******************************************************************************** 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/50/50.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10493 1.0000 500 11752 1.0000 500 2012 1.0000 500 20627 1.0000 500 20893 1.0000 500 21870 1.0000 500 24414 1.0000 500 25881 1.0000 500 263111 1.0000 500 264081 1.0000 500 264570 1.0000 500 28592 1.0000 500 31222 1.0000 500 3551 1.0000 500 35780 1.0000 500 36407 1.0000 500 36525 1.0000 500 37471 1.0000 500 41892 1.0000 500 4581 1.0000 500 bd1464 1.0000 500 bd875 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/50/50.seqs.fa -oc motifs/50 -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 0.244 C 0.235 G 0.257 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.244 C 0.235 G 0.257 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 16 llr = 221 E-value = 1.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 16:7:481644683383:831 pos.-specific C 837:86184562166:68:19 probability G :1311::::::11:1::113: matrix T 1::31:1111:111:21113: bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * ** * * * Entropy 1.0 * * **** * * ** * (19.9 bits) 0.8 ********* * **** ** * 0.6 ******************* * 0.4 ******************* * 0.2 ******************* * 0.0 --------------------- Multilevel CACACCACACCAACCACCAGC consensus CGT A CAA AA A T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36525 480 3.54e-10 AGCTGCTTGT CACACAACACAAAACTCCAGC 36407 480 3.54e-10 AGCTGCTTGT CACACAACACAAAACTCCAGC 264081 473 6.27e-10 TACAGCAAGG CACACCACATCAACGACCAAC TGACACC 11752 474 9.48e-10 CGACCCCTCC CCGACCACCACCACCACCATC ACCAAC bd1464 320 2.66e-09 CCACCCGCCT CGGACAACACCAACAAACATC AACAGAGGAC 10493 201 6.17e-09 TCTTTCCAAA CAGTCCACCCCATCCACCATC AGTGCTGCGG 31222 480 4.67e-08 GAGTCTCCAT TAGACCACACAAGCCAACAAC 28592 290 7.54e-08 GACAACCTCT ACCTCCACCACACCCAACAAC CATGAGCTCA 35780 476 3.94e-07 CCCTCCTCTC TCCACCACAAAAACATACGTC CAAC 2012 412 9.20e-07 TCCCTCGTGC CACACAAACCCTACCACTTGC CGAGCATACA 24414 480 1.42e-06 ACAACACCGC CACTGCACTCACAACATCACC 20893 31 1.42e-06 CTGGTTTGCT ACCGCCACCACTATCACCAAC TAATTCTCCT 20627 13 2.29e-06 AATCTCCTCC CACTCATCAAAGACGAACGTC TCGTGTCACC 25881 339 2.45e-06 ACGTGCTTCG CACAGATCAACACACACGAGA GATGTTAGAA 263111 417 5.22e-06 CCCGCCTTCC CACATCCACTCCAAAACCAGC TCCAGTAGCT 264570 314 9.30e-06 ATTGTGGATA CGGACAATACCAACAATGACA GCAGCAACCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36525 3.5e-10 479_[+1] 36407 3.5e-10 479_[+1] 264081 6.3e-10 472_[+1]_7 11752 9.5e-10 473_[+1]_6 bd1464 2.7e-09 319_[+1]_160 10493 6.2e-09 200_[+1]_279 31222 