******************************************************************************** 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/315/315.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10012 1.0000 500 10322 1.0000 500 11425 1.0000 500 18071 1.0000 500 1995 1.0000 500 22618 1.0000 500 24230 1.0000 500 24457 1.0000 500 24720 1.0000 500 25307 1.0000 500 269347 1.0000 500 269474 1.0000 500 31575 1.0000 500 36599 1.0000 500 36634 1.0000 500 8691 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/315/315.seqs.fa -oc motifs/315 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.251 C 0.232 G 0.246 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.232 G 0.246 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 16 llr = 154 E-value = 1.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :13::2:1:41: pos.-specific C 8::82:32a33a probability G 39::8::4:::: matrix T :1831884:36: bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 ** * * * * Entropy 1.1 ******* * * (13.8 bits) 0.8 ******* * * 0.6 ******* * ** 0.4 ******* **** 0.2 ************ 0.0 ------------ Multilevel CGTCGTTGCATC consensus G AT CT TC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10322 379 4.24e-07 TATTGACGTC CGTCGTTTCCTC TGCTGGTTCG 31575 155 2.54e-06 ACTATTTGGA GGTCGTTGCCTC GTACATTCAG 36634 25 3.42e-06 ATGCTCCTCC CGTCGTTCCTCC CACCGCATCC 36599 25 3.42e-06 ATGCTCCTCC CGTCGTTCCTCC CACCGCATCC 1995 274 6.45e-06 GGCCGAATAG CGATGTTTCATC AAAGATTTGC 269474 73 7.21e-06 AGTACCTTGT GGTTGTTTCATC GTGATTGAGA 24720 132 9.28e-06 ATAGACGGAC GGACGTTGCTTC ACTCACGTCT 10012 251 1.04e-05 GGGCTTGTTC CTTCGTTGCATC GTTGTGAAGT 24230 235 1.26e-05 GCCATCATAG CGTCGACTCTTC TTTTTGCTCC 24457 469 2.50e-05 TGACACAGCT CGTCTTCTCATC GATACAACAC 269347 59 3.18e-05 GCCCCCTCAT GGTTGTTGCAAC CAACCCGGCA 25307 268 3.44e-05 ACACCCATGC CGACGATGCAAC GTCTACCGAA 8691 286 4.33e-05 TCTTTGTATT CGATCTTTCCTC AGATGGTCAA 18071 436 4.33e-05 CCGACGTTGA CGTCCTCCCCCC CCTGCACTCT 11425 473 5.35e-05 CCAACACTTA CGTCCTCACTTC GTCACCTTCG 22618 413 6.79e-05 TCGTTCAATC CATCGATGCACC CTCTGCCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10322 4.2e-07 378_[+1]_110 31575 2.5e-06 154_[+1]_334 36634 3.4e-06 24_[+1]_464 36599 3.4e-06 24_[+1]_464 1995 6.4e-06 273_[+1]_215 269474 7.2e-06 72_[+1]_416 24720 9.3e-06 131_[+1]_357 10012 1e-05 250_[+1]_238 24230 1.3e-05 234_[+1]_254 24457 2.5e-05 468_[+1]_20 269347 3.2e-05 58_[+1]_430 25307 3.4e-05 267_[+1]_221 8691 4.3e-05 285_[+1]_203 18071 4.3e-05 435_[+1]_53 11425 5.4e-05 472_[+1]_16 22618 6.8e-05 412_[+1]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=16 10322 ( 379) CGTCGTTTCCTC 1 31575 ( 155) GGTCGTTGCCTC 1 36634 ( 25) CGTCGTTCCTCC 1 36599 ( 25) CGTCGTTCCTCC 1 1995 ( 274) CGATGTTTCATC 1 269474 ( 73) GGTTGTTTCATC 1 24720 ( 132) GGACGTTGCTTC 1 10012 ( 251) CTTCGTTGCATC 1 24230 ( 235) CGTCGACTCTTC 1 24457 ( 469) CGTCTTCTCATC 1 269347 ( 59) GGTTGTTGCAAC 1 25307 ( 268) CGACGATGCAAC 1 8691 ( 286) CGATCTTTCCTC 1 18071 ( 436) CGTCCTCCCCCC 1 11425 ( 473) CGTCCTCACTTC 1 22618 ( 413) CATCGATGCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 8.93074 E= 1.0e-002 -1064 169 2 -1064 -200 -1064 183 -211 -1 -1064 -1064 147 -1064 169 -1064 -12 -1064 -31 161 -211 -42 -1064 -1064 158 -1064 11 -1064 147 -200 -31 61 47 -1064 211 -1064 -1064 80 11 -1064 20 -100 11 -1064 120 -1064 211 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 1.0e-002 0.000000 0.750000 0.250000 0.000000 0.062500 0.000000 0.875000 0.062500 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.187500 0.750000 0.062500 0.187500 0.000000 0.000000 0.812500 0.000000 0.250000 0.000000 0.750000 0.062500 0.187500 0.375000 0.375000 0.000000 1.000000 0.000000 0.000000 0.437500 0.250000 0.000000 0.312500 0.125000 0.250000 0.000000 0.625000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]G[TA][CT]GT[TC][GT]C[ATC][TC]C -------------------------------------------------------------------------------- Time 2.21 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 92 E-value = 9.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::::::5::8333::33 pos.-specific C aa:aa:a::a::a3:::a588 probability G :::::5::8::8:::8::5:: matrix T ::a::5:a3:53::8:8:::: bits 2.1 ** ** * * * * 1.9 ***** ** * * * 1.7 ***** ** * * * 1.5 ***** ** * * * Relative 1.3 ***** **** *** * * ** Entropy 1.1 ********** ********** (33.1 bits) 0.8 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCTCCGCTGCAGCATGTCCCC consensus T T TT CAAA GAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36634 182 5.53e-13 TCATTCGGAT CCTCCGCTGCAGCATGTCGCC TATGCTGTAT 36599 182 5.53e-13 TCATTCGGAT CCTCCGCTGCAGCATGTCGCC TATGCTGTAT 31575 461 6.98e-11 AATGGCGGGA CCTCCTCTGCTGCAAGACCCA CCTGCCACAC 24720 440 2.69e-10 TAGCAATAGG CCTCCTCTTCTTCCTATCCAC GCGAATCTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36634 5.5e-13 181_[+2]_298 36599 5.5e-13 181_[+2]_298 31575 7e-11 460_[+2]_19 24720 2.7e-10 439_[+2]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 36634 ( 182) CCTCCGCTGCAGCATGTCGCC 1 36599 ( 182) CCTCCGCTGCAGCATGTCGCC 1 31575 ( 461) CCTCCTCTGCTGCAAGACCCA 1 24720 ( 440) CCTCCTCTTCTTCCTATCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.9061 E= 9.3e-001 -865 211 -865 -865 -865 211 -865 -865 -865 -865 -865 188 -865 211 -865 -865 -865 211 -865 -865 -865 -865 102 88 -865 211 -865 -865 -865 -865 -865 188 -865 -865 161 -12 -865 211 -865 -865 99 -865 -865 88 -865 -865 161 -12 -865 211 -865 -865 158 11 -865 -865 -1 -865 -865 147 -1 -865 161 -865 -1 -865 -865 147 -865 211 -865 -865 -865 111 102 -865 -1 169 -865 -865 -1 169 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 9.3e-001 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CCTCC[GT]CT[GT]C[AT][GT]C[AC][TA][GA][TA]C[CG][CA][CA] -------------------------------------------------------------------------------- Time 4.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 7 llr = 122 E-value = 5.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:67:193:13:77:11:1 pos.