******************************************************************************** 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/102/102.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10457 1.0000 500 10521 1.0000 500 11462 1.0000 500 14347 1.0000 500 16295 1.0000 500 1857 1.0000 500 19298 1.0000 500 19662 1.0000 500 20582 1.0000 500 21592 1.0000 500 21914 1.0000 500 24653 1.0000 500 24864 1.0000 500 24906 1.0000 500 261711 1.0000 500 262671 1.0000 500 262936 1.0000 500 263536 1.0000 500 264492 1.0000 500 31705 1.0000 500 33096 1.0000 500 34498 1.0000 500 4182 1.0000 500 4603 1.0000 500 5026 1.0000 500 5584 1.0000 500 5601 1.0000 500 5623 1.0000 500 5734 1.0000 500 5832 1.0000 500 7220 1.0000 500 7435 1.0000 500 7655 1.0000 500 7878 1.0000 500 8461 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/102/102.seqs.fa -oc motifs/102 -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= 35 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= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.246 C 0.249 G 0.239 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.246 C 0.249 G 0.239 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 35 llr = 361 E-value = 3.2e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3::22:1212313334133: pos.-specific C a1285:7648657437276:7 probability G ::311::1:11:::::2::2: matrix T :65117323:12233:23143 bits 2.1 1.9 * 1.7 * 1.4 * Relative 1.2 * * Entropy 1.0 * * ** * * * (14.9 bits) 0.8 ** * ** * * * * * 0.6 ** * ** * * * ** * 0.4 **** *** ***** * ** * 0.2 **************** **** 0.0 --------------------- Multilevel CTTCCTCCCCCCCCACACCTC consensus AG AATTT AATATAGTAAT sequence C A T TC C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5623 466 5.81e-08 TCCTCTCTCT CTTCCTCCCCCTCACACCCTT CCGTCAACAA 24906 453 5.81e-08 GTGGACACTT CTGCCTCCTCTCCCTCGTCTC CTCTCGGCTC 262671 20 9.29e-08 CCGAACGACC CTCCCTCCTCACCATCTCCTT CGCCACCGAC 24653 471 1.45e-07 ATTTCGCGGA CTGCCACAACCTCCACACCAC ACGTCGTCC 7435 468 2.94e-07 AGCCTGCGAT CTGCCTCCTCCACACTACCAC CTATCTACGA 31705 348 2.94e-07 CACTTTTCAC CTTCGTTCTCAACTTCACCAC CTCTCGTCCT 11462 452 2.94e-07 AGGACAAGTC CTCCCACCCCCCCAACTTCTT CAACATCGGA 5734 313 4.97e-07 GGGATCCCAG CTTCTTCTCCTCCTCCTCCTC TGTGATTGCC 263536 288 6.40e-07 TCTGGATAGC CTCCCTCCCCCCTCTCGTAAT TGTGGAGGAA 5601 417 8.19e-07 TACCACAAGC CAGCCTCCTCCACCCAAACAC CAAGCTTTCC 264492 215 1.31e-06 CCATCATCAT CATCATCATCATCCACCCATC ACCCCCAAAT 5832 460 1.47e-06 TTGAATCAAC CATCCTCCCCCCTCACTCGAC GTCAACCCTC 7220 9 2.06e-06 CCTCGCTT CAGCTTCTACCACTACCCCTT CAGCCTCCCC 19298 200 2.06e-06 CGAAGATACT CTTGCTCCTCCTCCTCCTCGT GGCACACCAG 21914 412 2.29e-06 TCCAAGCCTC CAGCCTCTTCCTCTTCAACGC AGCTCCATCT 7878 