4.7e-08 479_[+1] 28592 7.5e-08 289_[+1]_190 35780 3.9e-07 475_[+1]_4 2012 9.2e-07 411_[+1]_68 24414 1.4e-06 479_[+1] 20893 1.4e-06 30_[+1]_449 20627 2.3e-06 12_[+1]_467 25881 2.4e-06 338_[+1]_141 263111 5.2e-06 416_[+1]_63 264570 9.3e-06 313_[+1]_166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=16 36525 ( 480) CACACAACACAAAACTCCAGC 1 36407 ( 480) CACACAACACAAAACTCCAGC 1 264081 ( 473) CACACCACATCAACGACCAAC 1 11752 ( 474) CCGACCACCACCACCACCATC 1 bd1464 ( 320) CGGACAACACCAACAAACATC 1 10493 ( 201) CAGTCCACCCCATCCACCATC 1 31222 ( 480) TAGACCACACAAGCCAACAAC 1 28592 ( 290) ACCTCCACCACACCCAACAAC 1 35780 ( 476) TCCACCACAAAAACATACGTC 1 2012 ( 412) CACACAAACCCTACCACTTGC 1 24414 ( 480) CACTGCACTCACAACATCACC 1 20893 ( 31) ACCGCCACCACTATCACCAAC 1 20627 ( 13) CACTCATCAAAGACGAACGTC 1 25881 ( 339) CACAGATCAACACACACGAGA 1 263111 ( 417) CACATCCACTCCAAAACCAGC 1 264570 ( 314) CGGACAATACCAACAATGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10560 bayes= 9.36413 E= 1.1e-009 -97 168 -1064 -108 135 9 -104 -1064 -1064 155 28 -1064 149 -1064 -204 -8 -1064 179 -104 -207 84 126 -1064 -1064 173 -191 -1064 -108 -97 179 -1064 -207 120 68 -1064 -207 62 109 -1064 -108 62 141 -1064 -1064 135 -32 -204 -108 162 -91 -204 -207 35 141 -1064 -207 3 141 -104 -1064 173 -1064 -1064 -49 35 126 -1064 -108 -1064 179 -104 -207 173 -1064 -104 -207 3 -91 28 24 -97 190 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 1.1e-009 0.125000 0.750000 0.000000 0.125000 0.625000 0.250000 0.125000 0.000000 0.000000 0.687500 0.312500 0.000000 0.687500 0.000000 0.062500 0.250000 0.000000 0.812500 0.125000 0.062500 0.437500 0.562500 0.000000 0.000000 0.812500 0.062500 0.000000 0.125000 0.125000 0.812500 0.000000 0.062500 0.562500 0.375000 0.000000 0.062500 0.375000 0.500000 0.000000 0.125000 0.375000 0.625000 0.000000 0.000000 0.625000 0.187500 0.062500 0.125000 0.750000 0.125000 0.062500 0.062500 0.312500 0.625000 0.000000 0.062500 0.250000 0.625000 0.125000 0.000000 0.812500 0.000000 0.000000 0.187500 0.312500 0.562500 0.000000 0.125000 0.000000 0.812500 0.125000 0.062500 0.812500 0.000000 0.125000 0.062500 0.250000 0.125000 0.312500 0.312500 0.125000 0.875000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][CG][AT]C[CA]AC[AC][CA][CA]AA[CA][CA]A[CA]CA[GTA]C -------------------------------------------------------------------------------- Time 3.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 19 llr = 227 E-value = 4.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::21:1112122::::132 pos.