******************************************************************************** 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.radius75bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr10:117106347-11710649 1.0000 150 chr11:78069720-78069870 1.0000 150 chr11:78069792-78069942 1.0000 150 chr12:86800987-86801137 1.0000 150 chr1:86479304-86479454 1.0000 150 chr1:151953775-151953925 1.0000 150 chr2:168050409-168050559 1.0000 150 chr2:27344010-27344160 1.0000 150 chr2:27389674-27389824 1.0000 150 chr4:107008317-107008467 1.0000 150 chr4:155788382-155788532 1.0000 150 chr5:84811644-84811794 1.0000 150 chr6:72279647-72279797 1.0000 150 chr6:88189747-88189897 1.0000 150 chr7:128301163-128301313 1.0000 150 chr7:111179533-111179683 1.0000 150 chr7:127770637-127770787 1.0000 150 chr7:79358627-79358777 1.0000 150 chr7:120980099-120980249 1.0000 150 chr7:126042281-126042431 1.0000 150 chr7:103865818-103865968 1.0000 150 chr7:127091403-127091553 1.0000 150 chr7:125472297-125472447 1.0000 150 chr7:109115127-109115277 1.0000 150 chr7:123366187-123366337 1.0000 150 chr7:125428722-125428872 1.0000 150 chr7:66196788-66196938 1.0000 150 chr7:79742512-79742662 1.0000 150 chr8:80493895-80494045 1.0000 150 chr8:122314990-122315140 1.0000 150 chr8:36283726-36283876 1.0000 150 chr9:45803540-45803690 1.0000 150 chrX:150549776-150549926 1.0000 150 chrX:150564760-150564910 1.0000 150 ******************************************************************************** ******************************************************************************** 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.radius75bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATAWeakEnh.radius75bp.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= 5100 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.256 G 0.261 T 0.227 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.256 G 0.261 T 0.227 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 21 sites = 11 llr = 159 E-value = 3.9e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :14::2:1351a:42516571 pos.-specific C :53:7251457:11859:::6 probability G 1::::::51:2:55::::533 matrix T 944a36543:::41:::4::: bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * * * Entropy 1.1 * ** * * * **** * (20.9 bits) 0.9 * **** *** ****** 0.6 ** **** **** ******* 0.4 ******** **** ******* 0.2 ********************* 0.0 --------------------- Multilevel TCATCTTGCCCAGGCACAGAC consensus TT T CTAA TA C TAGG sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr11:78069792-78069942 38 2.79e-11 GGATCCCAGG TTATCTTGCCCAGGCCCAGAC TCTGTTCCTG chr11:78069720-78069870 110 2.79e-11 GGATCCCAGG TTATCTTGCCCAGGCCCAGAC TCTGTTCCTG chr7:79358627-79358777 15 5.39e-08 TGATTACATT TCCTCTCGTAAATACACTAAC CTAAAGGAAG chr7:103865818-103865968 22 5.94e-08 TTTGTGTCTA TCTTTTCTCAGAGTCACAGAC TCCACCCTGA chrX:150549776-150549926 8 8.63e-08 GGGTTCT TCTTCTCTCCCACGCCCTGGG CTCATCCTAG chrX:150564760-150564910 6 9.45e-08 AGTTA TTCTCCTAACCAGGCCCTAAC CAAGTAACAG chr12:86800987-86801137 22 1.03e-07 GGGGTAAAAA TAATCTCGTCCATACACAAGG AGATCACACA chr8:80493895-80494045 17 2.15e-07 CCTCTAGTTA TCTTTATTAACAGACACTAAA TAATGTTGCA chr10:117106347-11710649 26 5.30e-07 ACTGCATTTT TTCTTCTTTAGATAAACAGAC GCCCTCTGGG chr7:66196788-66196938 93 1.05e-06 CAGAGGCCCC TCATCTCCACCATCCCAAGGC TCCCCGCTGT chr2:27389674-27389824 109 1.28e-06 GCAGAGGCTG GCTTCATGGACAGGAACAAAG GTCCTAGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:78069792-78069942 2.8e-11 37_[+1]_92 chr11:78069720-78069870 2.8e-11 109_[+1]_20 chr7:79358627-79358777 5.4e-08 14_[+1]_115 chr7:103865818-103865968 5.9e-08 21_[+1]_108 chrX:150549776-150549926 8.6e-08 7_[+1]_122 chrX:150564760-150564910 9.4e-08 5_[+1]_124 chr12:86800987-86801137 1e-07 21_[+1]_108 chr8:80493895-80494045 