455 2.84e-06 CCACATCATC CATCATTCCCAACCACGCTTC CGTCTTGCGC 4603 334 2.84e-06 TGGTTGAGAC CTCCATTACCCCTCTCATATC AAATAAGTTT 16295 155 3.15e-06 ACCAAATACA CCTCCTCCTCCTTACAACAAC AGCCACAACC 8461 360 3.49e-06 ACGCAGCCTT CTTGATCTCACCCAACGCAAC GATGTTCAGC 4182 474 4.73e-06 TCGATAGCAG CATCGTTGCCCACCACCCAAC GACTCC 1857 467 5.22e-06 CACAACCTCC CTCCAACCCGACCTCCACCGC AACCACAGCA 19662 462 7.65e-06 ATTCTCTCAA CACCCTCTAACCCAACACTGC TACAACAACA 5026 348 1.10e-05 TGTTCTCTCT CACGTTCTCCCCCCACTCCGT AGAAACAAAC 21592 324 1.31e-05 TTACATCACG CTTCCATCTATTCTTCGCCGC TTCGGCCACA 10457 187 2.00e-05 AGTGTGTTCG GTTCATTCACCACCACTTATC CTATACCATA 7655 442 2.17e-05 CCCCTCACAT CTTCTACCACACTTCACCCTT CGTCGTTTTC 14347 33 2.17e-05 TTCGCTATTC CTCGCTCCTCGCAACAACCAC ACACTAAACA 261711 322 3.76e-05 GTTCATGAAC CTTCCATTCCCACTGAGCATT ATTCTCTGGG 262936 330 4.69e-05 GGGATTGTCC CTTCTGTCCACTTATCACCTC TCTCATATTG 10521 281 5.81e-05 TCGGGAAGCA CTGTATCAACTATCAAACATC CCAGTTGTCA 34498 358 6.22e-05 TATTTGCATT CTGTATTATCCCCTTAATATT TAATCTTATC 33096 417 6.22e-05 CCGTCGCAAC CAGCCACCACACATCCGCACC GGCACAAAGC 20582 470 7.14e-05 CTCCAGCTAC CAGCGTTTACTACACAATAGC TTCAGCAAGC 5584 432 1.36e-04 GCTCGCGCGC CCTTGACGCCCACATCCCCGC TCCCGTAAGC 24864 437 1.72e-04 GCCTCTTTCC CTTCCTCCGGGCAATCGTCAC AGTTATTTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5623 5.8e-08 465_[+1]_14 24906 5.8e-08 452_[+1]_27 262671 9.3e-08 19_[+1]_460 24653 1.5e-07 470_[+1]_9 7435 2.9e-07 467_[+1]_12 31705 2.9e-07 347_[+1]_132 11462 2.9e-07 451_[+1]_28 5734 5e-07 312_[+1]_167 263536 6.4e-07 287_[+1]_192 5601 8.2e-07 416_[+1]_63 264492 1.3e-06 214_[+1]_265 5832 1.5e-06 459_[+1]_20 7220 2.1e-06 8_[+1]_471 19298 2.1e-06 199_[+1]_280 21914 2.3e-06 411_[+1]_68 7878 2.8e-06 454_[+1]_25 4603 2.8e-06 333_[+1]_146 16295 3.2e-06 154_[+1]_325 8461 3.5e-06 359_[+1]_120 4182 4.7e-06 473_[+1]_6 1857 5.2e-06 466_[+1]_13 19662 7.6e-06 461_[+1]_18 5026 1.1e-05 347_[+1]_132 21592 1.3e-05 323_[+1]_156 10457 2e-05 186_[+1]_293 7655 2.2e-05 441_[+1]_38 14347 2.2e-05 32_[+1]_447 261711 3.8e-05 321_[+1]_158 262936 4.7e-05 329_[+1]_150 10521 5.8e-05 280_[+1]_199 34498 6.2e-05 357_[+1]_122 33096 6.2e-05 416_[+1]_63 20582 7.1e-05 469_[+1]_10 5584 0.00014 431_[+1]_48 24864 0.00017 436_[+1]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=35 5623 ( 466) CTTCCTCCCCCTCACACCCTT 1 24906 ( 453) CTGCCTCCTCTCCCTCGTCTC 1 262671 ( 20) CTCCCTCCTCACCATCTCCTT 1 24653 ( 471) CTGCCACAACCTCCACACCAC 1 7435 ( 468) CTGCCTCCTCCACACTACCAC 1 31705 ( 348) CTTCGTTCTCAACTTCACCAC 1 11462 ( 452) CTCCCACCCCCCCAACTTCTT 1 5734 ( 313) CTTCTTCTCCTCCTCCTCCTC 1 263536 ( 288) CTCCCTCCCCCCTCTCGTAAT 1 5601 ( 417) CAGCCTCCTCCACCCAAACAC 1 264492 ( 215) CATCATCATCATCCACCCATC 