******************************************************************************** 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/140/140.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17523 1.0000 500 31975 1.0000 500 43016 1.0000 500 17779 1.0000 500 43135 1.0000 500 47514 1.0000 500 48430 1.0000 500 39304 1.0000 500 39526 1.0000 500 15757 1.0000 500 16281 1.0000 500 40621 1.0000 500 40901 1.0000 500 16511 1.0000 500 16592 1.0000 500 16603 1.0000 500 16766 1.0000 500 33523 1.0000 500 51303 1.0000 500 10774 1.0000 500 10821 1.0000 500 44618 1.0000 500 11740 1.0000 500 45592 1.0000 500 27709 1.0000 500 20589 1.0000 500 41234 1.0000 500 45976 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/140/140.seqs.fa -oc motifs/140 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.245 G 0.225 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.245 G 0.225 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 85 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:::33:::::33:33::3: pos.-specific C ::88:3::3:::::::::3:: probability G a:3:a:5:8a5a88a88a883 matrix T :8:3:53a::5:::::::::8 bits 2.1 * * * * * * 1.9 * * * * * * * 1.7 * * * * * * * 1.5 * * * * * * * Relative 1.3 * *** *** ********** Entropy 1.1 ***** ************** (30.6 bits) 0.9 ***** ************** 0.6 ***** ************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTCCGTGTGGGGGGGGGGGGT consensus AGT AA C T AA AA CAG sequence CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 39304 23 2.84e-11 CACGGGTCCA GTCCGAATGGTGGGGGAGGGT TGGGTATATT 48430 176 4.99e-11 TGTATGTTAT GACCGTGTGGGGGGGAGGGGG GATTTCATTG 45592 170 1.36e-10 AGGTAGCAAA GTCTGCGTCGGGGGGGGGGAT GCTATCTGAA 40901 40 5.81e-10 GAAATTGTGG GTGCGTTTGGTGAAGGGGCGT TAGACGATGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39304 2.8e-11 22_[+1]_457 48430 5e-11 175_[+1]_304 45592 1.4e-10 169_[+1]_310 40901 5.8e-10 39_[+1]_440 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 39304 ( 23) GTCCGAATGGTGGGGGAGGGT 1 48430 ( 176) GACCGTGTGGGGGGGAGGGGG 1 45592 ( 170) GTCTGCGTCGGGGGGGGGGAT 1 40901 ( 40) GTGCGTTTGGTGAAGGGGCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 11.7138 E= 1.1e+002 -865 -865 215 -865 -11 -865 -865 153 -865 161 15 -865 -865 161 -865 -6 -865 -865 215 -865 -11 3 -865 94 -11 -865 115 -6 -865 -865 -865 194 -865 3 173 -865 -865 -865 215 -865 -865 -865 115 94 -865 -865 215 -865 -11 -865 173 -865 -11 -865 173 -865 -865 -865 215 -865 -11 -865 173 -865 -11 -865 173 -865 -865 -865 215 -865 -865 3 173 -865 -11 -865 173 -865 -865 -865 15 153 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.1e+002 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.250000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[TA][CG][CT]G[TAC][GAT]T[GC]G[GT]G[GA][GA]G[GA][GA]G[GC][GA][TG] -------------------------------------------------------------------------------- Time 7.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 14 llr = 146 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :6:::::34:1: pos.-specific C :::8:::11:62 probability G :1a:::944:25 matrix T a2:2aa121a:3 bits 2.1 * 1.9 * * ** * 1.7 * * ** * 1.5 * * *** * Relative 1.3 * ***** * Entropy 1.1 * ***** * (15.1 bits) 0.9 * ***** * 0.6 ******* *** 0.4 ******* *** 0.2 ******* **** 0.0 ------------ Multilevel TAGCTTGGGTCG consensus T T AA GT sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10774 305 1.45e-07 TTTCCACATC TAGCTTGAGTCG TTCTTTGGAA 48430 420 6.56e-07 CAATTTCTGG TAGCTTGAGTCT AGGCGGTACT 45976 344 1.91e-06 CGGGGATACC TAGTTTGGATCG CAGTACCAGT 16766 350 2.22e-06 TGCATACCGG TAGCTTGTTTCG TGACCAAGAG 43016 35 2.65e-06 GGTGCGGACA