******************************************************************************** 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/352/352.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10017 1.0000 500 10195 1.0000 500 11330 1.0000 500 263123 1.0000 500 264777 1.0000 500 3402 1.0000 500 8742 1.0000 500 9170 1.0000 500 9243 1.0000 500 9602 1.0000 500 bd1455 1.0000 500 bd517 1.0000 500 bd733 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/352/352.seqs.fa -oc motifs/352 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.280 C 0.228 G 0.229 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.280 C 0.228 G 0.229 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 8 llr = 106 E-value = 8.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::65:4:a3::31a pos.-specific C :a8::861:13a5:: probability G ::::33:8:3:::9: matrix T a:343::1:48:3:: bits 2.1 * * 1.9 ** * * * 1.7 ** * * * 1.5 ** * * ** Relative 1.3 *** * * * ** Entropy 1.1 *** **** ** ** (19.2 bits) 0.9 **** **** ** ** 0.6 **** **** ** ** 0.4 ********* ***** 0.2 ********* ***** 0.0 --------------- Multilevel TCCAACCGATTCCGA consensus TTGGA AC A sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- bd733 8 1.90e-08 CGGCTAT TCCAACCGAGTCAGA GTACACAGCT 3402 109 9.21e-08 TATCCAATGC TCCTGCCGATCCCGA GGCATTGGCG 9602 97 1.84e-07 GTTTTTTTTC TCCTTCCGAATCTGA AACGGAGACT bd1455 3 3.15e-07 TA TCCAACCTATCCCGA TCCTACCCCG 8742 174 4.51e-07 CTAACCAACA TCCAAGCCAATCCGA CCAGAGCAGA 10195 273 6.33e-07 GCAGACTTTT TCTATCAGACTCCGA CTATCTGATT 9170 329 8.59e-07 CTTTTACATA TCTTGCAGATTCAGA TATTGGCGTA 264777 183 2.12e-06 TCGAAGAAGA TCCAAGAGAGTCTAA GATGAGTATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd733 1.9e-08 7_[+1]_478 3402 9.2e-08 108_[+1]_377 9602 1.8e-07 96_[+1]_389 bd1455 3.1e-07 2_[+1]_483 8742 4.5e-07 173_[+1]_312 10195 6.3e-07 272_[+1]_213 9170 8.6e-07 328_[+1]_157 264777 2.1e-06 182_[+1]_303 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=8 bd733 ( 8) TCCAACCGAGTCAGA 1 3402 ( 109) TCCTGCCGATCCCGA 1 9602 ( 97) TCCTTCCGAATCTGA 1 bd1455 ( 3) TCCAACCTATCCCGA 1 8742 ( 174) TCCAAGCCAATCCGA 1 10195 ( 273) TCTATCAGACTCCGA 1 9170 ( 329) TCTTGCAGATTCAGA 1 264777 ( 183) TCCAAGAGAGTCTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6318 bayes= 9.62342 E= 8.7e+000 -965 -965 -965 193 -965 213 -965 -965 -965 171 -965 -7 116 -965 -965 52 84 -965 12 -7 -965 171 12 -965 42 145 -965 -965 -965 -87 171 -107 183 -965 -965 -965 -16 -87 12 52 -965 13 -965 152 -965 213 -965 -965 -16 113 -965 -7 -116 -965 193 -965 183 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 8.7e+000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.625000 0.000000 0.000000 0.375000 0.500000 0.000000 0.250000 0.250000 0.000000 0.750000 0.250000 0.000000 0.375000 0.625000 0.000000 0.000000 0.000000 0.125000 0.750000 0.125000 1.000000 0.000000 0.000000 0.000000 0.250000 0.125000 0.250000 0.375000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TC[CT][AT][AGT][CG][CA]GA[TAG][TC]C[CAT]GA -------------------------------------------------------------------------------- Time 1.62 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 5 llr = 69 E-value = 7.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2:8:a::::: pos.-specific C :6:a2a:a:a2a probability G ::2:::::::2: matrix T a46:::::a:6: bits 2.1 * * * * * 1.9 * * ***** * 1.7 * * ***** * 1.5 * * ***** * Relative 1.3 * ******* * Entropy 1.1 ** ******* * (19.8 bits) 0.9 ** ******* * 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCTCACACTCTC consensus TA C C sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 3402 440 5.19e-08 CGCTTCCTCC TCTCACACTCTC GACTCACTGC 264777 337 1.12e-07 TACATATTGG TTTCACACTCTC GAGGTAGAAC 263123 456 3.45e-07 ATCGGCCCCA TCACACACTCTC ATCACCATCG bd1455 398 5.01e-07 GTGACATGCT TTTCACACTCGC ACGTCAAGTC 10017 25 1.39e-06 TCTAAGGTAC TCGCCCACTCCC TCCCCCTAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3402 5.2e-08 439_[+2]_49 264777 