******************************************************************************** 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/157/157.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1354 1.0000 500 21256 1.0000 500 261803 1.0000 500 262350 1.0000 500 263002 1.0000 500 7048 1.0000 500 8232 1.0000 500 9278 1.0000 500 9435 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/157/157.seqs.fa -oc motifs/157 -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 0.274 C 0.232 G 0.223 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.232 G 0.223 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 9 llr = 129 E-value = 2.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6:18::332::::1::1::: pos.-specific C 726626841:::63823:::: probability G 21:::::111:1:6:33:::6 matrix T 1143:42147a9411439aa4 bits 2.2 1.9 * ** 1.7 * ** 1.5 ** ** Relative 1.3 * ** *** Entropy 1.1 * *** *** * **** (20.7 bits) 0.9 * * *** ***** **** 0.6 * ***** ****** **** 0.4 * ***** ************ 0.2 ********************* 0.0 --------------------- Multilevel CACCACCCTTTTCGCTCTTTG consensus GCTTCTTAAA TC GG T sequence CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9278 473 1.45e-12 CTGCATGGTG CACCACCCATTTCGCTGTTTG CAAATAC 8232 433 1.45e-12 CTGCATGGTG CACCACCCATTTCGCTGTTTG CAAATACATG 263002 167 5.52e-08 TCCTCATCTT CCTCCTCATATTCGCTTTTTT GGCTCATCAC 262350 93 1.34e-07 GAAGTTGGTT GTTTCTCCTTTTTGCTCTTTG TCGATGAGGC 261803 444 2.31e-07 TTCCCATCGA CACCATCTCATTCTCGTTTTG GCTGACAGCT 1354 362 3.81e-07 GTCCCAACGT CATCACCGTGTTTCAGGTTTT GCAGGTGATA 21256 251 4.97e-07 TAATTACGGG GACAACTAGTTTTCCGTTTTG AGACTGTACA 7048 423 1.18e-06 GTGGACATAA CGTTACTATTTGTCCCCTTTT CCGACGACTG 9435 12 2.08e-06 TGTTGGTGCT TCCTATCCATTTCGTCCATTT GCCTTACAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9278 1.5e-12 472_[+1]_7 8232 1.5e-12 432_[+1]_47 263002 5.5e-08 166_[+1]_313 262350 1.3e-07 92_[+1]_387 261803 2.3e-07 443_[+1]_36 1354 3.8e-07 361_[+1]_118 21256 5e-07 250_[+1]_229 7048 1.2e-06 422_[+1]_57 9435 2.1e-06 11_[+1]_468 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=9 9278 ( 473) CACCACCCATTTCGCTGTTTG 1 8232 ( 433) CACCACCCATTTCGCTGTTTG 1 263002 ( 167) CCTCCTCATATTCGCTTTTTT 1 262350 ( 93) GTTTCTCCTTTTTGCTCTTTG 1 261803 ( 444) CACCATCTCATTCTCGTTTTG 1 1354 ( 362) CATCACCGTGTTTCAGGTTTT 1 21256 ( 251) GACAACTAGTTTTCCGTTTTG 1 7048 ( 423) CGTTACTATTTGTCCCCTTTT 1 9435 ( 12) TCCTATCCATTTCGTCCATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 9.03845 E= 2.0e+000 -982 152 0 -129 102 -6 -100 -129 -982 126 -982 71 -130 126 -982 29 151 -6 -982 -982 -982 126 -982 71 -982 175 -982 -29 28 94 -100 -129 28 -106 -100 71 -30 -982 -100 129 -982 -982 -982 188 -982 -982 -100 171 -982 126 -982 71 -982 52 132 -129 -130 175 -982 -129 -982 -6 58 71 -982 52 58 29 -130 -982 -982 171 -982 -982 -982 188 -982 -982 -982 188 -982 -982 132 71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 2.0e+000 0.000000 0.666667 0.222222 0.111111 0.555556 0.222222 0.111111 0.111111 0.000000 0.555556 0.000000 0.444444 0.111111 0.555556 0.000000 0.333333 0.777778 0.222222 0.000000 0.000000 0.000000 0.555556 0.000000 0.444444 0.000000 0.777778 0.000000 0.222222 0.333333 0.444444 0.111111 0.111111 0.333333 0.111111 0.111111 0.444444 0.222222 0.000000 0.111111 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.555556 0.000000 0.444444 0.000000 0.333333 0.555556 0.111111 0.111111 0.777778 0.000000 0.111111 0.000000 0.222222 0.333333 0.444444 0.000000 0.333333 0.333333 0.333333 0.111111 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.444444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][AC][CT][CT][AC][CT][CT][CA][TA][TA]TT[CT][GC]C[TGC][CGT]TTT[GT] -------------------------------------------------------------------------------- Time 0.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 8 llr = 89 E-value = 4.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::3::9:4:9:3 pos.