-specific C 58495182535733a557737 probability G 22::3:1222::32:2::22: matrix T 3:61:816343224:353:31 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * ** * * Entropy 1.0 *** ** * * *** * (17.3 bits) 0.8 *** ** * * *** * 0.6 ******* ** ***** * 0.4 ********* ** ***** * 0.2 ************ ****** * 0.0 --------------------- Multilevel CCTCCTCTCTCCGTCCCCCAC consensus T C G CTCTTCC TTTGCA sequence A GA A T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35780 453 9.02e-11 GTAGAATGGG CCTCCTCTCTCCTCCCTCCTC TCTCCACCAC 264081 159 1.99e-08 TTCACAGCCA TCTCCTCTCGCTGTCCCTCAC CGCAGCTGGC 21870 362 4.07e-08 AAAGTTTTGT GCTCCTCGCTCCCGCCCCCGC TTCTACATCT 4581 437 2.30e-07 GAACTCAAGT CCTCGTCTGGCTGTCGTCCTC CTTTCGAGCT 20893 447 4.39e-07 GTTCCAGTTT CCTCCTGTCGTCGTCCTCCCA ACCAGGACAA 28592 262 4.87e-07 CTCGCGAATC TCTCGTCTCCTCAACCTTGAC AACCTCTACC 37471 429 5.96e-07 TGGAGGTGCC CCCCCTTTTCTCGTCTCCCTA TCATCTGTTT 36525 430 7.26e-07 GAGGCTTCTC CCCCAACCTCCCTGCCTCCAC GTGTCGTTCC 36407 430 7.26e-07 GAGGCTTCTC CCCCAACCTCCCTGCCTCCAC GTGTCGTTCC bd875 427 7.99e-07 ACCGACGACT GCCTCTCTTTTCGCCTCCCTC GGTGTCGTTG bd1464 294 7.99e-07 CACTTGCTAA CCCTCTCTCTCCCACCCCACC CGCCTCGGAC 2012 387 1.27e-06 GCCGTCGTCG TCTCGTCGATACCCCTCCCTC GTGCCACACA 10493 239 1.27e-06 CGGCCGTTGT TGTCCTCCGAACTTCCCCCAC GAATATTGGC 11752 411 3.50e-06 TTCATTTTTC TCTCCTTTTGTCACCCCTGCC GACGGTCGAA 20627 425 6.38e-06 CAACCACTTC CGTCGTCCGTCCGTCGTCCCT TTTGCCCATC 264570 469 8.44e-06 GTTGGGTGCA TCTCATCTTCATCTCTCTGAA CTCGTGAAGG 263111 391 9.65e-06 CGGCGCACCC GCCCATCGCCCAACCGCCCGC CTTCCCACAT 24414 13 1.10e-05 ACAACTTCGC CGCCGCCTCTCCATCTTCGCA CAATCGTACA 25881 423 1.81e-05 TAGCGGCTTT CCTCGTCACAATCACTTTCGC ATTCTTTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35780 9e-11 452_[+2]_27 264081 2e-08 158_[+2]_321 21870 4.1e-08 361_[+2]_118 4581 2.3e-07 436_[+2]_43 20893 4.4e-07 446_[+2]_33 28592 4.9e-07 261_[+2]_218 37471 6e-07 428_[+2]_51 36525 7.3e-07 429_[+2]_50 36407 7.3e-07 429_[+2]_50 bd875 8e-07 426_[+2]_53 bd1464 8e-07 293_[+2]_186 2012 1.3e-06 386_[+2]_93 10493 1.3e-06 238_[+2]_241 11752 3.5e-06 410_[+2]_69 20627 6.4e-06 424_[+2]_55 264570 8.4e-06 468_[+2]_11 263111 9.7e-06 390_[+2]_89 24414 1.1e-05 12_[+2]_467 25881 1.8e-05 422_[+2]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=19 35780 ( 453) CCTCCTCTCTCCTCCCTCCTC 1 264081 ( 159) TCTCCTCTCGCTGTCCCTCAC 1 21870 ( 362) GCTCCTCGCTCCCGCCCCCGC 1 4581 ( 437) CCTCGTCTGGCTGTCGTCCTC 1 20893 ( 447) CCTCCTGTCGTCGTCCTCCCA 1 28592 ( 262) TCTCGTCTCCTCAACCTTGAC 1 37471 ( 429) CCCCCTTTTCTCGTCTCCCTA 1 36525 ( 430) CCCCAACCTCCCTGCCTCCAC 1 36407 ( 430) CCCCAACCTCCCTGCCTCCAC 1 bd875 ( 427) GCCTCTCTTTTCGCCTCCCTC 