******************************************************************************** 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/95/95.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10991 1.0000 500 11129 1.0000 500 12133 1.0000 500 12196 1.0000 500 23656 1.0000 500 23707 1.0000 500 24184 1.0000 500 261657 1.0000 500 261788 1.0000 500 262203 1.0000 500 262827 1.0000 500 262828 1.0000 500 263035 1.0000 500 264587 1.0000 500 3183 1.0000 500 33270 1.0000 500 3349 1.0000 500 3516 1.0000 500 35245 1.0000 500 35407 1.0000 500 35423 1.0000 500 35611 1.0000 500 36139 1.0000 500 36811 1.0000 500 37309 1.0000 500 37357 1.0000 500 37409 1.0000 500 37431 1.0000 500 37432 1.0000 500 4551 1.0000 500 6947 1.0000 500 6948 1.0000 500 7307 1.0000 500 7355 1.0000 500 8199 1.0000 500 8338 1.0000 500 9067 1.0000 500 9737 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/95/95.seqs.fa -oc motifs/95 -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= 38 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= 19000 N= 38 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.228 G 0.244 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.228 G 0.244 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 196 E-value = 5.3e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::a::::::::::a: pos.-specific C aa:aa::::aa:6::aa:::a probability G :::::::::::::::::6a:: matrix T ::a::aaa:::a4aa::4::: bits 2.1 ** ** ** ** * * 1.9 ************ **** *** 1.7 ************ **** *** 1.5 ************ **** *** Relative 1.3 ************ **** *** Entropy 1.1 ********************* (40.3 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCTCCTTTACCTCTTCCGGAC consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37432 104 1.66e-13 GAGACCTTTG CCTCCTTTACCTCTTCCGGAC ATGATTGATT 36811 169 1.66e-13 GAGACCTTTG CCTCCTTTACCTCTTCCGGAC ATGATTGATG 35245 179 1.66e-13 GAGACCTTTG CCTCCTTTACCTCTTCCGGAC ATGATTGATT 3183 153 1.66e-13 GAGACCTTTG CCTCCTTTACCTCTTCCGGAC ATGATTGATT 6947 141 7.73e-13 CTCGCCGCGT CCTCCTTTACCTTTTCCTGAC ATGATTGATA 37309 147 7.73e-13 CTCGCCGCGT CCTCCTTTACCTTTTCCTGAC ATGGTTGAAA 35611 142 7.73e-13 CTCGCCGCGT CCTCCTTTACCTTTTCCTGAC ATGATTGATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37432 1.7e-13 103_[+1]_376 36811 1.7e-13 168_[+1]_311 35245 1.7e-13 178_[+1]_301 3183 1.7e-13 152_[+1]_327 6947 7.7e-13 140_[+1]_339 37309 7.7e-13 146_[+1]_333 35611 7.7e-13 141_[+1]_338 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 37432 ( 104) CCTCCTTTACCTCTTCCGGAC 1 36811 ( 169) CCTCCTTTACCTCTTCCGGAC 1 35245 ( 179) CCTCCTTTACCTCTTCCGGAC 1 3183 ( 153) CCTCCTTTACCTCTTCCGGAC 1 6947 ( 141) CCTCCTTTACCTTTTCCTGAC 1 37309 ( 147) CCTCCTTTACCTTTTCCTGAC 1 35611 ( 142) CCTCCTTTACCTTTTCCTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 11.1907 E= 5.3e-028 -945 213 -945 -945 -945 213 -945 -945 -945 -945 -945 187 -945 213 -945 -945 -945 213 -945 -945 -945 -945 -945 187 -945 -945 -945 187 -945 -945 -945 187 197 -945 -945 -945 -945 213 -945 -945 -945 213 -945 -945 -945 -945 -945 187 -945 132 -945 65 -945 -945 -945 187 -945 -945 -945 187 -945 213 -945 -945 -945 213 -945 -945 -945 -945 123 65 -945 -945 203 -945 197 -945 -945 -945 -945 213 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 5.3e-028 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 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 0.571429 0.000000 0.428571 0.000000 0.000000 0.000000 1.000000 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 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CCTCCTTTACCT[CT]TTCC[GT]GAC -------------------------------------------------------------------------------- Time 11.