******************************************************************************** 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/306/306.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10807 1.0000 500 21593 1.0000 500 22580 1.0000 500 22623 1.0000 500 24702 1.0000 500 264711 1.0000 500 2942 1.0000 500 35091 1.0000 500 6478 1.0000 500 6706 1.0000 500 6721 1.0000 500 6808 1.0000 500 9175 1.0000 500 bd296 1.0000 500 bd780 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/306/306.seqs.fa -oc motifs/306 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.232 G 0.240 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.232 G 0.240 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 10 llr = 152 E-value = 1.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 728:372:49::a6345:6:: pos.-specific C 16:a614a:19::43125268 probability G :22:113:5:1a::45121:2 matrix T 2::::11:1:::::::2314: bits 2.1 * * * 1.9 * * ** 1.7 * * *** 1.5 * * **** * Relative 1.3 ** * **** * Entropy 1.1 ** * ***** ** (21.9 bits) 0.8 * *** * ***** ** 0.6 ****** ******* * * ** 0.4 ****** ********* **** 0.2 ********************* 0.0 --------------------- Multilevel ACACCACCGACGAAGGACACC consensus TAG A G A CAACTCTG sequence G A C TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6721 471 1.81e-11 GCACCAACAC ACACCAGCAACGAACAACACC ATTATCAAC 22623 467 1.93e-10 CACGCCACAA ACACCAGCAACGACAGACCCC GAACACCCTC 10807 416 3.24e-09 AACAAACAGA ACACCACCAACGAACGTTGCC ATCGGCACCG 264711 373 1.31e-08 ACCAACGACA ACACAAACGCCGACGAACATC GCCTCAAAAA 21593 199 2.93e-08 GCCCCCTTCA AGACAGCCGACGACAGAGACC GCTCTACACA 24702 438 9.14e-08 TGCCACACAA TGACGACCGACGACGCACATC TCTCTCTGTC 2942 393 1.34e-07 GTGATCGTTC AAGCCTCCGACGAAGGTTCCC ACGCCTTCTC 9175 301 1.93e-07 TGAAATTCTC CAACCAACGAGGAACACCACC GTTGATCTCG 6478 57 7.85e-07 ATGCTGCCGA TCGCCAGCTACGAAGAGGATG GTCACCGCGG bd780 366 1.08e-06 CTCGCAAACA ACACACTCAACGAAAGCTTTG CACTTTCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6721 1.8e-11 470_[+1]_9 22623 1.9e-10 466_[+1]_13 10807 3.2e-09 415_[+1]_64 264711 1.3e-08 372_[+1]_107 21593 2.9e-08 198_[+1]_281 24702 9.1e-08 437_[+1]_42 2942 1.3e-07 392_[+1]_87 9175 1.9e-07 300_[+1]_179 6478 7.9e-07 56_[+1]_423 bd780 1.1e-06 365_[+1]_114 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=10 6721 ( 471) ACACCAGCAACGAACAACACC 1 22623 ( 467) ACACCAGCAACGACAGACCCC 1 10807 ( 416) ACACCACCAACGAACGTTGCC 1 264711 ( 373) ACACAAACGCCGACGAACATC 1 21593 ( 199) AGACAGCCGACGACAGAGACC 1 24702 ( 438) TGACGACCGACGACGCACATC 1 2942 ( 393) AAGCCTCCGACGAAGGTTCCC 1 9175 ( 301) CAACCAACGAGGAACACCACC 1 6478 ( 57) TCGCCAGCTACGAAGAGGATG 1 bd780 ( 366) ACACACTCAACGAAAGCTTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 10.4342 E= 1.0e-003 141 -121 -997 -40 -39 137 -27 -997 160 -997 -27 -997 -997 211 -997 -997 19 137 -126 -997 141 -121 -126 -140 -39 79 32 -140 -997 211 -997 -997 60 -997 106 -140 177 -121 -997 -997 -997 196 -126 -997 -997 -997 206 -997 193 -997 -997 -997 119 79 -997 -997 19 37 73 -997 60 -121 106 -997 93 -21 -126 -40 -997 111 -27 18 119 -21 -126 -140 -997 137 -997 60 -997 179 -27 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 10.0e-004 0.700000 0.100000 0.000000 0.200000 0.200000 0.600000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.600000 0.100000 0.000000 0.700000 0.100000 0.100000 0.100000 0.200000 0.400000 0.300000 0.100000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.500000 0.100000 0.900000 0.100000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.300000 0.300000 0.400000 0.000000 0.400000 0.100000 0.500000 0.000000 0.500000 0.200000 0.100000 0.200000 0.000000 0.500000 0.200000 0.300000 0.600000 0.200000 0.100000 0.100000 0.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][CAG][AG]C[CA]A[CGA]C[GA]ACGA[AC][GAC][GA][ACT][CTG][AC][CT][CG] -------------------------------------------------------------------------------- Time 2.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 12 llr = 161 E-value = 2.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 23::5::3::2616::51:6 pos.-specific C :351:3::7:23:::1:123 probability G 8129:2a::75:92:7::6: matrix T 133:55:73321:3a35831 bits 2.1 * 1.9 * * 1.7 * * * * 1.5 * * * * Relative 1.3 * * * * Entropy 1.1 * * **** * * * (19.4 bits) 0.8 * ** **** * **** 0.6 * ******** ********* 0.4 * ******** ********* 0.2 ******************** 0.0 -------------------- Multilevel GACGATGTCGGAGATGATGA consensus CT TC ATT C T TT TC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 35091 62 3.43e-09 CTACCCCGGA GATGACGTCGGAGATGATTC GTGACTTTTT 10807 49 3.43e-09 ACTCCGGGTT GCCGACGATGGCGATGATGA CGATATTGAT 24702 83 1.52e-08 CGAGCTTACT GCCGACGACGGCGGTGATGC AGTCTCCGTG 2942 127 2.27e-08 ACTTTTTATT GATGATGTCTCAGATTTTGA CTTATTACAA 6706 40 2.57e-08 AAGCAGTGTT GTCGTTGTTGAAGGTGTTGA TGTTTCAGGT 6808 15 4.70e-08 TCAATCGGTA GCCGTCGTCGTAGATTATTC AACGAAGGGC 22623 70 2.64e-07 GTTGATGACC GTTGTTGTTGCCGTTGATCA TATCGTCGTA 6721 314 7.63e-07 TACGACACAT ATCGTTGTCTGAATTGTTGC ACTGCCGAAC bd780 222 1.63e-06 AGTATTGTTG AACGATGACTAAGTTTTTCA GGTTGGGCTA bd296 334 1.85e-06 GAGGAAGCGA TCGCAGGTTGGAGATGTTGA GTTGGCAGAG 9175 220 3.47e-06 TGGGGGGAGT GAGGTGGACGGCGATCTCTA CCTTGTCACT 264711 51 7.70e-06 TTGTAATAGA GGTGTTGTCTTTGATGAAGT CACTCTTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35091 3.4e-09 61_[+2]_419 10807 3.4e-09 48_[+2]_432 24702 1.5e-08 82_[+2]_398 2942 2.3e-08 126_[+2]_354 6706 2.6e-08 39_[+2]_441 6808 4.7e-08 14_[+2]_466 22623 2.6e-07 69_[+2]_411 6721 7.6e-07 313_[+2]_167 bd780 1.6e-06 221_[+2]_259 bd296 1.8e-06 333_[+2]_147 9175 3.5e-06 219_[+2]_261 264711 7.7e-06 