******************************************************************************** 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= GATAWeakEnh.radius25bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr10:117106397-11710644 1.0000 50 chr11:78069770-78069820 1.0000 50 chr11:78069842-78069892 1.0000 50 chr12:86801037-86801087 1.0000 50 chr1:86479354-86479404 1.0000 50 chr1:151953825-151953875 1.0000 50 chr2:27389724-27389774 1.0000 50 chr2:168050459-168050509 1.0000 50 chr2:27344060-27344110 1.0000 50 chr4:107008367-107008417 1.0000 50 chr4:155788432-155788482 1.0000 50 chr5:84811694-84811744 1.0000 50 chr6:72279697-72279747 1.0000 50 chr6:88189797-88189847 1.0000 50 chr7:125472347-125472397 1.0000 50 chr7:103865868-103865918 1.0000 50 chr7:79742562-79742612 1.0000 50 chr7:126042331-126042381 1.0000 50 chr7:127091453-127091503 1.0000 50 chr7:123366237-123366287 1.0000 50 chr7:127770687-127770737 1.0000 50 chr7:111179583-111179633 1.0000 50 chr7:120980149-120980199 1.0000 50 chr7:109115177-109115227 1.0000 50 chr7:128301213-128301263 1.0000 50 chr7:79358677-79358727 1.0000 50 chr7:66196838-66196888 1.0000 50 chr7:125428772-125428822 1.0000 50 chr8:80493945-80493995 1.0000 50 chr8:36283776-36283826 1.0000 50 chr8:122315040-122315090 1.0000 50 chr9:45803590-45803640 1.0000 50 chrX:150564810-150564860 1.0000 50 chrX:150549826-150549876 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 GATAWeakEnh.radius25bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATAWeakEnh.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= 34 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= 1700 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.256 G 0.276 T 0.212 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.256 G 0.276 T 0.212 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 25 llr = 147 E-value = 3.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 37:4:25: pos.-specific C 7::::4:: probability G ::7632:a matrix T :33:715: bits 2.2 2.0 1.8 1.6 * Relative 1.3 * * Entropy 1.1 *** * ** (8.5 bits) 0.9 ***** ** 0.7 ***** ** 0.4 ***** ** 0.2 ******** 0.0 -------- Multilevel CAGGTCTG consensus ATTAGAA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:72279697-72279747 8 1.59e-05 CCACGCC CAGGTCTG TGAACTCCCG chr7:127770687-127770737 11 1.00e-04 TGATAAACTG CAGGTGTG GGAGGATAAT chr12:86801037-86801087 7 1.00e-04 CACTCA CAGATCAG CAACCAAATC chr7:127091453-127091503 17 1.96e-04 AGCAAGGTGA CAGGTGAG GTGAGGGGTG chr7:128301213-128301263 38 2.88e-04 CCCAAGCCAC CATATCTG ACCCC chr7:79358677-79358727 24 3.18e-04 GCTGCAAGAG CAGATAAG ATTGCAGAGG chr5:84811694-84811744 29 3.18e-04 TTTGTCGGCA CAGATAAG CCTATTGCAT chrX:150549826-150549876 34 5.96e-04 GGCTTTATCT ATGGTCTG CAGGCTCAG chr8:122315040-122315090 42 5.96e-04 TGTCTGTGGC CAGGGCAG G chr7:123366237-123366287 26 5.96e-04 CTGAGACTCT CAGGGCAG ACTCTCTGCC chr7:103865868-103865918 38 5.96e-04 TCTGAGCCAG CATGTAAG TGACC chr7:120980149-120980199 3 7.66e-04 TG AAGATGTG ACACCTTCAT chr1:86479354-86479404 33 8.55e-04 GTGGGGCTTG CAGGTTAG AGGCATTTCT chr7:125472347-125472397 43 9.65e-04 GGAGTGCTCA AAGATAAG chr2:168050459-168050509 19 9.65e-04 TGCGATAGAG CTTATCTG GCGGGTGTCA chr4:155788432-155788482 9 1.06e-03 TTCAAAGG AAGGGCTG CAATATGCTT chr11:78069770-78069820 1 1.06e-03 . CTGATAAG CACGTGCTAG chr8:80493945-80493995 15 1.17e-03 AATGCTAGCC AATGTGTG TCAACGGATA chr7:126042331-126042381 43 1.17e-03 CCTTCAAAAA AATATCAG chr10:117106397-11710644 2 1.17e-03 T CTGGGCTG AGGCCCACTT chrX:150564810-150564860 21 1.39e-03 AGTCATCACA CATGGCAG TATGTGACAG chr4:107008367-107008417 28 2.00e-03 AAAGGCAGGA CTGGGGTG TGGCTGTAAC chr7:79742562-79742612 17 3.11e-03 CTCCAAACTA CAGGTGTT CTGTTTCCTT chr8:36283776-36283826 33 3.36e-03 AACATGTTTC ATGAGATG CAAGCTGTAA chr7:109115177-109115227 5 3.48e-03 GGGT ATTGTTTG GGGACAGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:72279697-72279747 1.6e-05 7_[+1]_35 chr7:127770687-127770737 0.0001 10_[+1]_32 chr12:86801037-86801087 0.0001 6_[+1]_36 chr7:127091453-127091503 0.0002 16_[+1]_26 chr7:128301213-128301263 0.00029 37_[+1]_5 chr7:79358677-79358727 0.00032 23_[+1]_19 chr5:84811694-84811744 0.00032 28_[+1]_14 chrX:150549826-150549876 0.0006 33_[+1]_9 chr8:122315040-122315090 0.0006 41_[+1]_1 chr7:123366237-123366287 0.0006 25_[+1]_17 chr7:103865868-103865918 0.0006 37_[+1]_5 chr7:120980149-120980199 0.00077 2_[+1]_40 chr1:86479354-86479404 0.00085 32_[+1]_10 chr7:125472347-125472397 0.00097 42_[+1] chr2:168050459-168050509 0.00097 18_[+1]_24 chr4:155788432-155788482 0.0011 8_[+1]_34 chr11:78069770-78069820 0.0011 [+1]_42 chr8:80493945-80493995 0.0012 14_[+1]_28 chr7:126042331-126042381 0.0012 42_[+1] chr10:117106397-11710644 0.0012 1_[+1]_41 chrX:150564810-150564860 0.0014 20_[+1]_22 chr4:107008367-107008417 0.002 27_[+1]_15 chr7:79742562-79742612 0.0031 16_[+1]_26 chr8:36283776-36283826 0.0034 32_[+1]_10 chr7:109115177-109115227 0.0035 4_[+1]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=25 chr6:72279697-72279747 ( 8) CAGGTCTG 1 chr7:127770687-127770737 ( 11) CAGGTGTG 1 chr12:86801037-86801087 ( 7) CAGATCAG 1 chr7:127091453-127091503 ( 17) CAGGTGAG 1 chr7:128301213-128301263 ( 38) CATATCTG 1 chr7:79358677-79358727 ( 24) CAGATAAG 1 chr5:84811694-84811744 ( 29) CAGATAAG 1 chrX:150549826-150549876 ( 34) ATGGTCTG 1 chr8:122315040-122315090 ( 42) CAGGGCAG 1 chr7:123366237-123366287 ( 26) CAGGGCAG 1 chr7:103865868-103865918 ( 38) CATGTAAG 1 chr7:120980149-120980199 ( 3) AAGATGTG 1 chr1:86479354-86479404 ( 33) CAGGTTAG 1 chr7:125472347-125472397 ( 43) AAGATAAG 1 chr2:168050459-168050509 ( 19) CTTATCTG 1 chr4:155788432-155788482 ( 9) AAGGGCTG 1 chr11:78069770-78069820 ( 1) CTGATAAG 1 chr8:80493945-80493995 ( 15) AATGTGTG 1 chr7:126042331-126042381 ( 43) AATATCAG 1 chr10:117106397-11710644 ( 2) CTGGGCTG 1 chrX:150564810-150564860 ( 21) CATGGCAG 1 chr4:107008367-107008417 ( 28) CTGGGGTG 1 chr7:79742562-79742612 ( 17) CAGGTGTT 1 chr8:36283776-36283826 ( 33) ATGAGATG 1 chr7:109115177-109115227 ( 5) ATTGTTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1462 bayes= 6.99147 E= 3.7e+000 32 141 -1129 -1129 149 -1129 -1129 40 -1129 -1129 138 40 64 -1129 112 -1129 -1129 -1129 2 176 -9 78 -20 -141 91 -1129 -1129 129 -1129 -1129 180 -241 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 3.7e+000 0.320000 0.680000 0.000000 0.000000 0.720000 0.000000 0.000000 0.280000 0.000000 0.000000 0.720000 0.280000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 0.280000 0.720000 0.240000 0.440000 0.240000 0.080000 0.480000 0.000000 0.000000 0.520000 0.000000 0.000000 0.960000 0.040000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][AT][GT][GA][TG][CAG][TA]G -------------------------------------------------------------------------------- Time 0.74 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 21 sites = 3 llr = 65 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a:3:::::::::::3:7::3: pos.-specific C :333::33::::3::33:37a probability G :::::a:73:3:7:::::::: matrix T :737a:7:7a7a:a77:a7:: bits 2.2 * * * * * 2.0 * * * * * * * 1.8 * ** * * * * * 1.6 * ** * * * * * Relative 1.3 * ** * * * * * Entropy 1.1 ** **** **** ******** (31.2 bits) 0.9 ** ****************** 0.7 ** ****************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel ATATTGTGTTTTGTTTATTCC consensus CCC CCG G C ACC CA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr7:125472347-125472397 11 2.33e-11 GCCAATGCCA ATATTGTGGTTTCTTTCTTCC CGGAGTGCTC chr7:111179583-111179633 12 4.82e-11 CACAGAGAGC ATCCTGTGTTGTGTTCATTCC TGATAGCGTC chr10:117106397-11710644 16 3.47e-10 GCTGAGGCCC ACTTTGCCTTTTGTATATCAC ACGTGGCAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:125472347-125472397 