******************************************************************************** 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/485/485.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11629 1.0000 500 11710 1.0000 500 1194 1.0000 500 1481 1.0000 500 19048 1.0000 500 20951 1.0000 500 20989 1.0000 500 21400 1.0000 500 21613 1.0000 500 21673 1.0000 500 21983 1.0000 500 22227 1.0000 500 23396 1.0000 500 23777 1.0000 500 23786 1.0000 500 23803 1.0000 500 24011 1.0000 500 24428 1.0000 500 25378 1.0000 500 25414 1.0000 500 25422 1.0000 500 25423 1.0000 500 25553 1.0000 500 25591 1.0000 500 25608 1.0000 500 25637 1.0000 500 25679 1.0000 500 261839 1.0000 500 261895 1.0000 500 262535 1.0000 500 262597 1.0000 500 263782 1.0000 500 264271 1.0000 500 264399 1.0000 500 2647 1.0000 500 264918 1.0000 500 269115 1.0000 500 269386 1.0000 500 269948 1.0000 500 2916 1.0000 500 31001 1.0000 500 32738 1.0000 500 3637 1.0000 500 5909 1.0000 500 6832 1.0000 500 7379 1.0000 500 7830 1.0000 500 8732 1.0000 500 bd1749 1.0000 500 bd945 1.0000 500 bd954 1.0000 59 ******************************************************************************** ******************************************************************************** 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/485/485.seqs.fa -oc motifs/485 -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= 51 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= 25059 N= 51 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.231 G 0.234 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.231 G 0.234 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 18 llr = 242 E-value = 1.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 641:31:4851351:4113:: pos.-specific C 1:23:24::2:1:::2:::12 probability G :6517236228619a:87:98 matrix T 3:26:53::2114::412711 bits 2.1 * 1.9 * 1.7 ** 1.5 ** * Relative 1.3 * * ** * * Entropy 1.1 * * ** * ** ***** (19.4 bits) 0.8 * * ** * ** ***** 0.6 ** ** ** ***** ***** 0.4 ** ** *** *********** 0.2 ********************* 0.0 --------------------- Multilevel AGGTGTCGAAGGAGGTGGTGG consensus TACCACGAG AT A TA sequence GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 19048 173 6.34e-10 GTCATGTCGG AACTGTCAAAGGAGGAGGAGG AACCTTGGAG 1194 169 4.46e-09 AATCGTCGAG AGGTGGTAATGGAGGTGGAGG CGACACACTG 31001 218 1.16e-08 GATGTGGACG TGGCATCGGTGGTGGTGGTGG ACGTGGAGGC 11629 251 3.87e-08 AAAGAAGTGT CAACGTCAAAGAAGGTGGTGG GCAGAAACAC 25423 33 5.38e-08 ATAGCTGACT AGGTGCCAGAGGTGGTGTTGC CTTTGCTAAA 269115 25 1.35e-07 GATTGAGGTG AGGCGTGGGAGGAGGATTTGG ATGAATGTGG 23396 75 1.35e-07 GAGGAGGATG AAATAGCAACGGTGGCGGTGG