******************************************************************************** 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/8/8.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 13095 1.0000 500 46600 1.0000 500 21239 1.0000 500 38931 1.0000 500 9894 1.0000 500 40079 1.0000 500 10617 1.0000 500 45191 1.0000 500 34884 1.0000 500 45278 1.0000 500 46027 1.0000 500 46037 1.0000 500 12729 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/8/8.seqs.fa -oc motifs/8 -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 0.274 C 0.232 G 0.246 T 0.248 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.232 G 0.246 T 0.248 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 8 llr = 129 E-value = 2.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::31::::51::::31:::: pos.-specific C :91:::4a::16:813::64 probability G ::5:113::63:1:13::1: matrix T a119994:53649354aa36 bits 2.1 * * ** 1.9 * * ** 1.7 * * ** 1.5 ** *** * * ** Relative 1.3 ** *** * ** ** Entropy 1.1 ** *** * *** ** * (23.3 bits) 0.8 ** *** ** *** **** 0.6 ** *** ******* **** 0.4 ** *********** **** 0.2 ******************** 0.0 -------------------- Multilevel TCGTTTCCAGTCTCTTTTCT consensus A T TTGT TAC TC sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 34884 465 1.99e-11 TCGGCAATCA TCGTTTCCTTTCTCTTTTCT CCTCATCGGC 46037 271 4.68e-10 AATTCCTATT TCGTTTCCAGTTTCACTTCC AAAGATCGCC 46027 271 4.68e-10 AATTCCTATT TCGTTTCCAGTTTCACTTCC AAAGATCGCC 12729 286 1.26e-08 TTCACGCTTG TCCTTTTCTGTTTTGTTTCT TTCAGATCCA 45191 444 4.36e-08 ACCCTCGCCG TTGTTTTCTGTCTTTATTTC TCGGACCTAC 13095 217 8.11e-08 AGCTCGGGTA TCAATTGCAGCCTCTGTTTT GAAAGGAACA 21239 207 2.24e-07 TACTGGTCGA TCATGGTCTTGCTCCTTTCT CTGCGACCTA 40079 144 3.23e-07 AAGACGGCTG TCTTTTGCAAGCGCTGTTGT CCTCCCCTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34884 2e-11 464_[+1]_16 46037 4.7e-10 270_[+1]_210 46027 4.7e-10 270_[+1]_210 12729 1.3e-08 285_[+1]_195 45191 4.4e-08 443_[+1]_37 13095 8.1e-08 216_[+1]_264 21239 2.2e-07 206_[+1]_274 40079 3.2e-07 143_[+1]_337 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=8 34884 ( 465) TCGTTTCCTTTCTCTTTTCT 1 46037 ( 271) TCGTTTCCAGTTTCACTTCC 1 46027 ( 271) TCGTTTCCAGTTTCACTTCC 1 12729 ( 286) TCCTTTTCTGTTTTGTTTCT 1 45191 ( 444) TTGTTTTCTGTCTTTATTTC 1 13095 ( 217) TCAATTGCAGCCTCTGTTTT 1 21239 ( 207) TCATGGTCTTGCTCCTTTCT 1 40079 ( 144) TCTTTTGCAAGCGCTGTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 6253 bayes= 9.60849 E= 2.4e-002 -965 -965 -965 201 -965 191 -965 -98 -13 -89 102 -98 -113 -965 -965 182 -965 -965 -98 182 -965 -965 -98 182 -965 69 2 60 -965 211 -965 -965 87 -965 -965 101 -113 -965 134 1 -965 -89 2 133 -965 143 -965 60 -965 -965 -98 182 -965 169 -965 1 -13 -89 -98 101 -113 11 2 60 -965 -965 -965 201 -965 -965 -965 201 -965 143 -98 1 -965 69 -965 133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.4e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.000000 0.125000 0.250000 0.125000 0.500000 0.125000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.125000 0.875000 0.000000 0.375000 0.250000 0.375000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.125000 0.000000 0.625000 0.250000 0.000000 0.125000 0.250000 0.625000 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 0.125000 0.875000 0.000000 0.750000 0.000000 0.250000 0.250000 0.125000 0.125000 0.500000 0.125000 0.250000 0.250000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.125000 0.250000 0.000000 0.375000 0.000000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TC[GA]TTT[CTG]C[AT][GT][TG][CT]T[CT][TA][TCG]TT[CT][TC] -------------------------------------------------------------------------------- Time 1.42 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 9 llr = 105 E-value = 7.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 212a:3:::8:2 pos.