2.3e-11 10_[+2]_19 chr7:111179583-111179633 4.8e-11 11_[+2]_18 chr10:117106397-11710644 3.5e-10 15_[+2]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=3 chr7:125472347-125472397 ( 11) ATATTGTGGTTTCTTTCTTCC 1 chr7:111179583-111179633 ( 12) ATCCTGTGTTGTGTTCATTCC 1 chr10:117106397-11710644 ( 16) ACTTTGCCTTTTGTATATCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1020 bayes= 8.85373 E= 1.3e+002 196 -823 -823 -823 -823 38 -823 165 38 38 -823 65 -823 38 -823 165 -823 -823 -823 223 -823 -823 185 -823 -823 38 -823 165 -823 38 127 -823 -823 -823 27 165 -823 -823 -823 223 -823 -823 27 165 -823 -823 -823 223 -823 38 127 -823 -823 -823 -823 223 38 -823 -823 165 -823 38 -823 165 138 38 -823 -823 -823 -823 -823 223 -823 38 -823 165 38 138 -823 -823 -823 196 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 3 E= 1.3e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.333333 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[TC][ACT][TC]TG[TC][GC][TG]T[TG]T[GC]T[TA][TC][AC]T[TC][CA]C -------------------------------------------------------------------------------- Time 1.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 14 sites = 7 llr = 81 E-value = 4.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 9:::76:6:1:::9 pos.-specific C 1:41::7:::7a6: probability G :61:3131a:3:1: matrix T :449:3:3:9::31 bits 2.2 2.0 * 1.8 * * 1.6 * ** * Relative 1.3 * * ** * * Entropy 1.1 ** ** * **** * (16.6 bits) 0.9 ** ** * **** * 0.7 ************** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel AGCTAACAGTCCCA consensus TT GTGT G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:127770687-127770737 32 2.45e-07 GGATAATGTC AGCTAACGGTCCCA GCAGT chr7:120980149-120980199 31 3.24e-07 CTGGATCAGA AGTTAAGAGTGCCA CACATA chrX:150564810-150564860 30 1.28e-06 ACATGGCAGT ATGTGACAGTCCTA TCTCAGA chr1:86479354-86479404 3 2.03e-06 GA AGTTATCTGTCCTT GGGCAAGTGG chr7:109115177-109115227 18 4.49e-06 GTTTGGGGAC AGCTGGCAGTCCGA TAAGGGCCTG chr7:103865868-103865918 23 5.11e-06 AGACATGGTC ATCTATCTGAGCCA GCATGTAAGT chr2:27389724-27389774 13 7.95e-06 GCAGCCTAAC CTTCAAGAGTCCCA CCCCTGGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127770687-127770737 2.5e-07 31_[+3]_5 chr7:120980149-120980199 3.2e-07 30_[+3]_6 chrX:150564810-150564860 1.3e-06 29_[+3]_7 chr1:86479354-86479404 2e-06 2_[+3]_34 chr7:109115177-109115227 4.5e-06 17_[+3]_19 chr7:103865868-103865918 5.1e-06 22_[+3]_14 chr2:27389724-27389774 7.9e-06 12_[+3]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=7 chr7:127770687-127770737 ( 32) AGCTAACGGTCCCA 1 chr7:120980149-120980199 ( 31) AGTTAAGAGTGCCA 1 chrX:150564810-150564860 ( 30) ATGTGACAGTCCTA 1 chr1:86479354-86479404 ( 3) AGTTATCTGTCCTT 1 chr7:109115177-109115227 ( 18) AGCTGGCAGTCCGA 1 chr7:103865868-103865918 ( 23) ATCTATCTGAGCCA 1 chr2:27389724-27389774 ( 13) CTTCAAGAGTCCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1258 bayes= 7.32447 E= 4.5e+002 174 -84 -945 -945 -945 -945 105 101 -945 74 -95 101 -945 -84 -945 201 148 -945 5 -945 116 -945 -95 43 -945 148 5 -945 116 -945 -95 43 -945 -945 186 -945 -84 -945 -945 201 -945 148 5 -945 -945 196 -945 -945 -945 116 -95 43 174 -945 -945 -57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 7 E= 4.5e+002 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.428571 0.142857 0.428571 0.000000 0.142857 0.000000 0.857143 0.714286 0.000000 0.285714 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 0.714286 0.285714 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.714286 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.142857 0.285714 0.857143 0.000000 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[GT][CT]T[AG][AT][CG][AT]GT[CG]C[CT]A -------------------------------------------------------------------------------- Time 1.