******************************************************************************** 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/152/152.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 32178 1.0000 500 20809 1.0000 500 32524 1.0000 500 49608 1.0000 500 49610 1.0000 500 55177 1.0000 500 43940 1.0000 500 45621 1.0000 500 37105 1.0000 500 34225 1.0000 500 48044 1.0000 500 43334 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/152/152.seqs.fa -oc motifs/152 -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 0.258 C 0.252 G 0.226 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.252 G 0.226 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 12 llr = 134 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::83112:::81583 pos.-specific C :85::55::a7133:6 probability G ::531333::3:::1: matrix T a3::7225a::26211 bits 2.1 1.9 * ** 1.7 * ** 1.5 * ** Relative 1.3 * * ** Entropy 1.1 **** *** * (16.2 bits) 0.9 ***** **** * 0.6 ***** ****** ** 0.4 ***** ********* 0.2 **************** 0.0 ---------------- Multilevel TCCATCCTTCCATAAC consensus TGGAGGG G CC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 49608 221 2.65e-08 ATCCTTTCCT TCCATCCGTCCATCAA CTTGGTGCCC 55177 354 1.38e-07 GGTCGGCCGG TCGGTCGGTCCATCAC AGTCAGTTCA 34225 42 3.64e-07 CTTGAGCCAA TCGATGCATCCACAAA GGGACTTGCC 49610 471 5.26e-07 CAAATTCGTG TCCATTCTTCGACAAA ACAACGTAGG 32524 399 6.68e-07 CGCAGGATTG TCGATCCTTCCATTAT CGACACGCGT 20809 376 1.29e-06 ACGTGATCGA TCGATCGATCCTCAAC TTGAGACTCG 48044 305 1.43e-06 TACGAACCGA TCGAAGTTTCGATCAC ACGATCACAG 43940 417 6.35e-06 GGCAAACTCA TCCATCAGTCGATATC CACGGTCCCT 45621 374 7.37e-06 CTCTTTCTGT TTCGACCTTCGTTAAC AGTAAGATTC 32178 375 9.12e-06 GTCCGGTCAC TTCATGGTTCCATCGA GGGATGATCC 43334 405 2.91e-05 GACGGTGAGC TTCGAACGTCCAAAAC CGACTATGAG 37105 379 4.31e-05 AAAGACATTT TCGAGTTTTCCCCTAC CCTATGTTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49608 2.6e-08 220_[+1]_264 55177 1.4e-07 353_[+1]_131 34225 3.6e-07 41_[+1]_443 49610 5.3e-07 470_[+1]_14 32524 6.7e-07 398_[+1]_86 20809 1.3e-06 375_[+1]_109 48044 1.4e-06 304_[+1]_180 43940 6.4e-06 416_[+1]_68 45621 7.4e-06 373_[+1]_111 32178 9.1e-06 374_[+1]_110 43334 2.9e-05 404_[+1]_80 37105 4.3e-05 378_[+1]_106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=12 49608 ( 221) TCCATCCGTCCATCAA 1 55177 ( 354) TCGGTCGGTCCATCAC 1 34225 ( 42) TCGATGCATCCACAAA 1 49610 ( 471) TCCATTCTTCGACAAA 1 32524 ( 399) TCGATCCTTCCATTAT 1 20809 ( 376) TCGATCGATCCTCAAC 1 48044 ( 305) TCGAAGTTTCGATCAC 1 43940 ( 417) TCCATCAGTCGATATC 1 45621 ( 374) TTCGACCTTCGTTAAC 1 32178 ( 375) TTCATGGTTCCATCGA 1 43334 ( 405) TTCGAACGTCCAAAAC 1 37105 ( 379) TCGAGTTTTCCCCTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.36712 E= 1.1e+001 -1023 -1023 -1023 192 -1023 157 -1023 -8 -1023 99 114 -1023 154 -1023 15 -1023 -5 -1023 -144 134 -163 99 15 -66 -163 99 15 -66 -63 -1023 56 92 -1023 -1023 -1023 192 -1023 199 -1023 -1023 -1023 140 56 -1023 154 -160 -1023 -66 -163 40 -1023 114 95 40 -1023 -66 169 -1023 -144 -166 37 121 -1023 -166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 1.1e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.500000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.083333 0.666667 0.083333 0.500000 0.250000 0.166667 0.083333 0.500000 0.250000 0.166667 0.166667 0.000000 0.333333 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.750000 0.083333 0.000000 0.166667 0.083333 0.333333 0.000000 0.583333 0.500000 0.333333 0.000000 0.166667 0.833333 0.000000 0.083333 0.083333 0.333333 0.583333 0.000000 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CT][CG][AG][TA][CG][CG][TG]TC[CG]A[TC][AC]A[CA] -------------------------------------------------------------------------------- Time 1.