******************************************************************************** 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/32/32.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17276 1.0000 500 9157 1.0000 500 9570 1.0000 500 32441 1.0000 500 48767 1.0000 500 32791 1.0000 500 30502 1.0000 500 31140 1.0000 500 44176 1.0000 500 8024 1.0000 500 35304 1.0000 500 20034 1.0000 500 45676 1.0000 500 35590 1.0000 500 46188 1.0000 500 46289 1.0000 500 42970 1.0000 500 43356 1.0000 500 34807 1.0000 500 44205 1.0000 500 45609 1.0000 500 44249 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/32/32.seqs.fa -oc motifs/32 -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= 22 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= 11000 N= 22 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.280 C 0.232 G 0.213 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.280 C 0.232 G 0.213 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 16 llr = 173 E-value = 1.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 11:6813941::793: pos.-specific C :814::5:2236:138 probability G ::9::9212:743:3: matrix T 91::3:11271:1:23 bits 2.2 2.0 1.8 1.6 * * Relative 1.3 * * * * * Entropy 1.1 * * ** * ** * * (15.6 bits) 0.9 ****** * **** * 0.7 ****** * ***** * 0.4 ******** ***** * 0.2 ******** ***** * 0.0 ---------------- Multilevel TCGAAGCAATGCAAGC consensus CT A CGG AT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9570 107 2.49e-08 ACGAAATGAA TCGCAGCAATCGAAGC TACTTCCTTC 45609 324 1.37e-07 CCAACAAGAA TCGCAGAAATGGGAAC ACACACTCGA 46289 140 5.06e-07 CGCGCACGCG TCGAAGAAACGCGATC GAAGGCAACC 32791 325 1.11e-06 GCGAACCTGT TCGATGGAATCCGACC GAGTATCCGG 42970 198 1.37e-06 AAGGAAAGGT TCCCAGCAATGGAAAT GAAAAAGCAG 34807 163 1.52e-06 GTATGGGACA TTGCTGCATTGCAAAC AAAACAAACA 46188 404 1.52e-06 CGGGCGGGGA TCGCAGCAGTTCGACC ATTCACACTA 32441 47 1.69e-06 CGGAGTGTTG TCGAAGGATTGGACAC AAAACCGTCT 43356 368 3.01e-06 GTATTCACAG ACGCAGCAAAGCAAGT CGGTAAAGCA 31140 447 5.63e-06 CTCCATTGGA TAGAAACACTGCAATC GCGTGCAGCA 44205 121 7.23e-06 TGTGGGGCGC TCGAAACACTGGACTC GCTATTTTAC 8024 317 9.20e-06 GCTGGCACCG TCGCAGTACACCAACC ACACACGAAG 44249 399 1.80e-05 CTCCGTGTGG TCGATGGGTTGGAAGT GCATCCATCA 44176 220 1.93e-05 TCCGACGAAG ACGAAGAAGCGCTAGC CAAAGAATTG 9157 312 2.36e-05 GTAGGTAGAC TTGAAGATGCGCAAGC GCCTTTGAAC 20034 53 3.07e-05 GATTTTGCTC TACATGCAATCCAACT TTGAAGATAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9570 2.5e-08 106_[+1]_378 45609 1.4e-07 323_[+1]_161 46289 5.1e-07 139_[+1]_345 32791 1.1e-06 324_[+1]_160 42970 1.4e-06 197_[+1]_287 34807 1.5e-06 162_[+1]_322 46188 1.5e-06 403_[+1]_81 32441 1.7e-06 46_[+1]_438 43356 3e-06 367_[+1]_117 31140 5.6e-06 446_[+1]_38 44205 7.2e-06 120_[+1]_364 8024 9.2e-06 316_[+1]_168 44249 1.8e-05 398_[+1]_86 44176 1.9e-05 219_[+1]_265 9157 2.4e-05 311_[+1]_173 20034 3.1e-05 52_[+1]_432 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=16 9570 ( 