-06 TATATTCATA CGAAACCGCAACGGT ATACATATCC 10747 74 7.50e-06 TAATTCCCCC GGAAAATGCAAGGGT TGTTCGACTT 45190 315 1.16e-05 ATGAGATAAG GGAGGAAGCAACAAG TGGTTGTCAA 32071 68 1.57e-05 TGAAGTTGCG GCCAGAAGTAAACGA CATGCTGCCT 9312 145 1.74e-05 GACGGCATCC AGAAAAAGCGACCCA AAGGGCGTCC 54134 280 2.11e-05 CTCCTCGCCG GGAAGAAGAAAAACG CTCCGGCGGA 42494 433 3.33e-05 AGATACGATT CGCAATCGTAACAAA ACACTCTGCA 55046 422 3.63e-05 CTAATCGAGT GCAAAACGTGAGCGA TTGCTTTTCA 49229 5 3.96e-05 AATA AGAAAGAGTCAGGGG AGATGGATTG 11048 404 4.30e-05 ATGTTCAGCA GGAAATAGTACCGGC ACGCTCAGTA 46608 417 5.96e-05 CCGTCGCTCG CAAAAGAGTAAACAA CGCCTTTGAG 49639 273 1.50e-04 GCTAGAAACG CAAGAAAGCGAAGGG CGGCAACACA 41878 146 1.60e-04 GACGTGTCTT GGAAGGAGGACAGGT GATTGACTTT 47575 123 1.81e-04 TCGGACCCGA CCAAATCGACAGGAA GATCGTTTTG 38124 437 3.88e-04 CCAGAGTACC ACCATACGCAACAAG TTCGTTCGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34536 6.1e-09 71_[+1]_414 47006 1.2e-07 262_[+1]_223 48875 7e-07 150_[+1]_335 43587 2.5e-06 133_[+1]_352 18769 6e-06 126_[+1]_359 8747 6e-06 130_[+1]_355 8091 7.5e-06 198_[+1]_287 10747 7.5e-06 73_[+1]_412 45190 1.2e-05 314_[+1]_171 32071 1.6e-05 67_[+1]_418 9312 1.7e-05 144_[+1]_341 54134 2.1e-05 279_[+1]_206 42494 3.3e-05 432_[+1]_53 55046 3.6e-05 421_[+1]_64 49229 4e-05 4_[+1]_481 11048 4.3e-05 403_[+1]_82 46608 6e-05 416_[+1]_69 49639 0.00015 272_[+1]_213 41878 0.00016 145_[+1]_340 47575 0.00018 122_[+1]_363 38124 0.00039 436_[+1]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=21 34536 ( 72) GGAAGAAGCAACGGA 1 47006 ( 263) GGCAAGAGCAACGGA 1 48875 ( 151) CCAAAAAGCAACAAA 1 43587 ( 134) GGAAATAGAAACGAT 1 18769 ( 127) GGAAGAAGCCACACA 1 8747 ( 131) GCCAACAGCAAAGGA 1 8091 ( 199) CGAAACCGCAACGGT 1 10747 ( 74) GGAAAATGCAAGGGT 1 45190 ( 315) GGAGGAAGCAACAAG 1 32071 ( 68) GCCAGAAGTAAACGA 1 9312 ( 145) AGAAAAAGCGACCCA 1 54134 ( 280) GGAAGAAGAAAAACG 1 42494 ( 433) CGCAATCGTAACAAA 1 55046 ( 422) GCAAAACGTGAGCGA 1 49229 ( 5) AGAAAGAGTCAGGGG 1 11048 ( 404) GGAAATAGTACCGGC 1 46608 ( 417) CAAAAGAGTAAACAA 1 49639 ( 273) CAAGAAAGCGAAGGG 1 41878 ( 146) GGAAGGAGGACAGGT 1 47575 ( 123) CCAAATCGACAGGAA 1 38124 ( 437) ACCATACGCAACAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 10206 bayes= 9.22726 E= 2.5e+001 -82 16 129 -1104 -140 16 141 -1104 160 -10 -1104 -1104 184 -1104 -129 -1104 140 -1104 29 -244 105 -142 -29 -44 150 -10 -1104 -244 -1104 -1104 210 -1104 -82 104 -229 14 150 -84 -71 -1104 184 -142 -1104 -1104 18 104 -29 -1104 18 -42 117 -1104 40 -84 117 -1104 105 -242 3 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 21 E= 2.5e+001 0.142857 0.285714 0.571429 0.000000 0.095238 0.285714 0.619048 0.000000 0.761905 0.238095 0.000000 0.000000 0.904762 0.000000 