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 13 llr = 248 E-value = 1.7e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::33::::1::3::::::22: pos.-specific C 1::1273a::5::6:2:3819 probability G :a7:4:7::34::4::9::7: matrix T 9::653::9717a:a817::1 bits 2.1 * * 1.9 * * * * 1.7 * * * * * * 1.5 ** ** * * * * * Relative 1.3 ** *** * * * * * Entropy 1.1 *** ***** ******** * (27.5 bits) 0.9 *** **************** 0.6 **** **************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGGTTCGCTTCTTCTTGTCGC consensus AAGTC GGA G C C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6948 85 2.64e-12 ACACGCTTCT TGGAGCGCTTCTTCTTGTCGC CGGAGGCGGC 37431 91 2.64e-12 ACACGCTTCT TGGAGCGCTTCTTCTTGTCGC CGGAGGCGGC 35407 86 2.64e-12 ACACGCTTCT TGGAGCGCTTCTTCTTGTCGC CGGAGGCGGC 33270 74 2.64e-12 ACACGCTTCT TGGAGCGCTTCTTCTTGTCGC CGGTCGCGGC 37309 124 1.67e-10 GCGGAAGAGC TGGTTTGCTTCTTCTCGCCGC GTCCTCCTTT 35611 119 5.53e-10 GCGGAAGAGC TGGTCTGCTTCTTCTCGCCGC GTCCTCCTTT 35245 111 8.07e-10 GCGGGCTTGG TGATTCCCTGGATGTTGTCGC GAAGGACCTT 37432 36 2.37e-09 GCGGGCTTGG TGATTCCCTGGATGTTGTCAC GAAGGACCTT 36811 101 2.37e-09 GCGGGCTTAG TGATTCCCTGGATGTTGTCAC GAAGGACCTT 3183 85 2.37e-09 GCGGGCTTAG TGATTCCCTGGATGTTGTCAC GAAGGACCTT 6947 118 4.17e-09 GCGGAAGAGC TGGTCTGCTTTTTCTCGCCGC GTCCTCCTTT 37409 450 3.66e-08 GTCTTTCCTT CGGTGCGCTTCTTCTTTCACC AACACCAACA 23707 147 5.80e-08 ATGCATGTAC TGGCTTGCATGTTGTTGTAGT CACTCTAGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6948 2.6e-12 84_[+2]_395 37431 2.6e-12 90_[+2]_389 35407 2.6e-12 85_[+2]_394 33270 2.6e-12 73_[+2]_406 37309 1.7e-10 123_[+2]_356 35611 5.5e-10 118_[+2]_361 35245 8.1e-10 110_[+2]_369 37432 2.4e-09 35_[+2]_444 36811 2.4e-09 100_[+2]_379 3183 2.4e-09 84_[+2]_395 6947 4.2e-09 117_[+2]_362 37409 3.7e-08 449_[+2]_30 23707 5.8e-08 146_[+2]_333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=13 6948 ( 85) TGGAGCGCTTCTTCTTGTCGC 1 37431 ( 91) TGGAGCGCTTCTTCTTGTCGC 1 35407 ( 86) TGGAGCGCTTCTTCTTGTCGC 1 33270 ( 74) TGGAGCGCTTCTTCTTGTCGC 1 37309 ( 124) TGGTTTGCTTCTTCTCGCCGC 1 35611 ( 119) TGGTCTGCTTCTTCTCGCCGC 1 35245 ( 111) TGATTCCCTGGATGTTGTCGC 1 37432 ( 36) TGATTCCCTGGATGTTGTCAC 1 36811 ( 101) TGATTCCCTGGATGTTGTCAC 1 3183 ( 85) TGATTCCCTGGATGTTGTCAC 1 6947 ( 118) TGGTCTGCTTTTTCTCGCCGC 1 37409 ( 450) CGGTGCGCTTCTTCTTTCACC 1 23707 ( 147) TGGCTTGCATGTTGTTGTAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 10.9842 E= 1.7e-025 -1035 -157 -1035 176 -1035 -1035 203 -1035 27 -1035 150 -1035 27 -157 -1035 117 -1035 -57 65 76 -1035 160 -1035 17 -1035 43 150 -1035 -1035 213 -1035 -1035 -173 -1035 -1035 176 -1035 -1035 33 134 -1035 124 65 -182 27 -1035 -1035 134 -1035 -1035 -1035 187 -1035 143 65 -1035 -1035 -1035 -1035 187 -1035 2 -1035 150 -1035 -1035 192 -182 -1035 43 -1035 134 -73 189 -1035 -1035 -14 -157 150 -1035 -1035 202 -1035 -182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 1.7e-025 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 1.000000 0.000000 0.307692 0.000000 0.692308 0.000000 0.307692 0.076923 0.000000 0.615385 0.000000 0.153846 0.384615 0.461538 0.000000 0.692308 0.000000 0.307692 0.000000 0.307692 0.692308 0.000000 0.000000 1.000000 0.000000 0.000000 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 0.307692 0.692308 0.000000 0.538462 0.384615 0.076923 0.307692 0.000000 0.000000 0.692308 0.000000 0.000000 0.000000 1.000000 0.000000 0.615385 0.384615 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.230769 0.000000 0.769231 0.000000 0.000000 0.923077 0.076923 0.000000 0.307692 0.000000 0.692308 0.153846 0.846154 0.000000 0.000000 0.230769 0.076923 0.692308 0.000000 0.000000 0.923077 0.000000 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[GA][TA][TG][CT][GC]CT[TG][CG][TA]T[CG]T[TC]G[TC]C[GA]C -------------------------------------------------------------------------------- Time 22.