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 9 sites = 3 llr = 35 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A :3:::a::: pos.-specific C a73:a::a: probability G ::::::::: matrix T ::7a::a:a bits 2.2 * * * 2.0 * ****** 1.8 * ****** 1.6 * ****** Relative 1.3 * ****** Entropy 1.1 ********* (16.8 bits) 0.9 ********* 0.7 ********* 0.4 ********* 0.2 ********* 0.0 --------- Multilevel CCTTCATCT consensus AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- chr7:120980149-120980199 14 2.22e-06 AGATGTGACA CCTTCATCT GGATCAGAAG chr2:27344060-27344110 13 4.44e-06 CAGCCACCAC CATTCATCT GAACGCACTC chr7:66196838-66196888 40 7.12e-06 ACCCAGAGGC CCCTCATCT CC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:120980149-120980199 2.2e-06 13_[+4]_28 chr2:27344060-27344110 4.4e-06 12_[+4]_29 chr7:66196838-66196888 7.1e-06 39_[+4]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=9 seqs=3 chr7:120980149-120980199 ( 14) CCTTCATCT 1 chr2:27344060-27344110 ( 13) CATTCATCT 1 chr7:66196838-66196888 ( 40) CCCTCATCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 1428 bayes= 8.54994 E= 1.5e+003 -823 196 -823 -823 38 138 -823 -823 -823 38 -823 165 -823 -823 -823 223 -823 196 -823 -823 196 -823 -823 -823 -823 -823 -823 223 -823 196 -823 -823 -823 -823 -823 223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 3 E= 1.5e+003 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- C[CA][TC]TCATCT -------------------------------------------------------------------------------- Time 2.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 12 sites = 2 llr = 31 E-value = 6.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A :::5:::::a:a pos.-specific C :a::5aa::::: probability G a:::::::a::: matrix T ::a55::a::a: bits 2.2 * * * 2.0 ** *** *** 1.8 *** ******* 1.6 *** ******* Relative 1.3 *** ******* Entropy 1.1 ************ (22.5 bits) 0.9 ************ 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GCTACCCTGATA consensus TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ chr4:155788432-155788482 39 3.59e-08 GAACGATGCG GCTTTCCTGATA chr11:78069770-78069820 22 1.75e-07 GTGCTAGGCT GCTACCCTGATA GTGGTCAGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:155788432-155788482 3.6e-08 38_[+5] chr11:78069770-78069820 1.7e-07 21_[+5]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=12 seqs=2 chr4:155788432-155788482 ( 39) GCTTTCCTGATA 1 chr11:78069770-78069820 ( 22) GCTACCCTGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1326 bayes= 9.37069 E= 6.2e+003 -765 -765 185 -765 -765 196 -765 -765 -765 -765 -765 223 96 -765 -765 123 -765 96 -765 123 -765 196 -765 -765 -765 196 -765 -765 -765 -765 -765 223 -765 -765 185 -765 196 -765 -765 -765 -765 -765 -765 223 196 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 2 E= 6.2e+003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- GCT[AT][CT]CCTGATA -------------------------------------------------------------------------------- Time 2.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 8 sites = 2 llr = 22 E-value = 3.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::5:aa: probability G :a:::::: matrix T a:a5a::a bits 2.2 * * * * 2.0 * * **** 1.8 *** **** 1.6 *** **** Relative 1.3 *** **** Entropy 1.1 ******** (15.8 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGTCTCCT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:79742562-79742612 26 7.75e-06 ACAGGTGTTC TGTTTCCT TAGCTACAAA chr7:126042331-126042381 21 1.71e-05 GCTGGAGGCT TGTCTCCT AGACCCTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:79742562-79742612 7.7e-06 25_[+6]_17 chr7:126042331-126042381 1.7e-05 20_[+6]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=8 seqs=2 chr7:79742562-79742612 ( 26) TGTTTCCT 1 chr7:126042331-126042381 ( 21) TGTCTCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1462 bayes= 9.51175 E= 3.3e+003 -765 -765 -765 223 -765 -765 185 -765 -765 -765 -765 223 -765 96 -765 123 -765 -765 -765 223 -765 196 -765 -765 -765 196 -765 -765 -765 -765 -765 223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.3e+003 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 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- TGT[CT]TCCT -------------------------------------------------------------------------------- Time 3.