******************************************************************************** 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/292/292.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10979 1.0000 500 11219 1.0000 500 18104 1.0000 500 20932 1.0000 500 20992 1.0000 500 2116 1.0000 500 21922 1.0000 500 22189 1.0000 500 22627 1.0000 500 23269 1.0000 500 2390 1.0000 500 23951 1.0000 500 24177 1.0000 500 24483 1.0000 500 25722 1.0000 500 260941 1.0000 500 262457 1.0000 500 262512 1.0000 500 262580 1.0000 500 262975 1.0000 500 263072 1.0000 500 263583 1.0000 500 264623 1.0000 500 268179 1.0000 500 269798 1.0000 500 270116 1.0000 500 31259 1.0000 500 31627 1.0000 500 31764 1.0000 500 32741 1.0000 500 3494 1.0000 500 35108 1.0000 500 36506 1.0000 500 38149 1.0000 500 42533 1.0000 500 4940 1.0000 500 5318 1.0000 500 5332 1.0000 500 5387 1.0000 500 5694 1.0000 500 6190 1.0000 500 8366 1.0000 500 8397 1.0000 500 8438 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/292/292.seqs.fa -oc motifs/292 -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= 44 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= 22000 N= 44 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.239 G 0.239 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.239 G 0.240 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 39 llr = 433 E-value = 1.4e-030 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 34146217128733542372 pos.-specific C 52863882982375336518 probability G :31::::1::::12:1121: matrix T 221:1:1::::1::221:21 bits 2.1 1.9 1.7 * 1.4 * Relative 1.2 * *** Entropy 1.0 ** ** *** * * (16.0 bits) 0.8 ** ** ***** * 0.6 * *********** * **** 0.4 * ************* **** 0.2 * ****************** 0.0 -------------------- Multilevel CACCACCACCAACCAACCAC consensus AG ACA CCAACCAA sequence TC T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 20932 470 1.58e-11 TCACCTCCCT CCCCACCACCAACCCACCAC TCTCCTGCTC 8438 449 2.42e-09 AACATCCACT CCCCACCACCACCCACCCTC TCCATCTTGC 262975 449 6.97e-09 AAACACCGAG CGCCACCACAAAACACCCAC TCCACCTCGA 36506 476 4.37e-08 TCACCTTCTC TCCAACCACCAACATCCGAC GACGG 22627 416 5.03e-08 TCCCGTCGAC CACCACCACAACCGCACAAC TTGGAGTGGT 2116 449 6.61e-08 ACCAACGACG TCCACACACCAACAAACAAC AAATACAACT 31259 371 7.57e-08 TGTCCCACGT CCCCCCCCCCAAAAAAACAC ACCAGCACCA 262580 367 8.65e-08 CTGGTCCGCT CTCCCCCACCAACCCAACGC ACCACAACCA 42533 277 9.86e-08 GCCGAAGCCA CTCCACCACCACACCACCGC AATGGACGAA 35108 209 1.12e-07 ACACAGCCGA CGCCACCACCAAACTGAAAC GCACCTGCCT 5332 307 1.45e-07 TTCCGCTCAC CACCAACGCCAACACACCAA CCGTCCAAAA 5318 111 2.68e-07 CCAGATCACC CACCACCACCAACGATGAAA TTCCTACCAC 4940 425 4.28e-07 CGTCCTCTTC CACCGCCACCAACCTTCCTC AATCTTCCTC 8366 218 6.70e-07 AGGAGCACCG AGCACCCACCCACGAGCGAC