******************************************************************************** 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/176/176.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 20016 1.0000 500 24206 1.0000 500 24538 1.0000 500 24784 1.0000 500 264023 1.0000 500 264137 1.0000 500 38578 1.0000 500 4655 1.0000 500 5686 1.0000 500 7079 1.0000 500 7775 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/176/176.seqs.fa -oc motifs/176 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.262 G 0.225 T 0.248 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.262 G 0.225 T 0.248 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 7 llr = 85 E-value = 2.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1613:a4:a::a pos.-specific C ::::1:1::::: probability G 914:9:4a:9a: matrix T :347:::::1:: bits 2.1 * * 1.9 * ** ** 1.7 * ** ** 1.5 * ** ***** Relative 1.3 * ** ***** Entropy 1.1 * *** ***** (17.5 bits) 0.9 * *** ***** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GAGTGAAGAGGA consensus TTA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 264023 148 7.51e-08 ATACAATTGT GATTGAGGAGGA GTTGCCTCCC 7079 294 5.56e-07 AAGGAGAAAC GAGAGAAGAGGA AAACGAAGCT 38578 187 8.45e-07 GATGTATCCT GTGAGAGGAGGA ATAGTGGTGG 24538 36 1.26e-06 AGATGTATTG GAGTCAGGAGGA AGAAGCATGC 24784 2 1.44e-06 T GTATGAAGAGGA AGAGAAGAAT 20016 213 3.96e-06 TGAGCTGAAT GATTGACGATGA TTGGTACCGA 7775 115 4.69e-06 GAACGCATCA AGTTGAAGAGGA AGCATTTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264023 7.5e-08 147_[+1]_341 7079 5.6e-07 293_[+1]_195 38578 8.4e-07 186_[+1]_302 24538 1.3e-06 35_[+1]_453 24784 1.4e-06 1_[+1]_487 20016 4e-06 212_[+1]_276 7775 4.7e-06 114_[+1]_374 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=7 264023 ( 148) GATTGAGGAGGA 1 7079 ( 294) GAGAGAAGAGGA 1 38578 ( 187) GTGAGAGGAGGA 1 24538 ( 36) GAGTCAGGAGGA 1 24784 ( 2) GTATGAAGAGGA 1 20016 ( 213) GATTGACGATGA 1 7775 ( 115) AGTTGAAGAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.42755 E= 2.9e+001 -89 -945 193 -945 111 -945 -66 20 -89 -945 93 79 11 -945 -945 152 -945 -87 193 -945 192 -945 -945 -945 69 -87 93 -945 -945 -945 215 -945 192 -945 -945 -945 -945 -945 193 -79 -945 -945 215 -945 192 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.9e+001 0.142857 0.000000 0.857143 0.000000 0.571429 0.000000 0.142857 0.285714 0.142857 0.000000 0.428571 0.428571 0.285714 0.000000 0.000000 0.714286 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.142857 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AT][GT][TA]GA[AG]GAGGA -------------------------------------------------------------------------------- Time 1.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 105 E-value = 5.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 5:1141::1363:1:: pos.