-specific C ::6:51:1:::6 probability G 9a:a3:a351a1 matrix T 1:1:3::35::: bits 2.2 * * * * 1.9 * * * * 1.7 * * * * 1.5 ** * * * Relative 1.3 ** * ** ** Entropy 1.1 ** * ** *** (16.1 bits) 0.9 ** * ** *** 0.6 ******* **** 0.4 ******* **** 0.2 ******* **** 0.0 ------------ Multilevel GGCGCAGAGAGC consensus A G GT A sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9278 311 2.27e-07 TTTTGACACA GGCGCAGTTAGC GCAATTCGAT 8232 271 2.27e-07 TTTTGACACA GGCGCAGTTAGC GTTTTTCTTT 9435 473 8.58e-07 GATGTGGTGA GGAGCAGGGAGC ATCACATACC 21256 160 1.29e-06 AGCAGGCGGA GGCGGAGAGAGA AGGGGCGGAA 263002 247 5.33e-06 ATAAGTCTCT GGCGTCGATAGC TCCACCAACA 7048 296 9.73e-06 GTGGCGGCGT GGTGCAGGGAGG GAGAGGAGAG 262350 223 1.03e-05 TGTCGTCGTC GGAGGAGATGGC AGTGCCTCGT 261803 393 2.38e-05 GCTTTTGGCT TGCGTAGCGAGA TTTTCTACGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9278 2.3e-07 310_[+2]_178 8232 2.3e-07 270_[+2]_218 9435 8.6e-07 472_[+2]_16 21256 1.3e-06 159_[+2]_329 263002 5.3e-06 246_[+2]_242 7048 9.7e-06 295_[+2]_193 262350 1e-05 222_[+2]_266 261803 2.4e-05 392_[+2]_96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=8 9278 ( 311) GGCGCAGTTAGC 1 8232 ( 271) GGCGCAGTTAGC 1 9435 ( 473) GGAGCAGGGAGC 1 21256 ( 160) GGCGGAGAGAGA 1 263002 ( 247) GGCGTCGATAGC 1 7048 ( 296) GGTGCAGGGAGG 1 262350 ( 223) GGAGGAGATGGC 1 261803 ( 393) TGCGTAGCGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4401 bayes= 9.83901 E= 4.6e+000 -965 -965 197 -112 -965 -965 216 -965 -13 143 -965 -112 -965 -965 216 -965 -965 111 17 -12 168 -89 -965 -965 -965 -965 216 -965 45 -89 17 -12 -965 -965 116 88 168 -965 -83 -965 -965 -965 216 -965 -13 143 -83 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 4.6e+000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.250000 0.625000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.125000 0.250000 0.250000 0.000000 0.000000 0.500000 0.500000 0.875000 0.000000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.625000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GG[CA]G[CGT]AG[AGT][GT]AG[CA] -------------------------------------------------------------------------------- Time 1.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 7 llr = 86 E-value = 4.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1:6::::3::: pos.-specific C :79:a31a6:9a probability G :11::6::1:1: matrix T a::4:19::a:: bits 2.2 * * * 1.9 * * * * * 1.7 * * * * * 1.5 * * * * *** Relative 1.3 * * * ** *** Entropy 1.1 * * * ** *** (17.7 bits) 0.9 ***** ** *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCCACGTCCTCC consensus T C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 263002 148 8.86e-08 CACCTGCTCT TCCTCGTCCTCC TCATCTTCCT 9435 86 1.35e-07 AAGGCCAATA TCCACCTCCTCC ATCCTATCCG 262350 49 6.98e-07 CCAGTGCAAT TCCACGTCCTGC TTGTATCATG 8232 485 1.15e-06 CCGGAGTTGG TGCACCTCCTCC AGCA 1354 474 1.66e-06 CCTTTCAATC TACACGTCATCC ATCACATTAT 21256 88 3.50e-06 GAGTAGAATG TCGTCGTCGTCC ATTGTGGAGA 7048 12 6.34e-06 TTTCACAGCA TCCTCTCCATCC CTCACGCCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263002 8.9e-08 147_[+3]_341 9435 1.3e-07 85_[+3]_403 262350 7e-07 48_[+3]_440 8232 1.2e-06 484_[+3]_4 1354 1.7e-06 473_[+3]_15 21256 3.5e-06 87_[+3]_401 7048 6.3e-06 11_[+3]_477 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=7 263002 ( 148) TCCTCGTCCTCC 1 9435 ( 86) TCCACCTCCTCC 1 262350 ( 49) TCCACGTCCTGC 1 8232 ( 485) TGCACCTCCTCC 1 1354 ( 474) TACACGTCATCC 1 21256 ( 88) TCGTCGTCGTCC 1 7048 ( 12) TCCTCTCCATCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4401 bayes= 9.90047 E= 4.9e+000 -945 -945 -945 188 -94 162 -64 -945 -945 189 -64 -945 106 -945 -945 66 -945 211 -945 -945 -945 30 136 -93 -945 -70 -945 166 -945 211 -945 -945 6 130 -64 -945 -945 -945 -945 188 -945 189 -64 -945 -945 211 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 4.9e+000 0.000000 0.000000 0.000000 1.000000 0.142857 0.714286 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.571429 0.142857 0.000000 0.142857 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.285714 0.571429 0.142857 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TCC[AT]C[GC]TC[CA]TCC -------------------------------------------------------------------------------- Time 2.75 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1354 1.93e-05 361_[+1(3.81e-07)]_91_\ [+3(1.66e-06)]_15 21256 6.89e-08 87_[+3(3.50e-06)]_60_[+2(1.29e-06)]_\ 79_[+1(4.97e-07)]_229 261803 6.87e-05 392_[+2(2.38e-05)]_39_\ [+1(2.31e-07)]_36 262350 3.16e-08 48_[+3(6.98e-07)]_32_[+1(1.34e-07)]_\ 109_[+2(1.03e-05)]_266 263002 1.14e-09 147_[+3(8.86e-08)]_7_[+1(5.52e-08)]_\ 59_[+2(5.33e-06)]_242 7048 1.60e-06 11_[+3(6.34e-06)]_272_\ [+2(9.73e-06)]_115_[+1(1.18e-06)]_57 8232 3.27e-14 270_[+2(2.27e-07)]_150_\ [+1(1.45e-12)]_31_[+3(1.15e-06)]_4 9278 3.61e-11 310_[+2(2.27e-07)]_150_\ [+1(1.45e-12)]_7 9435 8.87e-09 11_[+1(2.08e-06)]_53_[+3(1.35e-07)]_\ 375_[+2(8.58e-07)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************