GCACCCTCCC 32741 411 6.70e-07 GTTGGGCTCG CCCAACGACCAACCACAGAC CTTCCACAAA 18104 479 6.70e-07 TGCTCCGCCT CACCACCACCACAGACTGAC CA 21922 459 8.33e-07 GCCAACCCAG AAGCCCAACCAACCAACAAC TCTGCTCTCC 269798 454 9.27e-07 AGTTTCTTCC ATCCACCACCCACACCCACC CCTTCTAAAC 31627 467 1.03e-06 ACATTCCTCC TCCAACCCCCACAACAACAC AAACTGAAAC 24483 211 1.03e-06 CCTTTGTGTA CACCACCACCAACCACTCTT AAACCCCTCT 20992 458 2.55e-06 ACTCACCCGT CACCACCTCCACCCATCACC ACTCCACCAA 5387 289 3.09e-06 GCACTGCTCC ATCACCCACCACCAATCCTA CCTCCTCCTC 263072 341 3.09e-06 CGACGATCGC CCCCCCCGCCCTCCACCATC CGCTCTCCGA 24177 395 3.73e-06 CCCGTCCGTA ACAAACCACCAAAAAACGTC TCCCGTCGTC 268179 372 6.42e-06 ATGCCACCAT CGTCACCACAAAGACACGAC GTTTCCACCA 31764 472 1.16e-05 CGACTCTCTC CGACACAACCCTCCATCCAC AATAATTGA 23269 355 1.26e-05 TATCCAATGG AACAAACCCAAACGACGAAC GAGCAGCCTC 38149 144 1.37e-05 CCAATCGCCA AGCCAACGCCCACCTGACTC ACAACACACC 260941 231 1.37e-05 GGATGCAGCA TGCAACAAACAACAAACGAA AGCATTGTTA 25722 232 1.88e-05 CCCCTGTCTT CTCCTCCACCATACTACCAT CACTTATATC 22189 441 3.19e-05 CCATTGGTTT TGCAACTCCCAACTATCCAA TTGAATCCGT 5694 434 3.43e-05 GCTGCTTTGC TACACACACCCCGACTACAC AACAGTGCAC 262512 196 3.69e-05 GATCTACTCA TATCAACAAAAACCCAAAAC TACACACTTC 8397 478 5.24e-05 CAACGCCGCA AAGCAACAAACCCCACCAAC ATA 3494 476 5.24e-05 ACTCGTCACC TGCACCTGCCACACATGCAC CGCGG 10979 246 5.24e-05 TCCCCTGTTT AATCTCCCCCAACGTCACAA CCAGAGACGG 11219 454 6.00e-05 ATCCACGGCG TTGACCCCCCAACATGCAAA TGCATCTGCG 262457 480 8.33e-05 TTGACTGTGT CGCCTACGCTCACCCACCGC A 264623 220 8.88e-05 TGCATTCCCA AACAAATCCCCAAGAACGGC TTGTTCATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20932 1.6e-11 469_[+1]_11 8438 2.4e-09 448_[+1]_32 262975 7e-09 448_[+1]_32 36506 4.4e-08 475_[+1]_5 22627 5e-08 415_[+1]_65 2116 6.6e-08 448_[+1]_32 31259 7.6e-08 370_[+1]_110 262580 8.6e-08 366_[+1]_114 42533 9.9e-08 276_[+1]_204 35108 1.1e-07 208_[+1]_272 5332 1.5e-07 306_[+1]_174 5318 2.7e-07 110_[+1]_370 4940 4.3e-07 424_[+1]_56 8366 6.7e-07 217_[+1]_263 32741 6.7e-07 410_[+1]_70 18104 6.7e-07 478_[+1]_2 21922 8.3e-07 458_[+1]_22 269798 9.3e-07 453_[+1]_27 31627 1e-06 466_[+1]_14 24483 1e-06 210_[+1]_270 20992 2.6e-06 457_[+1]_23 5387 3.1e-06 288_[+1]_192 263072 3.1e-06 340_[+1]_140 24177 3.7e-06 394_[+1]_86 268179 6.4e-06 371_[+1]_109 31764 1.2e-05 471_[+1]_9 23269 1.3e-05 354_[+1]_126 38149 1.4e-05 143_[+1]_337 260941 1.4e-05 230_[+1]_250 25722 1.9e-05 231_[+1]_249 22189 3.2e-05 440_[+1]_40 5694 3.4e-05 433_[+1]_47 262512 3.7e-05 195_[+1]_285 8397 5.2e-05 477_[+1]_3 3494 5.2e-05 475_[+1]_5 10979 5.2e-05 245_[+1]_235 11219 6e-05 453_[+1]_27 262457 8.3e-05 479_[+1]_1 264623 8.9e-05 219_[+1]_261 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=39 20932 ( 470) CCCCACCACCAACCCACCAC 1 