******************************************************************************** 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/465/465.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10487 1.0000 500 11038 1.0000 500 11057 1.0000 500 12116 1.0000 500 12149 1.0000 500 22070 1.0000 500 22625 1.0000 500 2282 1.0000 500 24101 1.0000 500 24747 1.0000 500 24870 1.0000 500 25181 1.0000 500 25429 1.0000 500 25882 1.0000 500 262679 1.0000 500 36490 1.0000 500 40335 1.0000 500 5769 1.0000 500 6636 1.0000 500 6798 1.0000 500 6823 1.0000 500 8974 1.0000 500 9657 1.0000 500 9661 1.0000 500 9959 1.0000 500 bd1075 1.0000 500 bd1100 1.0000 500 bd1870 1.0000 500 bd731 1.0000 500 bd911 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/465/465.seqs.fa -oc motifs/465 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.245 G 0.215 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.245 G 0.215 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 10 llr = 163 E-value = 1.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3::9:48774553::5::311 pos.-specific C ::a1:622153271a13a124 probability G :::::::1:::1::::::6:: matrix T 7a::a:::2122:9:47::75 bits 2.2 2.0 * * * 1.8 ** * * * 1.6 **** * * Relative 1.3 **** ** * Entropy 1.1 ****** *** ** (23.5 bits) 0.9 ******** *** *** 0.7 ********** *** ***** 0.4 *********** ********* 0.2 ********************* 0.0 --------------------- Multilevel TTCATCAAACAACTCATCGTT consensus A ACCTACCA TC ACC sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9661 461 4.12e-12 TCTAACTGGA TTCATAAAACAACTCATCGTT CATTTCAACC bd1870 461 5.64e-12 TTCAACTGTA TTCATAAAACAACTCATCGTC CATTCCAACC 9657 212 5.64e-12 TTCAACTGCA TTCATAAAACAACTCATCGTC CATTTTAATC bd731 322 5.22e-08 ATCGCTAGCC TTCATCAGAACCATCATCGAT GGTGAGTGCA 24870 145 5.59e-08 GGGGGGAGCC TTCCTCAAACAAATCTTCCCT CATTTATACA 25181 280 6.40e-08 CCACCACGAG TTCATCAAATTGCTCCCCGTC AAGACGACGG bd1075 291 7.78e-08 ATGTTATTGT ATCATCCCTAAACTCTCCATT CATCACTTAA 6823 313 8.28e-08 TAACTATTTG TTCATAAAAATTACCATCATC ATGCTCTTTA 40335 466 9.94e-08 CAACCACTGC ATCATCAACCCTCTCTTCGCA CATCTATAAT 11057 428 1.90e-07 ATGTTATTGT ATCATCCCTACCCTCTCCATT CATCGCTTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9661 4.1e-12 460_[+1]_19 bd1870 5.6e-12 460_[+1]_19 9657 5.6e-12 211_[+1]_268 bd731 5.2e-08 321_[+1]_158 24870 5.6e-08 144_[+1]_335 25181 6.4e-08 279_[+1]_200 bd1075 7.8e-08 290_[+1]_189 6823 8.3e-08 312_[+1]_167 40335 9.9e-08 465_[+1]_14 11057 1.9e-07 427_[+1]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=10 9661 ( 461) TTCATAAAACAACTCATCGTT 1 bd1870 ( 461) TTCATAAAACAACTCATCGTC 1 9657 ( 212) TTCATAAAACAACTCATCGTC 1 bd731 ( 322) TTCATCAGAACCATCATCGAT 1 24870 ( 145) TTCCTCAAACAAATCTTCCCT 1 25181 ( 280) TTCATCAAATTGCTCCCCGTC 1 bd1075 ( 291) ATCATCCCTAAACTCTCCATT 1 6823 ( 313) TTCATAAAAATTACCATCATC 1 40335 ( 466) ATCATCAACCCTCTCTTCGCA 1 11057 ( 428) ATCATCCCTACCCTCTCCATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 10.7426 E= 1.1e-002 17 -997 -997 135 -997 -997 -997 187 -997 203 -997 -997 175 -129 -997 -997 -997 -997 -997 187 58 129 -997 -997 158 -29 -997 -997 139 -29 -110 -997 139 -129 -997 -45 58 103 -997 -145 91 29 -997 -45 91 -29 -110 -45 17 152 -997 -997 -997 -129 -997 171 -997 203 -997 -997 91 -129 -997 55 -997 29 -997 135 -997 203 -997 -997 17 -129 148 -997 -141 -29 -997 135 -141 71 -997 87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 1.1e-002 0.300000 0.000000 0.000000 0.700000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.400000 0.600000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.700000 0.200000 0.100000 0.000000 0.700000 0.100000 0.000000 0.200000 0.400000 0.500000 0.000000 0.100000 0.500000 0.300000 0.000000 0.200000 0.500000 0.200000 0.100000 0.200000 0.300000 0.700000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 1.000000 0.000000 0.000000 0.500000 0.100000 0.000000 0.400000 0.000000 0.300000 0.000000 0.700000 0.000000 1.000000 0.000000 0.000000 0.300000 0.100000 0.600000 0.000000 0.100000 0.200000 0.000000 0.700000 0.100000 0.400000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA]TCAT[CA][AC][AC][AT][CA][ACT][ACT][CA]TC[AT][TC]C[GA][TC][TC] -------------------------------------------------------------------------------- Time 6.