-specific C ::::::::::34:::4 probability G :699:8:848:1a116 matrix T 54::61a35:13:89: bits 2.1 * 1.9 * * 1.7 * * 1.5 ** * * * Relative 1.3 ** ** * * * Entropy 1.1 ******* * * ** (19.0 bits) 0.9 ******** * **** 0.6 *********** **** 0.4 *********** **** 0.2 *********** **** 0.0 ---------------- Multilevel AGGGTGTGTGACGTTG consensus TT A TGACA C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 7079 256 1.30e-08 TGTAGACGAC ATGGTGTGTGATGTTC ATGTTGTTGA 38578 165 5.29e-08 GAGAAAGGAG AGGGTGTGGGAAGATG TATCCTGTGA 5686 46 5.92e-08 CAGGTGGAAT TTGGAGTGTGCAGTTG GTTGATACAG 4655 79 3.16e-07 GATACAGACA TGGGAATTGGACGTTG TCGCACTCAA 264137 74 3.80e-07 TCCTATGCGG AGGGTGTGGAAGGGTG AGGCAGTAGG 20016 421 1.53e-06 GGACCGCGGG TGAGTGTGTGCCGTGC ACTGCATGCT 24538 104 1.63e-06 ACATCATTCT TTGGTTTTTGTTGTTG CACTCGGTCA 7775 57 2.24e-06 AATGAAACTG AGGAAGTGAAACGTTC ATCTAGTCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7079 1.3e-08 255_[+2]_229 38578 5.3e-08 164_[+2]_320 5686 5.9e-08 45_[+2]_439 4655 3.2e-07 78_[+2]_406 264137 3.8e-07 73_[+2]_411 20016 1.5e-06 420_[+2]_64 24538 1.6e-06 103_[+2]_381 7775 2.2e-06 56_[+2]_428 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 7079 ( 256) ATGGTGTGTGATGTTC 1 38578 ( 165) AGGGTGTGGGAAGATG 1 5686 ( 46) TTGGAGTGTGCAGTTG 1 4655 ( 79) TGGGAATTGGACGTTG 1 264137 ( 74) AGGGTGTGGAAGGGTG 1 20016 ( 421) TGAGTGTGTGCCGTGC 1 24538 ( 104) TTGGTTTTTGTTGTTG 1 7775 ( 57) AGGAAGTGAAACGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 10.7023 E= 5.9e+001 92 -965 -965 101 -965 -965 147 60 -108 -965 195 -965 -108 -965 195 -965 50 -965 -965 133 -108 -965 173 -99 -965 -965 -965 201 -965 -965 173 1 -108 -965 73 101 -8 -965 173 -965 124 -7 -965 -99 -8 52 -85 1 -965 -965 215 -965 -108 -965 -85 160 -965 -965 -85 182 -965 52 147 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 5.9e+001 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.625000 0.375000 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.875000 0.000000 0.375000 0.000000 0.000000 0.625000 0.125000 0.000000 0.750000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.125000 0.000000 0.375000 0.500000 0.250000 0.000000 0.750000 0.000000 0.625000 0.250000 0.000000 0.125000 0.250000 0.375000 0.125000 0.250000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.125000 0.750000 0.000000 0.000000 0.125000 0.875000 0.000000 0.375000 0.625000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][GT]GG[TA]GT[GT][TG][GA][AC][CAT]GTT[GC] -------------------------------------------------------------------------------- Time 2.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 130 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 14294:17:3:71233684:7 pos.-specific C 1681294::79328744:4a: probability G ::::2::2::1:2::1::::1 matrix T 8:::1141a:::4::1:21:2 bits 2.1 1.9 * * 1.7 * * 1.5 * * * * * Relative 1.3 * * * * * Entropy 1.1 * ** * **** ** * * (20.8 bits) 0.9 **** * ***** ** ** * 0.6 **** ******* ** ***** 0.4 **** ******* ** ***** 0.2 ********************* 0.0 --------------------- Multilevel TCCAACCATCCATCCCAAACA consensus AA C TG A CCAAACTC T sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5686 436 4.04e-10 ACTTTATATG TCCAACTATCCATCACAACCT GTCACCTCCT 20016 354 6.63e-09 ATGAATCCTT TCCAGCTTTACATCCAAAACA GTGATGGTAC 4655 311 1.39e-08 TACAGTCAAG TCCACCTGTCCCTCCCCTACA AACAAGACGC 7775 451 6.11e-08 