******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.6.1 (Release date: Mon Mar 21 15:08:38 EST 2011) 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= GATATopEnh.radius25bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr12:32050294-32050344 1.0000 50 chr13:14543015-14543065 1.0000 50 chr14:118194779-11819482 1.0000 50 chr15:66826304-66826354 1.0000 50 chr18:38495027-38495077 1.0000 50 chr18:32542596-32542646 1.0000 50 chr1:130300261-130300311 1.0000 50 chr1:134093055-134093105 1.0000 50 chr3:146405913-146405963 1.0000 50 chr6:88203156-88203206 1.0000 50 chr6:88117084-88117134 1.0000 50 chr7:103861092-103861142 1.0000 50 chr7:103861104-103861154 1.0000 50 chr7:97210195-97210245 1.0000 50 chr7:16295063-16295113 1.0000 50 chr7:111004333-111004383 1.0000 50 chr8:122313437-122313487 1.0000 50 chr9:123958119-123958169 1.0000 50 chrX:7971530-7971580 1.0000 50 chrX:7841203-7841253 1.0000 50 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme GATATopEnh.radius25bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATATopEnh.radius25bp.meme.maxw25 model: mod= zoops nmotifs= 10 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 25 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 20 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= 1000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.227 C 0.253 G 0.281 T 0.239 Background letter frequencies (from dataset with add-one prior applied): A 0.227 C 0.253 G 0.281 T 0.239 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 20 sites = 11 llr = 128 E-value = 1.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 33:::3:542:25:9:5524 pos.-specific C :5::4:534:45::1113:: probability G 12:a2421276:19::3255 matrix T 6:a:544211:441:92:32 bits 2.1 * 1.9 ** 1.7 ** ** 1.5 ** *** Relative 1.3 ** *** Entropy 1.1 ** *** (16.8 bits) 0.9 * ** ** **** 0.6 **** ******* * 0.4 ******* ******* *** 0.2 ******************** 0.0 -------------------- Multilevel TCTGTGCAAGGCAGATAAGG consensus AA CTTCC CTT GCTA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- chr6:88203156-88203206 31 1.93e-08 TATCCGGACA TCTGCAGCCGGTAGATAAGG chr3:146405913-146405963 4 1.93e-08 CCA TCTGTACAGGGAAGATAATA GGTCCAGGGA chr7:103861104-103861154 4 3.04e-07 TGC TGTGCTCAAGCTAGATGCTG GCTCACAAGG chr7:103861092-103861142 16 3.04e-07 TCAGCACTGC TGTGCTCAAGCTAGATGCTG GCTCACAAGG chr14:118194779-11819482 8 4.31e-07 TCCAACA TATGTTTTTGCCAGATAAGT AAACAGTGTG chr18:32542596-32542646 23 2.28e-06 AGGCTCAGCT ACTGTTTCAGGCTTATCAGA GGCAGACC chr7:111004333-111004383 15 5.37e-06 GATATGGGCT TATGGGCTCACTAGATGGGG CCAGGCCAGC chr1:130300261-130300311 14 6.19e-06 GCAGTTGGTT AATGTGTGCTGCTGATAAAA GCAGTTTAAC chr7:97210195-97210245 29 6.63e-06 AGCCACAGAA TCTGGAGAAAGATGATTGGA GG chr8:122313437-122313487 10 8.63e-06 GTTATCTAG ACTGTGTCCGGCTGACTAAT CTTGCAGGCC chr1:134093055-134093105 23 2.13e-05 GGGCGGGGCT GCTGCGCAGGGCGGCTACGG CCACGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:88203156-88203206 1.9e-08 30_[+1] chr3:146405913-146405963 1.9e-08 3_[+1]_27 chr7:103861104-103861154 3e-07 3_[+1]_27 chr7:103861092-103861142 3e-07 15_[+1]_15 chr14:118194779-11819482 4.3e-07 7_[+1]_23 chr18:32542596-32542646 2.3e-06 22_[+1]_8 chr7:111004333-111004383 5.4e-06 14_[+1]_16 chr1:130300261-130300311 6.2e-06 13_[+1]_17 chr7:97210195-97210245 6.6e-06 28_[+1]_2 chr8:122313437-122313487 8.6e-06 9_[+1]_21 chr1:134093055-134093105 2.1e-05 