******************************************************************************** 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/327/327.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 14792 1.0000 500 51128 1.0000 500 29456 1.0000 500 48415 1.0000 500 43312 1.0000 500 15815 1.0000 500 55018 1.0000 500 49453 1.0000 500 30519 1.0000 500 50525 1.0000 500 11204 1.0000 500 45028 1.0000 500 51970 1.0000 500 31740 1.0000 500 44725 1.0000 500 47973 1.0000 500 47823 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/327/327.seqs.fa -oc motifs/327 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.251 C 0.252 G 0.225 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.252 G 0.225 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 17 llr = 157 E-value = 4.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 22:1:3::12:1 pos.-specific C 16:::3193::4 probability G ::a9:11:4::3 matrix T 72::a48138a2 bits 2.2 * 1.9 * * * 1.7 *** * 1.5 *** * * Relative 1.3 *** * ** Entropy 1.1 *** * ** (13.3 bits) 0.9 *** ** ** 0.6 ***** ** ** 0.4 ***** ** ** 0.2 ************ 0.0 ------------ Multilevel TCGGTTTCGTTC consensus A C G sequence C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 47973 347 2.14e-07 TGACCCCTTT TCGGTCTCGTTC GATGCGTCGC 30519 354 1.68e-06 GCAAAGTTCC TCGGTTTCCTTT ACACAAGGAT 29456 307 2.13e-06 TGCAGTTCGC TCGGTATCTTTT TCTAGGATCT 51128 307 2.13e-06 TGCAGTTCGC TCGGTATCTTTT TCTAGGATCT 47823 465 4.33e-06 ACCCTCGGTT ACGGTATCCTTC TACCGGAATC 44725 24 4.33e-06 CGGTTCGGAT TCGGTTGCGTTC CGACACGCGG 49453 293 6.51e-06 GATCGTAGCC TCGGTCTCCATC GATCCAACTT 14792 272 9.88e-06 GCTGTTCCGC ACGGTATCTTTG ACGTACAGTT 31740 480 1.25e-05 AACGTGTCAC TCGGTCTCATTG CAAATAATC 51970 68 2.25e-05 TCGTTCGCGG CAGGTTTCGTTC GATCCACATC 55018 182 2.99e-05 GTGACGCGGG TCGGTTCCGATC CTGCGCGTCC 11204 382 6.49e-05 CTTCTCCCCG CCGGTGTCTTTG AATGCTCTAC 50525 132 7.44e-05 TAAGGTGATA TAGGTCTTGTTT TTGCAAGGAG 45028 37 9.89e-05 GAGCATCCCG TTGGTTCCGATC GATGCAAACC 15815 186 1.12e-04 CGGTGCGGCC TTGATCTCCTTG CTCTTTGTGC 43312 337 1.20e-04 GTTTCCGAAA AAGGTATCCTTA TGTCCTCACG 48415 80 2.10e-04 GTTGCCATCG TTGGTTGTTTTG TTGCTTTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47973 2.1e-07 346_[+1]_142 30519 1.7e-06 353_[+1]_135 29456 2.1e-06 306_[+1]_182 51128 2.1e-06 306_[+1]_182 47823 4.3e-06 464_[+1]_24 44725 4.3e-06 23_[+1]_465 49453 6.5e-06 292_[+1]_196 14792 9.9e-06 271_[+1]_217 31740 1.3e-05 479_[+1]_9 51970 2.3e-05 67_[+1]_421 55018 3e-05 181_[+1]_307 11204 6.5e-05 381_[+1]_107 50525 7.4e-05 131_[+1]_357 45028 9.9e-05 36_[+1]_452 15815 0.00011 185_[+1]_303 43312 0.00012 336_[+1]_152 48415 0.00021 79_[+1]_409 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=17 47973 ( 347) TCGGTCTCGTTC 1 30519 ( 354) TCGGTTTCCTTT 1 29456 ( 307) TCGGTATCTTTT 1 51128 ( 307) TCGGTATCTTTT 1 47823 ( 465) ACGGTATCCTTC 1 44725 ( 24) TCGGTTGCGTTC 1 49453 ( 293) TCGGTCTCCATC 1 14792 ( 272) ACGGTATCTTTG 1 31740 ( 480) TCGGTCTCATTG 1 51970 ( 68) CAGGTTTCGTTC 1 55018 ( 182) TCGGTTCCGATC 1 11204 ( 382) CCGGTGTCTTTG 1 50525 ( 132) TAGGTCTTGTTT 1 45028 ( 37) TTGGTTCCGATC 1 15815 ( 186) TTGATCTCCTTG 1 43312 ( 337) AAGGTATCCTTA 1 48415 ( 80) TTGGTTGTTTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 8.93074 E= 4.0e-002 -51 -110 -1073 137 -51 136 -1073 -63 -1073 -1073 215 -1073 -209 -1073 207 -1073 -1073 -1073 -1073 187 23 22 -193 37 -1073 -110 -93 149 -1073 181 -1073 -121 -209 22 65 11 -51 -1073 -1073 159 -1073 -1073 -1073 187 -209 71 39 -21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 