1.1e-07 336_[+2]_152 263123 3.5e-07 455_[+2]_33 bd1455 5e-07 397_[+2]_91 10017 1.4e-06 24_[+2]_464 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=5 3402 ( 440) TCTCACACTCTC 1 264777 ( 337) TTTCACACTCTC 1 263123 ( 456) TCACACACTCTC 1 bd1455 ( 398) TTTCACACTCGC 1 10017 ( 25) TCGCCCACTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 10.5628 E= 7.8e+001 -897 -897 -897 193 -897 139 -897 61 -48 -897 -20 119 -897 213 -897 -897 151 -19 -897 -897 -897 213 -897 -897 183 -897 -897 -897 -897 213 -897 -897 -897 -897 -897 193 -897 213 -897 -897 -897 -19 -20 119 -897 213 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 7.8e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 0.200000 0.000000 0.200000 0.600000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CT][TAG]C[AC]CACTC[TCG]C -------------------------------------------------------------------------------- Time 3.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 98 E-value = 7.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2a4:8:::26:2:2a:2:: pos.-specific C :46::22::24:2:::::4:: probability G 46:::8::684468a8:a:aa matrix T 6:2:6::a4:::2:::::4:: bits 2.1 * * ** 1.9 * * * ** ** 1.7 * * * ** ** 1.5 * * * * * ** ** Relative 1.3 * *** * ***** ** Entropy 1.1 ** * ***** * ***** ** (28.3 bits) 0.9 ** ******* * ***** ** 0.6 ****************** ** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGCATGATGGCAGGGGAGCGG consensus GCA ACC TCGGCA A T sequence T A T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1455 152 2.17e-10 AGAGATTTCT GGAAAGATTGCAGGGGAGTGG AGTTAGTGCT 9602 32 2.67e-10 GTGACGATGA TGCATGATGCGAGAGGAGCGG CCCAATTTAT bd733 201 3.70e-10 CGAAGGTAAT TGCAAGATTGCATGGGAGAGG TTAGTGCATA 263123 201 4.88e-10 ATCGTAACGT GCCATCATGGGGCGGGAGCGG GCGAAAGCGG 9170 451 3.58e-09 GATATCGATG TCTATGCTGGAGGGGAAGTGG ATGTGGGCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1455 2.2e-10 151_[+3]_328 9602 2.7e-10 31_[+3]_448 bd733 3.7e-10 200_[+3]_279 263123 4.9e-10 200_[+3]_279 9170 3.6e-09 450_[+3]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 bd1455 ( 152) GGAAAGATTGCAGGGGAGTGG 1 9602 ( 32) TGCATGATGCGAGAGGAGCGG 1 bd733 ( 201) TGCAAGATTGCATGGGAGAGG 1 263123 ( 201) GCCATCATGGGGCGGGAGCGG 1 9170 ( 451) TCTATGCTGGAGGGGAAGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.536 E= 7.9e+001 -897 -897 80 119 -897 81 138 -897 -48 139 -897 -39 183 -897 -897 -897 51 -897 -897 119 -897 -19 180 -897 151 -19 -897 -897 -897 -897 -897 193 -897 -897 138 61 -897 -19 180 -897 -48 81 80 -897 110 -897 80 -897 -897 -19 138 -39 -48 -897 180 -897 -897 -897 212 -897 -48 -897 180 -897 183 -897 -897 -897 -897 -897 212 -897 -48 81 -897 61 -897 -897 212 -897 -897 -897 212 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 7.9e+001 0.000000 0.000000 0.400000 0.600000 0.000000 0.400000 0.600000 0.000000 0.200000 0.600000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.200000 0.800000 0.000000 0.200000 0.400000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.200000 0.600000 0.200000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG][GC][CAT]A[TA][GC][AC]T[GT][GC][CGA][AG][GCT][GA]G[GA]AG[CTA]GG -------------------------------------------------------------------------------- Time 4.39 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10017 1.01e-02 24_[+2(1.39e-06)]_464 10195 1.98e-04 122_[+3(3.35e-05)]_129_\ [+1(6.33e-07)]_213 11330 8.20e-01 500 263123 1.04e-08 200_[+3(4.88e-10)]_234_\ [+2(3.45e-07)]_33 264777 4.56e-06 182_[+1(2.12e-06)]_139_\ [+2(1.12e-07)]_152 3402 2.33e-07 108_[+1(9.21e-08)]_316_\ [+2(5.19e-08)]_49 8742 5.77e-03 173_[+1(4.51e-07)]_312 9170 1.41e-07 328_[+1(8.59e-07)]_107_\ [+3(3.58e-09)]_29 9243 6.28e-01 500 9602 3.25e-09 31_[+3(2.67e-10)]_44_[+1(1.84e-07)]_\ 389 bd1455 2.28e-12 2_[+1(3.15e-07)]_134_[+3(2.17e-10)]_\ 225_[+2(5.01e-07)]_91 bd517 7.97e-01 500 bd733 6.44e-10 7_[+1(1.90e-08)]_178_[+3(3.70e-10)]_\ 279 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************