CAGTTGTGGG 21983 278 1.35e-07 TTTGATAATG AAGCACTGGAGGAGGCGTTGG TTTGGTACGG 264399 140 1.64e-07 GCCGCGACTG TGGTGAGGAGGGTGGTGTAGG CGAGGGTGGA 25553 417 1.64e-07 GTTGTTAGAG AGGCAGGGAGGGAGGCAGTGG CAAAACCGAG 2916 312 2.59e-07 GTGAGGGGGG TGGGGGGAAAGTAGGTGGAGG AAGCAGGCGA 262597 208 3.38e-07 TGGGTGGGCG AGTTGTTGAAGAGAGAGGTGG GTGTGGTTGG 20951 313 4.01e-07 GCTCAGTTTG CACCGCCGACGGAGGTGATGG TTACTGATAT 7830 331 9.66e-07 TGTCAACGAC AACTGTTGAGTGTGGAGGTTG ATGGTCCCAT bd1749 178 1.21e-06 TGATTTCAGT TGTTATCAAATAAGGAGGAGC TCTTCACCTA 3637 326 1.85e-06 GGTTTTCAAG AAGTGTCGAAAAGGGAGGACG GAATTTGCGT 264271 3 2.42e-06 AA TACTGCTGATGCTGGTGGTGT GCACAAGGAT 20989 155 4.80e-06 AATCTGCTCA TGTGATGGACGATGGAAGTGC TTTCAGAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19048 6.3e-10 172_[+1]_307 1194 4.5e-09 168_[+1]_311 31001 1.2e-08 217_[+1]_262 11629 3.9e-08 250_[+1]_229 25423 5.4e-08 32_[+1]_447 269115 1.3e-07 24_[+1]_455 23396 1.3e-07 74_[+1]_405 21983 1.3e-07 277_[+1]_202 264399 1.6e-07 139_[+1]_340 25553 1.6e-07 416_[+1]_63 2916 2.6e-07 311_[+1]_168 262597 3.4e-07 207_[+1]_272 20951 4e-07 312_[+1]_167 7830 9.7e-07 330_[+1]_149 bd1749 1.2e-06 177_[+1]_302 3637 1.8e-06 325_[+1]_154 264271 2.4e-06 2_[+1]_477 20989 4.8e-06 154_[+1]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=18 19048 ( 173) AACTGTCAAAGGAGGAGGAGG 1 1194 ( 169) AGGTGGTAATGGAGGTGGAGG 1 31001 ( 218) TGGCATCGGTGGTGGTGGTGG 1 11629 ( 251) CAACGTCAAAGAAGGTGGTGG 1 25423 ( 33) AGGTGCCAGAGGTGGTGTTGC 1 269115 ( 25) AGGCGTGGGAGGAGGATTTGG 1 23396 ( 75) AAATAGCAACGGTGGCGGTGG 1 21983 ( 278) AAGCACTGGAGGAGGCGTTGG 1 264399 ( 140) TGGTGAGGAGGGTGGTGTAGG 1 25553 ( 417) AGGCAGGGAGGGAGGCAGTGG 1 2916 ( 312) TGGGGGGAAAGTAGGTGGAGG 1 262597 ( 208) AGTTGTTGAAGAGAGAGGTGG 1 20951 ( 313) CACCGCCGACGGAGGTGATGG 1 7830 ( 331) AACTGTTGAGTGTGGAGGTTG 1 bd1749 ( 178) TGTTATCAAATAAGGAGGAGC 1 3637 ( 326) AAGTGTCGAAAAGGGAGGACG 1 264271 ( 3) TACTGCTGATGCTGGTGGTGT 1 20989 ( 155) TGTGATGGACGATGGAAGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24039 bayes= 10.5165 E= 1.2e-003 105 -105 -1081 32 73 -1081 125 -1081 -127 -6 109 -68 -1081 53 -107 106 31 -1081 151 -1081 -227 -6 -8 91 -1081 94 25 6 54 -1081 138 -1081 154 -1081 -8 -1081 90 -47 -49 -68 -227 -1081 183 -126 5 -205 138 -226 90 -1081 -107 54 -227 -1081 201 -1081 -1081 -1081 209 -1081 54 -47 -1081 74 -127 -1081 183 -226 -227 -1081 162 -26 31 -1081 -1081 132 -1081 -205 192 -226 -1081 -47 173 -226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 1.2e-003 0.555556 0.111111 0.000000 0.333333 0.444444 0.000000 0.555556 0.000000 0.111111 0.222222 0.500000 0.166667 0.000000 0.333333 