8438 ( 449) CCCCACCACCACCCACCCTC 1 262975 ( 449) CGCCACCACAAAACACCCAC 1 36506 ( 476) TCCAACCACCAACATCCGAC 1 22627 ( 416) CACCACCACAACCGCACAAC 1 2116 ( 449) TCCACACACCAACAAACAAC 1 31259 ( 371) CCCCCCCCCCAAAAAAACAC 1 262580 ( 367) CTCCCCCACCAACCCAACGC 1 42533 ( 277) CTCCACCACCACACCACCGC 1 35108 ( 209) CGCCACCACCAAACTGAAAC 1 5332 ( 307) CACCAACGCCAACACACCAA 1 5318 ( 111) CACCACCACCAACGATGAAA 1 4940 ( 425) CACCGCCACCAACCTTCCTC 1 8366 ( 218) AGCACCCACCCACGAGCGAC 1 32741 ( 411) CCCAACGACCAACCACAGAC 1 18104 ( 479) CACCACCACCACAGACTGAC 1 21922 ( 459) AAGCCCAACCAACCAACAAC 1 269798 ( 454) ATCCACCACCCACACCCACC 1 31627 ( 467) TCCAACCCCCACAACAACAC 1 24483 ( 211) CACCACCACCAACCACTCTT 1 20992 ( 458) CACCACCTCCACCCATCACC 1 5387 ( 289) ATCACCCACCACCAATCCTA 1 263072 ( 341) CCCCCCCGCCCTCCACCATC 1 24177 ( 395) ACAAACCACCAAAAAACGTC 1 268179 ( 372) CGTCACCACAAAGACACGAC 1 31764 ( 472) CGACACAACCCTCCATCCAC 1 23269 ( 355) AACAAACCCAAACGACGAAC 1 38149 ( 144) AGCCAACGCCCACCTGACTC 1 260941 ( 231) TGCAACAAACAACAAACGAA 1 25722 ( 232) CTCCTCCACCATACTACCAT 1 22189 ( 441) TGCAACTCCCAACTATCCAA 1 5694 ( 434) TACACACACCCCGACTACAC 1 262512 ( 196) TATCAACAAAAACCCAAAAC 1 8397 ( 478) AAGCAACAAACCCCACCAAC 1 3494 ( 476) TGCACCTGCCACACATGCAC 1 10979 ( 246) AATCTCCCCCAACGTCACAA 1 11219 ( 454) TTGACCCCCCAACATGCAAA 1 262457 ( 480) CGCCTACGCTCACCCACCGC 1 264623 ( 220) AACAAATCCCCAAGAACGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 21164 bayes= 9.30527 E= 1.4e-030 -3 110 -1193 -18 46 -5 10 -76 -235 174 -164 -176 46 142 -1193 -1193 130 10 -322 -176 -18 169 -1193 -1193 -176 178 -322 -176 135 -41 -90 -334 -176 195 -1193 -1193 -76 178 -1193 -334 156 -5 -1193 -1193 135 10 -1193 -176 -3 154 -222 -1193 24 103 -42 -334 104 24 -1193 -54 65 24 -122 -35 -18 142 -164 -234 24 103 -22 -1193 135 -222 -122 -54 -54 169 -1193 -234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 39 E= 1.4e-030 0.256410 0.512821 0.000000 0.230769 0.358974 0.230769 0.256410 0.153846 0.051282 0.794872 0.076923 0.076923 0.358974 0.641026 0.000000 0.000000 0.641026 0.256410 0.025641 0.076923 0.230769 0.769231 0.000000 0.000000 0.076923 0.820513 0.025641 0.076923 0.666667 0.179487 0.128205 0.025641 0.076923 0.923077 0.000000 0.000000 0.153846 0.820513 0.000000 0.025641 0.769231 0.230769 0.000000 0.000000 0.666667 0.256410 0.000000 0.076923 0.256410 0.692308 0.051282 0.000000 0.307692 0.487179 0.179487 0.025641 0.538462 0.282051 0.000000 0.179487 0.410256 0.282051 0.102564 0.205128 0.230769 0.641026 0.076923 0.051282 0.307692 0.487179 0.205128 0.000000 0.666667 0.051282 0.102564 0.179487 0.179487 0.769231 0.000000 0.051282 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CAT][AGC]C[CA][AC][CA]CACC[AC][AC][CA][CA][AC][ACT][CA][CAG]AC -------------------------------------------------------------------------------- Time 16.