******************************************************************************** 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/100/100.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10871 1.0000 500 11543 1.0000 500 21155 1.0000 500 2496 1.0000 500 2550 1.0000 500 2965 1.0000 500 31247 1.0000 500 31747 1.0000 500 36649 1.0000 500 38574 1.0000 500 39615 1.0000 500 4501 1.0000 500 5035 1.0000 500 5605 1.0000 500 7304 1.0000 500 9052 1.0000 500 9587 1.0000 500 bd793 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/100/100.seqs.fa -oc motifs/100 -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= 18 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= 9000 N= 18 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.249 C 0.232 G 0.250 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.249 C 0.232 G 0.250 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 15 llr = 176 E-value = 7.3e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::21::1:::: pos.-specific C ::2::2131:1:::: probability G 7139175277:a9:9 matrix T 39519135338:1a1 bits 2.1 1.9 * * 1.7 * * * 1.5 * * **** Relative 1.3 * ** **** Entropy 1.1 ** ** ****** (17.0 bits) 0.8 ** *** ******* 0.6 ** *** ******* 0.4 ****** ******* 0.2 *************** 0.0 --------------- Multilevel GTTGTGGTGGTGGTG consensus T G CTCTT sequence C AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 39615 231 2.85e-09 TGATTGATTG GTGGTGGTGGTGGTG GTTGATGGAT 21155 295 1.11e-08 GTGCGGGGTT GTTGTGGGGGTGGTG CTTATCCTTT 11543 274 1.26e-08 GTGTTGGGAG GTTGTGATGGTGGTG TGGTTGTCTT 7304 141 5.85e-08 AGAGAGCGTG GTGGTGGCTGTGGTG CCTTTTGGCG 31247 207 1.33e-07 GGGATTGCTG TTGGTGGTGTTGGTG TTGATTACGG 38574 166 3.17e-07 GGTGGGAGGA GTGGGGTTGGTGGTG TTGGCTCCTA 2550 73 1.39e-06 GTTACACCTC GTTGTCTCGGAGGTG CTTCCAGATT 5035 129 5.13e-06 ATATTCCGAA GGGGTGAGTGTGGTG TGAGTCCAAG 31747 300 5.13e-06 TGAAGGGATA TTTGTTGCCGTGGTG AAACATGTGG 2965 436 5.53e-06 TCCTTCGTGC TTCGTCATTTTGGTG ACCAGAAATC bd793 273 5.96e-06 GTTGTTTGCG TTTGGGGTGTTGTTG GCAGTGGTCT 36649 310 9.42e-06 GTTATAGTGT GTCTTGTCTTTGGTG TGTAGTACAT 10871 88 1.01e-05 TAACCATGCA GTTGTTTTGGTGTTT GCTACTAAGG 4501 193 1.07e-05 AGGCGAGTTC GTCGTCGGGGAGGTT TAGGATGAAG 5605 309 1.52e-05 TCCGCGGCCT GTTGTGCAGTCGGTG TTGCTGACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39615 2.8e-09 230_[+1]_255 21155 1.1e-08 294_[+1]_191 11543 1.3e-08 273_[+1]_212 7304 5.8e-08 140_[+1]_345 31247 1.3e-07 206_[+1]_279 38574 3.2e-07 165_[+1]_320 2550 1.4e-06 72_[+1]_413 5035 5.1e-06 128_[+1]_357 31747 5.1e-06 299_[+1]_186 2965 5.5e-06 435_[+1]_50 bd793 6e-06 272_[+1]_213 36649 9.4e-06 309_[+1]_176 10871 1e-05 87_[+1]_398 4501 1.1e-05 192_[+1]_293 5605 1.5e-05 308_[+1]_177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=15 39615 ( 231) GTGGTGGTGGTGGTG 1 21155 ( 295) GTTGTGGGGGTGGTG 1 11543 ( 274) GTTGTGATGGTGGTG 1 7304 ( 141) GTGGTGGCTGTGGTG 1 31247 ( 207) TTGGTGGTGTTGGTG 1 38574 ( 166) GTGGGGTTGGTGGTG 1 2550 ( 73) GTTGTCTCGGAGGTG 1 5035 ( 129) GGGGTGAGTGTGGTG 1 31747 ( 300) TTTGTTGCCGTGGTG 1 2965 ( 436) TTCGTCATTTTGGTG 1 bd793 ( 273) TTTGGGGTGTTGTTG 1 36649 ( 