0.111111 0.555556 0.333333 0.000000 0.666667 0.000000 0.055556 0.222222 0.222222 0.500000 0.000000 0.444444 0.277778 0.277778 0.388889 0.000000 0.611111 0.000000 0.777778 0.000000 0.222222 0.000000 0.500000 0.166667 0.166667 0.166667 0.055556 0.000000 0.833333 0.111111 0.277778 0.055556 0.611111 0.055556 0.500000 0.000000 0.111111 0.388889 0.055556 0.000000 0.944444 0.000000 0.000000 0.000000 1.000000 0.000000 0.388889 0.166667 0.000000 0.444444 0.111111 0.000000 0.833333 0.055556 0.055556 0.000000 0.722222 0.222222 0.333333 0.000000 0.000000 0.666667 0.000000 0.055556 0.888889 0.055556 0.000000 0.166667 0.777778 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][GA][GC][TC][GA][TCG][CGT][GA][AG]AG[GA][AT]GG[TA]G[GT][TA]GG -------------------------------------------------------------------------------- Time 17.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 36 llr = 342 E-value = 7.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :71584419367:783 pos.-specific C 8194:548:52:63:6 probability G :::111:11113111: matrix T 22::111::11:2:21 bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * * Entropy 1.1 * * * ** * (13.7 bits) 0.8 *** * ** ***** 0.6 ***** *** ***** 0.4 ********** ***** 0.2 **************** 0.0 ---------------- Multilevel CACAACACACAACAAC consensus T C AC ACGTC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2647 367 1.54e-07 GACCGCAACC CACAACCCACGGCAAC AACGTTCTCT 25422 18 1.54e-07 CTCTTCCATC CACAACTCACAAGAAC ATGTTCTTCT 264271 248 2.13e-07 CAATTCATCT CACAACACGCAATAAC CAGTGATGGA 21613 470 2.46e-07 TTTACACACA CACCTCTCACAACAAC TCATTCAACA 24428 132 5.76e-07 ACAAGAAACT CACAAGCCACAGCAAA CTCACAAGCT 7830 148 7.56e-07 TACCCATCAA CACCAAACACAACGAA CGGCAGACTG 6832 485 1.26e-06 TCTGCCTTTG CACATCACATCACAAC 269115 454 1.26e-06 AACACGATAA CACGACTCGCAACAAC CAAGAGCACT 261839 474 1.44e-06 CGCAGCCTCT CACAACACAAAAGCAA ACACTACAAA 11629 93 2.07e-06 CAACATTGAC CACCACTCATGACAAC CTGACACTTT 25414 129 2.95e-06 AGTGAAATTA TTCAACACAAAACCAC TTGCTGTAGA 1481 437 5.73e-06 CGCCCACCGC CACCAACCAAACCAAA CTCATCACCC 23777 186 6.37e-06 CGAGCAACGA TACGATCCACAACAAA ACATCCTTGG 7379 450 7.07e-06 CCGTTGTCCT CTCCTCCCACTACAAA CGCCAACGCC 262535 261 7.07e-06 AACCCGCCTT CCCAACACACCATCAA CTGGCTGGCG 21983 71 7.85e-06 CGATCGTTAG CACAATCCATAGCATC GGGAGAACTG 2916 481 8.71e-06 CTCGTTTCCA TCACAAACACAACAAC AGCC 25608 333 8.71e-06 GCATGGGACG TACAAACCACAACATT TAACGGACAA 264918 436 1.06e-05 CATACTTCGA CACAAGAGACAATCAC AATCAATATA 23786 454 1.89e-05 TTCGTACGAA CACAAAAAGCTACCAC CAACTAAACG 32738 441 2.27e-05 CAAAGTCTTC TTCCACCCATAGCATC AAATCATTTA 25591 406 2.27e-05 CTCACCGCAC