0.095238 0.000000 0.666667 0.000000 0.285714 0.047619 0.523810 0.095238 0.190476 0.190476 0.714286 0.238095 0.000000 0.047619 0.000000 0.000000 1.000000 0.000000 0.142857 0.523810 0.047619 0.285714 0.714286 0.142857 0.142857 0.000000 0.904762 0.095238 0.000000 0.000000 0.285714 0.523810 0.190476 0.000000 0.285714 0.190476 0.523810 0.000000 0.333333 0.142857 0.523810 0.000000 0.523810 0.047619 0.238095 0.190476 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][GC][AC]A[AG]A[AC]G[CT]AA[CA][GA][GA][AG] -------------------------------------------------------------------------------- Time 4.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 21 llr = 200 E-value = 1.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::3:23::::2::1 pos.-specific C 51331:63115:2:4: probability G :227171:6::8::67 matrix T 575:531439426a:2 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * * * Entropy 1.0 * * * * * ** (13.8 bits) 0.8 ** * * *** *** 0.6 ** * * ******** 0.4 **** ** ******** 0.2 **************** 0.0 ---------------- Multilevel TTTGTGCTGTCGTTGG consensus C CCAT AT T C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 55046 132 7.77e-08 TTGCAGGTCC CTTGTGACGTTGTTGG CGGCATCCGG 43587 195 1.40e-07 AGAATTTTCC TTCGGGCTGTCGTTGG CAAATGACGC 34536 369 1.11e-06 AGTACGTCGG CGTGTGCTCTCGTTCG GTCGAGATGG 8747 342 2.16e-06 AACTTGGCTT TTTGTGCTGCTGATGG CGACCACTGT 32071 6 2.76e-06 TTGAA CTCGTTATTTTGTTCG GTGAAGACCA 8091 19 5.57e-06 AAACCTTGGT TTCGTTCCGGCGTTGG ATGGGCAAAC 49639 433 6.22e-06 CTTTGCCAGA CTTGTGTTCTCGTTGT GGATTCGTAG 47006 444 7.70e-06 AAGGGTGGCT TTCGAGCAGTAGCTGG ACCAAACATG 46608 478 1.16e-05 CGATCGAACT TTTCTGCATTTTCTGG AACAATC 54134 247 1.28e-05 CTGACGGTAC CGTGCGGTGTCGTTCG GCCTTCCCTC 38124 133 1.55e-05 CAATTTTCGT CGGCTGGTGTCGTTCG ATATCGGTCT 9312 102 1.86e-05 ATTGCTCTCC TCCGATCAGTTGTTGT ACGCTGGAGG 48875 470 2.43e-05 CTTGTCCTTG TTTCATCAGTCATTCG CCCAGTAATA 42494 398 2.65e-05 CAGTTAGTTC CTTCATCCGTTTATCG TCCACCAATA 45190 148 2.88e-05 TTACTGTTGA TTTCTGACGTTGATGA GGATGGCGCG 10747 24 3.13e-05 TAATTTTGTA TTTCCGCTTTCGTTCA TGGAAACATT 47575 437 3.13e-05 CTTATTGTCA CTGGAGTCGTCGCTCT TTTGACCGGC 49229 82 5.84e-05 ATACCGTATG TTGGAGAGTTTGTTGT ACGAGAGGGC 18769 143 6.74e-05 AGCCACACAA TCCGTTCATCCGTTCG AGACGTTGGA 11048 346 8.29e-05 GCATCACTTG CGCGGGCATTTTATGG ATTGAGTTTG 41878 441 1.46e-04 CGCTCCTTCC CTGGATTCCTCTCTGG TTAGTTCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 55046 7.8e-08 131_[+2]_353 43587 1.4e-07 194_[+2]_290 34536 1.1e-06 368_[+2]_116 8747 2.2e-06 341_[+2]_143 32071 2.8e-06 5_[+2]_479 8091 5.6e-06 18_[+2]_466 49639 6.2e-06 432_[+2]_52 47006 7.7e-06 443_[+2]_41 46608 1.2e-05 477_[+2]_7 54134 1.3e-05 246_[+2]_238 38124 1.5e-05 