107) TCGCAGCAATCGAAGC 1 45609 ( 324) TCGCAGAAATGGGAAC 1 46289 ( 140) TCGAAGAAACGCGATC 1 32791 ( 325) TCGATGGAATCCGACC 1 42970 ( 198) TCCCAGCAATGGAAAT 1 34807 ( 163) TTGCTGCATTGCAAAC 1 46188 ( 404) TCGCAGCAGTTCGACC 1 32441 ( 47) TCGAAGGATTGGACAC 1 43356 ( 368) ACGCAGCAAAGCAAGT 1 31140 ( 447) TAGAAACACTGCAATC 1 44205 ( 121) TCGAAACACTGGACTC 1 8024 ( 317) TCGCAGTACACCAACC 1 44249 ( 399) TCGATGGGTTGGAAGT 1 44176 ( 220) ACGAAGAAGCGCTAGC 1 9157 ( 312) TTGAAGATGCGCAAGC 1 20034 ( 53) TACATGCAATCCAACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10670 bayes= 10.1169 E= 1.6e+001 -116 -1064 -1064 167 -116 169 -1064 -114 -1064 -89 204 -1064 101 91 -1064 -1064 142 -1064 -1064 -14 -116 -1064 204 -1064 -16 111 -18 -213 164 -1064 -177 -213 64 -31 -18 -55 -116 -31 -1064 132 -1064 11 169 -213 -1064 143 82 -1064 129 -1064 23 -213 164 -89 -1064 -1064 -16 11 55 -55 -1064 169 -1064 -14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 16 E= 1.6e+001 0.125000 0.000000 0.000000 0.875000 0.125000 0.750000 0.000000 0.125000 0.000000 0.125000 0.875000 0.000000 0.562500 0.437500 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.125000 0.000000 0.875000 0.000000 0.250000 0.500000 0.187500 0.062500 0.875000 0.000000 0.062500 0.062500 0.437500 0.187500 0.187500 0.187500 0.125000 0.187500 0.000000 0.687500 0.000000 0.250000 0.687500 0.062500 0.000000 0.625000 0.375000 0.000000 0.687500 0.000000 0.250000 0.062500 0.875000 0.125000 0.000000 0.000000 0.250000 0.250000 0.312500 0.187500 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TCG[AC][AT]G[CA]AAT[GC][CG][AG]A[GAC][CT] -------------------------------------------------------------------------------- Time 3.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 10 llr = 129 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 77:51312:9:9a4:3 pos.-specific C 3:::13:42:8::1:: probability G :1::8:::4121:5a7 matrix T :2a5:4944::::::: bits 2.2 * 2.0 * 1.8 * * * 1.6 * * * Relative 1.3 * * * **** ** Entropy 1.1 * * * * **** ** (18.7 bits) 0.9 * *** * **** ** 0.7 ***** * ******* 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel AATAGTTCGACAAGGG consensus CT T A TT G A A sequence C AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44176 241 7.12e-09 CTAGCCAAAG AATTGCTCGACAAAGG GATGGGTATG 48767 38 8.97e-09 TGCCTTTACG AATAGATTTACAAGGG CAATTAGAGA 35304 362 2.83e-08 CTCTTGTTCA AATAGATTTACAAAGG CCTTTCTCTC 45676 401 1.41e-07 GACAAATGTA AATTGCTCTGCAAGGG TTCAACGACG 9157 470 6.80e-07 AGTCTGAAGC AATAGCTATAGAAGGA GCACCCAGCA 45609 20 1.11e-06 GACATCTTTT CTTTGATTGACAACGG GATCAAAAAG 9570 308 1.70e-06 TTGACTGTGA AATAGTACCACAAAGA GCAAATCAGG 20034 411 2.20e-06 GCTTTTAAAA AGTTGTTACACAAAGA AAAAATCAGC 43356 140 2.35e-06 TGGTCGAAGA CATAATTTGACGAGGG TTCAAGCTTA 31140 286 2.98e-06 CAACCCTTTC CTTTCTTCGAGAAGGG TTCACTATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44176 7.1e-09 240_[+2]_244 48767 9e-09 37_[+2]_447 35304 2.8e-08 361_[+2]_123 