CACAGCCCAGAGCATC CGGTTCCCTT bd945 430 2.96e-05 CTCACCGCCT CACGAAAAAACACATC CCTCCGATAA 23803 485 3.23e-05 CAGAAACTCA CACCAGCGACGAGAAC 25637 143 3.52e-05 CGTTATTTAC CACAAAAAAATACCTC TTCCAGTGGG 25378 484 3.84e-05 GACGAAGCCA CACCAAAGAACGTCAC C 19048 26 4.92e-05 GACGTGCTAA TTCCAACAACAATAAA GATTTGCCTC 269386 194 6.75e-05 TAGGTGCCGA CACCTCCCGCCATAAT TCGAATACAC 21400 407 6.75e-05 ATCACTCAAT CACCAATCACTAGAGA CGTCTCTCTC 264399 458 7.29e-05 TCTGATTTCT CTCCACACATCGCGAA ACTACATGCA 20951 449 7.29e-05 CACTATATCG CAACATCCAGTACAAA ATCTACTCAA 269948 433 8.48e-05 TCAATTTTGT CTCCTAACAAAATCTC AAATGTCGTC 23396 483 8.48e-05 TCTCGAGGCA TCAAAACCAACACCAC AA 25553 438 9.14e-05 GAGGCAGTGG CAAAACCGAGAGGAAC TTATCAAGTG 3637 132 1.22e-04 GTGGCATAAC CAAGACACGCAATAGC AGCATCGATT 25423 342 1.50e-04 AGAAGGCGCC TCCAGAACAACGCAAC CACGACCACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2647 1.5e-07 366_[+2]_118 25422 1.5e-07 17_[+2]_467 264271 2.1e-07 247_[+2]_237 21613 2.5e-07 469_[+2]_15 24428 5.8e-07 131_[+2]_353 7830 7.6e-07 147_[+2]_337 6832 1.3e-06 484_[+2] 269115 1.3e-06 453_[+2]_31 261839 1.4e-06 473_[+2]_11 11629 2.1e-06 92_[+2]_392 25414 2.9e-06 128_[+2]_356 1481 5.7e-06 436_[+2]_48 23777 6.4e-06 185_[+2]_299 7379 7.1e-06 449_[+2]_35 262535 7.1e-06 260_[+2]_224 21983 7.9e-06 70_[+2]_414 2916 8.7e-06 480_[+2]_4 25608 8.7e-06 332_[+2]_152 264918 1.1e-05 435_[+2]_49 23786 1.9e-05 453_[+2]_31 32738 2.3e-05 440_[+2]_44 25591 2.3e-05 405_[+2]_79 bd945 3e-05 429_[+2]_55 23803 3.2e-05 484_[+2] 25637 3.5e-05 142_[+2]_342 25378 3.8e-05 483_[+2]_1 19048 4.9e-05 25_[+2]_459 269386 6.8e-05 193_[+2]_291 21400 6.8e-05 406_[+2]_78 264399 7.3e-05 457_[+2]_27 20951 7.3e-05 448_[+2]_36 269948 8.5e-05 432_[+2]_52 23396 8.5e-05 482_[+2]_2 25553 9.1e-05 437_[+2]_47 3637 0.00012 131_[+2]_353 25423 0.00015 341_[+2]_143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=36 2647 ( 367) CACAACCCACGGCAAC 1 25422 ( 18) CACAACTCACAAGAAC 1 264271 ( 248) CACAACACGCAATAAC 1 21613 ( 470) CACCTCTCACAACAAC 1 24428 ( 132) CACAAGCCACAGCAAA 1 7830 ( 148) CACCAAACACAACGAA 1 6832 ( 485) CACATCACATCACAAC 1 269115 ( 454) CACGACTCGCAACAAC 1 261839 ( 474) CACAACACAAAAGCAA 1 11629 ( 93) CACCACTCATGACAAC 1 25414 ( 129) TTCAACACAAAACCAC 1 1481 ( 437) CACCAACCAAACCAAA 1 23777 ( 186) TACGATCCACAACAAA 1 7379 ( 450) CTCCTCCCACTACAAA 1 262535 ( 261) CCCAACACACCATCAA 1 21983 ( 71) CACAATCCATAGCATC 1 2916 ( 481) TCACAAACACAACAAC 1 25608 ( 333) TACAAACCACAACATT 1 264918 ( 436) CACAAGAGACAATCAC 1 23786 ( 454) CACAAAAAGCTACCAC 1 32738 ( 441) TTCCACCCATAGCATC 1 25591 ( 406) CACAGCCCAGAGCATC 1 bd945 ( 430) CACGAAAAAACACATC 1 23803 ( 