1 5832 ( 460) CATCCTCCCCCCTCACTCGAC 1 7220 ( 9) CAGCTTCTACCACTACCCCTT 1 19298 ( 200) CTTGCTCCTCCTCCTCCTCGT 1 21914 ( 412) CAGCCTCTTCCTCTTCAACGC 1 7878 ( 455) CATCATTCCCAACCACGCTTC 1 4603 ( 334) CTCCATTACCCCTCTCATATC 1 16295 ( 155) CCTCCTCCTCCTTACAACAAC 1 8461 ( 360) CTTGATCTCACCCAACGCAAC 1 4182 ( 474) CATCGTTGCCCACCACCCAAC 1 1857 ( 467) CTCCAACCCGACCTCCACCGC 1 19662 ( 462) CACCCTCTAACCCAACACTGC 1 5026 ( 348) CACGTTCTCCCCCCACTCCGT 1 21592 ( 324) CTTCCATCTATTCTTCGCCGC 1 10457 ( 187) GTTCATTCACCACCACTTATC 1 7655 ( 442) CTTCTACCACACTTCACCCTT 1 14347 ( 33) CTCGCTCCTCGCAACAACCAC 1 261711 ( 322) CTTCCATTCCCACTGAGCATT 1 262936 ( 330) CTTCTGTCCACTTATCACCTC 1 10521 ( 281) CTGTATCAACTATCAAACATC 1 34498 ( 358) CTGTATTATCCCCTTAATATT 1 33096 ( 417) CAGCCACCACACATCCGCACC 1 20582 ( 470) CAGCGTTTACTACACAATAGC 1 5584 ( 432) CCTTGACGCCCACATCCCCGC 1 24864 ( 437) CTTCCTCCGGGCAATCGTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16800 bayes= 9.72704 E= 3.2e-016 -1177 196 -306 -1177 36 -212 -1177 124 -1177 -12 26 86 -1177 168 -106 -164 -10 105 -106 -90 -10 -1177 -306 148 -1177 152 -1177 10 -78 120 -206 -22 -10 68 -306 36 -110 174 -206 -1177 -30 127 -206 -90 36 88 -1177 -22 -152 152 -1177 -42 48 58 -1177 10 48 20 -306 36 7 152 -1177 -322 70 -31 -6 -64 -210 146 -1177 -5 48 120 -306 -222 36 -312 -6 68 -1177 152 -1177 10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 35 E= 3.2e-016 0.000000 0.971429 0.028571 0.000000 0.314286 0.057143 0.000000 0.628571 0.000000 0.228571 0.285714 0.485714 0.000000 0.800000 0.114286 0.085714 0.228571 0.514286 0.114286 0.142857 0.228571 0.000000 0.028571 0.742857 0.000000 0.714286 0.000000 0.285714 0.142857 0.571429 0.057143 0.228571 0.228571 0.400000 0.028571 0.342857 0.114286 0.828571 0.057143 0.000000 0.200000 0.600000 0.057143 0.142857 0.314286 0.457143 0.000000 0.228571 0.085714 0.714286 0.000000 0.200000 0.342857 0.371429 0.000000 0.285714 0.342857 0.285714 0.028571 0.342857 0.257143 0.714286 0.000000 0.028571 0.400000 0.200000 0.228571 0.171429 0.057143 0.685714 0.000000 0.257143 0.342857 0.571429 0.028571 0.057143 0.314286 0.028571 0.228571 0.428571 0.000000 0.714286 0.000000 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[TA][TGC]C[CA][TA][CT][CT][CTA]C[CA][CAT][CT][CAT][ATC][CA][AGC][CT][CA][TAG][CT] -------------------------------------------------------------------------------- Time 11.65 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 32 llr = 292 E-value = 2.0e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::3:::::112 pos.