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 10 sites = 2 llr = 26 E-value = 8.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A :5:::::::a pos.-specific C :5a:a:5aa: probability G :::::::::: matrix T a::a:a5::: bits 2.2 * * * 2.0 * **** *** 1.8 * **** *** 1.6 * **** *** Relative 1.3 * **** *** Entropy 1.1 * ******** (18.6 bits) 0.9 ********** 0.7 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel TACTCTCCCA consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- chr7:128301213-128301263 17 1.14e-06 TGGCGAGGAG TACTCTTCCA ACCCAAGCCA chr4:107008367-107008417 5 2.51e-06 TAGA TCCTCTCCCA GATAAAGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:128301213-128301263 1.1e-06 16_[+7]_24 chr4:107008367-107008417 2.5e-06 4_[+7]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=10 seqs=2 chr7:128301213-128301263 ( 17) TACTCTTCCA 1 chr4:107008367-107008417 ( 5) TCCTCTCCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1394 bayes= 9.44294 E= 8.9e+003 -765 -765 -765 223 96 96 -765 -765 -765 196 -765 -765 -765 -765 -765 223 -765 196 -765 -765 -765 -765 -765 223 -765 96 -765 123 -765 196 -765 -765 -765 196 -765 -765 196 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 2 E= 8.9e+003 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 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 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- T[AC]CTCT[CT]CCA -------------------------------------------------------------------------------- Time 3.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 10 sites = 2 llr = 26 E-value = 1.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A a::::::::: pos.-specific C :a:a:5::aa probability G :::::5:5:: matrix T ::a:a:a5:: bits 2.2 * * * 2.0 ***** * ** 1.8 ***** * ** 1.6 ***** * ** Relative 1.3 ***** * ** Entropy 1.1 ***** **** (18.5 bits) 0.9 ********** 0.7 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel ACTCTCTGCC consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- chr11:78069842-78069892 7 1.18e-06 GCCCAG ACTCTGTTCC TGCTCCACAC chr7:123366237-123366287 34 1.92e-06 CTCAGGGCAG ACTCTCTGCC AGGGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:78069842-78069892 1.2e-06 6_[+8]_34 chr7:123366237-123366287 1.9e-06 33_[+8]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=10 seqs=2 chr11:78069842-78069892 ( 7) ACTCTGTTCC 1 chr7:123366237-123366287 ( 34) ACTCTCTGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1394 bayes= 9.44294 E= 1.2e+004 196 -765 -765 -765 -765 196 -765 -765 -765 -765 -765 223 -765 196 -765 -765 -765 -765 -765 223 -765 96 85 -765 -765 -765 -765 223 -765 -765 85 123 -765 196 -765 -765 -765 196 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 2 E= 1.2e+004 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- ACTCT[CG]T[GT]CC -------------------------------------------------------------------------------- Time 3.88 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 8 sites = 2 llr = 22 E-value = 1.