485) CACCAGCGACGAGAAC 1 25637 ( 143) CACAAAAAAATACCTC 1 25378 ( 484) CACCAAAGAACGTCAC 1 19048 ( 26) TTCCAACAACAATAAA 1 269386 ( 194) CACCTCCCGCCATAAT 1 21400 ( 407) CACCAATCACTAGAGA 1 264399 ( 458) CTCCACACATCGCGAA 1 20951 ( 449) CAACATCCAGTACAAA 1 269948 ( 433) CTCCTAACAAAATCTC 1 23396 ( 483) TCAAAACCAACACCAC 1 25553 ( 438) CAAAACCGAGAGGAAC 1 3637 ( 132) CAAGACACGCAATAGC 1 25423 ( 342) TCCAGAACAACGCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 24294 bayes= 10.2452 E= 7.8e-003 -1181 175 -1181 -26 143 -106 -1181 -68 -95 190 -1181 -1181 82 85 -107 -1181 159 -1181 -207 -94 43 103 -149 -168 73 85 -1181 -94 -127 175 -107 -1181 168 -1181 -75 -1181 -10 119 -149 -94 105 -6 -149 -94 143 -305 9 -1181 -1181 147 -75 -26 137 11 -207 -1181 148 -1181 -207 -46 19 147 -1181 -226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 36 E= 7.8e-003 0.000000 0.777778 0.000000 0.222222 0.722222 0.111111 0.000000 0.166667 0.138889 0.861111 0.000000 0.000000 0.472222 0.416667 0.111111 0.000000 0.805556 0.000000 0.055556 0.138889 0.361111 0.472222 0.083333 0.083333 0.444444 0.416667 0.000000 0.138889 0.111111 0.777778 0.111111 0.000000 0.861111 0.000000 0.138889 0.000000 0.250000 0.527778 0.083333 0.138889 0.555556 0.222222 0.083333 0.138889 0.722222 0.027778 0.250000 0.000000 0.000000 0.638889 0.138889 0.222222 0.694444 0.250000 0.055556 0.000000 0.750000 0.000000 0.055556 0.194444 0.305556 0.638889 0.000000 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]AC[AC]A[CA][AC]CA[CA][AC][AG][CT][AC]A[CA] -------------------------------------------------------------------------------- Time 34.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 15 llr = 191 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:2::::1::31:13: pos.-specific C :71929274837:5:a probability G :::::::1:11::3:: matrix T 837181816121a17: bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * Relative 1.3 ** **** * * * Entropy 1.1 ** **** ** ** ** (18.4 bits) 0.8 ** **** ** ** ** 0.6 ********** ***** 0.4 ********** ***** 0.2 ********** ***** 0.0 ---------------- Multilevel TCTCTCTCTCACTCTC consensus ATA C C C C GA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 263782 436 1.34e-09 CGCTCATACT TCTCTCTCTCTCTCTC TCTCTCTCTC 25423 110 1.34e-09 TCAGTTCAAT TCTCTCTCTCTCTCTC GTAGGATAAT 21983 474 2.25e-08 CACCGTCCTG TCTCTCTGTCACTGTC AAAGAACAAC 262597 389 6.27e-08 TAAAGCAGCC TCCCTCCCCCCCTCTC CTTCACACGA 7379 396 1.56e-07 TTCTCCCCTG TCACTCCCTCACTCAC CAGCCATGCG 23803 388 2.90e-07 AACGGCTCGC TTTCTTTCTCGCTCTC ACATTTCACC 25553 296 5.10e-07 GATAGCTTCT TCTCTTTCCCCTTGTC ATGCATGATA 25591 439 5.45e-07 CTTGCTTTCG