45676 1.4e-07 400_[+2]_84 9157 6.8e-07 469_[+2]_15 45609 1.1e-06 19_[+2]_465 9570 1.7e-06 307_[+2]_177 20034 2.2e-06 410_[+2]_74 43356 2.3e-06 139_[+2]_345 31140 3e-06 285_[+2]_199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=10 44176 ( 241) AATTGCTCGACAAAGG 1 48767 ( 38) AATAGATTTACAAGGG 1 35304 ( 362) AATAGATTTACAAAGG 1 45676 ( 401) AATTGCTCTGCAAGGG 1 9157 ( 470) AATAGCTATAGAAGGA 1 45609 ( 20) CTTTGATTGACAACGG 1 9570 ( 308) AATAGTACCACAAAGA 1 20034 ( 411) AGTTGTTACACAAAGA 1 43356 ( 140) CATAATTTGACGAGGG 1 31140 ( 286) CTTTCTTCGAGAAGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10670 bayes= 10.3097 E= 1.7e+002 132 37 -997 -997 132 -997 -109 -46 -997 -997 -997 186 84 -997 -997 86 -148 -121 191 -997 10 37 -997 54 -148 -997 -997 171 -49 78 -997 54 -997 -22 91 54 168 -997 -109 -997 -997 178 -9 -997 168 -997 -109 -997 184 -997 -997 -997 51 -121 123 -997 -997 -997 223 -997 10 -997 172 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 1.7e+002 0.700000 0.300000 0.000000 0.000000 0.700000 0.000000 0.100000 0.200000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.100000 0.100000 0.800000 0.000000 0.300000 0.300000 0.000000 0.400000 0.100000 0.000000 0.000000 0.900000 0.200000 0.400000 0.000000 0.400000 0.000000 0.200000 0.400000 0.400000 0.900000 0.000000 0.100000 0.000000 0.000000 0.800000 0.200000 0.000000 0.900000 0.000000 0.100000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.100000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.000000 0.700000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC][AT]T[AT]G[TAC]T[CTA][GTC]A[CG]AA[GA]G[GA] -------------------------------------------------------------------------------- Time 7.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 12 llr = 127 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::69:3::695: pos.-specific C 7:::a:1:::18 probability G :141::9:2131 matrix T 39:::8:a3:12 bits 2.2 2.0 * 1.8 * ** 1.6 * ** ** * Relative 1.3 * ** ** * Entropy 1.1 ******** * * (15.3 bits) 0.9 ******** * * 0.7 ******** * * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTAACTGTAAAC consensus T G A T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43356 177 1.68e-07 TTTCCTAGCC CTAACTGTAAAC TGGATCTATC 17276 309 1.68e-07 ATGCTCGCAG CTAACTGTAAAC CTGTCTGTGA 34807 37 9.11e-07 AAGAAATAAA CTGACTGTGAAC ACGTTCAAGG 45676 127 2.78e-06 CTCTCGATAG CTAACTGTAAGT TCCTTCGTCC 48767 90 3.35e-06 TTGAACTTGA CTGACAGTGAAC AACTTGACTG 35590 489 5.23e-06 TTTGCCTGAG TTGACTGTAACC 8024 120 8.33e-06 ATATTGCTCG CTAGCTGTTAAC AAAAACCATT 9157 162 9.12e-06 AATTAACTGC TTAACTGTAAAG TGAAAGATCG 42970 237 1.74e-05 GTGGGATTAG CTGACAGTTAGT CACTAGCTAG 20034 141 1.98e-05 AGATCTTAGC TTGACTGTTGGC TCCGTCAGTA 31140 258 1.98e-05 GAGAGCCTCA CGAACTGTAATC GCCTCTCAAC 44205 169 3.12e-05 ACTGCAGCTC TTAACACTAAGC AGCGCGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43356 1.7e-07 176_[+3]_312 17276 1.7e-07 308_[+3]_180 34807 