1 bd1464 ( 294) CCCTCTCTCTCCCACCCCACC 1 2012 ( 387) TCTCGTCGATACCCCTCCCTC 1 10493 ( 239) TGTCCTCCGAACTTCCCCCAC 1 11752 ( 411) TCTCCTTTTGTCACCCCTGCC 1 20627 ( 425) CGTCGTCCGTCCGTCGTCCCT 1 264570 ( 469) TCTCATCTTCATCTCTCTGAA 1 263111 ( 391) GCCCATCGCCCAACCGCCCGC 1 24414 ( 13) CGCCGCCTCTCCATCTTCGCA 1 25881 ( 423) CCTCGTCACAATCACTTTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10560 bayes= 9.31094 E= 4.2e-006 -1089 116 -70 26 -1089 184 -70 -1089 -1089 65 -1089 126 -1089 193 -1089 -132 -22 101 30 -1089 -121 -215 -1089 167 -1089 184 -228 -132 -221 -16 -70 113 -221 101 -70 26 -121 43 -29 48 -22 116 -1089 0 -221 165 -1089 -33 -22 16 30 -33 -63 16 -70 67 -1089 209 -1089 -1089 -1089 116 -70 26 -1089 116 -1089 84 -1089 165 -1089 0 -221 165 -29 -1089 37 16 -70 0 -22 165 -1089 -232 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 19 E= 4.2e-006 0.000000 0.526316 0.157895 0.315789 0.000000 0.842105 0.157895 0.000000 0.000000 0.368421 0.000000 0.631579 0.000000 0.894737 0.000000 0.105263 0.210526 0.473684 0.315789 0.000000 0.105263 0.052632 0.000000 0.842105 0.000000 0.842105 0.052632 0.105263 0.052632 0.210526 0.157895 0.578947 0.052632 0.473684 0.157895 0.315789 0.105263 0.315789 0.210526 0.368421 0.210526 0.526316 0.000000 0.263158 0.052632 0.736842 0.000000 0.210526 0.210526 0.263158 0.315789 0.210526 0.157895 0.263158 0.157895 0.421053 0.000000 1.000000 0.000000 0.000000 0.000000 0.526316 0.157895 0.315789 0.000000 0.526316 0.000000 0.473684 0.000000 0.736842 0.000000 0.263158 0.052632 0.736842 0.210526 0.000000 0.315789 0.263158 0.157895 0.263158 0.210526 0.736842 0.000000 0.052632 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]C[TC]C[CGA]TC[TC][CT][TCG][CTA][CT][GCAT][TC]C[CT][CT][CT][CG][ACT][CA] -------------------------------------------------------------------------------- Time 8.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 17 llr = 208 E-value = 2.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::12233:2312371:25: pos.-specific C ::3:15::51121::1:11: probability G 9:29126227555738a549 matrix T 1a5:711521112::::2:1 bits 2.1 1.9 * * 1.7 * * * 1.5 ** * * * Relative 1.3 ** * * * Entropy 1.0 ** * **** * (17.6 bits) 0.8 ** * **** ** 0.6 ** ** * ** **** ** 0.4 ***** ***** **** ** 0.2 ******************** 0.0 -------------------- Multilevel GTTGTCGTCGGGGGAGGGAG consensus C AAAG ACTAG TG sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 36525 368 3.75e-10 GAAAAAAGGA GTTGTCGACGAGTGAGGGAG TGGAGTAGAC 36407 368 3.75e-10 GAAAAAAGGA GTTGTCGACGAGTGAGGGAG TGGAGTAGAC 20627 65 4.68e-10 CGGTGGCGGC