******************************************************************************** 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/125/125.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9278 1.0000 500 12969 1.0000 500 14412 1.0000 500 43486 1.0000 500 40650 1.0000 500 41016 1.0000 500 43950 1.0000 500 50885 1.0000 500 11934 1.0000 500 35625 1.0000 500 44450 1.0000 500 47926 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/125/125.seqs.fa -oc motifs/125 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.255 G 0.228 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.255 G 0.228 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 12 llr = 115 E-value = 6.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:::7::3:3: pos.-specific C :39:23a6276: probability G 3518:1:43:1a matrix T 8::28:::33:: bits 2.1 * 1.9 * * 1.7 * * 1.5 ** * * Relative 1.3 * *** * * Entropy 1.1 * *** ** * * (13.8 bits) 0.9 * ****** * * 0.6 ******** *** 0.4 ******** *** 0.2 ******** *** 0.0 ------------ Multilevel TGCGTACCACCG consensus GA C GGTA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43950 313 2.73e-06 AGTAAAAGTG TACGTACCACAG CATGCAATCC 35625 459 3.64e-06 TGTCTCTTTG TACGTACCATCG CAACCCATCA 41016 36 5.81e-06 GGCTTCATGT GGCGTACGATCG TGTCGGCCTG 40650 160 1.00e-05 AACGTACAGT TCCGTCCGTCCG GCAACGAGCT 50885 190 1.24e-05 CTTCCGCCCT TCCGTCCCCCCG CTTGTACAAC 43486 31 1.53e-05 TCTTCATGAT TGCTTACGGCAG TTGAAACTTC 14412 304 1.53e-05 TTCACGCATT TCCGTACCACGG CAGCAGCAGG 44450 42 1.71e-05 AGCCATCCGA TGCGTGCCGCAG AAAGTCTACC 47926 343 2.42e-05 GTCAGATCGA TGGGTACCCCCG TCTCCCGTTG 12969 257 2.61e-05 ACTTTACCAT GGCGTCCGTTCG TGTTATGGGT 9278 470 6.59e-05 GTCCATCCTC GACGCACCGTCG TCCTGCTCGG 11934 117 6.98e-05 ACGTCCAATC TGCTCACGTCAG TCGTCGGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43950 2.7e-06 312_[+1]_176 35625 3.6e-06 458_[+1]_30 41016 5.8e-06 35_[+1]_453 40650 1e-05 159_[+1]_329 50885 1.2e-05 189_[+1]_299 43486 1.5e-05 30_[+1]_458 14412 1.5e-05 303_[+1]_185 44450 1.7e-05 41_[+1]_447 47926 2.4e-05 342_[+1]_146 12969 2.6e-05 256_[+1]_232 9278 6.6e-05 469_[+1]_19 11934 7e-05 116_[+1]_372 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=12 43950 ( 313) TACGTACCACAG 1 35625 ( 459) TACGTACCATCG 1 41016 ( 36) GGCGTACGATCG 1 40650 ( 160) TCCGTCCGTCCG 1 50885 ( 190) TCCGTCCCCCCG 1 43486 ( 31) TGCTTACGGCAG 1 14412 ( 304) TCCGTACCACGG 1 44450 ( 42) TGCGTGCCGCAG 1 47926 ( 343) TGGGTACCCCCG 1 12969 ( 257) GGCGTCCGTTCG 1 9278 ( 470) GACGCACCGTCG 1 11934 ( 117) TGCTCACGTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 9.37898 E= 6.6e+001 -1023 -1023 13 152 -4 -3 113 -1023 -1023 185 -145 -1023 -1023 -1023 187 -64 -1023 -61 -1023 168 138 -3 -145 -1023 -1023 197 -1023 -1023 -1023 120 87 -1023 38 -61 13 -6 -1023 139 -1023 35 38 120 -145 -1023 -1023 -1023 213 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 6.6e+001 0.000000 0.000000 0.250000 0.750000 0.250000 0.250000 0.500000 0.000000 0.000000 0.916667 0.083333 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.833333 0.666667 0.250000 0.083333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.583333 0.416667 0.000000 0.333333 0.166667 0.250000 0.250000 0.000000 0.666667 0.000000 0.333333 0.333333 0.583333 0.083333 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][GAC]CGT[AC]C[CG][AGT][CT][CA]G -------------------------------------------------------------------------------- Time 1.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 107 E-value = 2.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 8:a3:28:5:2:8:5:3:85: pos.-specific C :a:7:5:a:3:3:a:522::2 probability G 2::::22::7:3:::5:525: matrix T ::::a2::5:832:5:53::8 bits 2.1 1.9 ** * * * 1.7 ** * * * 1.5 ** * * * Relative 1.3 *** * ** * ** * * Entropy 1.1 ***** ** ** ** * *** (25.7 bits) 0.9 ***** ***** **** *** 0.6 ***** ***** **** **** 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel ACACTCACAGTCACACTGAAT consensus A TC G TGAT G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50885 234 3.30e-10 GCGATACTTT ACACTTACTGTTACTGTTAGT TAGGTAGCCG 40650 303 4.12e-10 CCTTGGTTTG ACAATGACTGTGACAGTGAGT AACCCTATCG 41016 305 2.31e-09 ACTTACTCAC ACACTCACACTCACACAGAGC CGAAAAGGAA 43950 238 9.72e-09 CTATGTTTTC ACAATAACACTTACTGCTAAT ATAATTGTAA 47926 108 1.20e-08 ACAATCGTGT ACACTCACAGACACACTCGAT CGATAGAGCC 9278 230 2.14e-08 CACGAAATGG GCACTCGCTGTGTCTCAGAAT GATTGATCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50885 