22_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=11 chr6:88203156-88203206 ( 31) TCTGCAGCCGGTAGATAAGG 1 chr3:146405913-146405963 ( 4) TCTGTACAGGGAAGATAATA 1 chr7:103861104-103861154 ( 4) TGTGCTCAAGCTAGATGCTG 1 chr7:103861092-103861142 ( 16) TGTGCTCAAGCTAGATGCTG 1 chr14:118194779-11819482 ( 8) TATGTTTTTGCCAGATAAGT 1 chr18:32542596-32542646 ( 23) ACTGTTTCAGGCTTATCAGA 1 chr7:111004333-111004383 ( 15) TATGGGCTCACTAGATGGGG 1 chr1:130300261-130300311 ( 14) AATGTGTGCTGCTGATAAAA 1 chr7:97210195-97210245 ( 29) TCTGGAGAAAGATGATTGGA 1 chr8:122313437-122313487 ( 10) ACTGTGTCCGGCTGACTAAT 1 chr1:134093055-134093105 ( 23) GCTGCGCAGGGCGGCTACGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 620 bayes= 6.15164 E= 1.2e-003 26 -1010 -162 141 26 111 -63 -1010 -1010 -1010 -1010 206 -1010 -1010 183 -1010 -1010 52 -63 93 26 -1010 37 60 -1010 84 -63 60 100 11 -162 -39 68 52 -63 -139 -32 -1010 137 -139 -1010 52 118 -1010 -32 84 -1010 60 126 -1010 -162 60 -1010 -1010 169 -139 200 -147 -1010 -1010 -1010 -147 -1010 193 100 -147 -4 -39 126 11 -63 -1010 -32 -1010 96 19 68 -1010 69 -39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 11 E= 1.2e-003 0.272727 0.000000 0.090909 0.636364 0.272727 0.545455 0.181818 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.363636 0.181818 0.454545 0.272727 0.000000 0.363636 0.363636 0.000000 0.454545 0.181818 0.363636 0.454545 0.272727 0.090909 0.181818 0.363636 0.363636 0.181818 0.090909 0.181818 0.000000 0.727273 0.090909 0.000000 0.363636 0.636364 0.000000 0.181818 0.454545 0.000000 0.363636 0.545455 0.000000 0.090909 0.363636 0.000000 0.000000 0.909091 0.090909 0.909091 0.090909 0.000000 0.000000 0.000000 0.090909 0.000000 0.909091 0.454545 0.090909 0.272727 0.181818 0.545455 0.272727 0.181818 0.000000 0.181818 0.000000 0.545455 0.272727 0.363636 0.000000 0.454545 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA][CA]TG[TC][GTA][CT][AC][AC]G[GC][CT][AT]GAT[AG][AC][GT][GA] -------------------------------------------------------------------------------- Time 0.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 12 sites = 9 llr = 89 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::616146::1: pos.-specific C 3a:7266::19: probability G 7::22:::a6:: matrix T ::4::3:4:3:a bits 2.1 * 1.9 * * * 1.7 * * * 1.5 * * ** Relative 1.3 * * ** Entropy 1.1 *** *** ** (14.2 bits) 0.9 *** *** ** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GCACACCAGGCT consensus C TGCTAT T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ chr7:103861104-103861154 24 5.43e-07 CTAGATGCTG GCTCACAAGGCT GAACACACCC chr7:103861092-103861142 36 5.43e-07 CTAGATGCTG GCTCACAAGGCT GAA chr18:38495027-38495077 17 1.22e-05 GAGCTTGGCA GCACCTCTGTCT GGTGTGGGGA chrX:7841203-7841253 19 1.34e-05 TCAGTACGGT GCACGTCTGTCT ATCGGTTGGC chr15:66826304-66826354 28 1.34e-05 TCTTGTGTCT GCAGCCCAGGCT CTCTGGCCTT chr13:14543015-14543065 6 1.34e-05 CTCCA GCTCAAATGGCT CCTGGGAGTC chr6:88117084-88117134 25 2.78e-05 ACCTTCTTTA CCACATCAGGAT ACAGAGCATT chr9:123958119-123958169 3 3.66e-05 GG CCTAACATGTCT GTTTGTTTTT chr7:111004333-111004383 35 7.09e-05 CTAGATGGGG CCAGGCCAGCCT GCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103861104-103861154 5.4e-07 23_[+2]_15 chr7:103861092-103861142 5.4e-07 35_[+2]_3 chr18:38495027-38495077 1.2e-05 16_[+2]_22 chrX:7841203-7841253 1.3e-05 18_[+2]_20 chr15:66826304-66826354 1.3e-05 27_[+2]_11 chr13:14543015-14543065 1.3e-05 5_[+2]_33 