-specific C 11::41:::1:: probability G 3:a2:83:9316 matrix T 69:5627a1482 bits 2.1 * 1.9 * * 1.7 * * 1.4 ** ** Relative 1.2 ** ** * Entropy 1.0 ** * *** * (13.1 bits) 0.8 ** ***** * 0.6 *** ***** ** 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel TTGTTGTTGTTG consensus G AC G G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 5584 352 8.43e-08 CTCGCTCCCA TTGTTGTTGTTG GCGTTGTACT 4603 290 1.60e-07 GTCGTGGCTG TTGTTGTTGGTG AAGCGTCAGT 263536 428 3.81e-07 ATTGAGCAGT TTGTCGTTGTTG TCCTCAACCT 7878 176 9.55e-07 AACTGCCAAT GTGTCGTTGTTG ATCCCTGTGG 5734 18 2.51e-06 CCCTTCTCCG TTGTTGTTGCTG TTGCGAGCGT 7655 80 3.04e-06 GATGATTGAG TTGGTGGTGGTG CTTGTACGTC 4182 285 3.04e-06 TGGAGTTCGG GTGGCGTTGTTG AGAGATCGAC 20582 10 3.04e-06 TGTATTGTT GTGTTGTTGTTA TTGTTGCGTT 24653 42 3.69e-06 CACTCTAATG TTGATGTTGATG GGTTGTGATT 10457 127 7.26e-06 TCATCAGGAG GTGACGGTGTTG CAAGAGGTTG 5026 1 1.18e-05 . CTGGTGTTGGTG GAGTGTGTTG 262936 144 1.31e-05 CCATGACGTT GTGACGTTGTTA GGATGTAGCG 21914 36 1.57e-05 CCTGATGTGA CTGTTGTTGATG CTTCGTTGTT 24906 293 1.99e-05 AAGAGGCCTG TTGTTTTTGTTT GACGAATGGA 10521 62 1.99e-05 TGGCAGGAGA GTGATGTTGTGG TGAGGAGGGG 5623 38 2.37e-05 AGAGTTGATA TTGATGTTGCTA TCGTCGTGTG 24864 178 2.87e-05 AGACGACGTT TTGTCGGTGGGG CGGCGCGTTG 5832 259 3.14e-05 CCCAATCCCC TTGTTGTTTGTT TGTTTGATGT 33096 227 3.42e-05 AAGGTTCATG GTGACGGTGGTT GTGAAAAGGA 7435 70 3.72e-05 TGTCCATAAC GTGGTTGTGGTG AGGAGATGGC 7220 158 6.25e-05 TGGCATGATC TTGATCTTGATG ATGATGTGCC 34498 234 6.25e-05 ACGACCTGCC TTGTTGGTTGTT TGGACTCTGC 5601 167 6.80e-05 GTAAGCGTGG TTGTCCTTGTTT TGTGTTCTCG 14347 385 6.80e-05 AGCGTTTGCG TTGGCGGTGATA GTGTTTTACA 11462 382 6.80e-05 GGCTACTCTT TTGATTTTGTGG GGAATATTAT 1857 131 7.31e-05 CTCGTTGACA GCGTCGTTGCTG CTCTCCACGG 264492 127 7.88e-05 AGGTGGAAGG TTGTTATTGGTA TGTGTGTTTG 19298 416 9.80e-05 CAGACGATGA GTGGTGTTGTAA AGTAAGAAAA 16295 51 1.21e-04 AGCCACAACG GCGTTTGTGGTG TAGCCTCCTC 262671 308 1.29e-04 GTTTTCCCTT CTGATGGTTGTG TGCAGTGTCA 21592 218 1.55e-04 GGGTGTCTCA TCGGCGTTTTTG GAAATAGCCG 8461 133 2.08e-04 GTTTTTATCA TTGTCTTTGTAT CTGAGGGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5584 8.4e-08 351_[+2]_137 4603 1.6e-07 289_[+2]_199 263536 3.8e-07 427_[+2]_61 7878 9.6e-07 175_[+2]_313 5734 2.5e-06 17_[+2]_471 7655 3e-06 79_[+2]_409 4182 3e-06 284_[+2]_204 20582 3e-06 9_[+2]_479 24653 3.7e-06 41_[+2]_447 10457 7.3e-06 126_[+2]_362 5026 1.2e-05 [+2]_488 262936 1.3e-05 143_[+2]_345 21914 1.6e-05 35_[+2]_453 24906 2e-05 292_[+2]_196 10521 2e-05 61_[+2]_427 5623 2.4e-05 37_[+2]_451 24864 2.9e-05 177_[+2]_311 5832 3.1e-05 258_[+2]_230 33096 3.4e-05 226_[+2]_262 7435 3.7e-05 69_[+2]_419 7220 6.2e-05 157_[+2]_331 34498 6.2e-05 233_[+2]_255 5601 6.8e-05 166_[+2]_322 14347 6.8e-05 384_[+2]_104 11462 6.8e-05 381_[+2]_107 1857 7.3e-05 130_[+2]_358 264492 7.9e-05 126_[+2]_362 19298 9.8e-05 415_[+2]_73 