TCACTCTCCGCCTGAC GATGATTCCC 21613 270 7.16e-07 TATAGGGGAC TCTCCCTCTGAATCTC CCTTTTATTT 25414 309 1.65e-06 GTCCGTGATT TTTTTCTGCCACTCTC TTTCTCAGGT 20989 356 2.54e-06 TTCACCAACG TCCCCCCTCCCCTGTC TCGACAAGCC 11710 456 3.60e-06 ATCTCATCGT ATTCTCTCTCATTTTC ATTCAGCCAA 261895 117 4.61e-06 ATCTGTTACT TCTCCCTTTCGCTAAC ATGCAGTACG 264271 201 4.92e-06 ATGAAGCTCA ACTCTCTATCCATGAC TCGGCACACC 23777 429 4.92e-06 TGGTCAAACG ATACTCTCCTTCTCTC CACCGGTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263782 1.3e-09 435_[+3]_49 25423 1.3e-09 109_[+3]_375 21983 2.2e-08 473_[+3]_11 262597 6.3e-08 388_[+3]_96 7379 1.6e-07 395_[+3]_89 23803 2.9e-07 387_[+3]_97 25553 5.1e-07 295_[+3]_189 25591 5.4e-07 438_[+3]_46 21613 7.2e-07 269_[+3]_215 25414 1.6e-06 308_[+3]_176 20989 2.5e-06 355_[+3]_129 11710 3.6e-06 455_[+3]_29 261895 4.6e-06 116_[+3]_368 264271 4.9e-06 200_[+3]_284 23777 4.9e-06 428_[+3]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=15 263782 ( 436) TCTCTCTCTCTCTCTC 1 25423 ( 110) TCTCTCTCTCTCTCTC 1 21983 ( 474) TCTCTCTGTCACTGTC 1 262597 ( 389) TCCCTCCCCCCCTCTC 1 7379 ( 396) TCACTCCCTCACTCAC 1 23803 ( 388) TTTCTTTCTCGCTCTC 1 25553 ( 296) TCTCTTTCCCCTTGTC 1 25591 ( 439) TCACTCTCCGCCTGAC 1 21613 ( 270) TCTCCCTCTGAATCTC 1 25414 ( 309) TTTTTCTGCCACTCTC 1 20989 ( 356) TCCCCCCTCCCCTGTC 1 11710 ( 456) ATTCTCTCTCATTTTC 1 261895 ( 117) TCTCCCTTTCGCTAAC 1 264271 ( 201) ACTCTCTATCCATGAC 1 23777 ( 429) ATACTCTCCTTCTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 24294 bayes= 12.3664 E= 1.6e-001 -42 -1055 -1055 158 -1055 167 -1055 0 -42 -79 -1055 132 -1055 201 -1055 -200 -1055 -21 -1055 158 -1055 191 -1055 -100 -1055 -21 -1055 158 -201 153 -81 -100 -1055 79 -1055 117 -1055 179 -81 -200 31 53 -81 -41 -101 167 -1055 -100 -1055 -1055 -1055 191 -201 121 51 -200 -1 -1055 -1055 146 -1055 211 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 15 E= 1.6e-001 0.200000 0.000000 0.000000 0.800000 0.000000 0.733333 0.000000 0.266667 0.200000 0.133333 0.000000 0.666667 0.000000 0.933333 0.000000 0.066667 0.000000 0.200000 0.000000 0.800000 0.000000 0.866667 0.000000 0.133333 0.000000 0.200000 0.000000 0.800000 0.066667 0.666667 0.133333 0.133333 0.000000 0.400000 0.000000 0.600000 0.000000 0.800000 0.133333 0.066667 0.333333 0.333333 0.133333 0.200000 0.133333 0.733333 0.000000 0.133333 0.000000 0.000000 0.000000 1.000000 0.066667 0.533333 0.333333 0.066667 0.266667 0.000000 0.000000 0.733333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA][CT][TA]C[TC]C[TC]C[TC]C[ACT]CT[CG][TA]C -------------------------------------------------------------------------------- Time 51.