******************************************************************************** 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/314/314.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10129 1.0000 500 11234 1.0000 500 24004 1.0000 500 260906 1.0000 500 33600 1.0000 500 3943 1.0000 500 4824 1.0000 500 5692 1.0000 500 bd825 1.0000 500 bd942 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/314/314.seqs.fa -oc motifs/314 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.216 G 0.248 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.216 G 0.248 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 8 llr = 110 E-value = 5.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1:4::4::49:43:: pos.-specific C a9a63834a5:94888 probability G ::::1:33:1::1::: matrix T ::::6314::111:33 bits 2.2 * * * 2.0 * * * 1.8 * * * 1.5 *** * * Relative 1.3 *** * * ** *** Entropy 1.1 **** * * ** *** (19.8 bits) 0.9 **** * * ** *** 0.7 ****** **** *** 0.4 ****** ***** *** 0.2 ****** ********* 0.0 ---------------- Multilevel CCCCTCACCCACACCC consensus ACTCT A CATT sequence GG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 4824 423 1.59e-09 CCGTGAGCTG CCCATCACCCACACCC AACATCCTCG 10129 455 2.51e-09 ATTCCTTCTT CCCCTCCTCAACACCC TACAAAGACT 33600 358 4.18e-08 GAGACTTCTT CCCCTTCCCCACCCTC TGTTTGTCAA 24004 465 4.18e-07 TCACGCCGCC CCCCTCTGCAACCACT CAGTTGTAGC 5692 294 4.85e-07 GGGTCAATAT CCCCCCATCCACTCTT TTCTCCAGCC 11234 397 6.48e-07 CCATGGCAGT CCCCGTAGCGACACCC CATAGTGCAC 260906 435 7.40e-07 AGGACTCGAA CACACCGTCCACCACC ATCTCGTCGC bd942 376 2.19e-06 CAACTTCTAT CCCATCGCCATTGCCC TCTGAAACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4824 1.6e-09 422_[+1]_62 10129 2.5e-09 454_[+1]_30 33600 4.2e-08 357_[+1]_127 24004 4.2e-07 464_[+1]_20 5692 4.8e-07 293_[+1]_191 11234 6.5e-07 396_[+1]_88 260906 7.4e-07 434_[+1]_50 bd942 2.2e-06 375_[+1]_109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=8 4824 ( 423) CCCATCACCCACACCC 1 10129 ( 455) CCCCTCCTCAACACCC 1 33600 ( 358) CCCCTTCCCCACCCTC 1 24004 ( 465) CCCCTCTGCAACCACT 1 5692 ( 294) CCCCCCATCCACTCTT 1 11234 ( 397) CCCCGTAGCGACACCC 1 260906 ( 435) CACACCGTCCACCACC 1 bd942 ( 376) CCCATCGCCATTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 10.5647 E= 5.2e-002 -965 221 -965 -965 -109 202 -965 -965 -965 221 -965 -965 49 153 -965 -965 -965 21 -98 121 -965 179 -965 -11 49 21 1 -111 -965 79 1 48 -965 221 -965 -965 49 121 -98 -965 171 -965 -965 -111 -965 202 -965 -111 49 79 -98 -111 -9 179 -965 -965 -965 179 -965 -11 -965 179 -965 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 5.2e-002 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.000000 0.250000 0.125000 0.625000 0.000000 0.750000 0.000000 0.250000 0.375000 0.250000 0.250000 0.125000 0.000000 0.375000 0.250000 0.375000 0.000000 1.000000 0.000000 0.000000 0.375000 0.500000 0.125000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.375000 0.375000 0.125000 0.125000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CCC[CA][TC][CT][ACG][CTG]C[CA]AC[AC][CA][CT][CT] -------------------------------------------------------------------------------- Time 0.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 10 llr = 109 E-value = 1.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :13:332:::932a pos.-specific C ::1:7337a1:51: probability G :911:222:9:17: matrix T a:59:231::11:: bits 2.2 * 2.0 * * * 1.8 * * * 1.5 ** ** * Relative 1.3 ** ** *** * Entropy 1.1 ** ** *** * (15.8 bits) 0.9 ** ** **** ** 0.7 ** ** **** ** 0.4 ** ** ******* 0.2 ***** ******* 0.0 -------------- Multilevel TGTTCACCCGACGA consensus A ACTG AA sequence GA TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- bd825 187 7.48e-09 TTGAAGGCAA TGTTCACCCGACGA CTATGAAGTC 4824 26 7.65e-07 TTCCCCTTCT TGTTCGTCCGAGGA GGAAGCACAT 10129 9 1.82e-06 GCTGACGA TGGTACACCGACGA CGTTGGGCTG bd942 136 2.69e-06 CAGTCGTCGC TGTTCAGCCCAAGA CAACTGAAAA 260906 59 3.82e-06 TTCCACCATC TGTTCCCGCGAACA ATGCCCTCAA 11234 27 4.17e-06 AAGCAGAACA TGCTCATCCGTCGA ACGAGGAAAT 5692 331 6.86e-06 TAGTCTCCCA TGAGAGTCCGACGA GGAATCAAAC 33600 385 7.99e-06 GTTTGTCAAC TGATCTCTCGACAA CGTCCGTCGT 3943 188 1.31e-05 TTGTTGTATG TAATACACCGAAGA GGTACACGGT 24004 314 2.02e-05 AATCAGCTTT TGTTCTGGCGATAA ATATTGAACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd825 7.5e-09 186_[+2]_300 4824 7.7e-07 