2.2e-07 16_[+1]_113 chr10:117106347-11710649 5.3e-07 25_[+1]_104 chr7:66196788-66196938 1.1e-06 92_[+1]_37 chr2:27389674-27389824 1.3e-06 108_[+1]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=11 chr11:78069792-78069942 ( 38) TTATCTTGCCCAGGCCCAGAC 1 chr11:78069720-78069870 ( 110) TTATCTTGCCCAGGCCCAGAC 1 chr7:79358627-79358777 ( 15) TCCTCTCGTAAATACACTAAC 1 chr7:103865818-103865968 ( 22) TCTTTTCTCAGAGTCACAGAC 1 chrX:150549776-150549926 ( 8) TCTTCTCTCCCACGCCCTGGG 1 chrX:150564760-150564910 ( 6) TTCTCCTAACCAGGCCCTAAC 1 chr12:86800987-86801137 ( 22) TAATCTCGTCCATACACAAGG 1 chr8:80493895-80494045 ( 17) TCTTTATTAACAGACACTAAA 1 chr10:117106347-11710649 ( 26) TTCTTCTTTAGATAAACAGAC 1 chr7:66196788-66196938 ( 93) TCATCTCCACCATCCCAAGGC 1 chr2:27389674-27389824 ( 109) GCTTCATGGACAGGAACAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4420 bayes= 8.19804 E= 3.9e-003 -1010 -1010 -152 200 -149 109 -1010 68 50 9 -1010 68 -1010 -1010 -1010 214 -1010 151 -1010 27 -50 -49 -1010 149 -1010 83 -1010 126 -149 -149 80 68 9 51 -152 27 83 109 -1010 -1010 -149 151 -52 -1010 196 -1010 -1010 -1010 -1010 -149 106 68 50 -149 80 -132 -50 168 -1010 -1010 109 83 -1010 -1010 -149 183 -1010 -1010 131 -1010 -1010 68 83 -1010 106 -1010 150 -1010 6 -1010 -149 131 6 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 3.9e-003 0.000000 0.000000 0.090909 0.909091 0.090909 0.545455 0.000000 0.363636 0.363636 0.272727 0.000000 0.363636 0.000000 0.000000 0.000000 1.000000 0.000000 0.727273 0.000000 0.272727 0.181818 0.181818 0.000000 0.636364 0.000000 0.454545 0.000000 0.545455 0.090909 0.090909 0.454545 0.363636 0.272727 0.363636 0.090909 0.272727 0.454545 0.545455 0.000000 0.000000 0.090909 0.727273 0.181818 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.545455 0.363636 0.363636 0.090909 0.454545 0.090909 0.181818 0.818182 0.000000 0.000000 0.545455 0.454545 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.636364 0.000000 0.000000 0.363636 0.454545 0.000000 0.545455 0.000000 0.727273 0.000000 0.272727 0.000000 0.090909 0.636364 0.272727 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CT][ATC]T[CT]T[TC][GT][CAT][CA]CA[GT][GA]C[AC]C[AT][GA][AG][CG] -------------------------------------------------------------------------------- Time 3.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 25 sites = 11 llr = 170 E-value = 3.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 8:41351:29212:6:5422:6::: pos.-specific C :23:1::56::5::255:::11396 probability G 123545912184671::6869:51: matrix T 161431:5::::2315:::2:33:4 bits 2.1 1.9 1.7 1.5 * * * * Relative 1.3 * ** * * * Entropy 1.1 * * ** * **** * ** (22.3 bits) 0.9 ** * ** * **** ** ** 0.6 ** * ********* ******* ** 0.4 ** * ******************** 0.2 ** ********************** 0.0 ------------------------- Multilevel ATAGGAGCCAGCGGATAGGGGAGCC consensus CTAG T G T CCA TC T sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr11:78069792-78069942 9 4.22e-12 CTACCCTG ATAGTGGTCAGCGTATCGGGGATCC CAGGTTATCT chr11:78069720-78069870 81 4.22e-12 TGCTACCCTG ATAGTGGTCAGCGTATCGGGGATCC CAGGTTATCT chr10:117106347-11710649 114 1.42e-09 GTTTTAACAG AGATTAGCCAGGGGACAGAGGACCC CCCCCAAGTG chr7:111179533-111179683 96 1.44e-08 TAGCGTCAAG ATGGAGGCGAGGGGCCCAGAGAGCT TGGGGACATG chr7:103865818-103865968 77 2.27e-08 ATGGTCATCT ATCTGAGCCAGCATGTAAGTGACCC TTCTTGATAG chr8:80493895-80494045 66 4.86e-08 ATGCTAGCCA ATGTGTGTCAACGGATAGAGGCCCC GGGAAGGTGG chr7:127091403-127091553 52 1.21e-07 GAAATCCAAG ATTGAAGCAAGGTGACAGGTGAGGT GAGGGGTGCG chr7:127770637-127770787 14 2.71e-07 GGAAGCTGCT GGGGAAGGAAGCTGATCAGGGAGCT AGCAGATAAG chr7:109115127-109115277 8 3.26e-07 GGAGGCA ACCAGAGTGAGCGGCCAGGGCTGCT GCCCCAGCTG chr7:120980099-120980249 69 4.94e-07 TGACACCTTC ATCTGGATCAGAAGTTAAGAGTGCC ACACATAGCA