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 29 llr = 338 E-value = 3.7e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2::4:15:2:221::12::: pos.-specific C :1::2:1:::52:2121:4:: probability G 917828815722812861463 matrix T 163221:45:33:77:27247 bits 2.1 1.9 1.7 1.4 * * Relative 1.2 * ** * * Entropy 1.0 * ** ** * * * (16.8 bits) 0.8 * ** ** ** * * ** 0.6 * ** ****** **** * ** 0.4 **** ****** ********* 0.2 **** ****** ********* 0.0 --------------------- Multilevel GTGGAGGAGGCTGTTGGTCGT consensus ATTC TTATC G GTG sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 18104 52 1.24e-10 GAGGGAAGAA GTGGAGGTTGCTGTTGCTCGT TGTTGTGTAA 23269 69 4.43e-10 CGTAGTCTTC GTGGAGGATGCCGTGGGTTGT GTGGGCGGTT 24177 244 5.20e-09 GCAGCGCAGC GTGGCGGTGGCTGTGGCTCTT GACCCCTCCT 260941 164 5.00e-08 AAGCGGGAGG GTTGGGGATGTCATTGGTTGT GGTTGTTGTG 38149 338 5.68e-08 GATGGCAGCG GCGGTGGTGGCAGTTCGTCGT CGATTCCATC 4940 152 1.68e-07 CGGTGGTGGT GTTTCGGAGGTGATTGGTGTT GATAACTTAA 2116 66 3.63e-07 TGTTGATGAT GTTGCTGATGCTGCTGTTGTT GTTGATACCG 268179 88 5.51e-07 AGAAGTTGGT GTGTGGGTGGCAGGCGGTGGT CTGTTGTTCC 262457 380 5.51e-07 GTTGTCAGGC GTTGAGCTGAGGGTTGGTTGT CACGTGAAAT 25722 324 6.10e-07 GTTGTGTTTT GATTTGGATGCTGTTGATGTG TGTCACATGT 21922 24 6.10e-07 GTGGTGCACT GTTGCGGTGGCGCTTGGACGG GTTCGTTGTC 3494 118 8.22e-07 GAATTTGTCG TTGGGGGTGGTCGTTGTGGGG ATGGGTGGAT 6190 394 1.75e-06 TTTGTTTGGG GAGGAGCAGGGAGCTGGAGGT CGGGCGGGCG 23951 276 1.75e-06 GTCTTTTGTG GAGGAGGATGCGGTGGCACCT ACGCCGAGTC 20932 273 1.75e-06 CGTGACATCC TTGGAGATGGTGGCTGCTGGT GTAGACGTAG 2390 13 1.92e-06 ACATGGATAT GTTGTCGTTGCTGCTGTTGTT TACGTCAGAT 5318 180 2.10e-06 CAATGCCCCT GTGCAGGAGATCGTTCGACGT CAATGTTTTT 22627 196 2.10e-06 GAGGTATATT GTGGTGGATGTCATGGTGTTT GTTCGTTTGA 11219 216 2.10e-06 GTGTTCCATT TCGGAGGGTGCTGTTCGTCTT GTGCTGTTGA 32741 233 2.29e-06 CTGATTCAAA GTGGTGGTGACGATCGTTTGG GAGATGCAAT 10979 83 2.98e-06 CGCCAGTGGG GAGGCGGATCCTGCGCGTGGT GGTGGAGGGC 269798 326 3.53e-06 TCTGCTATCT GTTGCTGTTGGTATCGGTCGG GAGCAGGAAG 264623 11 7.91e-06 CTTCCTCCCC GTGGCTGTTGTCGTGGATGTA TCTCATGCAA 31764 168 9.93e-06 GGCGGGGAGG GATGATAATGGCGATGGTCGT GCCATTGTTG 8366 68 1.33e-05 GCGGAGGGTA GGGGAGGGGTCGGTTGGGCTG TTAAGCTGGA 35108 98 1.65e-05 GTGCATCAGA GAGTGGGAGATAGTTGGCTTG AGGCTCTTAC 5694 14 1.89e-05 GTTCCGAGGT GGGTGGGTGAGAGGTGGACGT CGACAGATTC 36506 372 2.48e-05 TGTAAGCTTG GAGGAGGAGATTGAAGAGCGT GGCGGCCTTT 31259 257 4.41e-05 CAATAGCTTA TTGTTGAATACTGTTCATGTG CAAACTAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 18104 1.2e-10 51_[+2]_428 23269 4.4e-10 68_[+2]_411 24177 5.2e-09 243_[+2]_236 260941 5e-08 163_[+2]_316 38149 5.7e-08 337_[+2]_142 4940 1.7e-07 151_[+2]_328 