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C ::a:::aa probability G :a:::a:: matrix T a::a:::: bits 2.2 * * 2.0 * *** ** 1.8 ******** 1.6 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.1 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGCTAGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:80493945-80493995 7 1.47e-05 TTTAAA TGCTAGCC AATGTGTGTC chr7:109115177-109115227 40 1.47e-05 GATAAGGGCC TGCTAGCC CGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:80493945-80493995 1.5e-05 6_[+9]_36 chr7:109115177-109115227 1.5e-05 39_[+9]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=8 seqs=2 chr8:80493945-80493995 ( 7) TGCTAGCC 1 chr7:109115177-109115227 ( 40) TGCTAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1462 bayes= 8.66217 E= 1.2e+004 -765 -765 -765 223 -765 -765 185 -765 -765 196 -765 -765 -765 -765 -765 223 196 -765 -765 -765 -765 -765 185 -765 -765 196 -765 -765 -765 196 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.2e+004 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- TGCTAGCC -------------------------------------------------------------------------------- Time 4.23 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 8 sites = 2 llr = 22 E-value = 1.7e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A a:aaaa:: pos.-specific C ::::::aa probability G :::::::: matrix T :a:::::: bits 2.2 * 2.0 ******** 1.8 ******** 1.6 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.0 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ATAAAACC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr9:45803590-45803640 34 1.53e-05 GGAGGCAGAG ATAAAACC CCAGCTACT chr7:66196838-66196888 10 1.53e-05 GAGAGAGGA ATAAAACC AAAGGTTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:45803590-45803640 1.5e-05 33_[+10]_9 chr7:66196838-66196888 1.5e-05 9_[+10]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=8 seqs=2 chr9:45803590-45803640 ( 34) ATAAAACC 1 chr7:66196838-66196888 ( 10) ATAAAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1462 bayes= 8.66217 E= 1.7e+004 196 -765 -765 -765 -765 -765 -765 223 196 -765 -765 -765 196 -765 -765 -765 196 -765 -765 -765 196 -765 -765 -765 -765 196 -765 -765 -765 196 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.7e+004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- ATAAAACC -------------------------------------------------------------------------------- Time 4.61 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:117106397-11710644 2.78e-05 15_[+2(3.47e-10)]_14 chr11:78069770-78069820 3.41e-04 21_[+5(1.75e-07)]_17 chr11:78069842-78069892 3.13e-03 6_[+8(1.18e-06)]_34 chr12:86801037-86801087 5.50e-01 50 chr1:86479354-86479404 6.41e-04 2_[+3(2.03e-06)]_34 chr1:151953825-151953875 9.76e-01 50 chr2:27389724-27389774 7.76e-02 12_[+3(7.95e-06)]_24 chr2:168050459-168050509 2.95e-01 50 chr2:27344060-27344110 1.55e-01 12_[+4(4.44e-06)]_29 chr4:107008367-107008417 3.34e-04 4_[+7(2.51e-06)]_36 chr4:155788432-155788482 7.51e-04 38_[+5(3.59e-08)] chr5:84811694-84811744 1.60e-01 50 chr6:72279697-72279747 4.26e-02 7_[+1(1.59e-05)]_35 chr6:88189797-88189847 7.83e-01 50 chr7:125472347-125472397 9.89e-09 10_[+2(2.33e-11)]_19 chr7:103865868-103865918 6.36e-04 22_[+3(5.11e-06)]_14 chr7:79742562-79742612 5.24e-03 25_[+6(7.75e-06)]_17 chr7:126042331-126042381 1.54e-04 20_[+6(1.71e-05)]_22 chr7:127091453-127091503 9.13e-01 50 chr7:123366237-123366287 3.47e-03 33_[+8(1.92e-06)]_7 chr7:127770687-127770737 5.77e-04 31_[+3(2.45e-07)]_5 chr7:111179583-111179633 1.23e-07 11_[+2(4.82e-11)]_18 chr7:120980149-120980199 1.65e-05 13_[+4(2.22e-06)]_8_[+3(3.24e-07)]_6 chr7:109115177-109115227 2.08e-03 17_[+3(4.49e-06)]_8_[+9(1.47e-05)]_3 chr7:128301213-128301263 2.03e-03 16_[+7(1.14e-06)]_24 chr7:79358677-79358727 2.16e-01 50 chr7:66196838-66196888 7.49e-04 9_[+10(1.53e-05)]_22_[+4(7.12e-06)]_2 chr7:125428772-125428822 7.53e-01 50 chr8:80493945-80493995 4.11e-02 6_[+9(1.47e-05)]_36 chr8:36283776-36283826 1.86e-02 50 chr8:122315040-122315090 3.49e-02 50 chr9:45803590-45803640 5.26e-01 33_[+10(1.53e-05)]_9 chrX:150564810-150564860 3.60e-04 29_[+3(1.28e-06)]_7 chrX:150549826-150549876 9.98e-02 50 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************