TTTGTCATCT TCCAGCCATCCACAATCAACA TCACGCTGGA 38578 67 2.20e-07 CAACGATCGT TAAACTTGTACATCCAAACCA AATCGCAATT 264023 60 2.76e-07 CCTCCTCCTT TACCACCATCCACACCCAACG AAAAGACCAA 24538 301 3.93e-07 AACGCTGGCC ACAAACCATACCACCACACCA GCTCCGACAA 264137 448 5.13e-07 TGCACCGTCT TACATCCATCGCGCCCATCCT AAAAAACAAC 24784 435 7.43e-07 CATAACTGCC CACAACAATCCAGCAGAATCA GAATAAAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5686 4e-10 435_[+3]_44 20016 6.6e-09 353_[+3]_126 4655 1.4e-08 310_[+3]_169 7775 6.1e-08 450_[+3]_29 38578 2.2e-07 66_[+3]_413 264023 2.8e-07 59_[+3]_420 24538 3.9e-07 300_[+3]_179 264137 5.1e-07 447_[+3]_32 24784 7.4e-07 434_[+3]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 5686 ( 436) TCCAACTATCCATCACAACCT 1 20016 ( 354) TCCAGCTTTACATCCAAAACA 1 4655 ( 311) TCCACCTGTCCCTCCCCTACA 1 7775 ( 451) TCCAGCCATCCACAATCAACA 1 38578 ( 67) TAAACTTGTACATCCAAACCA 1 264023 ( 60) TACCACCATCCACACCCAACG 1 24538 ( 301) ACAAACCATACCACCACACCA 1 264137 ( 448) TACATCCATCGCGCCCATCCT 1 24784 ( 435) CACAACAATCCAGCAGAATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.32846 E= 1.1e+002 -125 -123 -982 165 75 108 -982 -982 -25 157 -982 -982 175 -123 -982 -982 75 -24 -2 -116 -982 176 -982 -116 -125 76 -982 84 133 -982 -2 -116 -982 -982 -982 201 33 135 -982 -982 -982 176 -102 -982 133 35 -982 -982 -125 -24 -2 84 -25 157 -982 -982 33 135 -982 -982 33 76 -102 -116 107 76 -982 -982 155 -982 -982 -16 75 76 -982 -116 -982 193 -982 -982 133 -982 -102 -16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.1e+002 0.111111 0.111111 0.000000 0.777778 0.444444 0.555556 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.444444 0.222222 0.222222 0.111111 0.000000 0.888889 0.000000 0.111111 0.111111 0.444444 0.000000 0.444444 0.666667 0.000000 0.222222 0.111111 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.666667 0.333333 0.000000 0.000000 0.111111 0.222222 0.222222 0.444444 0.222222 0.777778 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.444444 0.111111 0.111111 0.555556 0.444444 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.444444 0.444444 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.111111 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CA][CA]A[ACG]C[CT][AG]T[CA]C[AC][TCG][CA][CA][CA][AC][AT][AC]C[AT] -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20016 1.68e-09 212_[+1(3.96e-06)]_129_\ [+3(6.63e-09)]_46_[+2(1.53e-06)]_64 24206 6.86e-01 500 24538 2.67e-08 35_[+1(1.26e-06)]_56_[+2(1.63e-06)]_\ 181_[+3(3.93e-07)]_179 24784 1.91e-05 1_[+1(1.44e-06)]_421_[+3(7.43e-07)]_\ 45 264023 4.88e-07 33_[+1(1.53e-05)]_14_[+3(2.76e-07)]_\ 67_[+1(7.51e-08)]_341 264137 2.67e-06 73_[+2(3.80e-07)]_358_\ [+3(5.13e-07)]_32 38578 4.55e-10 66_[+3(2.20e-07)]_77_[+2(5.29e-08)]_\ 6_[+1(8.45e-07)]_302 4655 7.44e-08 78_[+2(3.16e-07)]_216_\ [+3(1.39e-08)]_169 5686 1.41e-09 45_[+2(5.92e-08)]_374_\ [+3(4.04e-10)]_44 7079 2.15e-07 255_[+2(1.30e-08)]_22_\ [+1(5.56e-07)]_195 7775 2.16e-08 56_[+2(2.24e-06)]_42_[+1(4.69e-06)]_\ 324_[+3(6.11e-08)]_29 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************