chr6:88117084-88117134 2.8e-05 24_[+2]_14 chr9:123958119-123958169 3.7e-05 2_[+2]_36 chr7:111004333-111004383 7.1e-05 34_[+2]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=9 chr7:103861104-103861154 ( 24) GCTCACAAGGCT 1 chr7:103861092-103861142 ( 36) GCTCACAAGGCT 1 chr18:38495027-38495077 ( 17) GCACCTCTGTCT 1 chrX:7841203-7841253 ( 19) GCACGTCTGTCT 1 chr15:66826304-66826354 ( 28) GCAGCCCAGGCT 1 chr13:14543015-14543065 ( 6) GCTCAAATGGCT 1 chr6:88117084-88117134 ( 25) CCACATCAGGAT 1 chr9:123958119-123958169 ( 3) CCTAACATGTCT 1 chr7:111004333-111004383 ( 35) CCAGGCCAGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 780 bayes= 6.55646 E= 1.2e+000 -982 40 125 -982 -982 198 -982 -982 129 -982 -982 89 -103 140 -34 -982 129 -19 -34 -982 -103 113 -982 48 97 113 -982 -982 129 -982 -982 89 -982 -982 183 -982 -982 -119 98 48 -103 181 -982 -982 -982 -982 -982 206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 1.2e+000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.111111 0.666667 0.222222 0.000000 0.555556 0.222222 0.222222 0.000000 0.111111 0.555556 0.000000 0.333333 0.444444 0.555556 0.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.555556 0.333333 0.111111 0.888889 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC]C[AT][CG][ACG][CT][CA][AT]G[GT]CT -------------------------------------------------------------------------------- Time 0.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 11 sites = 4 llr = 46 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a:8:8::a:3: pos.-specific C :a:5::a:5:: probability G :::3:a::3:a matrix T ::333:::38: bits 2.1 * * 1.9 ** *** * 1.7 ** *** * 1.5 ** *** * Relative 1.3 *** **** ** Entropy 1.1 *** **** ** (16.7 bits) 0.9 *** **** ** 0.6 *** **** ** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel ACACAGCACTG consensus TGT GA sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr13:14543015-14543065 28 5.93e-07 CCTGGGAGTC ACATAGCACTG TTCCTAGAAA chr7:103861092-103861142 4 1.68e-06 ATG ACTCAGCACTG CTGTGCTCAA chr6:88117084-88117134 37 2.29e-06 ACATCAGGAT ACAGAGCATTG CAT chr18:38495027-38495077 38 1.05e-05 TGGTGTGGGG ACACTGCAGAG CC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:14543015-14543065 5.9e-07 27_[+3]_12 chr7:103861092-103861142 1.7e-06 3_[+3]_36 chr6:88117084-88117134 2.3e-06 36_[+3]_3 chr18:38495027-38495077 1.1e-05 37_[+3]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=11 seqs=4 chr13:14543015-14543065 ( 28) ACATAGCACTG 1 chr7:103861092-103861142 ( 4) ACTCAGCACTG 1 chr6:88117084-88117134 ( 37) ACAGAGCATTG 1 chr18:38495027-38495077 ( 38) ACACTGCAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 800 bayes= 7.63662 E= 1.8e+002 214 -865 -865 -865 -865 198 -865 -865 172 -865 -865 6 -865 98 -17 6 172 -865 -865 6 -865 -865 183 -865 -865 198 -865 -865 214 -865 -865 -865 -865 98 -17 6 14 -865 -865 165 -865 -865 183 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 4 E= 1.8e+002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AC[AT][CGT][AT]GCA[CGT][TA]G -------------------------------------------------------------------------------- Time 0.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 8 sites = 2 llr = 23 E-value = 7.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A a:a::a:: pos.