GTTGTCGTCGGGAGAGGTAG CAGTAGCCTG 11752 337 1.67e-08 CTGTGTGTGT GTGGTGGAGGGGGAAGGGAG CTATTGGATA bd875 119 6.24e-08 GCAGGGCAAC GTCGTCATGGGGGGGCGGAG GGACTTCATG 37471 385 1.13e-07 TTGGCATAGT GTCGTAGTCGAAGAGGGGGG TGCTAGGTGT 2012 65 1.47e-06 AAGACTTGAG GTTGGCAGGAGGAGAGGGAG GTTGAAGAAG 10493 99 1.59e-06 TGACGTTTCG GTTGCCTTCGGGGGAGGAGT TCATTGTGAT 3551 170 2.04e-06 AGTTGAATTG GTGGTAGTTGGTGAGGGCAG ACGAGAACGA 24414 142 3.01e-06 AAGGCTCGTC GTGGTCTTCGTCGGAGGTCG AGAACGAAGG 41892 140 3.50e-06 GTTTGTTGTT GTTGTTGTTGCGTGGAGGAG ATGAGGTGTA 21870 110 3.76e-06 GTTGTGTGTG GTGATTGTGGGTGGAGGTGG TGAGATCCCC 31222 172 5.01e-06 GATCGTACAT GTCGAGATCAAAGGGGGTGG AGAATAGTGG 263111 324 5.76e-06 AAGTTTGTAT TTTGTGGGTGCGCGAGGGGG GTTACACCTG 264081 355 7.05e-06 TGCACGCAGG GTCGACGACCGCTGACGAGG GCGATGACAT 35780 341 1.39e-05 GTGTAGAAAG TTCGAAAGTAGCGAAGGGGG GTTGAGTCAT 20893 401 1.66e-05 GTAAACTGTA GTTGTAAACTACAAAGGAAT ATTTAATATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36525 3.8e-10 367_[+3]_113 36407 3.8e-10 367_[+3]_113 20627 4.7e-10 64_[+3]_416 11752 1.7e-08 336_[+3]_144 bd875 6.2e-08 118_[+3]_362 37471 1.1e-07 384_[+3]_96 2012 1.5e-06 64_[+3]_416 10493 1.6e-06 98_[+3]_382 3551 2e-06 169_[+3]_311 24414 3e-06 141_[+3]_339 41892 3.5e-06 139_[+3]_341 21870 3.8e-06 109_[+3]_371 31222 5e-06 171_[+3]_309 263111 5.8e-06 323_[+3]_157 264081 7e-06 354_[+3]_126 35780 1.4e-05 340_[+3]_140 20893 1.7e-05 400_[+3]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=17 36525 ( 368) GTTGTCGACGAGTGAGGGAG 1 36407 ( 368) GTTGTCGACGAGTGAGGGAG 1 20627 ( 65) GTTGTCGTCGGGAGAGGTAG 1 11752 ( 337) GTGGTGGAGGGGGAAGGGAG 1 bd875 ( 119) GTCGTCATGGGGGGGCGGAG 1 37471 ( 385) GTCGTAGTCGAAGAGGGGGG 1 2012 ( 65) GTTGGCAGGAGGAGAGGGAG 1 10493 ( 99) GTTGCCTTCGGGGGAGGAGT 1 3551 ( 170) GTGGTAGTTGGTGAGGGCAG 1 24414 ( 142) GTGGTCTTCGTCGGAGGTCG 1 41892 ( 140) GTTGTTGTTGCGTGGAGGAG 1 21870 ( 110) GTGATTGTGGGTGGAGGTGG 1 31222 ( 172) GTCGAGATCAAAGGGGGTGG 1 263111 ( 324) TTTGTGGGTGCGCGAGGGGG 1 264081 ( 355) GTCGACGACCGCTGACGAGG 1 35780 ( 341) TTCGAAAGTAGCGAAGGGGG 1 20893 ( 401) GTTGTAAACTACAAAGGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 10582 bayes= 10.0752 E= 2.1e-004 -1073 -1073 178 -116 -1073 -1073 -1073 192 -1073 33 -13 83 -205 -1073 187 -1073 -47 -199 -212 142 -6 100 -54 -116 27 -1073 119 -116 27 -1073 -54 100 -1073 117 -13 -16 -47 -199 146 -216 27 -100 104 -216 -105 0 104 -116 -47 -199 104 -16 27 -1073 146 -1073 153 -1073 19 -1073 -205 -100 168 -1073 -1073 -1073 196 -1073 -47 -199 104 -16 111 -199 68 -1073 -1073 -1073 178 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 