132_[+2]_352 9312 1.9e-05 101_[+2]_383 48875 2.4e-05 469_[+2]_15 42494 2.7e-05 397_[+2]_87 45190 2.9e-05 147_[+2]_337 10747 3.1e-05 23_[+2]_461 47575 3.1e-05 436_[+2]_48 49229 5.8e-05 81_[+2]_403 18769 6.7e-05 142_[+2]_342 11048 8.3e-05 345_[+2]_139 41878 0.00015 440_[+2]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=21 55046 ( 132) CTTGTGACGTTGTTGG 1 43587 ( 195) TTCGGGCTGTCGTTGG 1 34536 ( 369) CGTGTGCTCTCGTTCG 1 8747 ( 342) TTTGTGCTGCTGATGG 1 32071 ( 6) CTCGTTATTTTGTTCG 1 8091 ( 19) TTCGTTCCGGCGTTGG 1 49639 ( 433) CTTGTGTTCTCGTTGT 1 47006 ( 444) TTCGAGCAGTAGCTGG 1 46608 ( 478) TTTCTGCATTTTCTGG 1 54134 ( 247) CGTGCGGTGTCGTTCG 1 38124 ( 133) CGGCTGGTGTCGTTCG 1 9312 ( 102) TCCGATCAGTTGTTGT 1 48875 ( 470) TTTCATCAGTCATTCG 1 42494 ( 398) CTTCATCCGTTTATCG 1 45190 ( 148) TTTCTGACGTTGATGA 1 10747 ( 24) TTTCCGCTTTCGTTCA 1 47575 ( 437) CTGGAGTCGTCGCTCT 1 49229 ( 82) TTGGAGAGTTTGTTGT 1 18769 ( 143) TCCGTTCATCCGTTCG 1 11048 ( 346) CGCGGGCATTTTATGG 1 41878 ( 441) CTGGATTCCTCTCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10185 bayes= 8.91886 E= 1.0e+001 -1104 90 -1104 102 -1104 -142 -29 146 -1104 38 -29 88 -1104 16 161 -1104 40 -142 -129 88 -1104 -1104 151 36 -40 116 -129 -86 18 16 -229 56 -1104 -84 129 14 -1104 -142 -229 173 -240 104 -1104 73 -240 -1104 171 -44 -40 -42 -1104 126 -1104 -1104 -1104 195 -1104 75 129 -1104 -140 -1104 161 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 21 E= 1.0e+001 0.000000 0.476190 0.000000 0.523810 0.000000 0.095238 0.190476 0.714286 0.000000 0.333333 0.190476 0.476190 0.000000 0.285714 0.714286 0.000000 0.333333 0.095238 0.095238 0.476190 0.000000 0.000000 0.666667 0.333333 0.190476 0.571429 0.095238 0.142857 0.285714 0.285714 0.047619 0.380952 0.000000 0.142857 0.571429 0.285714 0.000000 0.095238 0.047619 0.857143 0.047619 0.523810 0.000000 0.428571 0.047619 0.000000 0.761905 0.190476 0.190476 0.190476 0.000000 0.619048 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.571429 0.000000 0.095238 0.000000 0.714286 0.190476 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]T[TC][GC][TA][GT]C[TAC][GT]T[CT]GTT[GC]G -------------------------------------------------------------------------------- Time 7.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 21 llr = 195 E-value = 8.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :464381987335973 pos.