310) GTCTTGTCTTTGGTG 1 10871 ( 88) GTTGTTTTGGTGTTT 1 4501 ( 193) GTCGTCGGGGAGGTT 1 5605 ( 309) GTTGTGCAGTCGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8748 bayes= 9.86053 E= 7.3e-007 -1055 -1055 155 -2 -1055 -1055 -191 179 -1055 -21 41 79 -1055 -1055 190 -201 -1055 -1055 -91 168 -1055 -21 141 -101 -31 -179 90 -2 -190 20 -32 79 -1055 -179 141 -2 -1055 -1055 141 31 -90 -179 -1055 157 -1055 -1055 200 -1055 -1055 -1055 179 -101 -1055 -1055 -1055 189 -1055 -1055 179 -101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 15 E= 7.3e-007 0.000000 0.000000 0.733333 0.266667 0.000000 0.000000 0.066667 0.933333 0.000000 0.200000 0.333333 0.466667 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.133333 0.866667 0.000000 0.200000 0.666667 0.133333 0.200000 0.066667 0.466667 0.266667 0.066667 0.266667 0.200000 0.466667 0.000000 0.066667 0.666667 0.266667 0.000000 0.000000 0.666667 0.333333 0.133333 0.066667 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.866667 0.133333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.866667 0.133333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT]T[TGC]GT[GC][GTA][TCG][GT][GT]TGGTG -------------------------------------------------------------------------------- Time 2.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 17 llr = 185 E-value = 7.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2562a51258:8a462 pos.-specific C 72:6:48242a2:517 probability G :1:1::12::::::11 matrix T 1341:1:411:::121 bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * * Relative 1.3 * * *** Entropy 1.1 * * * * **** (15.7 bits) 0.8 * * * * **** * 0.6 * ***** ****** * 0.4 * ***** ******** 0.2 ******* ******** 0.0 ---------------- Multilevel CAACAACTAACAACAC consensus ATT C CC C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9587 480 1.11e-08 CGTTTAGCAA CTACACCCAACAACAC AGCAG 2965 457 2.75e-08 GGTGACCAGA AATCAACTCACAACAC TTCTTCGTTC 7304 323 1.57e-07 CCCCACCCAT CCTCAACTCACAACTC TCTCTCTCAA 21155 21 6.45e-07 AATCAGGAGC CAAAAACGAACAACGC ACAGCCGCAA 2496 461 1.27e-06 TGCTATTGCA CATAAAACAACAACAC GCATACACTC 31247 49 2.14e-06 GACGACAATA ATACAACTCACAAAAT GAACAACTCC 9052 53 2.59e-06 CACCGCAGTA CAACAACAACCCAAAA GCACAAATTG 38574 14 3.15e-06 TCCACAAAAA CTTCACCGCCCAAATC AAAAGAAGAA bd793 331 3.46e-06 TCCACGTTTT CTTCATCGTACAAAAC GAATTCAGTC 31747 484 5.44e-06 CGCAACTCTC CCACAACAACCAACAG C 5605 403 6.46e-06 AATATATAAG AGAGAACCAACAAAAC GTTTAGTTAG 10871 59 6.46e-06 CTCCGAACCA AAACATCTAACCAAGC GTCTAACCAT 36649 22 1.32e-05 GTTTTCTCCT CCATAACTTACAATAC AACGACAGTG 2550 460 1.65e-05 GTGCTTGCTA CAAAACCACACCAACA CTCGCTACTG 11543 144 1.65e-05 TGTCATCACA CATCACATCTCAACTC ACCTGCACTG 4501 480 2.67e-05 CAACTCTCCA CTAGACGCAACAATAC TCAGA 39615 38 2.85e-05 ACACACGTAG TATCACCTCACCACCA ATCGTAGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9587 1.1e-08 479_[+2]_5 2965 2.8e-08 456_[+2]_28 7304 1.6e-07 322_[+2]_162 21155 6.4e-07 20_[+2]_464 2496 1.3e-06 460_[+2]_24 31247 2.1e-06 48_[+2]_436 9052 2.6e-06 52_[+2]_432 38574 3.2e-06 13_[+2]_471 bd793 3.5e-06 330_[+2]_154 31747 5.4e-06 483_[+2]_1 5605 6.5e-06 402_[+2]_82 