25_[+2]_461 10129 1.8e-06 8_[+2]_478 bd942 2.7e-06 135_[+2]_351 260906 3.8e-06 58_[+2]_428 11234 4.2e-06 26_[+2]_460 5692 6.9e-06 330_[+2]_156 33600 8e-06 384_[+2]_102 3943 1.3e-05 187_[+2]_299 24004 2e-05 313_[+2]_173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=10 bd825 ( 187) TGTTCACCCGACGA 1 4824 ( 26) TGTTCGTCCGAGGA 1 10129 ( 9) TGGTACACCGACGA 1 bd942 ( 136) TGTTCAGCCCAAGA 1 260906 ( 59) TGTTCCCGCGAACA 1 11234 ( 27) TGCTCATCCGTCGA 1 5692 ( 331) TGAGAGTCCGACGA 1 33600 ( 385) TGATCTCTCGACAA 1 3943 ( 188) TAATACACCGAAGA 1 24004 ( 314) TGTTCTGGCGATAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 4870 bayes= 9.17683 E= 1.9e+000 -997 -997 -997 189 -141 -997 186 -997 17 -111 -131 89 -997 -997 -131 174 17 170 -997 -997 17 47 -31 -43 -42 47 -31 16 -997 170 -31 -143 -997 221 -997 -997 -997 -111 186 -997 175 -997 -997 -143 17 121 -131 -143 -42 -111 150 -997 190 -997 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 10 E= 1.9e+000 0.000000 0.000000 0.000000 1.000000 0.100000 0.000000 0.900000 0.000000 0.300000 0.100000 0.100000 0.500000 0.000000 0.000000 0.100000 0.900000 0.300000 0.700000 0.000000 0.000000 0.300000 0.300000 0.200000 0.200000 0.200000 0.300000 0.200000 0.300000 0.000000 0.700000 0.200000 0.100000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.900000 0.000000 0.000000 0.100000 0.300000 0.500000 0.100000 0.100000 0.200000 0.100000 0.700000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[TA]T[CA][ACGT][CTAG][CG]CGA[CA][GA]A -------------------------------------------------------------------------------- Time 1.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 7 llr = 85 E-value = 8.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 19:1:a:::::: pos.-specific C :1::a:1:9::9 probability G 3:9:::4:1a31 matrix T 6:19::4a::7: bits 2.2 * 2.0 ** * * 1.8 ** * * 1.5 ** *** * Relative 1.3 ***** *** * Entropy 1.1 ***** ***** (17.4 bits) 0.9 ***** ***** 0.7 ***** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TAGTCAGTCGTC consensus G T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 4824 221 5.74e-08 TGCGAGGTGG TAGTCAGTCGTC GTCGGAAATT 3943 454 3.90e-07 ACGCAAGAAA TAGTCACTCGTC ACATCACTCA bd825 103 6.11e-07 TTATTCCGAG AAGTCATTCGTC AGGCTTGTGT bd942 122 1.71e-06 TCGTATACTG GAGACAGTCGTC GCTGTTCAGC 11234 147 2.63e-06 AATCAACCTC TATTCATTCGGC TCAAGTCGCT 24004 148 3.01e-06 GGGTTTTCCA GCGTCAGTCGGC ATTTGGTCTT 5692 432 6.22e-06 GGCGGTGAGC TAGTCATTGGTG TCATCAAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4824 5.7e-08 220_[+3]_268 3943 3.9e-07 453_[+3]_35 bd825 6.1e-07 102_[+3]_386 bd942 1.7e-06 121_[+3]_367 11234 2.6e-06 146_[+3]_342 24004 3e-06 147_[+3]_341 5692 6.2e-06 431_[+3]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=7 4824 ( 221) TAGTCAGTCGTC 1 3943 ( 454) TAGTCACTCGTC 1 bd825 ( 103) AAGTCATTCGTC 1 bd942 ( 122) GAGACAGTCGTC 1 11234 ( 147) TATTCATTCGGC 1 24004 ( 148) GCGTCAGTCGGC 1 5692 ( 432) TAGTCATTGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 9.28984 E= 8.5e+000 -90 -945 21 108 168 -60 -945 -945 -945 -945 179 -91 -90 -945 -945 167 -945 221 -945 -945 190 -945 -945 -945 -945 -60 79 67 -945 -945 -945 189 -945 199 -79 -945 -945 -945 201 -945 -945 -945 21 141 -945 199 -79 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 8.5e+000 0.142857 0.000000 0.285714 0.571429 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.428571 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.857143 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG]AGTCA[GT]TCG[TG]C -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10129 6.63e-08 8_[+2(1.82e-06)]_34_[+2(9.03e-05)]_\ 384_[+1(2.51e-09)]_30 11234 1.97e-07 26_[+2(4.17e-06)]_106_\ [+3(2.63e-06)]_238_[+1(6.48e-07)]_88 24004 6.26e-07 147_[+3(3.01e-06)]_154_\ [+2(2.02e-05)]_137_[+1(4.18e-07)]_20 260906 5.17e-05 58_[+2(3.82e-06)]_362_\ [+1(7.40e-07)]_50 33600 6.43e-06 357_[+1(4.18e-08)]_11_\ [+2(7.99e-06)]_102 3943 9.54e-05 187_[+2(1.31e-05)]_252_\ [+3(3.90e-07)]_35 4824 4.51e-12 6_[+1(5.27e-05)]_3_[+2(7.65e-07)]_\ 181_[+3(5.74e-08)]_190_[+1(1.59e-09)]_62 5692 5.19e-07 293_[+1(4.85e-07)]_21_\ [+2(6.86e-06)]_87_[+3(6.22e-06)]_57 bd825 2.55e-07 102_[+3(6.11e-07)]_72_\ [+2(7.48e-09)]_300 bd942 2.71e-07 121_[+3(1.71e-06)]_2_[+2(2.69e-06)]_\ 226_[+1(2.19e-06)]_109 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************