2116 3.6e-07 65_[+2]_414 268179 5.5e-07 87_[+2]_392 262457 5.5e-07 379_[+2]_100 25722 6.1e-07 323_[+2]_156 21922 6.1e-07 23_[+2]_456 3494 8.2e-07 117_[+2]_362 6190 1.8e-06 393_[+2]_86 23951 1.8e-06 275_[+2]_204 20932 1.8e-06 272_[+2]_207 2390 1.9e-06 12_[+2]_467 5318 2.1e-06 179_[+2]_300 22627 2.1e-06 195_[+2]_284 11219 2.1e-06 215_[+2]_264 32741 2.3e-06 232_[+2]_247 10979 3e-06 82_[+2]_397 269798 3.5e-06 325_[+2]_154 264623 7.9e-06 10_[+2]_469 31764 9.9e-06 167_[+2]_312 8366 1.3e-05 67_[+2]_412 35108 1.6e-05 97_[+2]_382 5694 1.9e-05 13_[+2]_466 36506 2.5e-05 371_[+2]_108 31259 4.4e-05 256_[+2]_223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=29 18104 ( 52) GTGGAGGTTGCTGTTGCTCGT 1 23269 ( 69) GTGGAGGATGCCGTGGGTTGT 1 24177 ( 244) GTGGCGGTGGCTGTGGCTCTT 1 260941 ( 164) GTTGGGGATGTCATTGGTTGT 1 38149 ( 338) GCGGTGGTGGCAGTTCGTCGT 1 4940 ( 152) GTTTCGGAGGTGATTGGTGTT 1 2116 ( 66) GTTGCTGATGCTGCTGTTGTT 1 268179 ( 88) GTGTGGGTGGCAGGCGGTGGT 1 262457 ( 380) GTTGAGCTGAGGGTTGGTTGT 1 25722 ( 324) GATTTGGATGCTGTTGATGTG 1 21922 ( 24) GTTGCGGTGGCGCTTGGACGG 1 3494 ( 118) TTGGGGGTGGTCGTTGTGGGG 1 6190 ( 394) GAGGAGCAGGGAGCTGGAGGT 1 23951 ( 276) GAGGAGGATGCGGTGGCACCT 1 20932 ( 273) TTGGAGATGGTGGCTGCTGGT 1 2390 ( 13) GTTGTCGTTGCTGCTGTTGTT 1 5318 ( 180) GTGCAGGAGATCGTTCGACGT 1 22627 ( 196) GTGGTGGATGTCATGGTGTTT 1 11219 ( 216) TCGGAGGGTGCTGTTCGTCTT 1 32741 ( 233) GTGGTGGTGACGATCGTTTGG 1 10979 ( 83) GAGGCGGATCCTGCGCGTGGT 1 269798 ( 326) GTTGCTGTTGGTATCGGTCGG 1 264623 ( 11) GTGGCTGTTGTCGTGGATGTA 1 31764 ( 168) GATGATAATGGCGATGGTCGT 1 8366 ( 68) GGGGAGGGGTCGGTTGGGCTG 1 35108 ( 98) GAGTGGGAGATAGTTGGCTTG 1 5694 ( 14) GGGTGGGTGAGAGGTGGACGT 1 36506 ( 372) GAGGAGGAGATTGAAGAGCGT 1 31259 ( 257) TTGTTGAATACTGTTCATGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 10.1478 E= 3.7e-013 -1150 -1150 185 -92 -11 -179 -179 125 -1150 -1150 153 25 -1150 -279 166 -33 54 2 -47 -33 -1150 -279 179 -92 -133 -179 179 -1150 89 -1150 -179 78 -1150 -1150 111 89 -11 -279 153 -292 -1150 112 -47 25 -60 2 1 40 -60 -279 173 -1150 -192 -47 -179 140 -292 -121 -21 133 -1150 -47 179 -1150 -92 -79 120 -60 -60 -279 -80 133 -1150 79 66 -33 -1150 -279 129 54 -292 -1150 20 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 29 E= 3.7e-013 0.000000 0.000000 0.862069 0.137931 0.241379 0.068966 0.068966 0.620690 0.000000 0.000000 0.689655 0.310345 0.000000 0.034483 0.758621 0.206897 0.379310 0.241379 0.172414 0.206897 0.000000 0.034483 0.827586 0.137931 0.103448 0.068966 0.827586 0.000000 0.482759 0.000000 0.068966 0.448276 0.000000 0.000000 0.517241 0.482759 0.241379 0.034483 0.689655 0.034483 0.000000 0.517241 0.172414 0.310345 0.172414 0.241379 0.241379 0.344828 0.172414 0.034483 0.793103 0.000000 0.068966 