******************************************************************************** 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/348/348.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10566 1.0000 500 18954 1.0000 500 2033 1.0000 500 21686 1.0000 500 2513 1.0000 500 25813 1.0000 500 263792 1.0000 500 3223 1.0000 500 4033 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/348/348.seqs.fa -oc motifs/348 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.230 G 0.242 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.230 G 0.242 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 6 llr = 105 E-value = 8.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3::::2:::8::3::::5: pos.-specific C 2232:::22:::2::5:3:: probability G 8:28:78::a2:8355:7:7 matrix T :55:a3:88::a:35:a:53 bits 2.1 * 1.9 * * * * 1.7 * * * * 1.5 * ** * ** * Relative 1.3 * ** ******* * Entropy 1.1 * ********** **** * (25.2 bits) 0.8 * ********** ****** 0.6 * *********** ****** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GTTGTGGTTGATGAGCTGAG consensus AC T GTG CTT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 10566 176 1.12e-10 CTGGTTCTGT GTTGTGGTTGATGGGCTGAT GTGTTGTATC 18954 198 2.29e-09 TGTTGGTTGG GTTGTTGTTGGTGTTGTGTG CTTTGTGGAG 263792 373 9.03e-09 TCTTAGTCTT GACGTTGTCGATGGTGTCAG AAGGCTCAAC 2033 338 9.64e-09 TCTAGAAGAC GAGGTGGTTGATCTTCTCAG CATTGCCTGT 21686 45 1.49e-08 TTGCCGACGG CTCCTGGTTGATGAGCTGTT GGAGTGCCGC 4033 162 1.60e-08 GGTGGTTCTG GCTGTGACTGATGAGGTGTG GTTGAAATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10566 1.1e-10 175_[+1]_305 18954 2.3e-09 197_[+1]_283 263792 9e-09 372_[+1]_108 2033 9.6e-09 337_[+1]_143 21686 1.5e-08 44_[+1]_436 4033 1.6e-08 161_[+1]_319 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=6 10566 ( 176) GTTGTGGTTGATGGGCTGAT 1 18954 ( 198) GTTGTTGTTGGTGTTGTGTG 1 263792 ( 373) GACGTTGTCGATGGTGTCAG 1 2033 ( 338) GAGGTGGTTGATCTTCTCAG 1 21686 ( 45) CTCCTGGTTGATGAGCTGTT 1 4033 ( 162) GCTGTGACTGATGAGGTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4329 bayes= 9.15128 E= 8.7e+000 -923 -46 178 -923 32 -46 -923 94 -923 53 -54 94 -923 -46 178 -923 -923 -923 -923 194 -923 -923 146 36 -68 -923 178 -923 -923 -46 -923 168 -923 -46 -923 168 -923 -923 204 -923 164 -923 -54 -923 -923 -923 -923 194 -923 -46 178 -923 32 -923 46 36 -923 -923 104 94 -923 112 104 -923 -923 -923 -923 194 -923 53 146 -923 90 -923 -923 94 -923 -923 146 36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 8.7e+000 0.000000 0.166667 0.833333 0.000000 0.333333 0.166667 0.000000 0.500000 0.000000 0.333333 0.166667 0.500000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.833333 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.666667 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[TA][TC]GT[GT]GTTGATG[AGT][GT][CG]T[GC][AT][GT] -------------------------------------------------------------------------------- Time 1.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 4 llr = 69 E-value = 3.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::85a5:8::::3:a: pos.-specific C a833:3a38aa:8a:8 probability G :::3:3::3::a:::: matrix T :3:::::::::::::3 bits 2.1 * * *** * 1.9 * * * *** ** 1.7 * * * *** ** 1.5 * * * *** ** Relative 1.3 ** * * ******** Entropy 1.1 *** * ********** (24.8 bits) 0.8 *** * ********** 0.6 *** * ********** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCAAAACACCCGCCAC consensus TCC C CG A T sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2513 476 5.09e-09 ACTCATCTCA CTACAACACCCGCCAC CTGCACACC 3223 110 7.65e-09 GACACGTCAA CCAGAGCCCCCGCCAC AAGACGACCA 21686 2 8.89e-09 T CCAAAACAGCCGCCAT CGCCTTTTGC 25813 453 1.62e-08 AAGTTGGCAA CCCAACCACCCGACAC GAACCCGAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2513 5.1e-09 475_[+2]_9 3223 7.7e-09 109_[+2]_375 21686 8.9e-09 1_[+2]_483 25813 1.6e-08 452_[+2]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=4 2513 ( 476) CTACAACACCCGCCAC 1 3223 ( 110) CCAGAGCCCCCGCCAC 1 21686 ( 2) CCAAAACAGCCGCCAT 1 25813 ( 453) CCCAACCACCCGACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4365 bayes= 10.0904 E= 3.4e+001 -865 212 -865 -865 -865 170 -865 -6 148 12 -865 -865 90 12 4 -865 190 -865 -865 -865 90 12 4 -865 -865 212 -865 -865 148 12 -865 -865 -865 170 4 -865 -865 212 -865 -865 -865 212 -865 -865 -865 -865 204 -865 -10 170 -865 -865 -865 212 -865 -865 190 -865 -865 -865 -865 170 -865 -6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 3.4e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[CT][AC][ACG]A[ACG]C[AC][CG]CCG[CA]CA[CT] -------------------------------------------------------------------------------- Time 1.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 9 llr = 105 E-value = 6.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::a818a7416872 pos.-specific C 128::9::2:1312: probability G ::2:::2:1:2:::7 matrix T 98::2::::661111 bits 2.1 1.9 * * 1.7 * * * 1.5 * * * * Relative 1.3 **** *** Entropy 1.1 ******** (16.8 bits) 0.8 ******** * * * 0.6 ********** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TTCAACAAATTAAAG consensus CG T G CAGC CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 18954 437 4.80e-08 GTATACATAT TTGAACAAATTCAAG GGTGGAGAAA 4033 484 1.18e-07 CACAATACAT TTCAACAAATTAACA AT 263792 180 3.76e-07 CATCCCAAGT CTCAACAAAAGAAAG CACGGTAGGT 2033 278 3.76e-07 TTGACTCTGT TCCAACAAATGAACG TGGAGGAAGG 25813 376 1.95e-06 CAAACTCGAA TTCATCAACTTCAAT CAGGTCAAAT 2513 323 3.43e-06 CAGAATAATG TTGAAAAAAATAAAA TACATTTCCA 10566 109 4.58e-06 ATGTCGGCTT TTCAACAACATCTTG ATGAGATTGA 21686 432 8.88e-06 CGATTGGACA TTCAACGAGTATAAG GACACAATGT 3223 290 1.75e-05 AGACAGAGCG TCCATCGAAACACAG AAGGTGAGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 18954 4.8e-08 436_[+3]_49 4033 1.2e-07 483_[+3]_2 263792 3.8e-07 179_[+3]_306 2033 3.8e-07 277_[+3]_208 25813 2e-06 375_[+3]_110 2513 3.4e-06 322_[+3]_163 10566 4.6e-06 108_[+3]_377 21686 8.9e-06 431_[+3]_54 3223 1.7e-05 289_[+3]_196 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=9 18954 ( 437) TTGAACAAATTCAAG 1 4033 ( 484) TTCAACAAATTAACA 1 263792 ( 180) CTCAACAAAAGAAAG 1 2033 ( 278) TCCAACAAATGAACG 1 25813 ( 376) TTCATCAACTTCAAT 1 2513 ( 323) TTGAAAAAAATAAAA 1 10566 ( 109) TTCAACAACATCTTG 1 21686 ( 432) TTCAACGAGTATAAG 1 3223 ( 290) TCCATCGAAACACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4374 bayes= 9.05641 E= 6.0e+001 -982 -105 -982 177 -982 -5 -982 158 -982 176 -13 -982 190 -982 -982 -982 154 -982 -982 -22 -127 195 -982 -982 154 -982 -13 -982 190 -982 -982 -982 132 -5 -112 -982 73 -982 -982 110 -127 -105 -13 110 105 53 -982 -122 154 -105 -982 -122 132 -5 -982 -122 -27 -982 146 -122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.0e+001 0.000000 0.111111 0.000000 0.888889 0.000000 0.222222 0.000000 0.777778 0.000000 0.777778 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.111111 0.888889 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.222222 0.111111 0.000000 0.444444 0.000000 0.000000 0.555556 0.111111 0.111111 0.222222 0.555556 0.555556 0.333333 0.000000 0.111111 0.777778 0.111111 0.000000 0.111111 0.666667 0.222222 0.000000 0.111111 0.222222 0.000000 0.666667 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TC][CG]A[AT]C[AG]A[AC][TA][TG][AC]A[AC][GA] -------------------------------------------------------------------------------- Time 2.61 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10566 2.82e-08 108_[+3(4.58e-06)]_52_\ [+1(1.12e-10)]_305 18954 3.65e-09 197_[+1(2.29e-09)]_219_\ [+3(4.80e-08)]_49 2033 6.61e-08 277_[+3(3.76e-07)]_45_\ [+1(9.64e-09)]_143 21686 6.24e-11 1_[+2(8.89e-09)]_27_[+1(1.49e-08)]_\ 367_[+3(8.88e-06)]_54 2513 1.77e-07 322_[+3(3.43e-06)]_138_\ [+2(5.09e-09)]_9 25813 1.21e-06 375_[+3(1.95e-06)]_62_\ [+2(1.62e-08)]_32 263792 1.45e-07 179_[+3(3.76e-07)]_178_\ [+1(9.03e-09)]_108 3223 3.73e-06 109_[+2(7.65e-09)]_164_\ [+3(1.75e-05)]_196 4033 8.48e-08 161_[+1(1.60e-08)]_237_\ [+3(5.63e-05)]_50_[+3(1.18e-07)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************