-specific C :a:a:::a probability G :::::::: matrix T ::::a:a: bits 2.1 * * *** 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.5 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACACTATC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:7841203-7841253 3 1.08e-05 AA ACACTATC AGTACGGTGC chr15:66826304-66826354 12 1.08e-05 CTGCTACCTC ACACTATC TTGTGTCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:7841203-7841253 1.1e-05 2_[+4]_40 chr15:66826304-66826354 1.1e-05 11_[+4]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=8 seqs=2 chrX:7841203-7841253 ( 3) ACACTATC 1 chr15:66826304-66826354 ( 12) ACACTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 860 bayes= 8.74483 E= 7.3e+002 213 -765 -765 -765 -765 198 -765 -765 213 -765 -765 -765 -765 198 -765 -765 -765 -765 -765 206 213 -765 -765 -765 -765 -765 -765 206 -765 198 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.3e+002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- ACACTATC -------------------------------------------------------------------------------- Time 0.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 8 sites = 2 llr = 21 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A :5a:a:a: pos.-specific C :5:::::: probability G :::a:::: matrix T a::::a:a bits 2.1 * * **** 1.9 * ****** 1.7 * ****** 1.5 * ****** Relative 1.3 * ****** Entropy 1.1 ******** (15.5 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TAAGATAT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:32050294-32050344 20 1.02e-05 TATACCATAT TAAGATAT CAGCGATTCC chr7:111004333-111004383 2 2.15e-05 C TCAGATAT GGGCTTATGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:32050294-32050344 1e-05 19_[+5]_23 chr7:111004333-111004383 2.2e-05 1_[+5]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=8 seqs=2 chr12:32050294-32050344 ( 20) TAAGATAT 1 chr7:111004333-111004383 ( 2) TCAGATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 860 bayes= 8.74483 E= 1.4e+003 -765 -765 -765 206 113 98 -765 -765 213 -765 -765 -765 -765 -765 183 -765 213 -765 -765 -765 -765 -765 -765 206 213 -765 -765 -765 -765 -765 -765 206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.4e+003 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- T[AC]AGATAT -------------------------------------------------------------------------------- Time 0.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 11 sites = 2 llr = 27 E-value = 2.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A ::a5:5a:a:a pos.-specific C ::::a5:5::: probability G :::5:::5:a: matrix T aa::::::::: bits 2.1 *** * * * 1.9 *** * * *** 1.7 *** * * *** 1.5 *** * * *** Relative 1.3 *** * * *** Entropy 1.1 ******* *** (19.5 bits) 0.9 *********** 0.6 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel TTAACAACAGA consensus G C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr1:130300261-130300311 39 2.97e-07 TAAAAGCAGT TTAACAAGAGA C chr7:97210195-97210245 17 1.19e-06 TTCTACAGCT TTAGCCACAGA ATCTGGAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:130300261-130300311 3e-07 38_[+6]_1 chr7:97210195-97210245 1.2e-06 16_[+6]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=11 seqs=2 chr1:130300261-130300311 ( 39) TTAACAAGAGA 1 chr7:97210195-97210245 ( 17) TTAGCCACAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 800 bayes= 8.64024 E= 2.7e+003 -765 -765 -765 206 -765 -765 -765 206 213 -765 -765 -765 113 -765 83 -765 -765 198 -765 -765 113 98 -765 -765 213 -765 -765 -765 -765 98 83 -765 213 -765 -765 -765 -765 -765 183 -765 213 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2 E= 2.7e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- TTA[AG]C[AC]A[CG]AGA -------------------------------------------------------------------------------- Time 1.