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 12 llr = 117 E-value = 4.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::146:::18 pos.-specific C 3:18::313::2 probability G 51::862:139: matrix T 29922::968:: bits 2.1 1.9 1.7 * 1.5 ** * * Relative 1.3 *** * ** Entropy 1.1 ***** * *** (14.1 bits) 0.9 ***** * *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GTTCGGATTTGA consensus C AC CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43940 108 2.91e-07 GGCATTCTTG GTTCGGCTTTGA CTGGGTCGGC 45621 329 1.10e-06 AGTTTTTGCG GTTCGGATTTGC AAATATCTCC 32178 336 1.61e-06 TTTGCTCGGA TTTCGAATTTGA ATATTTGGAT 55177 113 5.35e-06 CAATCAAACC GTTCTAATCTGA ATTATCGGAA 32524 101 5.74e-06 ATTCACGAAG CTTCGACTTGGA CAGCGAATCC 37105 166 6.63e-06 TGAATTGCAA CTCCGGATTTGA CAGAATAAGC 34225 25 1.44e-05 AAAGAGCGTT TTTCGGACTTGA GCCAATCGAT 43334 471 1.85e-05 GCAATCCACT GTTTTGATCTGA ATCTGATCCT 20809 464 2.69e-05 TTCTTCTAGC CGTCGGGTCTGA TCTTGTAAAT 49608 101 3.09e-05 ATCTAACAAA GTTCGAATCGAA TGGGTCCGAT 48044 63 4.98e-05 AAACGGTAAA CTTTGGGTGTGA TACAGTCCTA 49610 49 1.05e-04 CGATCGCGAG GTTCAACTTGGC GGTCCACGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43940 2.9e-07 107_[+2]_381 45621 1.1e-06 328_[+2]_160 32178 1.6e-06 335_[+2]_153 55177 5.3e-06 112_[+2]_376 32524 5.7e-06 100_[+2]_388 37105 6.6e-06 165_[+2]_323 34225 1.4e-05 24_[+2]_464 43334 1.9e-05 470_[+2]_18 20809 2.7e-05 463_[+2]_25 49608 3.1e-05 100_[+2]_388 48044 5e-05 62_[+2]_426 49610 0.0001 48_[+2]_440 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=12 43940 ( 108) GTTCGGCTTTGA 1 45621 ( 329) GTTCGGATTTGC 1 32178 ( 336) TTTCGAATTTGA 1 55177 ( 113) GTTCTAATCTGA 1 32524 ( 101) CTTCGACTTGGA 1 37105 ( 166) CTCCGGATTTGA 1 34225 ( 25) TTTCGGACTTGA 1 43334 ( 471) GTTTTGATCTGA 1 20809 ( 464) CGTCGGGTCTGA 1 49608 ( 101) GTTCGAATCGAA 1 48044 ( 63) CTTTGGGTGTGA 1 49610 ( 49) GTTCAACTTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 9.37898 E= 4.7e+001 -1023 40 114 -66 -1023 -1023 -144 180 -1023 -160 -1023 180 -1023 172 -1023 -66 -163 -1023 173 -66 69 -1023 137 -1023 118 -1 -44 -1023 -1023 -160 -1023 180 -1023 40 -144 114 -1023 -1023 15 151 -163 -1023 202 -1023 169 -60 -1023 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 4.7e+001 0.000000 0.333333 0.500000 0.166667 0.000000 0.000000 0.083333 0.916667 0.000000 0.083333 0.000000 0.916667 0.000000 0.833333 0.000000 0.166667 0.083333 0.000000 0.750000 0.166667 0.416667 0.000000 0.583333 0.000000 0.583333 0.250000 0.166667 0.000000 0.000000 0.083333 0.000000 0.916667 0.000000 0.333333 0.083333 0.583333 0.000000 0.000000 0.250000 0.750000 0.083333 0.000000 0.916667 0.000000 0.833333 0.166667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC]TTCG[GA][AC]T[TC][TG]GA -------------------------------------------------------------------------------- Time 3.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 12 llr = 114 E-value = 2.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 32a8:4:1:3:3 pos.