9.1e-07 36_[+3]_452 45676 2.8e-06 126_[+3]_362 48767 3.4e-06 89_[+3]_399 35590 5.2e-06 488_[+3] 8024 8.3e-06 119_[+3]_369 9157 9.1e-06 161_[+3]_327 42970 1.7e-05 236_[+3]_252 20034 2e-05 140_[+3]_348 31140 2e-05 257_[+3]_231 44205 3.1e-05 168_[+3]_320 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=12 43356 ( 177) CTAACTGTAAAC 1 17276 ( 309) CTAACTGTAAAC 1 34807 ( 37) CTGACTGTGAAC 1 45676 ( 127) CTAACTGTAAGT 1 48767 ( 90) CTGACAGTGAAC 1 35590 ( 489) TTGACTGTAACC 1 8024 ( 120) CTAGCTGTTAAC 1 9157 ( 162) TTAACTGTAAAG 1 42970 ( 237) CTGACAGTTAGT 1 20034 ( 141) TTGACTGTTGGC 1 31140 ( 258) CGAACTGTAATC 1 44205 ( 169) TTAACACTAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 10758 bayes= 10.2544 E= 1.1e+003 -1023 152 -1023 28 -1023 -1023 -135 174 106 -1023 97 -1023 171 -1023 -135 -1023 -1023 211 -1023 -1023 -16 -1023 -1023 145 -1023 -148 211 -1023 -1023 -1023 -1023 186 106 -1023 -35 -14 171 -1023 -135 -1023 84 -148 65 -172 -1023 169 -135 -72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 1.1e+003 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.083333 0.916667 0.583333 0.000000 0.416667 0.000000 0.916667 0.000000 0.083333 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.083333 0.916667 0.000000 0.000000 0.000000 0.000000 1.000000 0.583333 0.000000 0.166667 0.250000 0.916667 0.000000 0.083333 0.000000 0.500000 0.083333 0.333333 0.083333 0.000000 0.750000 0.083333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]T[AG]AC[TA]GT[AT]A[AG]C -------------------------------------------------------------------------------- Time 11.92 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17276 2.71e-03 308_[+3(1.68e-07)]_180 9157 3.00e-06 161_[+3(9.12e-06)]_138_\ [+1(2.36e-05)]_142_[+2(6.80e-07)]_15 9570 2.69e-07 106_[+1(2.49e-08)]_185_\ [+2(1.70e-06)]_177 32441 1.44e-02 46_[+1(1.69e-06)]_438 48767 9.79e-07 37_[+2(8.97e-09)]_36_[+3(3.35e-06)]_\ 399 32791 1.10e-02 324_[+1(1.11e-06)]_160 30502 8.00e-01 500 31140 6.21e-06 257_[+3(1.98e-05)]_16_\ [+2(2.98e-06)]_145_[+1(5.63e-06)]_38 44176 1.95e-06 219_[+1(1.93e-05)]_5_[+2(7.12e-09)]_\ 244 8024 3.86e-04 119_[+3(8.33e-06)]_185_\ [+1(9.20e-06)]_4_[+1(5.27e-05)]_148 35304 3.56e-04 361_[+2(2.83e-08)]_123 20034 2.12e-05 52_[+1(3.07e-05)]_72_[+3(1.98e-05)]_\ 258_[+2(2.20e-06)]_74 45676 9.43e-06 39_[+3(3.12e-05)]_75_[+3(2.78e-06)]_\ 262_[+2(1.41e-07)]_84 35590 8.41e-03 488_[+3(5.23e-06)] 46188 6.71e-03 403_[+1(1.52e-06)]_81 46289 1.91e-03 139_[+1(5.06e-07)]_345 42970 3.71e-04 197_[+1(1.37e-06)]_23_\ [+3(1.74e-05)]_252 43356 3.84e-08 139_[+2(2.35e-06)]_21_\ [+3(1.68e-07)]_179_[+1(3.01e-06)]_117 34807 2.06e-05 36_[+3(9.11e-07)]_114_\ [+1(1.52e-06)]_322 44205 1.85e-03 120_[+1(7.23e-06)]_32_\ [+3(3.12e-05)]_39_[+1(9.41e-05)]_265 45609 4.21e-06 19_[+2(1.11e-06)]_288_\ [+1(1.37e-07)]_161 44249 9.08e-02 158_[+1(4.97e-05)]_224_\ [+1(1.80e-05)]_86 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************