0.172414 0.068966 0.689655 0.034483 0.103448 0.206897 0.655172 0.000000 0.172414 0.827586 0.000000 0.137931 0.137931 0.551724 0.172414 0.172414 0.034483 0.137931 0.655172 0.000000 0.413793 0.379310 0.206897 0.000000 0.034483 0.586207 0.379310 0.034483 0.000000 0.275862 0.689655 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TA][GT][GT][ACT]GG[AT][GT][GA][CT][TCG]GT[TG]GGT[CGT][GT][TG] -------------------------------------------------------------------------------- Time 31.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 19 llr = 252 E-value = 6.7e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 6:229129:37:525343448 pos.-specific C 168::91:8:1a145123411 probability G 3418::81162:34:641241 matrix T 11::1:::21::1:1::3:11 bits 2.1 * 1.9 * * 1.7 * * 1.4 ** * * Relative 1.2 *** * * Entropy 1.0 ******* * (19.1 bits) 0.8 *********** ** * 0.6 *********** ** * 0.4 ***************** * * 0.2 ***************** *** 0.0 --------------------- Multilevel ACCGACGACGACAGAGAACGA consensus GG A A GCCAGCAA sequence A CTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 22627 95 1.93e-09 TCGGCGGACG ACCGACGACGACCGAGGACAA TTCCGTGAAT 32741 125 2.25e-09 GAACTTGGGT ACCGACGACGGCGGAGGCGGA GGGAAGGCGA 38149 117 1.32e-08 GACGGGGTGA ACCGACGACGACGACCGCCAA TCGCCAAGCC 5694 475 1.91e-08 ACTCGCTTCC ACCGACGACGACTCTGGACGA TCAAT 42533 242 5.95e-08 GAAACCATCA GCAAACGACAACACCGACAGA CGAAGCCGAA 262457 155 8.17e-08 ATCGGCGAGT AGCGTCGATGACAGAGAAGAA CACGACATCA 5387 264 1.11e-07 AAACAAAACG GCCGACGACGACACAGCACTG CTCCATCACC 31259 169 1.49e-07 CAAAGGAGTT TGCGACGAGGACAGAGATGGA AAGCATTCTT 262512 134 1.81e-07 ATCAACGCGA AGCGACAACTACAGCACTAAA CGTCTTGAAC 24177 43 2.40e-07 GCAAAGGCAG AGAGACCACGACGCCGATGGA ACGAGGTGGT 25722 412 4.90e-07 ACGATTGTGC AGCAAAGACGACACCGCAACA GATTCACATG 260941 379 6.87e-07 CATAGTTTTA GCAGACAACAACGGCACTCAA GAAGAACCTC 262975 474 8.09e-07 CCCACTCCAC CTCGACGACAACAACAACAGA GGCACC 262580 456 1.03e-06 CTGATAACAG TCCAACGACAGCACAAGGCAA ACAATTCTAT 23269 171 1.30e-06 TGTTGCTGGA GGCGTCGACGCCGCAGGTCGT CATCGTCTGG 4940 266 1.40e-06 TAGTGGGTGG ACGGACGGTGACGGCAAAAAA AACAGGGGAC 263072 169 1.75e-06 CTTTTTGCCC AGCAACGATTCCAGAGAGCGA AGTGCAACAC 21922 145 2.88e-06 CTCTCCAACT GCCGACAACGACTACAACACT GCAACACTCT 270116 195 4.31e-06 AAGAGGATCA ACCGACGGCAGCAAAGGCATC TCCGTTCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22627 1.9e-09 94_[+3]_385 32741 2.2e-09 124_[+3]_355 38149 1.3e-08 116_[+3]_363 5694 1.9e-08 474_[+3]_5 42533 5.9e-08 241_[+3]_238 262457 8.2e-08 154_[+3]_325 5387 1.1e-07 263_[+3]_216 31259 1.5e-07 168_[+3]_311 262512 1.8e-07 133_[+3]_346 24177 2.4e-07 42_[+3]_437 25722 4.9e-07 411_[+3]_68 260941 6.9e-07 378_[+3]_101 262975 8.1e-07 473_[+3]_6 262580 1e-06 455_[+3]_24 