16295 0.00012 50_[+2]_438 262671 0.00013 307_[+2]_181 21592 0.00016 217_[+2]_271 8461 0.00021 132_[+2]_356 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=32 5584 ( 352) TTGTTGTTGTTG 1 4603 ( 290) TTGTTGTTGGTG 1 263536 ( 428) TTGTCGTTGTTG 1 7878 ( 176) GTGTCGTTGTTG 1 5734 ( 18) TTGTTGTTGCTG 1 7655 ( 80) TTGGTGGTGGTG 1 4182 ( 285) GTGGCGTTGTTG 1 20582 ( 10) GTGTTGTTGTTA 1 24653 ( 42) TTGATGTTGATG 1 10457 ( 127) GTGACGGTGTTG 1 5026 ( 1) CTGGTGTTGGTG 1 262936 ( 144) GTGACGTTGTTA 1 21914 ( 36) CTGTTGTTGATG 1 24906 ( 293) TTGTTTTTGTTT 1 10521 ( 62) GTGATGTTGTGG 1 5623 ( 38) TTGATGTTGCTA 1 24864 ( 178) TTGTCGGTGGGG 1 5832 ( 259) TTGTTGTTTGTT 1 33096 ( 227) GTGACGGTGGTT 1 7435 ( 70) GTGGTTGTGGTG 1 7220 ( 158) TTGATCTTGATG 1 34498 ( 234) TTGTTGGTTGTT 1 5601 ( 167) TTGTCCTTGTTT 1 14347 ( 385) TTGGCGGTGATA 1 11462 ( 382) TTGATTTTGTGG 1 1857 ( 131) GCGTCGTTGCTG 1 264492 ( 127) TTGTTATTGGTA 1 19298 ( 416) GTGGTGTTGTAA 1 16295 ( 51) GCGTTTGTGGTG 1 262671 ( 308) CTGATGGTTGTG 1 21592 ( 218) TCGGCGTTTTTG 1 8461 ( 133) TTGTCTTTGTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17115 bayes= 9.79832 E= 2.0e-011 -1164 -141 53 108 -1164 -141 -1164 176 -1164 -1164 207 -1164 20 -1164 -13 91 -1164 59 -1164 123 -297 -199 165 -77 -1164 -1164 24 143 -1164 -1164 -1164 191 -1164 -1164 187 -109 -97 -141 53 71 -197 -1164 -135 166 -39 -1164 139 -51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 32 E= 2.0e-011 0.000000 0.093750 0.343750 0.562500 0.000000 0.093750 0.000000 0.906250 0.000000 0.000000 1.000000 0.000000 0.281250 0.000000 0.218750 0.500000 0.000000 0.375000 0.000000 0.625000 0.031250 0.062500 0.750000 0.156250 0.000000 0.000000 0.281250 0.718750 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.125000 0.093750 0.343750 0.437500 0.062500 0.000000 0.093750 0.843750 0.187500 0.000000 0.625000 0.187500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]TG[TAG][TC]G[TG]TG[TG]TG -------------------------------------------------------------------------------- Time 21.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 30 llr = 313 E-value = 6.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 4316:21:1432722213821 pos.-specific C 141:::12:13::2::4::3: probability G 438188369337343737118 matrix T 1::32:52:121:3512:141 bits 2.1 1.9 1.7 * 1.4 * * Relative 1.2 * ** * Entropy 1.0 * ** * * * ** * (15.0 bits) 0.8 **** * ** * ** * 0.6 **** ** ** * ** * 0.4 ****** ** ** ** ** * 0.2 ********** ** ******* 0.0 --------------------- Multilevel ACGAGGTGGACGAGTGCGATG consensus GG TT GC GAAGTG GA C sequence A T G T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262936 298 1.24e-09 AAGAAGAGGA GGGAGGTGGAGGACTGGGAAG TGGGATTGTC 