50_[+2]_430 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=12 35091 ( 62) GATGACGTCGGAGATGATTC 1 10807 ( 49) GCCGACGATGGCGATGATGA 1 24702 ( 83) GCCGACGACGGCGGTGATGC 1 2942 ( 127) GATGATGTCTCAGATTTTGA 1 6706 ( 40) GTCGTTGTTGAAGGTGTTGA 1 6808 ( 15) GCCGTCGTCGTAGATTATTC 1 22623 ( 70) GTTGTTGTTGCCGTTGATCA 1 6721 ( 314) ATCGTTGTCTGAATTGTTGC 1 bd780 ( 222) AACGATGACTAAGTTTTTCA 1 bd296 ( 334) TCGCAGGTTGGAGATGTTGA 1 9175 ( 220) GAGGTGGACGGCGATCTCTA 1 264711 ( 51) GGTGTTGTCTTTGATGAAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7215 bayes= 10.816 E= 2.6e-001 -66 -1023 164 -166 34 52 -153 -8 -1023 111 -53 33 -1023 -147 193 -1023 93 -1023 -1023 92 -1023 52 -53 92 -1023 -1023 206 -1023 34 -1023 -1023 133 -1023 152 -1023 33 -1023 -1023 147 33 -66 -48 106 -67 115 52 -1023 -166 -166 -1023 193 -1023 115 -1023 -53 -8 -1023 -1023 -1023 192 -1023 -147 147 -8 93 -1023 -1023 92 -166 -147 -1023 165 -1023 -48 128 -8 115 52 -1023 -166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 12 E= 2.6e-001 0.166667 0.000000 0.750000 0.083333 0.333333 0.333333 0.083333 0.250000 0.000000 0.500000 0.166667 0.333333 0.000000 0.083333 0.916667 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.166667 0.166667 0.500000 0.166667 0.583333 0.333333 0.000000 0.083333 0.083333 0.000000 0.916667 0.000000 0.583333 0.000000 0.166667 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.083333 0.666667 0.250000 0.500000 0.000000 0.000000 0.500000 0.083333 0.083333 0.000000 0.833333 0.000000 0.166667 0.583333 0.250000 0.583333 0.333333 0.000000 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[ACT][CT]G[AT][TC]G[TA][CT][GT]G[AC]G[AT]T[GT][AT]T[GT][AC] -------------------------------------------------------------------------------- Time 4.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 12 llr = 124 E-value = 5.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1::2:::3312: pos.-specific C 8:a552a3:9:5 probability G 1::11::::::1 matrix T :a:348:58:84 bits 2.1 * * 1.9 ** * 1.7 ** * * 1.5 ** * * Relative 1.3 *** ** ** Entropy 1.1 *** ** *** (14.9 bits) 0.8 *** ** *** 0.6 *** *** **** 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel CTCCCTCTTCTC consensus TT AA T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9175 411 4.73e-08 GTTCTCCGGT CTCCCTCTTCTC TGCTGCACCG 264711 321 4.54e-07 GTGTTGTTCC CTCTCTCTTCTC CGCACTTTAT 35091 480 5.61e-07 CATCGTAACA CTCCCTCATCTT TTCAGGTTC 10807 377 3.94e-06 TATGTTGCCC CTCCTCCCTCTC AAACAAACAA 24702 478 4.15e-06 CTCTCTCTCT CTCTCTCTTCAC ACCCCACCAC 6706 454 9.30e-06 CACTCCTCTG CTCACTCCACTT TCGTTTTGCA 6478 435 1.00e-05 AGTTGTGGTA CTCCTTCTACTG CATCCGGAGA 22623 139 1.53e-05 CAAAAGCATC GTCCTTCATCTT GTTGAACGTA bd780 270 1.65e-05 CCAGTTAGTC CTCCGTCCACTT CGCCGCTACT 2942 265 2.16e-05 TTGATTTTCT CTCATTCATCAT TAGCTACCGA 