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 7 llr = 173 E-value = 1.6e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::a:a::6:::a:::::44:: pos.-specific C a::::a::a4::4::6:::a: probability G :a:6::a::6a::aa4a66:: matrix T :::4:::4::::6:::::::a bits 2.1 ** ** * * ** * * 1.9 *** *** * ** ** * ** 1.7 *** *** * ** ** * ** 1.5 *** *** * ** ** * ** Relative 1.3 *** *** * ** ** * ** Entropy 1.1 ******* ************* (35.7 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGAGACGACGGATGGCGGGCT consensus T T C C G AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37432 12 1.45e-13 CCACGACGAG CGAGACGACGGATGGCGGGCT TGGTGATTCC 36811 77 1.45e-13 CCACGACGAG CGAGACGACGGATGGCGGGCT TAGTGATTCC 35245 87 1.45e-13 CCACGACGAG CGAGACGACGGATGGCGGGCT TGGTGATTCC 3183 61 1.45e-13 CCACGACGAG CGAGACGACGGATGGCGGGCT TAGTGATTCC 6947 73 1.96e-11 AGGTACCTTC CGATACGTCCGACGGGGAACT GAAGTCCAGC 37309 79 1.96e-11 AGGTACCTTC CGATACGTCCGACGGGGAACT GAAGTCCGGC 35611 74 1.96e-11 AGGTACCTTC CGATACGTCCGACGGGGAACT GAAGTCCAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37432 1.5e-13 11_[+3]_468 36811 1.5e-13 76_[+3]_403 35245 1.5e-13 86_[+3]_393 3183 1.5e-13 60_[+3]_419 6947 2e-11 72_[+3]_407 37309 2e-11 78_[+3]_401 35611 2e-11 73_[+3]_406 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=7 37432 ( 12) CGAGACGACGGATGGCGGGCT 1 36811 ( 77) CGAGACGACGGATGGCGGGCT 1 35245 ( 87) CGAGACGACGGATGGCGGGCT 1 3183 ( 61) CGAGACGACGGATGGCGGGCT 1 6947 ( 73) CGATACGTCCGACGGGGAACT 1 37309 ( 79) CGATACGTCCGACGGGGAACT 1 35611 ( 74) CGATACGTCCGACGGGGAACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18240 bayes= 11.1907 E= 1.6e-017 -945 213 -945 -945 -945 -945 203 -945 197 -945 -945 -945 -945 -945 123 65 197 -945 -945 -945 -945 213 -945 -945 -945 -945 203 -945 116 -945 -945 65 -945 213 -945 -945 -945 91 123 -945 -945 -945 203 -945 197 -945 -945 -945 -945 91 -945 107 -945 -945 203 -945 -945 -945 203 -945 -945 132 81 -945 -945 -945 203 -945 75 -945 123 -945 75 -945 123 -945 -945 213 -945 -945 -945 -945 -945 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.6e-017 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CGA[GT]ACG[AT]C[GC]GA[TC]GG[CG]G[GA][GA]CT -------------------------------------------------------------------------------- Time 34.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10991 3.39e-01 500 11129 7.15e-01 500 12133 8.91e-01 500 12196 8.08e-01 500 23656 5.53e-01 500 23707 3.56e-04 146_[+2(5.80e-08)]_333 24184 4.24e-01 500 261657 8.13e-01 500 261788 6.86e-01 500 262203 7.76e-01 500 262827 4.49e-01 500 262828 5.64e-01 500 263035 1.60e-01 436_[+2(6.41e-05)]_43 264587 1.93e-01 500 3183 1.19e-23 60_[+3(1.45e-13)]_3_[+2(2.37e-09)]_\ 47_[+1(1.66e-13)]_327 33270 1.25e-07 73_[+2(2.64e-12)]_406 3349 2.37e-01 500 3516 3.66e-01 500 35245 4.20e-24 86_[+3(1.45e-13)]_3_[+2(8.07e-10)]_\ 47_[+1(1.66e-13)]_301 35407 1.14e-07 85_[+2(2.64e-12)]_394 35423 2.65e-01 500 35611 1.47e-21 73_[+3(1.96e-11)]_24_[+2(5.53e-10)]_\ 2_[+1(7.73e-13)]_338 36139 1.78e-01 500 36811 1.19e-23 76_[+3(1.45e-13)]_3_[+2(2.37e-09)]_\ 47_[+1(1.66e-13)]_311 37309 4.62e-22 78_[+3(1.96e-11)]_24_[+2(1.67e-10)]_\ 2_[+1(7.73e-13)]_333 37357 4.53e-01 500 37409 1.95e-04 449_[+2(3.66e-08)]_30 37431 5.33e-08 90_[+2(2.64e-12)]_389 37432 1.19e-23 11_[+3(1.45e-13)]_3_[+2(2.37e-09)]_\ 47_[+1(1.66e-13)]_55_[+2(6.26e-05)]_300 4551 4.52e-01 500 6947 1.03e-20 72_[+3(1.96e-11)]_24_[+2(4.17e-09)]_\ 2_[+1(7.73e-13)]_339 6948 1.14e-07 84_[+2(2.64e-12)]_395 7307 8.70e-01 500 7355 8.49e-01 500 8199 6.37e-01 500 8338 8.86e-01 500 9067 1.41e-01 500 9737 1.77e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************