11462 43 1.67e-07 CACAATCATG ACGATGCGGATGATTGCAACG ATAGCACGAC 262671 162 1.91e-07 GGAGACGTTG GCGAGGGTGGGGGGTGTGAGG GTGGGTGATT 7878 259 2.48e-07 TTTCGCTCCG AGAAGGCGGAGGAGAGCGACG CCTCCCTGGT 10457 140 4.64e-07 ACGGTGTTGC AAGAGGTTGCAGATTGCGTTG TGCTCACTTG 10521 98 1.46e-06 GCATTACATG ACGGTGTCGACGATAGGAATG CGGATGTTGC 7435 151 1.81e-06 GAGCGATATC CCGAGGCGGAGGAGCGAGATG CCGCTGCTGC 4603 144 1.81e-06 GGCTGTCCCG AGGAGGTTGGAAAGTGTGAAT CGGTTGCCTG 4182 332 2.47e-06 GAGGGAAGAG AAGAGAGGGAATAGGGGAAAG AACCTAGAAA 7220 324 2.74e-06 CTCTTTCTTT GGGAGGCGGCAAGGTACGAAG GCGCCTCATC 5584 63 2.74e-06 AATTGCAGCA ACGTTGGCGTAGAGTAGGATG GCAAAGATTG 24906 137 3.35e-06 GATGTTGGAT GCCAGGTGGGCGGCGGCGGTG GAGGGTGTGG 31705 476 3.69e-06 TGAGTGTTTG ACGAGGTCGTTGAATGTGACA CGTG 24653 282 4.49e-06 GATGGAAGGG GAGAGAGCGATGAGGGTGACT GCCGCTGGGG 264492 154 4.94e-06 GTTTGTGTAT GAATGATGGGCGATGGAGATG GATGGATGAG 24864 115 4.94e-06 TGTGATTTTA CGGTGGTGGTGGGGTGGGGCG GTGTGTGTGT 14347 86 4.94e-06 ACACAAAGAG GAGAGATGGTGGACGTCAACG GCAACGATAG 261711 394 5.43e-06 CACACAAGAT GCGTGGGCGGAGGATGAGATT GATACTTGGA 21914 138 7.86e-06 GGTGTATCGG GCGATGAGGAGGAAGGCACTG TCATCTTTTC 21592 382 7.86e-06 CGTCATCGGC AGGGGGGGGATGAAGAGAAGG TGCTAAACAA 19298 357 7.86e-06 CGGTCTACGA GCGTGGTGGCGAAGATGAAAG GAAACCGAGG 34498 318 1.03e-05 AGGGGAGACT AGGAGGAGGACCATGGGGACA AGTTGACGAT 1857 282 1.03e-05 GGAATGAGGA GCATGGGCGGCGGTAGTAATG GTTATGACGG 5026 285 1.33e-05 TGGATCGGCT GAGGGGAGGGCGGATACGAGG GCACTTATTG 33096 194 1.86e-05 AGATCCTGCG AGCAGGGTGGAAATAGCAAAG GAAAGGTTCA 16295 362 1.86e-05 CAGGATTATC CAGAGGTGAGTTGTTGCGATG TGATACATTG 5623 110 3.00e-05 GAGCTGCAGC AAGTTGTTGACAGCGTGGATG GCACACAGTT 19662 263 3.00e-05 AGGACGAGTG ACGAGATCAACAACGACGACG AACCCCACCC 8461 97 5.05e-05 GTCTCGGGGC TGGAGGTGGCAGATTGTGTCC ACAATGTTTT 7655 100 1.07e-04 TGCTTGTACG TCGTTGTTGACGGGTGGATTT GATTCCATGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262936 1.2e-09 297_[+3]_182 11462 1.7e-07 42_[+3]_437 262671 1.9e-07 161_[+3]_318 7878 2.5e-07 258_[+3]_221 10457 4.6e-07 139_[+3]_340 10521 1.5e-06 97_[+3]_382 7435 1.8e-06 150_[+3]_329 4603 1.8e-06 143_[+3]_336 4182 2.5e-06 331_[+3]_148 7220 2.7e-06 323_[+3]_156 5584 2.7e-06 62_[+3]_417 24906 3.3e-06 136_[+3]_343 31705 3.7e-06 475_[+3]_4 24653 4.5e-06 281_[+3]_198 264492 4.9e-06 153_[+3]_326 24864 4.9e-06 114_[+3]_365 14347 4.9e-06 85_[+3]_394 261711 5.4e-06 393_[+3]_86 21914 7.9e-06 137_[+3]_342 21592 7.9e-06 381_[+3]_98 19298 7.9e-06 356_[+3]_123 34498 1e-05 317_[+3]_162 1857 1e-05 281_[+3]_198 5026 1.3e-05 284_[+3]_195 33096 1.9e-05 193_[+3]_286 16295 1.9e-05 361_[+3]_118 5623 3e-05 109_[+3]_370 19662 3e-05 262_[+3]_217 8461 5e-05 96_[+3]_383 7655 0.00011 99_[+3]_380 