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 9 llr = 151 E-value = 5.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 827:63a72a3:811:::621 pos.-specific C 1:3a12:37:2a13::::23: probability G 1:::1:::::3::63::a::: matrix T :8::24::1:1:1:6aa:249 bits 2.2 * 2.0 * * * * * 1.8 * * * * *** 1.6 * * * * *** Relative 1.3 * * * * *** * Entropy 1.1 *** ** * * *** * (24.1 bits) 0.9 **** ** * ** *** * 0.7 **** **** ******* * 0.4 **** ***** ********** 0.2 ********************* 0.0 --------------------- Multilevel ATACATAACAACAGTTTGATT consensus AC TA CA G CG CC sequence C C TA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1870 314 3.56e-11 ACACTGCCGA ATACTAAACAGCAGTTTGATT CAGGGGATAT 9661 313 3.56e-11 ACACCGCCGA ATACTAAACAGCAGTTTGATT CAGGGGATAT bd1100 472 2.57e-09 TTCTCATTCC ATACATACAAACAGGTTGTCT CTGCAAGT 25882 472 2.57e-09 TTCTCATTCC ATACATACAAACAGGTTGTCT CTGCTAGT 25429 260 1.78e-08 GCGGTGAAAA ATACACAACAGCCAGTTGAAT TTCGGAGCAT 6823 122 2.09e-08 CGAACATCTC GTCCATAACACCAGATTGCTT GCAGCCCTCA 36490 327 4.93e-08 ATTGTGACCT AACCACACTACCACTTTGATT CAATCATATC 5769 87 8.44e-08 AAGCCACGCA ATACCTAACAACTCTTTGAAA TAAATGATGT 9657 394 1.73e-07 TATCACTTCT CACCGAAACATCACTTTGCCT TGTGACTCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1870 3.6e-11 313_[+2]_166 9661 3.6e-11 312_[+2]_167 bd1100 2.6e-09 471_[+2]_8 25882 2.6e-09 471_[+2]_8 25429 1.8e-08 259_[+2]_220 6823 2.1e-08 121_[+2]_358 36490 4.9e-08 326_[+2]_153 5769 8.4e-08 86_[+2]_393 9657 1.7e-07 393_[+2]_86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=9 bd1870 ( 314) ATACTAAACAGCAGTTTGATT 1 9661 ( 313) ATACTAAACAGCAGTTTGATT 1 bd1100 ( 472) ATACATACAAACAGGTTGTCT 1 25882 ( 472) ATACATACAAACAGGTTGTCT 1 25429 ( 260) ATACACAACAGCCAGTTGAAT 1 6823 ( 122) GTCCATAACACCAGATTGCTT 1 36490 ( 327) AACCACACTACCACTTTGATT 1 5769 ( 87) ATACCTAACAACTCTTTGAAA 1 9657 ( 394) CACCGAAACATCACTTTGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 9.94442 E= 5.3e-002 154 -114 -95 -982 -26 -982 -982 150 132 45 -982 -982 -982 203 -982 -982 106 -114 -95 -30 32 -14 -982 70 191 -982 -982 -982 132 45 -982 -982 -26 145 -982 -130 191 -982 -982 -982 32 -14 64 -130 -982 203 -982 -982 154 -114 -982 -130 -126 45 137 -982 -126 -982 64 102 -982 -982 -982 187 -982 -982 -982 187 -982 -982 222 -982 106 -14 -982 -30 -26 45 -982 70 -126 -982 -982 170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 5.3e-002 0.777778 0.111111 0.111111 0.000000 0.222222 0.000000 0.000000 0.777778 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.111111 0.111111 0.222222 0.333333 0.222222 0.000000 0.444444 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.222222 0.666667 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.333333 0.222222 0.333333 0.111111 0.000000 1.000000 0.000000 0.000000 0.777778 0.111111 0.000000 0.111111 0.111111 0.333333 0.555556 0.000000 0.111111 0.000000 0.333333 0.555556 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.555556 0.222222 0.000000 0.222222 0.222222 0.333333 0.000000 0.444444 0.111111 0.000000 0.000000 0.888889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[TA][AC]C[AT][TAC]A[AC][CA]A[AGC]CA[GC][TG]TTG[ACT][TCA]T -------------------------------------------------------------------------------- Time 13.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 7 llr = 127 E-value = 7.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 7:1::1:1:31::::::6:1 pos.