3.3e-10 233_[+2]_246 40650 4.1e-10 302_[+2]_177 41016 2.3e-09 304_[+2]_175 43950 9.7e-09 237_[+2]_242 47926 1.2e-08 107_[+2]_372 9278 2.1e-08 229_[+2]_250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 50885 ( 234) ACACTTACTGTTACTGTTAGT 1 40650 ( 303) ACAATGACTGTGACAGTGAGT 1 41016 ( 305) ACACTCACACTCACACAGAGC 1 43950 ( 238) ACAATAACACTTACTGCTAAT 1 47926 ( 108) ACACTCACAGACACACTCGAT 1 9278 ( 230) GCACTCGCTGTGTCTCAGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 9.56395 E= 2.5e+002 170 -923 -45 -923 -923 197 -923 -923 196 -923 -923 -923 38 139 -923 -923 -923 -923 -923 194 -62 97 -45 -64 170 -923 -45 -923 -923 197 -923 -923 96 -923 -923 94 -923 39 155 -923 -62 -923 -923 168 -923 39 55 35 170 -923 -923 -64 -923 197 -923 -923 96 -923 -923 94 -923 97 113 -923 38 -61 -923 94 -923 -61 113 35 170 -923 -45 -923 96 -923 113 -923 -923 -61 -923 168 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 2.5e+002 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.500000 0.166667 0.166667 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.333333 0.666667 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.333333 0.333333 0.333333 0.833333 0.000000 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.500000 0.000000 0.333333 0.166667 0.000000 0.500000 0.000000 0.166667 0.500000 0.333333 0.833333 0.000000 0.166667 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.166667 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ACA[CA]TCAC[AT][GC]T[CGT]AC[AT][CG][TA][GT]A[AG]T -------------------------------------------------------------------------------- Time 3.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 3 llr = 70 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :aa:7a:3333a:::::a::a pos.-specific C :::a:::373:::3::7:a:: probability G a:::3:a::37:3:aa:::a: matrix T :::::::3::::77::3:::: bits 2.1 * * ** * 1.9 **** ** * ** **** 1.7 **** ** * ** **** 1.5 **** ** * ** **** Relative 1.3 **** ** * ** **** Entropy 1.1 ******* * *********** (33.7 bits) 0.9 ******* * *********** 0.6 ******* * *********** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAACAAGACAGATTGGCACGA consensus G CACA GC T sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9278 204 1.71e-12 CGAAAGTACA GAACAAGACAGATTGGCACGA AATGGGCACT 44450 337 2.66e-11 TGCCTACCTT GAACAAGTCCAAGTGGCACGA CCTTATAGAG 41016 428 7.74e-11 ATCTGGACGT GAACGAGCAGGATCGGTACGA ACCACAGGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9278 1.7e-12 203_[+3]_276 44450 2.7e-11 336_[+3]_143 41016 7.7e-11 427_[+3]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=3 9278 ( 204) GAACAAGACAGATTGGCACGA 1 44450 ( 337) GAACAAGTCCAAGTGGCACGA 1 41016 ( 428) GAACGAGCAGGATCGGTACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.5649 E= 1.3e+003 -823 -823 213 -823 196 -823 -823 -823 196 -823 -823 -823 -823 197 -823 -823 137 -823 55 -823 196 -823 -823 -823 -823 -823 213 -823 38 39 -823 35 38 139 -823 -823 38 39 55 -823 38 -823 155 -823 196 -823 -823 -823 -823 -823 55 135 -823 39 -823 135 -823 -823 213 -823 -823 -823 213 -823 -823 139 -823 35 196 -823 -823 -823 -823 197 -823 -823 -823 -823 213 -823 196 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 3 E= 1.3e+003 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 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 0.666667 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 1.000000 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 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GAAC[AG]AG[ACT][CA][ACG][GA]A[TG][TC]GG[CT]ACGA -------------------------------------------------------------------------------- Time 4.93 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9278 1.82e-13 203_[+3(1.71e-12)]_5_[+2(2.14e-08)]_\ 219_[+1(6.59e-05)]_19 12969 7.03e-02 256_[+1(2.61e-05)]_232 14412 8.56e-02 303_[+1(1.53e-05)]_185 43486 5.01e-02 30_[+1(1.53e-05)]_458 40650 1.42e-07 159_[+1(1.00e-05)]_131_\ [+2(4.12e-10)]_177 41016 8.29e-14 35_[+1(5.81e-06)]_134_\ [+3(9.21e-05)]_102_[+2(2.31e-09)]_21_[+3(4.42e-05)]_60_[+3(7.74e-11)]_52 43950 6.21e-07 237_[+2(9.72e-09)]_54_\ [+1(2.73e-06)]_176 50885 4.23e-08 189_[+1(1.24e-05)]_32_\ [+2(3.30e-10)]_246 11934 1.26e-01 116_[+1(6.98e-05)]_372 35625 3.71e-03 458_[+1(3.64e-06)]_30 44450 1.45e-08 41_[+1(1.71e-05)]_283_\ [+3(2.66e-11)]_143 47926 2.02e-06 107_[+2(1.20e-08)]_214_\ [+1(2.42e-05)]_113_[+2(2.24e-05)]_12 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************