-specific C 813:97::a:18 probability G :64:1:a:::9: matrix T :2:::::a:2:: 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 CGGACCGTCAGC consensus ATC A T A sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46037 383 1.40e-07 CGCGTCCTTT CGAACCGTCAGC ACTGCTGAGA 46027 383 1.40e-07 CGCGTCCTTT CGAACCGTCAGC ACTGCGGAGA 34884 193 4.16e-07 GGATGACACA CGCACCGTCTGC GTCATCTGGT 13095 81 1.07e-06 AGTATTTTCA CTCACAGTCAGC TAGAGAGCTG 10617 188 1.21e-06 TTGTAAGTGA CGGACCGTCACC GAGGCAGCAG 45191 153 2.43e-06 AAGCGAGCAC CCCACAGTCAGC GGTACCTTAA 38931 185 4.28e-06 GGTCTGTGCG CAGACCGTCAGA AACCTCAAGC 45278 210 8.00e-06 GTACAGGCTG AGGACCGTCTGA CGTGCGCTCC 12729 97 1.71e-05 TACCGCTGTA ATGAGAGTCAGC GCACCAGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46037 1.4e-07 382_[+2]_106 46027 1.4e-07 382_[+2]_106 34884 4.2e-07 192_[+2]_296 13095 1.1e-06 80_[+2]_408 10617 1.2e-06 187_[+2]_301 45191 2.4e-06 152_[+2]_336 38931 4.3e-06 184_[+2]_304 45278 8e-06 209_[+2]_279 12729 1.7e-05 96_[+2]_392 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=9 46037 ( 383) CGAACCGTCAGC 1 46027 ( 383) CGAACCGTCAGC 1 34884 ( 193) CGCACCGTCTGC 1 13095 ( 81) CTCACAGTCAGC 1 10617 ( 188) CGGACCGTCACC 1 45191 ( 153) CCCACAGTCAGC 1 38931 ( 185) CAGACCGTCAGA 1 45278 ( 210) AGGACCGTCTGA 1 12729 ( 97) ATGAGAGTCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 10.3111 E= 7.3e-001 -30 174 -982 -982 -130 -106 117 -16 -30 52 85 -982 187 -982 -982 -982 -982 194 -115 -982 28 152 -982 -982 -982 -982 202 -982 -982 -982 -982 201 -982 211 -982 -982 150 -982 -982 -16 -982 -106 185 -982 -30 174 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 7.3e-001 0.222222 0.777778 0.000000 0.000000 0.111111 0.111111 0.555556 0.222222 0.222222 0.333333 0.444444 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.000000 0.111111 0.888889 0.000000 0.222222 0.777778 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][GT][GCA]AC[CA]GTC[AT]G[CA] -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 104 E-value = 8.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::4:a:8:2:28:a6::4:2: pos.-specific C 826::a2:::::8:::6:::: probability G ::::::::62:22:2:26::a matrix T 28:a:::a288:::2a2:a8: bits 2.1 * * * * * * 1.9 *** * * * * * 1.7 *** * * * * * 1.5 *** * * * * * Relative 1.3 ** ***** ***** * *** Entropy 1.1 ******** ***** * **** (30.1 bits) 0.8 ******** ***** * **** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CTCTACATGTTACAATCGTTG consensus TCA C AGAGG G GA A sequence T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46037 227 1.13e-12 CACGATTCAT CTCTACATGTTACATTCGTTG CAACACAAAA 46027 227 1.13e-12 CACGATTCAT CTCTACATGTTACAGTCGTTG CAACACAGAA 21239 98 2.11e-10 TTCGTAGACT CCCTACATTTTACAATGATTG CTTTCAAGCT 34884 3 9.59e-10 TG CTATACCTAGAACAATCGTTG GCCTGTTAGT 46600 352 3.03e-09 AGTCACTTAT TTATACATGTTGGAATTATAG TTGCATTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46037 1.1e-12 226_[+3]_253 46027 1.1e-12 226_[+3]_253 21239 2.1e-10 97_[+3]_382 34884 9.6e-10 2_[+3]_477 46600 3e-09 351_[+3]_128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 46037 ( 227) CTCTACATGTTACATTCGTTG 1 46027 ( 227) CTCTACATGTTACAGTCGTTG 1 21239 ( 98) CCCTACATTTTACAATGATTG 1 34884 ( 3) CTATACCTAGAACAATCGTTG 1 46600 ( 352) TTATACATGTTGGAATTATAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.536 E= 8.1e-001 -897 178 -897 -31 -897 -21 -897 169 54 137 -897 -897 -897 -897 -897 201 187 -897 -897 -897 -897 211 -897 -897 154 -21 -897 -897 -897 -897 -897 201 -45 -897 128 -31 -897 -897 -30 169 -45 -897 -897 169 154 -897 -30 -897 -897 178 -30 -897 187 -897 -897 -897 113 -897 -30 -31 -897 -897 -897 201 -897 137 -30 -31 54 -897 128 -897 -897 -897 -897 201 -45 -897 -897 169 -897 -897 202 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 8.1e-001 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.600000 0.200000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.800000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.200000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][TC][CA]TAC[AC]T[GAT][TG][TA][AG][CG]A[AGT]T[CGT][GA]T[TA]G -------------------------------------------------------------------------------- Time 4.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13095 3.49e-06 80_[+2(1.07e-06)]_124_\ [+1(8.11e-08)]_264 46600 1.64e-05 351_[+3(3.03e-09)]_128 21239 1.28e-09 97_[+3(2.11e-10)]_88_[+1(2.24e-07)]_\ 274 38931 1.13e-02 184_[+2(4.28e-06)]_304 9894 2.04e-01 500 40079 2.79e-03 143_[+1(3.23e-07)]_337 10617 1.65e-02 187_[+2(1.21e-06)]_301 45191 5.17e-07 152_[+2(2.43e-06)]_279_\ [+1(4.36e-08)]_37 34884 8.13e-16 2_[+3(9.59e-10)]_169_[+2(4.16e-07)]_\ 260_[+1(1.99e-11)]_16 45278 5.31e-02 209_[+2(8.00e-06)]_279 46027 9.32e-18 226_[+3(1.13e-12)]_23_\ [+1(4.68e-10)]_92_[+2(1.40e-07)]_106 46037 9.32e-18 226_[+3(1.13e-12)]_23_\ [+1(4.68e-10)]_92_[+2(1.40e-07)]_106 12729 4.10e-06 96_[+2(1.71e-05)]_177_\ [+1(1.26e-08)]_195 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************