4.0e-002 0.176471 0.117647 0.000000 0.705882 0.176471 0.647059 0.000000 0.176471 0.000000 0.000000 1.000000 0.000000 0.058824 0.000000 0.941176 0.000000 0.000000 0.000000 0.000000 1.000000 0.294118 0.294118 0.058824 0.352941 0.000000 0.117647 0.117647 0.764706 0.000000 0.882353 0.000000 0.117647 0.058824 0.294118 0.352941 0.294118 0.176471 0.000000 0.000000 0.823529 0.000000 0.000000 0.000000 1.000000 0.058824 0.411765 0.294118 0.235294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TCGGT[TAC]TC[GCT]TT[CGT] -------------------------------------------------------------------------------- Time 2.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 104 E-value = 8.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2:2:228::::8::::::6: pos.-specific C ::48:::2:a282:a::28:: probability G a6::288:::8::::4:624a matrix T :26:8:::a::2:a:6a2::: bits 2.2 * * 1.9 * ** ** * * 1.7 * ** ** * * 1.5 * ** ** ** * * Relative 1.3 * ************ * * * Entropy 1.1 * ************** *** (30.1 bits) 0.9 * *************** *** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GGTCTGGATCGCATCTTGCAG consensus ACAGAAC CTC G CGG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 29456 377 7.08e-13 GTGGAAAAAA GGCCTGGATCGCATCTTGCAG GTGCAACGCT 51128 377 7.08e-13 GTGGAAAAAA GGCCTGGATCGCATCTTGCAG GTGCAACGCT 47823 322 6.12e-11 AAAGATCAAC GATCTGGATCGCATCGTTCGG AAAAAGACCC 47973 257 2.58e-09 ACATTTTGGC GGTATAAATCGTATCTTCCGG TCACGCGTCA 45028 264 3.61e-09 GAGGATTCGT GTTCGGGCTCCCCTCGTGGAG GATCTCCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29456 7.1e-13 376_[+2]_103 51128 7.1e-13 376_[+2]_103 47823 6.1e-11 321_[+2]_158 47973 2.6e-09 256_[+2]_223 45028 3.6e-09 263_[+2]_216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 29456 ( 377) GGCCTGGATCGCATCTTGCAG 1 51128 ( 377) GGCCTGGATCGCATCTTGCAG 1 47823 ( 322) GATCTGGATCGCATCGTTCGG 1 47973 ( 257) GGTATAAATCGTATCTTCCGG 1 45028 ( 264) GTTCGGGCTCCCCTCGTGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8160 bayes= 10.9232 E= 8.4e-001 -897 -897 215 -897 -33 -897 142 -45 -897 66 -897 114 -33 166 -897 -897 -897 -897 -17 155 -33 -897 183 -897 -33 -897 183 -897 167 -33 -897 -897 -897 -897 -897 187 -897 199 -897 -897 -897 -33 183 -897 -897 166 -897 -45 167 -33 -897 -897 -897 -897 -897 187 -897 199 -897 -897 -897 -897 83 114 -897 -897 -897 187 -897 -33 142 -45 -897 166 -17 -897 126 -897 83 -897 -897 -897 215 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 8.4e-001 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.600000 0.200000 0.000000 0.400000 0.000000 0.600000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.800000 0.200000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GAT][TC][CA][TG][GA][GA][AC]TC[GC][CT][AC]TC[TG]T[GCT][CG][AG]G -------------------------------------------------------------------------------- Time 5.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 9 llr = 142 E-value = 1.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::3:1:9:2:96:13:263 pos.-specific C :861:78::73::a21:336 probability G :1:6:2::::7:::6::4:1 matrix T a14:a:21a1:14:16a:1: bits 2.2 1.9 * * * * * 1.7 * * * * * 1.5 * * ** * * * Relative 1.3 * * *** * * * Entropy 1.1 ** * *** ** * * (22.8 bits) 0.9 *** ***** **** * 0.6 ************** ** ** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TCCGTCCATCGAACGTTGAC consensus TA GT AC T CA CCA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 29456 157 1.07e-10 GTCGTATACG TCTGTCCATAGAACGTTGAC TAATGTAAGA 51128 158 1.07e-10 GTCGTATACG TCTGTCCATAGAACGTTGAC