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 11 sites = 2 llr = 27 E-value = 3.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A :a::::::5:a pos.-specific C a:5a:5a:::: probability G ::::::::::: matrix T ::5:a5:a5a: bits 2.1 * * * ** 1.9 ** ** ** ** 1.7 ** ** ** ** 1.5 ** ** ** ** Relative 1.3 ** ** ** ** Entropy 1.1 *********** (19.6 bits) 0.9 *********** 0.6 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel CACCTCCTATA consensus T T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr12:32050294-32050344 3 6.16e-07 TC CATCTCCTATA CCATATTAAG chr6:88117084-88117134 14 1.11e-06 CCCCGTGGGC CACCTTCTTTA CCACATCAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:32050294-32050344 6.2e-07 2_[+7]_37 chr6:88117084-88117134 1.1e-06 13_[+7]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=11 seqs=2 chr12:32050294-32050344 ( 3) CATCTCCTATA 1 chr6:88117084-88117134 ( 14) CACCTTCTTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 800 bayes= 8.64024 E= 3.5e+003 -765 198 -765 -765 213 -765 -765 -765 -765 98 -765 106 -765 198 -765 -765 -765 -765 -765 206 -765 98 -765 106 -765 198 -765 -765 -765 -765 -765 206 113 -765 -765 106 -765 -765 -765 206 213 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2 E= 3.5e+003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- CA[CT]CT[CT]CT[AT]TA -------------------------------------------------------------------------------- Time 1.21 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 8 sites = 2 llr = 20 E-value = 3.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A :aaa::5a pos.-specific C :::::::: probability G 5::::a5: matrix T 5:::a::: bits 2.1 **** * 1.9 ***** * 1.7 ***** * 1.5 ***** * Relative 1.3 ***** * Entropy 1.1 ******* (14.4 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAATGAA consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:118194779-11819482 43 2.10e-05 GTGTGTGTCG GAAATGAA chr9:123958119-123958169 24 3.30e-05 TGTTTGTTTT TAAATGGA GTGCATTAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:118194779-11819482 2.1e-05 42_[+8] chr9:123958119-123958169 3.3e-05 23_[+8]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=8 seqs=2 chr14:118194779-11819482 ( 43) GAAATGAA 1 chr9:123958119-123958169 ( 24) TAAATGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 860 bayes= 8.74483 E= 3.9e+003 -765 -765 83 106 213 -765 -765 -765 213 -765 -765 -765 213 -765 -765 -765 -765 -765 -765 206 -765 -765 183 -765 113 -765 83 -765 213 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.9e+003 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- [GT]AAATG[AG]A -------------------------------------------------------------------------------- Time 1.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 8 sites = 2 llr = 19 E-value = 4.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A 5a:5aa:a pos.