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=30 262936 ( 298) GGGAGGTGGAGGACTGGGAAG 1 11462 ( 43) ACGATGCGGATGATTGCAACG 1 262671 ( 162) GCGAGGGTGGGGGGTGTGAGG 1 7878 ( 259) AGAAGGCGGAGGAGAGCGACG 1 10457 ( 140) AAGAGGTTGCAGATTGCGTTG 1 10521 ( 98) ACGGTGTCGACGATAGGAATG 1 7435 ( 151) CCGAGGCGGAGGAGCGAGATG 1 4603 ( 144) AGGAGGTTGGAAAGTGTGAAT 1 4182 ( 332) AAGAGAGGGAATAGGGGAAAG 1 7220 ( 324) GGGAGGCGGCAAGGTACGAAG 1 5584 ( 63) ACGTTGGCGTAGAGTAGGATG 1 24906 ( 137) GCCAGGTGGGCGGCGGCGGTG 1 31705 ( 476) ACGAGGTCGTTGAATGTGACA 1 24653 ( 282) GAGAGAGCGATGAGGGTGACT 1 264492 ( 154) GAATGATGGGCGATGGAGATG 1 24864 ( 115) CGGTGGTGGTGGGGTGGGGCG 1 14347 ( 86) GAGAGATGGTGGACGTCAACG 1 261711 ( 394) GCGTGGGCGGAGGATGAGATT 1 21914 ( 138) GCGATGAGGAGGAAGGCACTG 1 21592 ( 382) AGGGGGGGGATGAAGAGAAGG 1 19298 ( 357) GCGTGGTGGCGAAGATGAAAG 1 34498 ( 318) AGGAGGAGGACCATGGGGACA 1 1857 ( 282) GCATGGGCGGCGGTAGTAATG 1 5026 ( 285) GAGGGGAGGGCGGATACGAGG 1 33096 ( 194) AGCAGGGTGGAAATAGCAAAG 1 16295 ( 362) CAGAGGTGAGTTGTTGCGATG 1 5623 ( 110) AAGTTGTTGACAGCGTGGATG 1 19662 ( 263) ACGAGATCAACAACGACGACG 1 8461 ( 97) TGGAGGTGGCAGATTGTGTCC 1 7655 ( 100) TCGTTGTTGACGGGTGGATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16800 bayes= 9.0516 E= 6.0e-007 82 -131 74 -200 12 80 33 -1155 -130 -190 180 -1155 137 -1155 -126 0 -1155 -1155 174 -42 -56 -1155 180 -1155 -130 -90 16 91 -1155 -9 125 -42 -188 -1155 197 -1155 82 -90 33 -100 12 27 16 -68 -30 -290 155 -200 144 -1155 48 -1155 -56 -58 62 17 -56 -290 48 81 -56 -1155 162 -141 -130 56 48 -42 44 -1155 148 -1155 170 -290 -184 -141 -30 27 -126 58 -188 -290 168 -100 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 30 E= 6.0e-007 0.433333 0.100000 0.400000 0.066667 0.266667 0.433333 0.300000 0.000000 0.100000 0.066667 0.833333 0.000000 0.633333 0.000000 0.100000 0.266667 0.000000 0.000000 0.800000 0.200000 0.166667 0.000000 0.833333 0.000000 0.100000 0.133333 0.266667 0.500000 0.000000 0.233333 0.566667 0.200000 0.066667 0.000000 0.933333 0.000000 0.433333 0.133333 0.300000 0.133333 0.266667 0.300000 0.266667 0.166667 0.200000 0.033333 0.700000 0.066667 0.666667 0.000000 0.333333 0.000000 0.166667 0.166667 0.366667 0.300000 0.166667 0.033333 0.333333 0.466667 0.166667 0.000000 0.733333 0.100000 0.100000 0.366667 0.333333 0.200000 0.333333 0.000000 0.666667 0.000000 0.800000 0.033333 0.066667 0.100000 0.200000 0.300000 0.100000 0.400000 0.066667 0.033333 0.766667 0.133333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][CGA]G[AT][GT]G[TG][GCT]G[AG][CAG][GA][AG][GT][TG]G[CGT][GA]A[TCA]G -------------------------------------------------------------------------------- Time 31.97 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10457 