TAAGTAAGAG 44725 459 7.24e-09 TGTCTATTTA TCCATCTATCCAACGTTACC CTTGCTGGAA 45028 362 1.21e-08 GTGTTGTTAT TCCGTACATCGATCGATACA GTCTATATTC 11204 223 4.19e-08 AAGTCAAACC TCCGTGCTTCGATCGATGAG TCATCCTGCA 14792 141 5.30e-08 GCGAACCCAC TCTGTCTATCGTACCTTCAA CTCGCGAGCT 47823 436 1.01e-07 GTGTACTGCA TTCATCCATCCATCCATCCA CCCTCGGTTA 15815 428 2.61e-07 GCCTGTGATA TGCATGCATCCAACACTCAC CAACGCGTTT 50525 379 2.76e-07 GGCAGTTGTA TCTCTCCATTGATCTTTGTC CATGATAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29456 1.1e-10 156_[+3]_324 51128 1.1e-10 157_[+3]_323 44725 7.2e-09 458_[+3]_22 45028 1.2e-08 361_[+3]_119 11204 4.2e-08 222_[+3]_258 14792 5.3e-08 140_[+3]_340 47823 1e-07 435_[+3]_45 15815 2.6e-07 427_[+3]_53 50525 2.8e-07 378_[+3]_102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=9 29456 ( 157) TCTGTCCATAGAACGTTGAC 1 51128 ( 158) TCTGTCCATAGAACGTTGAC 1 44725 ( 459) TCCATCTATCCAACGTTACC 1 45028 ( 362) TCCGTACATCGATCGATACA 1 11204 ( 223) TCCGTGCTTCGATCGATGAG 1 14792 ( 141) TCTGTCTATCGTACCTTCAA 1 47823 ( 436) TTCATCCATCCATCCATCCA 1 15815 ( 428) TGCATGCATCCAACACTCAC 1 50525 ( 379) TCTCTCCATTGATCTTTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.96028 E= 1.3e-001 -982 -982 -982 187 -982 162 -101 -129 -982 114 -982 70 41 -118 131 -982 -982 -982 -982 187 -117 140 -2 -982 -982 162 -982 -29 182 -982 -982 -129 -982 -982 -982 187 -17 140 -982 -129 -982 40 157 -982 182 -982 -982 -129 115 -982 -982 70 -982 199 -982 -982 -117 -18 131 -129 41 -118 -982 103 -982 -982 -982 187 -17 40 98 -982 115 40 -982 -129 41 114 -101 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.3e-001 0.000000 0.000000 0.000000 1.000000 0.000000 0.777778 0.111111 0.111111 0.000000 0.555556 0.000000 0.444444 0.333333 0.111111 0.555556 0.000000 0.000000 0.000000 0.000000 1.000000 0.111111 0.666667 0.222222 0.000000 0.000000 0.777778 0.000000 0.222222 0.888889 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 1.000000 0.222222 0.666667 0.000000 0.111111 0.000000 0.333333 0.666667 0.000000 0.888889 0.000000 0.000000 0.111111 0.555556 0.000000 0.000000 0.444444 0.000000 1.000000 0.000000 0.000000 0.111111 0.222222 0.555556 0.111111 0.333333 0.111111 0.000000 0.555556 0.000000 0.000000 0.000000 1.000000 0.222222 0.333333 0.444444 0.000000 0.555556 0.333333 0.000000 0.111111 0.333333 0.555556 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TC[CT][GA]T[CG][CT]AT[CA][GC]A[AT]C[GC][TA]T[GCA][AC][CA] -------------------------------------------------------------------------------- Time 7.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14792 5.61e-06 73_[+1(2.99e-05)]_55_[+3(5.30e-08)]_\ 111_[+1(9.88e-06)]_217 51128 1.97e-17 157_[+3(1.07e-10)]_129_\ [+1(2.13e-06)]_58_[+2(7.08e-13)]_103 29456 1.97e-17 156_[+3(1.07e-10)]_130_\ [+1(2.13e-06)]_58_[+2(7.08e-13)]_103 48415 3.32e-01 500 43312 2.12e-01 500 15815 3.69e-04 427_[+3(2.61e-07)]_53 55018 1.32e-01 181_[+1(2.99e-05)]_307 49453 5.11e-04 292_[+1(6.51e-06)]_196 30519 2.92e-03 122_[+1(5.51e-06)]_219_\ [+1(1.68e-06)]_135 50525 3.17e-04 131_[+1(7.44e-05)]_235_\ [+3(2.76e-07)]_102 11204 4.04e-05 222_[+3(4.19e-08)]_139_\ [+1(6.49e-05)]_107 45028 2.05e-10 36_[+1(9.89e-05)]_215_\ [+2(3.61e-09)]_77_[+3(1.21e-08)]_119 51970 2.84e-02 67_[+1(2.25e-05)]_421 31740 8.41e-02 479_[+1(1.25e-05)]_9 44725 4.92e-07 23_[+1(4.33e-06)]_423_\ [+3(7.24e-09)]_22 47973 7.87e-09 256_[+2(2.58e-09)]_69_\ [+1(2.14e-07)]_142 47823 1.79e-12 321_[+2(6.12e-11)]_93_\ [+3(1.01e-07)]_9_[+1(4.33e-06)]_24 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************