-specific C ::::::5: probability G ::a::::: matrix T 5::5::5: bits 2.1 * ** * 1.9 ** ** * 1.7 ** ** * 1.5 ** ** * Relative 1.3 ** ** * Entropy 1.1 ******** (13.6 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAGAAACA consensus T T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr13:14543015-14543065 43 3.83e-05 GCACTGTTCC TAGAAATA chr3:146405913-146405963 36 6.89e-05 TCCAGGGATT AAGTAACA GGGCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:14543015-14543065 3.8e-05 42_[+9] chr3:146405913-146405963 6.9e-05 35_[+9]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=8 seqs=2 chr13:14543015-14543065 ( 43) TAGAAATA 1 chr3:146405913-146405963 ( 36) AAGTAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 860 bayes= 8.74483 E= 4.3e+003 113 -765 -765 106 213 -765 -765 -765 -765 -765 183 -765 113 -765 -765 106 213 -765 -765 -765 213 -765 -765 -765 -765 98 -765 106 213 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.3e+003 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- [AT]AG[AT]AA[CT]A -------------------------------------------------------------------------------- Time 1.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 8 sites = 2 llr = 22 E-value = 6.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C :::a:::a probability G ::a::aa: matrix T aa:::::: bits 2.1 ** * 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (15.7 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTGCAGGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:7971530-7971580 17 1.84e-05 GGGGAGCCCA TTGCAGGC GGGGGTGGGG chr8:122313437-122313487 31 1.84e-05 CTGACTAATC TTGCAGGC CCGGGGTTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:7971530-7971580 1.8e-05 16_[+10]_26 chr8:122313437-122313487 1.8e-05 30_[+10]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=8 seqs=2 chrX:7971530-7971580 ( 17) TTGCAGGC 1 chr8:122313437-122313487 ( 31) TTGCAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 860 bayes= 8.74483 E= 6.1e+003 -765 -765 -765 206 -765 -765 -765 206 -765 -765 183 -765 -765 198 -765 -765 213 -765 -765 -765 -765 -765 183 -765 -765 -765 183 -765 -765 198 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.1e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- TTGCAGGC -------------------------------------------------------------------------------- Time 1.53 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:32050294-32050344 7.71e-05 2_[+7(6.16e-07)]_6_[+5(1.02e-05)]_23 chr13:14543015-14543065 1.32e-06 5_[+2(1.34e-05)]_10_[+3(5.93e-07)]_4_[+9(3.83e-05)] chr14:118194779-11819482 3.65e-07 7_[+1(4.31e-07)]_15_[+8(2.10e-05)] chr15:66826304-66826354 6.68e-04 11_[+4(1.08e-05)]_8_[+2(1.34e-05)]_11 chr18:38495027-38495077 1.06e-03 16_[+2(1.22e-05)]_9_[+3(1.05e-05)]_2 chr18:32542596-32542646 9.90e-04 22_[+1(2.28e-06)]_8 chr1:130300261-130300311 8.08e-05 13_[+1(6.19e-06)]_5_[+6(2.97e-07)]_1 chr1:134093055-134093105 5.20e-01 22_[+1(2.13e-05)]_8 chr3:146405913-146405963 2.52e-05 3_[+1(1.93e-08)]_12_[+9(6.89e-05)]_7 chr6:88203156-88203206 1.39e-03 30_[+1(1.93e-08)] chr6:88117084-88117134 1.62e-06 13_[+7(1.11e-06)]_[+2(2.78e-05)]_[+3(2.29e-06)]_3 chr7:103861092-103861142 9.91e-08 3_[+3(1.68e-06)]_1_[+1(3.04e-07)]_[+2(5.43e-07)]_3 chr7:103861104-103861154 2.65e-05 3_[+1(3.04e-07)]_[+2(5.43e-07)]_15 chr7:97210195-97210245 2.29e-06 16_[+6(1.19e-06)]_1_[+1(6.63e-06)]_2 chr7:16295063-16295113 9.44e-01 50 chr7:111004333-111004383 3.04e-04 1_[+5(2.15e-05)]_5_[+1(5.37e-06)]_[+2(7.09e-05)]_4 chr8:122313437-122313487 1.72e-03 9_[+1(8.63e-06)]_1_[+10(1.84e-05)]_12 chr9:123958119-123958169 6.09e-03 2_[+2(3.66e-05)]_9_[+8(3.30e-05)]_19 chrX:7971530-7971580 3.22e-01 16_[+10(1.84e-05)]_26 chrX:7841203-7841253 6.26e-03 2_[+4(1.08e-05)]_8_[+2(1.34e-05)]_20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************