10871 6.5e-06 58_[+2]_426 36649 1.3e-05 21_[+2]_463 2550 1.7e-05 459_[+2]_25 11543 1.7e-05 143_[+2]_341 4501 2.7e-05 479_[+2]_5 39615 2.8e-05 37_[+2]_447 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=17 9587 ( 480) CTACACCCAACAACAC 1 2965 ( 457) AATCAACTCACAACAC 1 7304 ( 323) CCTCAACTCACAACTC 1 21155 ( 21) CAAAAACGAACAACGC 1 2496 ( 461) CATAAAACAACAACAC 1 31247 ( 49) ATACAACTCACAAAAT 1 9052 ( 53) CAACAACAACCCAAAA 1 38574 ( 14) CTTCACCGCCCAAATC 1 bd793 ( 331) CTTCATCGTACAAAAC 1 31747 ( 484) CCACAACAACCAACAG 1 5605 ( 403) AGAGAACCAACAAAAC 1 10871 ( 59) AAACATCTAACCAAGC 1 36649 ( 22) CCATAACTTACAATAC 1 2550 ( 460) CAAAACCACACCAACA 1 11543 ( 144) CATCACATCTCAACTC 1 4501 ( 480) CTAGACGCAACAATAC 1 39615 ( 38) TATCACCTCACCACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8730 bayes= 9.07116 E= 7.6e-005 -8 161 -1073 -219 92 -39 -209 13 124 -1073 -1073 61 -49 148 -109 -219 201 -1073 -1073 -1073 109 61 -1073 -119 -108 183 -209 -1073 -49 2 -50 61 92 83 -1073 -119 162 -39 -1073 -219 -1073 211 -1073 -1073 162 2 -1073 -1073 201 -1073 -1073 -1073 73 102 -1073 -119 124 -98 -109 -61 -49 161 -209 -219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 7.6e-005 0.235294 0.705882 0.000000 0.058824 0.470588 0.176471 0.058824 0.294118 0.588235 0.000000 0.000000 0.411765 0.176471 0.647059 0.117647 0.058824 1.000000 0.000000 0.000000 0.000000 0.529412 0.352941 0.000000 0.117647 0.117647 0.823529 0.058824 0.000000 0.176471 0.235294 0.176471 0.411765 0.470588 0.411765 0.000000 0.117647 0.764706 0.176471 0.000000 0.058824 0.000000 1.000000 0.000000 0.000000 0.764706 0.235294 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.411765 0.470588 0.000000 0.117647 0.588235 0.117647 0.117647 0.176471 0.176471 0.705882 0.058824 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][AT][AT]CA[AC]C[TC][AC]AC[AC]A[CA]AC -------------------------------------------------------------------------------- Time 6.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 10 llr = 127 E-value = 2.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::1::1:2:3142: pos.-specific C a:19339:18:3911a probability G :21:4::7::92:11: matrix T :88127129:12:46: bits 2.1 * * 1.9 * * 1.7 * * * * * 1.5 * * * * * * * Relative 1.3 ** * * *** * * Entropy 1.1 **** ** *** * * (18.3 bits) 0.8 **** ****** * * 0.6 **** ****** * * 0.4 **** ****** * ** 0.2 *********** **** 0.0 ---------------- Multilevel CTTCGTCGTCGACATC consensus G CC T A C TA sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5605 221 5.24e-08 GAGGTGATGC CTTCGTCGTCTCCATC CATGAGGACT bd793 54 8.27e-08 ACCAAGTCGC CTTCACCGTCGGCTTC TCAATCTGAA 4501 240 1.04e-07 TCATCTAGGG CTTCTTCGTAGGCTTC TTGGTTGATT 9587 408 1.94e-07 CGCCCGAAGG CTTCCTCGCCGACAAC GATGGCGACG 10871 142 2.85e-07 GAGCACCTTC CTTCGCCGTCGCCCGC GTTGTTGTGT 9052 477 4.24e-07 TAACTTCTCA CTTCCTCTTCGACGAC TAAACAGA 36649 164 5.96e-07 GTCTTCCTTC CTTCGTTTTCGTCATC AAACTTCTAC 11543 448 2.55e-06 ACGATCGAAA CGCCGCCATCGCCATC CCAGAAGGCC 2965 413 3.29e-06 CTGGTACGAT CTTCTTCGTAGAATCC TTCGTGCTTC 7304 185 4.24e-06 GTGGTGTGGT CGGTCTCGTCGTCTTC GGTGCATGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5605 5.2e-08 220_[+3]_264 bd793 8.3e-08 53_[+3]_431 4501 1e-07 239_[+3]_245 9587 1.9e-07 407_[+3]_77 10871 2.9e-07 141_[+3]_343 9052 4.2e-07 476_[+3]_8 36649 6e-07 163_[+3]_321 11543 2.6e-06 447_[+3]_37 2965 3.3e-06 412_[+3]_72 7304 4.2e-06 184_[+3]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=10 5605 ( 221) CTTCGTCGTCTCCATC 1 bd793 ( 54) CTTCACCGTCGGCTTC 1 4501 ( 240) CTTCTTCGTAGGCTTC 1 9587 ( 408) CTTCCTCGCCGACAAC 1 10871 ( 142) CTTCGCCGTCGCCCGC 1 9052 ( 477) CTTCCTCTTCGACGAC 1 36649 ( 164) CTTCGTTTTCGTCATC 1 11543 ( 448) CGCCGCCATCGCCATC 1 2965 ( 413) CTTCTTCGTAGAATCC 1 7304 ( 185) CGGTCTCGTCGTCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8730 bayes= 10.02 E= 2.6e+000 -997 211 -997 -997 -997 -997 -32 157 -997 -121 -132 157 -997 196 -997 -143 -131 37 68 -43 -997 37 -997 138 -997 196 -997 -143 -131 -997 148 -43 -997 -121 -997 174 -31 179 -997 -997 -997 -997 185 -143 27 37 -32 -43 -131 196 -997 -997 69 -121 -132 57 -31 -121 -132 115 -997 211 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 2.6e+000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.100000 0.100000 0.800000 0.000000 0.900000 0.000000 0.100000 0.100000 0.300000 0.400000 0.200000 0.000000 0.300000 0.000000 0.700000 0.000000 0.900000 0.000000 0.100000 0.100000 0.000000 0.700000 0.200000 0.000000 0.100000 0.000000 0.900000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.300000 0.300000 0.200000 0.200000 0.100000 0.900000 0.000000 0.000000 0.400000 0.100000 0.100000 0.400000 0.200000 0.100000 0.100000 0.600000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TG]TC[GCT][TC]C[GT]T[CA]G[ACGT]C[AT][TA]C -------------------------------------------------------------------------------- Time 9.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10871 4.65e-07 58_[+2(6.46e-06)]_13_[+1(1.01e-05)]_\ 39_[+3(2.85e-07)]_343 11543 1.82e-08 143_[+2(1.65e-05)]_114_\ [+1(1.26e-08)]_159_[+3(2.55e-06)]_37 21155 3.74e-07 20_[+2(6.45e-07)]_258_\ [+1(1.11e-08)]_191 2496 1.45e-02 460_[+2(1.27e-06)]_24 2550 2.60e-04 72_[+1(1.39e-06)]_225_\ [+1(4.65e-05)]_132_[+2(1.65e-05)]_25 2965 1.73e-08 412_[+3(3.29e-06)]_7_[+1(5.53e-06)]_\ 6_[+2(2.75e-08)]_28 31247 8.19e-06 48_[+2(2.14e-06)]_142_\ [+1(1.33e-07)]_279 31747 2.37e-04 299_[+1(5.13e-06)]_169_\ [+2(5.44e-06)]_1 36649 1.63e-06 21_[+2(1.32e-05)]_126_\ [+3(5.96e-07)]_130_[+1(9.42e-06)]_176 38574 3.31e-06 13_[+2(3.15e-06)]_136_\ [+1(3.17e-07)]_320 39615 2.85e-06 37_[+2(2.85e-05)]_177_\ [+1(2.85e-09)]_255 4501 7.10e-07 27_[+3(1.12e-05)]_149_\ [+1(1.07e-05)]_32_[+3(1.04e-07)]_76_[+3(3.29e-06)]_132_[+2(2.67e-05)]_5 5035 3.72e-02 128_[+1(5.13e-06)]_357 5605 1.45e-07 220_[+3(5.24e-08)]_8_[+3(1.28e-05)]_\ 48_[+1(1.52e-05)]_79_[+2(6.46e-06)]_82 7304 1.64e-09 140_[+1(5.85e-08)]_29_\ [+3(4.24e-06)]_122_[+2(1.57e-07)]_162 9052 3.07e-05 52_[+2(2.59e-06)]_408_\ [+3(4.24e-07)]_8 9587 1.06e-07 407_[+3(1.94e-07)]_56_\ [+2(1.11e-08)]_5 bd793 5.31e-08 34_[+2(3.23e-05)]_3_[+3(8.27e-08)]_\ 203_[+1(5.96e-06)]_43_[+2(3.46e-06)]_154 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************