TAGCTTGAGTAG TAGAGAGAGA 27709 479 5.99e-06 TGGGACATTG TAGCTTGGCTCT TTGCGAAACC 20589 161 9.15e-06 AAATGTACCC TAGCTTGAGTAC ATGCTAGATC 16592 44 1.05e-05 AATTTCAGCA TGGTTTGGATCG TTTTCGTCGT 39304 191 1.10e-05 CACGGAGTAA TAGTTTGGGTGT GCTGTGTTGG 40901 169 1.32e-05 CTGCAGGCTG TGGCTTGCGTCC CACCGTCGAC 47514 35 1.46e-05 TATTCAACCC TTGCTTGCATCC CGTATCCCTA 17779 240 1.46e-05 TCACAGAAAA TAGCTTTGATGG TTTCACGAAT 16511 94 2.40e-05 AACAATACAG TTGCTTGTTTGG TAGGTACAGC 43135 462 3.79e-05 CACGACCTTG TTGCTTTTATCT CATTCGTCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10774 1.5e-07 304_[+2]_184 48430 6.6e-07 419_[+2]_69 45976 1.9e-06 343_[+2]_145 16766 2.2e-06 349_[+2]_139 43016 2.7e-06 34_[+2]_454 27709 6e-06 478_[+2]_10 20589 9.1e-06 160_[+2]_328 16592 1e-05 43_[+2]_445 39304 1.1e-05 190_[+2]_298 40901 1.3e-05 168_[+2]_320 47514 1.5e-05 34_[+2]_454 17779 1.5e-05 239_[+2]_249 16511 2.4e-05 93_[+2]_395 43135 3.8e-05 461_[+2]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=14 10774 ( 305) TAGCTTGAGTCG 1 48430 ( 420) TAGCTTGAGTCT 1 45976 ( 344) TAGTTTGGATCG 1 16766 ( 350) TAGCTTGTTTCG 1 43016 ( 35) TAGCTTGAGTAG 1 27709 ( 479) TAGCTTGGCTCT 1 20589 ( 161) TAGCTTGAGTAC 1 16592 ( 44) TGGTTTGGATCG 1 39304 ( 191) TAGTTTGGGTGT 1 40901 ( 169) TGGCTTGCGTCC 1 47514 ( 35) TTGCTTGCATCC 1 17779 ( 240) TAGCTTTGATGG 1 16511 ( 94) TTGCTTGTTTGG 1 43135 ( 462) TTGCTTTTATCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13692 bayes= 11.1555 E= 1.1e+002 -1045 -1045 -1045 194 125 -1045 -66 -28 -1045 -1045 215 -1045 -1045 168 -1045 -28 -1045 -1045 -1045 194 -1045 -1045 -1045 194 -1045 -1045 193 -86 8 -78 66 -28 40 -177 93 -86 -1045 -1045 -1045 194 -92 139 -7 -1045 -1045 -19 115 14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 1.1e+002 0.000000 0.000000 0.000000 1.000000 0.642857 0.000000 0.142857 0.214286 0.000000 0.000000 1.000000 0.000000 0.000000 0.785714 0.000000 0.214286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 0.285714 0.142857 0.357143 0.214286 0.357143 0.071429 0.428571 0.142857 0.000000 0.000000 0.000000 1.000000 0.142857 0.642857 0.214286 0.000000 0.000000 0.214286 0.500000 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[AT]G[CT]TTG[GAT][GA]T[CG][GTC] -------------------------------------------------------------------------------- Time 15.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 12 llr = 167 E-value = 3.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 72:94826:583984591:91 pos.-specific C :8:143412523::65:37:7 probability G 1:a:::325::4:3::153:2 matrix T 31::2:123:1:1::::2:11 bits 2.1 * 1.9 * 1.7 * 1.5 ** * * * Relative 1.3 ** * * * Entropy 1.1 ** * *** * ** (20.1 bits) 0.9 *** * ** ***** ** 0.6 **** * *** ***** *** 0.4 ****** ************** 0.2 ********************* 0.0 --------------------- Multilevel ACGAAACAGAAGAACAAGCAC consensus T CCG TC C GAC CG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 47514 143 2.50e-10 ATCGTGGGAA ACGACAGATCAGAAACAGGAC GATTCTGGGC 16603 124 8.54e-09 GAAAAGAAAG ACGAAACGGAAGAAAAAGGAG ATTCTGACGA 27709 352 3.44e-08 TTTCGTGTTC ACGACAGACCCAAAACACCAC ACATGGGTCC 39304 163 4.71e-08 CGAGCGATGA TCGATAGATACAAACAAGCAC GGAGTAATAG 16281 195 5.22e-08 GGGCACGCAG TCGACCGTGCAGAGCAAGGAC GAGATCATGC 20589 86 7.75e-08 GCTCTGATCC ACGATACATAAGTGACAGCAC CTGGAAATTC 45592 351 1.48e-07 CGCACGTGAC AAGCAACAGCAGAACAAGGAG ATAAACGTTT 17779 325 2.68e-07 CGCGCTAAAC GTGAAACGGAACAACCACCAC ATCCACTCAG 17523 318 4.98e-07 ATGGGAAATC ACGACCCCTAACAACCATCAA ACACTTCCTT 41234 442 5.76e-07 TTTGGCAACC ACGAAAATCCACAACAATCAT CTTCTACCTT 15757 168 1.55e-06 GACAACTAGT TCGAAATAGCTAAACAGCCAC GTAGACTTTC 16592 460 3.19e-06 GGAGGAGAAC