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11629 2.62e-06 92_[+2(2.07e-06)]_142_\ [+1(3.87e-08)]_229 11710 2.77e-03 332_[+1(7.97e-05)]_102_\ [+3(3.60e-06)]_29 1194 1.54e-04 168_[+1(4.46e-09)]_311 1481 1.90e-02 436_[+2(5.73e-06)]_48 19048 1.36e-06 25_[+2(4.92e-05)]_131_\ [+1(6.34e-10)]_307 20951 1.31e-04 312_[+1(4.01e-07)]_115_\ [+2(7.29e-05)]_36 20989 1.17e-04 154_[+1(4.80e-06)]_180_\ [+3(2.54e-06)]_129 21400 2.18e-01 406_[+2(6.75e-05)]_78 21613 1.87e-06 269_[+3(7.16e-07)]_84_\ [+2(2.49e-05)]_84_[+2(2.46e-07)]_15 21673 8.05e-01 500 21983 1.03e-09 70_[+2(7.85e-06)]_191_\ [+1(1.35e-07)]_109_[+3(4.60e-05)]_50_[+3(2.25e-08)]_11 22227 1.16e-01 297_[+3(7.02e-05)]_187 23396 9.13e-05 74_[+1(1.35e-07)]_387_\ [+2(8.48e-05)]_2 23777 3.39e-04 185_[+2(6.37e-06)]_227_\ [+3(4.92e-06)]_56 23786 1.45e-02 453_[+2(1.89e-05)]_31 23803 2.13e-04 387_[+3(2.90e-07)]_81_\ [+2(3.23e-05)] 24011 2.42e-01 500 24428 1.04e-03 131_[+2(5.76e-07)]_353 25378 1.81e-01 483_[+2(3.84e-05)]_1 25414 1.97e-05 128_[+2(2.95e-06)]_164_\ [+3(1.65e-06)]_176 25422 1.42e-05 17_[+2(1.54e-07)]_3_[+3(3.91e-05)]_\ 448 25423 4.76e-10 32_[+1(5.38e-08)]_56_[+3(1.34e-09)]_\ 375 25553 2.02e-07 295_[+3(5.10e-07)]_105_\ [+1(1.64e-07)]_[+2(9.14e-05)]_47 25591 5.70e-05 405_[+2(2.27e-05)]_17_\ [+3(5.45e-07)]_46 25608 5.08e-03 332_[+2(8.71e-06)]_152 25637 3.93e-02 142_[+2(3.52e-05)]_342 25679 5.62e-01 500 261839 6.70e-04 473_[+2(1.44e-06)]_11 261895 2.64e-02 116_[+3(4.61e-06)]_368 262535 1.50e-02 260_[+2(7.07e-06)]_224 262597 8.06e-07 207_[+1(3.38e-07)]_160_\ [+3(6.27e-08)]_96 263782 3.43e-06 435_[+3(1.34e-09)]_[+3(1.34e-09)]_\ 33 264271 7.55e-08 2_[+1(2.42e-06)]_177_[+3(4.92e-06)]_\ 31_[+2(2.13e-07)]_237 264399 1.56e-04 139_[+1(1.64e-07)]_297_\ [+2(7.29e-05)]_27 2647 1.39e-03 14_[+2(3.84e-05)]_336_\ [+2(1.54e-07)]_118 264918 2.96e-02 435_[+2(1.06e-05)]_25_\ [+2(7.29e-05)]_8 269115 6.48e-06 24_[+1(1.35e-07)]_97_[+1(1.53e-05)]_\ 290_[+2(1.26e-06)]_31 269386 6.08e-03 193_[+2(6.75e-05)]_260_\ [+1(8.52e-05)]_10 269948 2.63e-02 312_[+3(7.24e-05)]_104_\ [+2(8.48e-05)]_52 2916 3.27e-05 311_[+1(2.59e-07)]_148_\ [+2(8.71e-06)]_4 31001 2.34e-04 217_[+1(1.16e-08)]_262 32738 4.07e-02 440_[+2(2.27e-05)]_44 3637 3.04e-03 325_[+1(1.85e-06)]_154 5909 3.94e-01 500 6832 1.40e-02 19_[+2(7.87e-05)]_449_\ [+2(1.26e-06)] 7379 2.05e-05 395_[+3(1.56e-07)]_38_\ [+2(7.07e-06)]_35 7830 1.29e-05 147_[+2(7.56e-07)]_139_\ [+2(6.25e-05)]_12_[+1(9.66e-07)]_149 8732 2.27e-01 500 bd1749 1.06e-03 177_[+1(1.21e-06)]_302 bd945 2.94e-02 429_[+2(2.96e-05)]_55 bd954 3.09e-01 59 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************