6721 137 3.33e-05 GCGTTTCTAA CTCGTTCTTATC ATAGTGGGAG 22580 463 3.57e-05 TGGTAACAAC ATCTCCCTTCTC GTGAGACGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9175 4.7e-08 410_[+3]_78 264711 4.5e-07 320_[+3]_168 35091 5.6e-07 479_[+3]_9 10807 3.9e-06 376_[+3]_112 24702 4.2e-06 477_[+3]_11 6706 9.3e-06 453_[+3]_35 6478 1e-05 434_[+3]_54 22623 1.5e-05 138_[+3]_350 bd780 1.7e-05 269_[+3]_219 2942 2.2e-05 264_[+3]_224 6721 3.3e-05 136_[+3]_352 22580 3.6e-05 462_[+3]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=12 9175 ( 411) CTCCCTCTTCTC 1 264711 ( 321) CTCTCTCTTCTC 1 35091 ( 480) CTCCCTCATCTT 1 10807 ( 377) CTCCTCCCTCTC 1 24702 ( 478) CTCTCTCTTCAC 1 6706 ( 454) CTCACTCCACTT 1 6478 ( 435) CTCCTTCTACTG 1 22623 ( 139) GTCCTTCATCTT 1 bd780 ( 270) CTCCGTCCACTT 1 2942 ( 265) CTCATTCATCAT 1 6721 ( 137) CTCGTTCTTATC 1 22580 ( 463) ATCTCCCTTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7335 bayes= 10.3541 E= 5.3e+000 -166 184 -153 -1023 -1023 -1023 -1023 192 -1023 211 -1023 -1023 -66 111 -153 -8 -1023 111 -153 65 -1023 -48 -1023 165 -1023 211 -1023 -1023 -7 11 -1023 92 -7 -1023 -1023 150 -166 198 -1023 -1023 -66 -1023 -1023 165 -1023 111 -153 65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 5.3e+000 0.083333 0.833333 0.083333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.500000 0.083333 0.250000 0.000000 0.500000 0.083333 0.416667 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 0.750000 0.083333 0.916667 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.500000 0.083333 0.416667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CTC[CT][CT]TC[TAC][TA]CT[CT] -------------------------------------------------------------------------------- Time 5.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10807 2.85e-12 48_[+2(3.43e-09)]_308_\ [+3(3.94e-06)]_27_[+1(3.24e-09)]_64 21593 5.49e-04 198_[+1(2.93e-08)]_281 22580 1.06e-01 462_[+3(3.57e-05)]_26 22623 4.23e-11 69_[+2(2.64e-07)]_49_[+3(1.53e-05)]_\ 316_[+1(1.93e-10)]_13 24702 2.76e-10 82_[+2(1.52e-08)]_335_\ [+1(9.14e-08)]_19_[+3(4.15e-06)]_11 264711 1.88e-09 50_[+2(7.70e-06)]_250_\ [+3(4.54e-07)]_40_[+1(1.31e-08)]_107 2942 2.62e-09 126_[+2(2.27e-08)]_118_\ [+3(2.16e-05)]_116_[+1(1.34e-07)]_87 35091 9.61e-08 61_[+2(3.43e-09)]_398_\ [+3(5.61e-07)]_9 6478 1.59e-04 56_[+1(7.85e-07)]_357_\ [+3(1.00e-05)]_54 6706 5.36e-06 39_[+2(2.57e-08)]_68_[+2(5.00e-05)]_\ 306_[+3(9.30e-06)]_35 6721 2.58e-11 136_[+3(3.33e-05)]_165_\ [+2(7.63e-07)]_105_[+1(6.47e-06)]_11_[+1(1.81e-11)]_9 6808 2.65e-04 14_[+2(4.70e-08)]_466 9175 1.34e-09 219_[+2(3.47e-06)]_61_\ [+1(1.93e-07)]_89_[+3(4.73e-08)]_78 bd296 1.00e-02 333_[+2(1.85e-06)]_147 bd780 6.92e-07 221_[+2(1.63e-06)]_28_\ [+3(1.65e-05)]_84_[+1(1.08e-06)]_114 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************