23269 1.3e-06 170_[+3]_309 4940 1.4e-06 265_[+3]_214 263072 1.7e-06 168_[+3]_311 21922 2.9e-06 144_[+3]_335 270116 4.3e-06 194_[+3]_285 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=19 22627 ( 95) ACCGACGACGACCGAGGACAA 1 32741 ( 125) ACCGACGACGGCGGAGGCGGA 1 38149 ( 117) ACCGACGACGACGACCGCCAA 1 5694 ( 475) ACCGACGACGACTCTGGACGA 1 42533 ( 242) GCAAACGACAACACCGACAGA 1 262457 ( 155) AGCGTCGATGACAGAGAAGAA 1 5387 ( 264) GCCGACGACGACACAGCACTG 1 31259 ( 169) TGCGACGAGGACAGAGATGGA 1 262512 ( 134) AGCGACAACTACAGCACTAAA 1 24177 ( 43) AGAGACCACGACGCCGATGGA 1 25722 ( 412) AGCAAAGACGACACCGCAACA 1 260941 ( 379) GCAGACAACAACGGCACTCAA 1 262975 ( 474) CTCGACGACAACAACAACAGA 1 262580 ( 456) TCCAACGACAGCACAAGGCAA 1 23269 ( 171) GGCGTCGACGCCGCAGGTCGT 1 4940 ( 266) ACGGACGGTGACGGCAAAAAA 1 263072 ( 169) AGCAACGATTCCAGAGAGCGA 1 21922 ( 145) GCCGACAACGACTACAACACT 1 270116 ( 195) ACCGACGGCAGCAAAGGCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21120 bayes= 11.5585 E= 6.7e-006 115 -218 14 -131 -1089 128 62 -231 -72 172 -218 -1089 -31 -1089 172 -1089 178 -1089 -1089 -131 -231 199 -1089 -1089 -72 -218 172 -1089 178 -1089 -119 -1089 -1089 172 -218 -72 1 -1089 140 -131 150 -118 -60 -1089 -1089 207 -1089 -1089 101 -218 40 -131 -31 63 81 -1089 86 99 -1089 -231 28 -218 140 -1089 69 -18 62 -1089 28 40 -119 1 50 82 -19 -1089 50 -118 81 -131 160 -218 -218 -131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 19 E= 6.7e-006 0.578947 0.052632 0.263158 0.105263 0.000000 0.578947 0.368421 0.052632 0.157895 0.789474 0.052632 0.000000 0.210526 0.000000 0.789474 0.000000 0.894737 0.000000 0.000000 0.105263 0.052632 0.947368 0.000000 0.000000 0.157895 0.052632 0.789474 0.000000 0.894737 0.000000 0.105263 0.000000 0.000000 0.789474 0.052632 0.157895 0.263158 0.000000 0.631579 0.105263 0.736842 0.105263 0.157895 0.000000 0.000000 1.000000 0.000000 0.000000 0.526316 0.052632 0.315789 0.105263 0.210526 0.368421 0.421053 0.000000 0.473684 0.473684 0.000000 0.052632 0.315789 0.052632 0.631579 0.000000 0.421053 0.210526 0.368421 0.000000 0.315789 0.315789 0.105263 0.263158 0.368421 0.421053 0.210526 0.000000 0.368421 0.105263 0.421053 0.105263 0.789474 0.052632 0.052632 0.105263 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][CG]C[GA]ACGAC[GA]AC[AG][GCA][AC][GA][AGC][ACT][CAG][GA]A -------------------------------------------------------------------------------- Time 48.62 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10979 1.88e-03 82_[+2(2.98e-06)]_142_\ [+1(5.24e-05)]_65_[+2(2.65e-05)]_149 11219 1.07e-04 215_[+2(2.10e-06)]_33_\ [+2(8.82e-05)]_40_[+3(7.12e-05)]_102_[+1(6.00e-05)]_27 18104 2.27e-09 51_[+2(1.24e-10)]_99_[+2(4.14e-05)]_\ 286_[+1(6.70e-07)]_2 20932 6.44e-11 