17 E= 2.1e-004 0.000000 0.000000 0.882353 0.117647 0.000000 0.000000 0.000000 1.000000 0.000000 0.294118 0.235294 0.470588 0.058824 0.000000 0.941176 0.000000 0.176471 0.058824 0.058824 0.705882 0.235294 0.470588 0.176471 0.117647 0.294118 0.000000 0.588235 0.117647 0.294118 0.000000 0.176471 0.529412 0.000000 0.529412 0.235294 0.235294 0.176471 0.058824 0.705882 0.058824 0.294118 0.117647 0.529412 0.058824 0.117647 0.235294 0.529412 0.117647 0.176471 0.058824 0.529412 0.235294 0.294118 0.000000 0.705882 0.000000 0.705882 0.000000 0.294118 0.000000 0.058824 0.117647 0.823529 0.000000 0.000000 0.000000 1.000000 0.000000 0.176471 0.058824 0.529412 0.235294 0.529412 0.058824 0.411765 0.000000 0.000000 0.000000 0.882353 0.117647 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GT[TCG]GT[CA][GA][TA][CGT]G[GA][GC][GT][GA][AG]GG[GT][AG]G -------------------------------------------------------------------------------- Time 12.15 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10493 5.57e-10 98_[+3(1.59e-06)]_25_[+3(2.39e-06)]_\ 37_[+1(6.17e-09)]_17_[+2(1.27e-06)]_169_[+2(8.68e-05)]_51 11752 3.50e-12 283_[+3(1.04e-06)]_33_\ [+3(1.67e-08)]_54_[+2(3.50e-06)]_42_[+1(9.48e-10)]_6 2012 5.21e-08 64_[+3(1.47e-06)]_257_\ [+2(9.39e-05)]_24_[+2(1.27e-06)]_4_[+1(9.20e-07)]_68 20627 3.16e-10 12_[+1(2.29e-06)]_31_[+3(4.68e-10)]_\ 340_[+2(6.38e-06)]_55 20893 2.66e-07 30_[+1(1.42e-06)]_349_\ [+3(1.66e-05)]_26_[+2(4.39e-07)]_33 21870 1.06e-06 109_[+3(3.76e-06)]_232_\ [+2(4.07e-08)]_118 24414 1.05e-06 12_[+2(1.10e-05)]_27_[+2(9.03e-05)]_\ 60_[+3(3.01e-06)]_318_[+1(1.42e-06)] 25881 8.94e-05 338_[+1(2.45e-06)]_63_\ [+2(1.81e-05)]_57 263111 5.35e-06 323_[+3(5.76e-06)]_47_\ [+2(9.65e-06)]_5_[+1(5.22e-06)]_63 264081 5.40e-12 158_[+2(1.99e-08)]_175_\ [+3(7.05e-06)]_98_[+1(6.27e-10)]_7 264570 8.78e-04 313_[+1(9.30e-06)]_134_\ [+2(8.44e-06)]_11 28592 1.61e-06 261_[+2(4.87e-07)]_7_[+1(7.54e-08)]_\ 100_[+1(6.99e-05)]_69 31222 8.46e-06 171_[+3(5.01e-06)]_288_\ [+1(4.67e-08)] 3551 2.77e-02 169_[+3(2.04e-06)]_311 35780 2.72e-11 340_[+3(1.39e-05)]_92_\ [+2(9.02e-11)]_2_[+1(3.94e-07)]_4 36407 8.60e-15 367_[+3(3.75e-10)]_42_\ [+2(7.26e-07)]_29_[+1(3.54e-10)] 36525 8.60e-15 367_[+3(3.75e-10)]_42_\ [+2(7.26e-07)]_29_[+1(3.54e-10)] 37471 8.50e-07 384_[+3(1.13e-07)]_24_\ [+2(5.96e-07)]_51 41892 3.68e-02 139_[+3(3.50e-06)]_341 4581 1.31e-03 436_[+2(2.30e-07)]_43 bd1464 5.90e-08 293_[+2(7.99e-07)]_5_[+1(2.66e-09)]_\ 160 bd875 4.16e-07 118_[+3(6.24e-08)]_248_\ [+2(8.68e-05)]_19_[+2(7.99e-07)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************