-specific C :8:2a1:68:33 probability G :1:::4::367: matrix T 7::::1a3:2:4 bits 2.1 1.9 * * * 1.7 * * * 1.5 * * * Relative 1.3 *** * * Entropy 1.1 * *** * * * (13.7 bits) 0.9 ***** * * * 0.6 ***** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCAACATCCGGT consensus A G TGACC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 55177 86 4.73e-07 GCGAATCGAG TCAACATCCGGA TAGACCAATC 34225 480 1.22e-06 CCTAAGCGAT TCAACATCCGCC GCCGGGCCA 45621 259 5.38e-06 CTTGTCGTGC TCAACTTCCGGC ACTTCGGAGG 49608 125 1.17e-05 GGTCCGATCT TCAACATCCTCC GAAATTGTGT 37105 38 1.72e-05 TCCGAGAGCT ACAACGTTGGGA TGTGCTTGGA 20809 345 2.06e-05 CATTCGCTAC AAAACATTCGGT ATTCACGGGA 49610 11 2.26e-05 TGGCTTGGAC TCACCGTCCAGA AGGAGTGAGA 32524 43 2.26e-05 GTTGGGTCGA TCAACCTTCGCT TGTCGAGCGC 43334 224 3.42e-05 TCTTGCAGTC AAAACATCCAGC AAATTGAAGC 32178 88 3.42e-05 TTCCTCCATA TGAACGTCCTGT CCTGTCTTGC 48044 483 5.67e-05 GATTCATAAA ACAACGTTGACT GTCATT 43940 159 8.11e-05 ATCCAATTGG TCACCGTAGGGT CGTGTGTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 55177 4.7e-07 85_[+3]_403 34225 1.2e-06 479_[+3]_9 45621 5.4e-06 258_[+3]_230 49608 1.2e-05 124_[+3]_364 37105 1.7e-05 37_[+3]_451 20809 2.1e-05 344_[+3]_144 49610 2.3e-05 10_[+3]_478 32524 2.3e-05 42_[+3]_446 43334 3.4e-05 223_[+3]_265 32178 3.4e-05 87_[+3]_401 48044 5.7e-05 482_[+3]_6 43940 8.1e-05 158_[+3]_330 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=12 55177 ( 86) TCAACATCCGGA 1 34225 ( 480) TCAACATCCGCC 1 45621 ( 259) TCAACTTCCGGC 1 49608 ( 125) TCAACATCCTCC 1 37105 ( 38) ACAACGTTGGGA 1 20809 ( 345) AAAACATTCGGT 1 49610 ( 11) TCACCGTCCAGA 1 32524 ( 43) TCAACCTTCGCT 1 43334 ( 224) AAAACATCCAGC 1 32178 ( 88) TGAACGTCCTGT 1 48044 ( 483) ACAACGTTGACT 1 43940 ( 159) TCACCGTAGGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 8.93074 E= 2.0e+003 37 -1023 -1023 134 -63 157 -144 -1023 195 -1023 -1023 -1023 169 -60 -1023 -1023 -1023 199 -1023 -1023 69 -160 88 -166 -1023 -1023 -1023 192 -163 121 -1023 34 -1023 157 15 -1023 -5 -1023 137 -66 -1023 40 156 -1023 -5 40 -1023 66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 2.0e+003 0.333333 0.000000 0.000000 0.666667 0.166667 0.750000 0.083333 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.416667 0.083333 0.416667 0.083333 0.000000 0.000000 0.000000 1.000000 0.083333 0.583333 0.000000 0.333333 0.000000 0.750000 0.250000 0.000000 0.250000 0.000000 0.583333 0.166667 0.000000 0.333333 0.666667 0.000000 0.250000 0.333333 0.000000 0.416667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]CAAC[AG]T[CT][CG][GA][GC][TCA] -------------------------------------------------------------------------------- Time 4.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32178 9.05e-06 87_[+3(3.42e-05)]_236_\ [+2(1.61e-06)]_27_[+1(9.12e-06)]_110 20809 1.23e-05 344_[+3(2.06e-05)]_19_\ [+1(1.29e-06)]_72_[+2(2.69e-05)]_25 32524 1.89e-06 42_[+3(2.26e-05)]_46_[+2(5.74e-06)]_\ 286_[+1(6.68e-07)]_86 49608 2.58e-07 100_[+2(3.09e-05)]_12_\ [+3(1.17e-05)]_84_[+1(2.65e-08)]_264 49610 1.98e-05 10_[+3(2.26e-05)]_448_\ [+1(5.26e-07)]_14 55177 1.26e-08 85_[+3(4.73e-07)]_15_[+2(5.35e-06)]_\ 229_[+1(1.38e-07)]_131 43940 3.05e-06 107_[+2(2.91e-07)]_39_\ [+3(8.11e-05)]_246_[+1(6.35e-06)]_68 45621 1.02e-06 258_[+3(5.38e-06)]_58_\ [+2(1.10e-06)]_33_[+1(7.37e-06)]_111 37105 6.67e-05 37_[+3(1.72e-05)]_116_\ [+2(6.63e-06)]_201_[+1(4.31e-05)]_106 34225 1.80e-07 24_[+2(1.44e-05)]_5_[+1(3.64e-07)]_\ 422_[+3(1.22e-06)]_9 48044 5.58e-05 62_[+2(4.98e-05)]_230_\ [+1(1.43e-06)]_162_[+3(5.67e-05)]_6 43334 2.09e-04 223_[+3(3.42e-05)]_169_\ [+1(2.91e-05)]_50_[+2(1.85e-05)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************