-specific C 63121:9::1415::3 probability G 433:5::11:16:11: matrix T :::4:1:::22:::14 bits 2.1 1.9 1.7 1.5 * * Relative 1.3 ** * Entropy 1.0 * **** ** (13.4 bits) 0.8 * **** *** 0.6 * * ****** **** 0.4 ********** ***** 0.2 ********** ***** 0.0 ---------------- Multilevel CAAAGACAAACGCAAT consensus GCGTA AAA A sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 42494 241 3.89e-09 GGCACGACGA CGAAGACAAACGAAAT AACGTATCAA 9312 308 1.90e-06 CCGAATCATC CAAAATCAAAGGCAAT CGCAGTGTAA 49229 211 3.09e-06 CAGACTGGTC CGGTATCAAAAGCAAT CCCGGATACC 8747 100 4.33e-06 AAACGTCCAT CCACGTCAAAAGAAAC ACCAAACAAG 43587 431 4.84e-06 ACGGAACATC CAATAACTAACGCAAC TGAAACTAGG 49639 18 5.39e-06 TCCGTATGTC GAACGACAAATGCATC TATGAAAGGT 38124 80 5.39e-06 GACGTATCTG CAGTGACAATTAAAAA GAAGTCAATG 11048 430 5.99e-06 CGCTCAGTAG CAGACACAAAAGAAGA GAGCTATGAA 45190 14 7.40e-06 TGTGAATTGT CGAAGAAAATTGAAAT TTTGTAGATC 8091 318 1.00e-05 TACAATGATG CAACAACAACAACAAC AACAACACGC 47006 321 1.11e-05 TGAGTACCTA CAATGAAAAATCCAAT GTCCGGGTTC 54134 75 1.22e-05 AGAGACGGTT GCCAGACAGACGCAAA AGTTGAACTT 55046 100 1.62e-05 CAGTCTATCT CGAACCCAAAAGAAAT CACGTATTGC 48875 86 2.54e-05 GCCTACGCCT GCGTGACAAACACACA CACGGTAAAA 34536 31 2.77e-05 TGAGTCAACG GAAAAACAGCCACAAA AAATCATGGA 18769 337 2.77e-05 GAAAGAAAAC GGGAAACGACCGAAAT ACGCTGAGAG 10747 380 6.12e-05 CCCCTTCGTC CAATGACGATGGCATC CACTCTGTCA 32071 221 9.39e-05 GCCCATTGTC GCATCACAGAAAAAGT GAGTTAGAAT 47575 293 1.15e-04 CGTCATATTC GGCAGACAAAGGAGGT ATTTGTCCGT 41878 99 2.25e-04 CAGCAGTGCA GCGCAAAAATCCCAAC AGCATGAACA 46608 334 3.62e-04 CGACTGTTGA CCGTGACACACAAGTA GTAACTCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42494 3.9e-09 240_[+3]_244 9312 1.9e-06 307_[+3]_177 49229 3.1e-06 210_[+3]_274 8747 4.3e-06 99_[+3]_385 43587 4.8e-06 430_[+3]_54 49639 5.4e-06 17_[+3]_467 38124 5.4e-06 79_[+3]_405 11048 6e-06 429_[+3]_55 45190 7.4e-06 13_[+3]_471 8091 1e-05 317_[+3]_167 47006 1.1e-05 320_[+3]_164 54134 1.2e-05 74_[+3]_410 55046 1.6e-05 99_[+3]_385 48875 2.5e-05 85_[+3]_399 34536 2.8e-05 30_[+3]_454 18769 2.8e-05 336_[+3]_148 10747 6.1e-05 379_[+3]_105 32071 9.4e-05 220_[+3]_264 47575 0.00011 292_[+3]_192 41878 0.00022 98_[+3]_386 46608 0.00036 333_[+3]_151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=21 42494 ( 241) CGAAGACAAACGAAAT 1 9312 ( 308) CAAAATCAAAGGCAAT 1 49229 ( 211) CGGTATCAAAAGCAAT 1 8747 ( 100) CCACGTCAAAAGAAAC 1 43587 ( 431) CAATAACTAACGCAAC 1 49639 ( 18) GAACGACAAATGCATC 1 38124 ( 80) CAGTGACAATTAAAAA 1 11048 ( 430) CAGACACAAAAGAAGA 1 45190 ( 14) CGAAGAAAATTGAAAT 1 8091 ( 318) CAACAACAACAACAAC 1 47006 ( 321) CAATGAAAAATCCAAT 1 54134 ( 75) GCCAGACAGACGCAAA 1 55046 ( 100) CGAACCCAAAAGAAAT 1 48875 ( 86) GCGTGACAAACACACA 1 34536 ( 31) GAAAAACAGCCACAAA 1 18769 ( 337) GGGAAACGACCGAAAT 1 10747 ( 380) CAATGACGATGGCATC 1 32071 ( 221) GCATCACAGAAAAAGT 1 47575 ( 293) GGCAGACAAAGGAGGT 1 41878 ( 99) GCGCAAAAATCCCAAC 1 46608 ( 334) CCGTGACACACAAGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10185 bayes= 8.91886 E= 8.8e+002 -1104 128 71 -1104 77 16 29 -1104 118 -142 51 -1104 77 -42 -1104 56 40 -84 117 -1104 168 -242 -1104 -86 -82 175 -1104 -1104 177 -1104 -129 -244 168 -242 -71 -1104 140 -84 -1104 -44 18 58 -71 -44 18 -142 141 -1104 92 104 -1104 -1104 184 -1104 -129 -1104 140 -242 -71 -86 18 16 -1104 73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 21 E= 8.8e+002 0.000000 0.619048 0.380952 0.000000 0.428571 0.285714 0.285714 0.000000 0.571429 0.095238 0.333333 0.000000 0.428571 0.190476 0.000000 0.380952 0.333333 0.142857 0.523810 0.000000 0.809524 0.047619 0.000000 0.142857 0.142857 0.857143 0.000000 0.000000 0.857143 0.000000 0.095238 0.047619 0.809524 0.047619 0.142857 0.000000 0.666667 0.142857 0.000000 0.190476 0.285714 0.380952 0.142857 0.190476 0.285714 0.095238 0.619048 0.000000 0.476190 0.523810 0.000000 0.000000 0.904762 0.000000 0.095238 0.000000 0.666667 0.047619 0.142857 0.142857 0.285714 0.285714 0.000000 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][ACG][AG][AT][GA]ACAAA[CA][GA][CA]AA[TAC] -------------------------------------------------------------------------------- Time 11.59 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42494 9.96e-08 240_[+3(3.89e-09)]_141_\ [+2(2.65e-05)]_19_[+1(3.33e-05)]_53 8747 1.26e-06 99_[+3(4.33e-06)]_15_[+1(5.97e-06)]_\ 196_[+2(2.16e-06)]_143 9312 1.06e-05 101_[+2(1.86e-05)]_27_\ [+1(1.74e-05)]_148_[+3(1.90e-06)]_177 32071 5.54e-05 5_[+2(2.76e-06)]_46_[+1(1.57e-05)]_\ 98_[+2(2.65e-05)]_24_[+3(9.39e-05)]_264 46608 1.74e-03 416_[+1(5.96e-05)]_46_\ [+2(1.16e-05)]_7 47575 3.89e-03 436_[+2(3.13e-05)]_48 38124 3.12e-04 79_[+3(5.39e-06)]_37_[+2(1.55e-05)]_\ 352 48875 7.79e-06 85_[+3(2.54e-05)]_49_[+1(7.01e-07)]_\ 304_[+2(2.43e-05)]_15 43587 5.34e-08 133_[+1(2.52e-06)]_46_\ [+2(1.40e-07)]_220_[+3(4.84e-06)]_54 54134 4.66e-05 74_[+3(1.22e-05)]_156_\ [+2(1.28e-05)]_17_[+1(2.11e-05)]_111_[+2(8.87e-05)]_79 49229 9.04e-05 4_[+1(3.96e-05)]_62_[+2(5.84e-05)]_\ 113_[+3(3.09e-06)]_274 55046 1.04e-06 99_[+3(1.62e-05)]_16_[+2(7.77e-08)]_\ 274_[+1(3.63e-05)]_64 49639 6.59e-05 17_[+3(5.39e-06)]_399_\ [+2(6.22e-06)]_52 18769 1.33e-04 126_[+1(5.97e-06)]_1_[+2(6.74e-05)]_\ 178_[+3(2.77e-05)]_148 11048 2.32e-04 345_[+2(8.29e-05)]_42_\ [+1(4.30e-05)]_11_[+3(5.99e-06)]_55 10747 1.66e-04 23_[+2(3.13e-05)]_34_[+1(7.50e-06)]_\ 291_[+3(6.12e-05)]_105 41878 1.95e-02 500 34536 6.90e-09 30_[+3(2.77e-05)]_25_[+1(6.06e-09)]_\ 282_[+2(1.11e-06)]_116 45190 3.62e-05 13_[+3(7.40e-06)]_118_\ [+2(2.88e-05)]_151_[+1(1.16e-05)]_171 8091 7.62e-06 18_[+2(5.57e-06)]_164_\ [+1(7.50e-06)]_104_[+3(1.00e-05)]_167 47006 2.80e-07 262_[+1(1.24e-07)]_43_\ [+3(1.11e-05)]_107_[+2(7.70e-06)]_41 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************