172_[+3(4.52e-05)]_79_\ [+2(1.75e-06)]_176_[+1(1.58e-11)]_11 20992 2.02e-02 457_[+1(2.55e-06)]_1_[+1(4.89e-05)]_\ 2 2116 7.90e-08 65_[+2(3.63e-07)]_9_[+2(2.29e-06)]_\ 18_[+2(1.60e-06)]_272_[+1(1.26e-05)]_1_[+1(6.61e-08)]_32 21922 4.50e-08 23_[+2(6.10e-07)]_100_\ [+3(2.88e-06)]_293_[+1(8.33e-07)]_22 22189 2.18e-02 374_[+3(9.66e-05)]_45_\ [+1(3.19e-05)]_40 22627 1.18e-11 94_[+3(1.93e-09)]_80_[+2(2.10e-06)]_\ 155_[+1(8.88e-05)]_24_[+1(5.03e-08)]_25_[+1(1.72e-06)]_20 23269 3.34e-10 68_[+2(4.43e-10)]_52_[+2(1.15e-05)]_\ 8_[+3(1.30e-06)]_163_[+1(1.26e-05)]_126 2390 2.32e-02 12_[+2(1.92e-06)]_467 23951 2.18e-02 245_[+2(9.83e-05)]_9_[+2(1.75e-06)]_\ 32_[+2(9.93e-06)]_151 24177 2.22e-10 42_[+3(2.40e-07)]_180_\ [+2(5.20e-09)]_130_[+1(3.73e-06)]_86 24483 4.98e-03 210_[+1(1.03e-06)]_270 25722 1.53e-07 231_[+1(1.88e-05)]_72_\ [+2(6.10e-07)]_67_[+3(4.90e-07)]_68 260941 1.59e-08 163_[+2(5.00e-08)]_46_\ [+1(1.37e-05)]_128_[+3(6.87e-07)]_101 262457 1.04e-07 154_[+3(8.17e-08)]_204_\ [+2(5.51e-07)]_79_[+1(8.33e-05)]_1 262512 4.98e-05 133_[+3(1.81e-07)]_41_\ [+1(3.69e-05)]_285 262580 3.15e-06 366_[+1(8.65e-08)]_69_\ [+3(1.03e-06)]_24 262975 1.63e-07 406_[+3(3.46e-05)]_21_\ [+1(6.97e-09)]_5_[+3(8.09e-07)]_6 263072 1.22e-04 168_[+3(1.75e-06)]_151_\ [+1(3.09e-06)]_140 263583 7.00e-01 500 264623 4.17e-03 10_[+2(7.91e-06)]_188_\ [+1(8.88e-05)]_261 268179 1.81e-05 87_[+2(5.51e-07)]_263_\ [+1(6.42e-06)]_109 269798 4.36e-05 325_[+2(3.53e-06)]_107_\ [+1(9.27e-07)]_27 270116 2.79e-02 194_[+3(4.31e-06)]_259_\ [+3(5.14e-05)]_5 31259 1.66e-08 168_[+3(1.49e-07)]_67_\ [+2(4.41e-05)]_93_[+1(7.57e-08)]_110 31627 6.97e-03 466_[+1(1.03e-06)]_14 31764 7.46e-04 24_[+1(2.75e-05)]_123_\ [+2(9.93e-06)]_283_[+1(1.16e-05)]_9 32741 1.68e-10 124_[+3(2.25e-09)]_27_\ [+2(8.82e-05)]_39_[+2(2.29e-06)]_157_[+1(6.70e-07)]_70 3494 7.47e-04 117_[+2(8.22e-07)]_337_\ [+1(5.24e-05)]_5 35108 2.26e-06 97_[+2(1.65e-05)]_90_[+1(1.12e-07)]_\ 272 36506 1.30e-06 299_[+3(5.58e-05)]_51_\ [+2(2.48e-05)]_83_[+1(4.37e-08)]_5 38149 4.63e-10 116_[+3(1.32e-08)]_6_[+1(1.37e-05)]_\ 174_[+2(5.68e-08)]_142 42533 7.48e-08 241_[+3(5.95e-08)]_14_\ [+1(9.86e-08)]_52_[+3(8.02e-06)]_131 4940 3.83e-09 151_[+2(1.68e-07)]_93_\ [+3(1.40e-06)]_138_[+1(4.28e-07)]_56 5318 1.63e-05 110_[+1(2.68e-07)]_49_\ [+2(2.10e-06)]_300 5332 4.50e-04 306_[+1(1.45e-07)]_174 5387 8.47e-06 263_[+3(1.11e-07)]_4_[+1(3.09e-06)]_\ 44_[+1(5.24e-05)]_128 5694 3.12e-07 13_[+2(1.89e-05)]_399_\ [+1(3.43e-05)]_21_[+3(1.91e-08)]_5 6190 2.33e-02 393_[+2(1.75e-06)]_86 8366 1.81e-04 67_[+2(1.33e-05)]_129_\ [+1(6.70e-07)]_263 8397 1.25e-01 477_[+1(5.24e-05)]_3 8438 6.56e-05 427_[+1(1.72e-06)]_1_[+1(2.42e-09)]_\ 32 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************