-specific C 77:a41a6:61:19:3a:69: probability G :3:::1:::::93::::73:7 matrix T 3:9::::3119:313::1:11 bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * * * * * * Relative 1.3 **** * * ** * ** * Entropy 1.1 ***** * * ** **** * (25.1 bits) 0.8 ******* * ** ***** ** 0.6 ************ ******** 0.4 ************ ******** 0.2 ************ ******** 0.0 --------------------- Multilevel CCTCAACCACTGACAACGCCG consensus TG C T A G TC G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36634 84 2.51e-12 ATAGTCATCG CCTCCACCACTGGCAACGGCG ACGCTCCCGA 36599 84 2.51e-12 ATAGTCATCG CCTCCACCACTGGCAACGGCG ACGCTCCCGA 22618 331 9.82e-09 AGAGAGATTG TGTCCACCAATAACAACGACG TTACTTGTGT 269474 411 1.06e-08 AATTGGCACT CCTCACCTATCGACACCGCCG ACAGAGTATT 1995 200 3.19e-08 GTCTAGTAAA CGTCAACTTATGCCTACACCG GCTCGTATAC 24720 379 5.15e-08 TGTCAACTTC CCTCAACCACTGTTTACTCTT GACTTCTCCT 11425 165 5.45e-08 AGCACAACAA TCACAGCAACTGTCACCGCCA TTAACAGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36634 2.5e-12 83_[+3]_396 36599 2.5e-12 83_[+3]_396 22618 9.8e-09 330_[+3]_149 269474 1.1e-08 410_[+3]_69 1995 3.2e-08 199_[+3]_280 24720 5.2e-08 378_[+3]_101 11425 5.5e-08 164_[+3]_315 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=7 36634 ( 84) CCTCCACCACTGGCAACGGCG 1 36599 ( 84) CCTCCACCACTGGCAACGGCG 1 22618 ( 331) TGTCCACCAATAACAACGACG 1 269474 ( 411) CCTCACCTATCGACACCGCCG 1 1995 ( 200) CGTCAACTTATGCCTACACCG 1 24720 ( 379) CCTCAACCACTGTTTACTCTT 1 11425 ( 165) TCACAGCAACTGTCACCGCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.7044 E= 5.3e-001 -945 162 -945 7 -945 162 22 -945 -81 -945 -945 166 -945 211 -945 -945 119 89 -945 -945 151 -70 -78 -945 -945 211 -945 -945 -81 130 -945 7 177 -945 -945 -92 19 130 -945 -92 -945 -70 -945 166 -81 -945 180 -945 19 -70 22 7 -945 188 -945 -92 151 -945 -945 7 151 30 -945 -945 -945 211 -945 -945 -81 -945 154 -92 -81 130 22 -945 -945 188 -945 -92 -81 -945 154 -92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 5.3e-001 0.000000 0.714286 0.000000 0.285714 0.000000 0.714286 0.285714 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.571429 0.000000 0.285714 0.857143 0.000000 0.000000 0.142857 0.285714 0.571429 0.000000 0.142857 0.000000 0.142857 0.000000 0.857143 0.142857 0.000000 0.857143 0.000000 0.285714 0.142857 0.285714 0.285714 0.000000 0.857143 0.000000 0.142857 0.714286 0.000000 0.000000 0.285714 0.714286 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.000000 0.714286 0.142857 0.142857 0.571429 0.285714 0.000000 0.000000 0.857143 0.000000 0.142857 0.142857 0.000000 0.714286 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CG]TC[AC]AC[CT]A[CA]TG[AGT]C[AT][AC]CG[CG]CG -------------------------------------------------------------------------------- Time 6.73 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10012 3.15e-02 250_[+1(1.04e-05)]_238 10322 1.37e-03 378_[+1(4.24e-07)]_110 11425 3.25e-05 164_[+3(5.45e-08)]_287_\ [+1(5.35e-05)]_16 18071 2.75e-02 435_[+1(4.33e-05)]_53 1995 1.86e-06 199_[+3(3.19e-08)]_53_\ [+1(6.45e-06)]_215 22618 3.08e-06 330_[+3(9.82e-09)]_61_\ [+1(6.79e-05)]_76 24230 3.18e-02 234_[+1(1.26e-05)]_254 24457 6.06e-02 468_[+1(2.50e-05)]_20 24720 7.83e-12 131_[+1(9.28e-06)]_235_\ [+3(5.15e-08)]_40_[+2(2.69e-10)]_40 25307 1.28e-01 267_[+1(3.44e-05)]_221 269347 4.50e-02 58_[+1(3.18e-05)]_430 269474 1.99e-06 72_[+1(7.21e-06)]_326_\ [+3(1.06e-08)]_69 31575 7.16e-09 154_[+1(2.54e-06)]_294_\ [+2(6.98e-11)]_19 36599 6.69e-19 24_[+1(3.42e-06)]_47_[+3(2.51e-12)]_\ 77_[+2(5.53e-13)]_298 36634 6.69e-19 24_[+1(3.42e-06)]_47_[+3(2.51e-12)]_\ 77_[+2(5.53e-13)]_298 8691 1.21e-01 285_[+1(4.33e-05)]_203 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************