1.47e-06 126_[+2(7.26e-06)]_1_[+3(4.64e-07)]_\ 26_[+1(2.00e-05)]_293 10521 2.54e-05 61_[+2(1.99e-05)]_24_[+3(1.46e-06)]_\ 162_[+1(5.81e-05)]_199 11462 9.58e-08 42_[+3(1.67e-07)]_318_\ [+2(6.80e-05)]_58_[+1(2.94e-07)]_28 14347 9.13e-05 32_[+1(2.17e-05)]_32_[+3(4.94e-06)]_\ 278_[+2(6.80e-05)]_104 16295 8.83e-05 154_[+1(3.15e-06)]_186_\ [+3(1.86e-05)]_83_[+1(4.05e-05)]_14 1857 5.31e-05 130_[+2(7.31e-05)]_139_\ [+3(1.03e-05)]_164_[+1(5.22e-06)]_13 19298 2.40e-05 199_[+1(2.06e-06)]_136_\ [+3(7.86e-06)]_38_[+2(9.80e-05)]_73 19662 2.54e-03 262_[+3(3.00e-05)]_178_\ [+1(7.65e-06)]_18 20582 1.71e-03 9_[+2(3.04e-06)]_448_[+1(7.14e-05)]_\ 10 21592 1.77e-04 323_[+1(1.31e-05)]_37_\ [+3(7.86e-06)]_98 21914 5.31e-06 35_[+2(1.57e-05)]_12_[+2(6.25e-05)]_\ 35_[+2(4.88e-05)]_19_[+3(7.86e-06)]_55_[+3(7.17e-05)]_81_[+1(2.55e-05)]_75_\ [+1(2.29e-06)]_68 24653 7.19e-08 41_[+2(3.69e-06)]_81_[+1(9.93e-05)]_\ 126_[+3(4.49e-06)]_168_[+1(1.45e-07)]_9 24864 2.52e-04 114_[+3(4.94e-06)]_42_\ [+2(2.87e-05)]_311 24906 1.10e-07 136_[+3(3.35e-06)]_135_\ [+2(1.99e-05)]_148_[+1(5.81e-08)]_27 261711 1.38e-03 321_[+1(3.76e-05)]_51_\ [+3(5.43e-06)]_86 262671 6.71e-08 19_[+1(9.29e-08)]_97_[+3(3.35e-06)]_\ 3_[+3(1.91e-07)]_318 262936 2.49e-08 143_[+2(1.31e-05)]_142_\ [+3(1.24e-09)]_11_[+1(4.69e-05)]_150 263536 3.32e-06 287_[+1(6.40e-07)]_119_\ [+2(3.81e-07)]_36_[+1(2.84e-06)]_4 264492 8.86e-06 126_[+2(7.88e-05)]_15_\ [+3(4.94e-06)]_40_[+1(1.31e-06)]_265 31705 1.26e-05 347_[+1(2.94e-07)]_107_\ [+3(3.69e-06)]_4 33096 3.89e-04 193_[+3(1.86e-05)]_12_\ [+2(3.42e-05)]_178_[+1(6.22e-05)]_63 34498 3.90e-04 233_[+2(6.25e-05)]_72_\ [+3(1.03e-05)]_19_[+1(6.22e-05)]_122 4182 8.27e-07 250_[+3(9.36e-05)]_13_\ [+2(3.04e-06)]_35_[+3(2.47e-06)]_121_[+1(4.73e-06)]_6 4603 2.68e-08 143_[+3(1.81e-06)]_125_\ [+2(1.60e-07)]_32_[+1(2.84e-06)]_146 5026 2.64e-05 [+2(1.18e-05)]_272_[+3(1.33e-05)]_\ 42_[+1(1.10e-05)]_132 5584 7.18e-07 62_[+3(2.74e-06)]_268_\ [+2(8.43e-08)]_137 5601 9.73e-04 166_[+2(6.80e-05)]_238_\ [+1(8.19e-07)]_63 5623 9.37e-07 37_[+2(2.37e-05)]_60_[+3(3.00e-05)]_\ 335_[+1(5.81e-08)]_14 5734 3.77e-05 17_[+2(2.51e-06)]_283_\ [+1(4.97e-07)]_167 5832 4.53e-04 258_[+2(3.14e-05)]_3_[+2(5.26e-05)]_\ 174_[+1(1.47e-06)]_20 7220 6.38e-06 8_[+1(2.06e-06)]_128_[+2(6.25e-05)]_\ 154_[+3(2.74e-06)]_156 7435 4.84e-07 69_[+2(3.72e-05)]_69_[+3(1.81e-06)]_\ 42_[+2(9.80e-05)]_242_[+1(2.94e-07)]_12 7655 8.78e-05 28_[+2(7.88e-05)]_39_[+2(3.04e-06)]_\ 350_[+1(2.17e-05)]_38 7878 2.24e-08 175_[+2(9.55e-07)]_71_\ [+3(2.48e-07)]_175_[+1(2.84e-06)]_25 8461 3.54e-04 96_[+3(5.05e-05)]_242_\ [+1(3.49e-06)]_120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************