AAGACCAAGAACAGACAACTC AACAGAATCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47514 2.5e-10 142_[+3]_337 16603 8.5e-09 123_[+3]_356 27709 3.4e-08 351_[+3]_128 39304 4.7e-08 162_[+3]_317 16281 5.2e-08 194_[+3]_285 20589 7.8e-08 85_[+3]_394 45592 1.5e-07 350_[+3]_129 17779 2.7e-07 324_[+3]_155 17523 5e-07 317_[+3]_162 41234 5.8e-07 441_[+3]_38 15757 1.5e-06 167_[+3]_312 16592 3.2e-06 459_[+3]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=12 47514 ( 143) ACGACAGATCAGAAACAGGAC 1 16603 ( 124) ACGAAACGGAAGAAAAAGGAG 1 27709 ( 352) ACGACAGACCCAAAACACCAC 1 39304 ( 163) TCGATAGATACAAACAAGCAC 1 16281 ( 195) TCGACCGTGCAGAGCAAGGAC 1 20589 ( 86) ACGATACATAAGTGACAGCAC 1 45592 ( 351) AAGCAACAGCAGAACAAGGAG 1 17779 ( 325) GTGAAACGGAACAACCACCAC 1 17523 ( 318) ACGACCCCTAACAACCATCAA 1 41234 ( 442) ACGAAAATCCACAACAATCAT 1 15757 ( 168) TCGAAATAGCTAAACAGCCAC 1 16592 ( 460) AAGACCAAGAACAGACAACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 9.78661 E= 3.9e+002 130 -1023 -143 -6 -69 161 -1023 -164 -1023 -1023 215 -1023 176 -155 -1023 -1023 63 77 -1023 -64 147 3 -1023 -1023 -69 77 56 -164 111 -155 -44 -64 -1023 -55 115 36 89 103 -1023 -1023 147 -55 -1023 -164 -11 44 89 -1023 176 -1023 -1023 -164 147 -1023 15 -1023 63 125 -1023 -1023 89 103 -1023 -1023 176 -1023 -143 -1023 -169 3 115 -64 -1023 144 56 -1023 176 -1023 -1023 -164 -169 144 -44 -164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 3.9e+002 0.666667 0.000000 0.083333 0.250000 0.166667 0.750000 0.000000 0.083333 0.000000 0.000000 1.000000 0.000000 0.916667 0.083333 0.000000 0.000000 0.416667 0.416667 0.000000 0.166667 0.750000 0.250000 0.000000 0.000000 0.166667 0.416667 0.333333 0.083333 0.583333 0.083333 0.166667 0.166667 0.000000 0.166667 0.500000 0.333333 0.500000 0.500000 0.000000 0.000000 0.750000 0.166667 0.000000 0.083333 0.250000 0.333333 0.416667 0.000000 0.916667 0.000000 0.000000 0.083333 0.750000 0.000000 0.250000 0.000000 0.416667 0.583333 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.916667 0.000000 0.083333 0.000000 0.083333 0.250000 0.500000 0.166667 0.000000 0.666667 0.333333 0.000000 0.916667 0.000000 0.000000 0.083333 0.083333 0.666667 0.166667 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AT]CGA[AC][AC][CG]A[GT][AC]A[GCA]A[AG][CA][AC]A[GC][CG]AC -------------------------------------------------------------------------------- Time 23.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17523 5.58e-04 317_[+3(4.98e-07)]_162 31975 9.67e-01 500 43016 2.78e-03 34_[+2(2.65e-06)]_454 17779 7.05e-05 239_[+2(1.46e-05)]_73_\ [+3(2.68e-07)]_155 43135 2.20e-02 461_[+2(3.79e-05)]_27 47514 1.40e-07 34_[+2(1.46e-05)]_96_[+3(2.50e-10)]_\ 337 48430 2.71e-09 175_[+1(4.99e-11)]_223_\ [+2(6.56e-07)]_69 39304 1.02e-12 22_[+1(2.84e-11)]_119_\ [+3(4.71e-08)]_7_[+2(1.10e-05)]_298 39526 2.37e-01 500 15757 1.50e-02 167_[+3(1.55e-06)]_312 16281 6.09e-04 194_[+3(5.22e-08)]_285 40621 6.34e-01 500 40901 1.38e-07 39_[+1(5.81e-10)]_108_\ [+2(1.32e-05)]_320 16511 1.08e-01 93_[+2(2.40e-05)]_395 16592 4.71e-04 43_[+2(1.05e-05)]_404_\ [+3(3.19e-06)]_20 16603 1.09e-04 123_[+3(8.54e-09)]_356 16766 1.12e-02 349_[+2(2.22e-06)]_139 33523 8.18e-01 500 51303 1.20e-01 500 10774 1.39e-03 304_[+2(1.45e-07)]_184 10821 1.58e-01 500 44618 3.37e-01 500 11740 7.77e-01 500 45592 1.23e-09 169_[+1(1.36e-10)]_50_\ [+3(7.21e-05)]_89_[+3(1.48e-07)]_129 27709 4.09e-06 351_[+3(3.44e-08)]_106_\ [+2(5.99e-06)]_10 20589 8.23e-06 85_[+3(7.75e-08)]_54_[+2(9.15e-06)]_\ 328 41234 7.14e-03 441_[+3(5.76e-07)]_38 45976 5.62e-03 343_[+2(1.91e-06)]_145 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************