-specific C :a6:363:47:::4:1a4:1 probability G 1:3a7::93:::::39:::: matrix T 1::::37:3:9aa67:::a7 bits 2.2 * 2.0 * * * 1.8 * * ** * * 1.6 * * * ** ** * Relative 1.3 * ** * *** ** * Entropy 1.1 * ** ** **** *** * (26.2 bits) 0.9 ** ** ** ********** 0.7 ******** *********** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ACCGGCTGCCTTTTTGCATT consensus G CTC GA CG C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- bd1870 433 2.94e-12 CTCCACAGTA ACCGGCTGCCTTTTTGCCTT CAACTGTATT 9657 184 2.55e-10 TACATAAACA ACCGGCTACCTTTTTGCCTT CAACTGCATT 9661 433 2.89e-10 TCCACAAGTA ACCGGCTGTCTTTCTGCATC TAACTGGATT 6823 189 5.22e-09 TGCAATGCCG TCGGGATGCATTTTTGCATT AGGTCTGCGT 10487 41 8.07e-09 TCAACTCGCC ACAGCCTGGCTTTCTCCCTT CCTCGTTTGA 36490 224 1.59e-08 GTTGGTTGTC GCCGGTCGGCATTCGGCATT TCTCATTCTT 12149 394 3.17e-08 GGCGAGCGAA ACGGCTCGTATTTTGGCATA CATCTAGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1870 2.9e-12 432_[+3]_48 9657 2.5e-10 183_[+3]_297 9661 2.9e-10 432_[+3]_48 6823 5.2e-09 188_[+3]_292 10487 8.1e-09 40_[+3]_440 36490 1.6e-08 223_[+3]_257 12149 3.2e-08 393_[+3]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=7 bd1870 ( 433) ACCGGCTGCCTTTTTGCCTT 1 9657 ( 184) ACCGGCTACCTTTTTGCCTT 1 9661 ( 433) ACCGGCTGTCTTTCTGCATC 1 6823 ( 189) TCGGGATGCATTTTTGCATT 1 10487 ( 41) ACAGCCTGGCTTTCTCCCTT 1 36490 ( 224) GCCGGTCGGCATTCGGCATT 1 12149 ( 394) ACGGCTCGTATTTTGGCATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14430 bayes= 11.6147 E= 7.5e-001 142 -945 -59 -94 -945 203 -945 -945 -90 122 41 -945 -945 -945 222 -945 -945 22 173 -945 -90 122 -945 6 -945 22 -945 138 -90 -945 200 -945 -945 81 41 6 10 154 -945 -945 -90 -945 -945 164 -945 -945 -945 187 -945 -945 -945 187 -945 81 -945 106 -945 -945 41 138 -945 -77 200 -945 -945 203 -945 -945 110 81 -945 -945 -945 -945 -945 187 -90 -77 -945 138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 7.5e-001 0.714286 0.000000 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 0.142857 0.571429 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.142857 0.571429 0.000000 0.285714 0.000000 0.285714 0.000000 0.714286 0.142857 0.000000 0.857143 0.000000 0.000000 0.428571 0.285714 0.285714 0.285714 0.714286 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.285714 0.714286 0.000000 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.142857 0.000000 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AC[CG]G[GC][CT][TC]G[CGT][CA]TTT[TC][TG]GC[AC]TT -------------------------------------------------------------------------------- Time 19.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10487 1.39e-05 40_[+3(8.07e-09)]_440 11038 4.85e-02 183_[+1(1.42e-05)]_296 11057 2.77e-03 190_[+1(9.92e-05)]_216_\ [+1(1.90e-07)]_52 12116 2.71e-01 401_[+1(9.07e-05)]_78 12149 6.92e-04 393_[+3(3.17e-08)]_87 22070 5.88e-02 500 22625 7.99e-01 500 2282 8.37e-01 500 24101 8.18e-01 500 24747 9.97e-01 500 24870 5.82e-04 144_[+1(5.59e-08)]_335 25181 1.00e-03 279_[+1(6.40e-08)]_200 25429 2.32e-05 259_[+2(1.78e-08)]_220 25882 4.08e-05 471_[+2(2.57e-09)]_8 262679 9.74e-01 500 36490 4.13e-08 223_[+3(1.59e-08)]_83_\ [+2(4.93e-08)]_153 40335 2.33e-04 114_[+1(2.86e-06)]_330_\ [+1(9.94e-08)]_14 5769 1.03e-03 86_[+2(8.44e-08)]_393 6636 9.34e-01 500 6798 1.24e-01 500 6823 6.34e-13 121_[+2(2.09e-08)]_46_\ [+3(5.22e-09)]_104_[+1(8.28e-08)]_167 8974 3.50e-01 500 9657 2.93e-17 56_[+2(1.33e-05)]_106_\ [+3(2.55e-10)]_8_[+1(5.64e-12)]_161_[+2(1.73e-07)]_86 9661 7.05e-21 312_[+2(3.56e-11)]_99_\ [+3(2.89e-10)]_8_[+1(4.12e-12)]_19 9959 6.90e-01 500 bd1075 3.58e-04 18_[+1(4.46e-06)]_251_\ [+1(7.78e-08)]_189 bd1100 5.58e-05 471_[+2(2.57e-09)]_8 bd1870 1.14e-22 313_[+2(3.56e-11)]_98_\ [+3(2.94e-12)]_8_[+1(5.64e-12)]_19 bd731 3.46e-04 321_[+1(5.22e-08)]_158 bd911 9.32e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************