chr2:168050409-168050559 91 5.85e-07 GTGTCAGGGT TCAGCGGCCGAGGGACCGGGGTTCC CGGAAGCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:78069792-78069942 4.2e-12 8_[+2]_117 chr11:78069720-78069870 4.2e-12 80_[+2]_45 chr10:117106347-11710649 1.4e-09 113_[+2]_12 chr7:111179533-111179683 1.4e-08 95_[+2]_30 chr7:103865818-103865968 2.3e-08 76_[+2]_49 chr8:80493895-80494045 4.9e-08 65_[+2]_60 chr7:127091403-127091553 1.2e-07 51_[+2]_74 chr7:127770637-127770787 2.7e-07 13_[+2]_112 chr7:109115127-109115277 3.3e-07 7_[+2]_118 chr7:120980099-120980249 4.9e-07 68_[+2]_57 chr2:168050409-168050559 5.9e-07 90_[+2]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=25 seqs=11 chr11:78069792-78069942 ( 9) ATAGTGGTCAGCGTATCGGGGATCC 1 chr11:78069720-78069870 ( 81) ATAGTGGTCAGCGTATCGGGGATCC 1 chr10:117106347-11710649 ( 114) AGATTAGCCAGGGGACAGAGGACCC 1 chr7:111179533-111179683 ( 96) ATGGAGGCGAGGGGCCCAGAGAGCT 1 chr7:103865818-103865968 ( 77) ATCTGAGCCAGCATGTAAGTGACCC 1 chr8:80493895-80494045 ( 66) ATGTGTGTCAACGGATAGAGGCCCC 1 chr7:127091403-127091553 ( 52) ATTGAAGCAAGGTGACAGGTGAGGT 1 chr7:127770637-127770787 ( 14) GGGGAAGGAAGCTGATCAGGGAGCT 1 chr7:109115127-109115277 ( 8) ACCAGAGTGAGCGGCCAGGGCTGCT 1 chr7:120980099-120980249 ( 69) ATCTGGATCAGAAGTTAAGAGTGCC 1 chr2:168050409-168050559 ( 91) TCAGCGGCCGAGGGACCGGGGTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 4284 bayes= 8.95751 E= 3.6e-001 167 -1010 -152 -132 -1010 -49 -52 149 50 9 6 -132 -149 -1010 106 68 9 -149 48 27 83 -1010 80 -132 -149 -1010 180 -1010 -1010 83 -152 100 -50 131 -52 -1010 182 -1010 -152 -1010 -50 -1010 165 -1010 -149 109 48 -1010 -50 -1010 129 -32 -1010 -1010 148 27 131 -49 -152 -132 -1010 83 -1010 126 109 83 -1010 -1010 50 -1010 129 -1010 -50 -1010 165 -1010 -50 -1010 129 -32 -1010 -149 180 -1010 131 -149 -1010 27 -1010 9 80 27 -1010 183 -152 -1010 -1010 131 -1010 68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 11 E= 3.6e-001 0.818182 0.000000 0.090909 0.090909 0.000000 0.181818 0.181818 0.636364 0.363636 0.272727 0.272727 0.090909 0.090909 0.000000 0.545455 0.363636 0.272727 0.090909 0.363636 0.272727 0.454545 0.000000 0.454545 0.090909 0.090909 0.000000 0.909091 0.000000 0.000000 0.454545 0.090909 0.454545 0.181818 0.636364 0.181818 0.000000 0.909091 0.000000 0.090909 0.000000 0.181818 0.000000 0.818182 0.000000 0.090909 0.545455 0.363636 0.000000 0.181818 0.000000 0.636364 0.181818 0.000000 0.000000 0.727273 0.272727 0.636364 0.181818 0.090909 0.090909 0.000000 0.454545 0.000000 0.545455 0.545455 0.454545 0.000000 0.000000 0.363636 0.000000 0.636364 0.000000 0.181818 0.000000 0.818182 0.000000 0.181818 0.000000 0.636364 0.181818 0.000000 0.090909 0.909091 0.000000 0.636364 0.090909 0.000000 0.272727 0.000000 0.272727 0.454545 0.272727 0.000000 0.909091 0.090909 0.000000 0.000000 0.636364 0.000000 0.363636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AT[ACG][GT][GAT][AG]G[CT]CAG[CG]G[GT]A[TC][AC][GA]GGG[AT][GCT]C[CT] -------------------------------------------------------------------------------- Time 6.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 11 sites = 10 llr = 105 E-value = 1.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::3::22: pos.-specific C 2aa::7:a827 probability G ::::6:3::33 matrix T 8::a4:7::3: bits 2.1 * 1.9 *** * 1.7 *** * 1.5 *** * Relative 1.3 **** *** Entropy 1.1 ********* * (15.1 bits) 0.9 ********* * 0.6 ********* * 0.4 ********* * 0.2 ********* * 0.0 ----------- Multilevel TCCTGCTCCGC consensus C TAG ATG sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr8:122314990-122315140 132 7.84e-07 TCAAGTCACT TCCTTCTCCGC CCTCCCAC chr11:78069792-78069942 64 1.22e-06 CAGACTCTGT TCCTGCTCCAC ACCCTGATTG chr11:78069720-78069870 136 1.22e-06 CAGACTCTGT TCCTGCTCCAC ACCC chr7:123366187-123366337 135 3.02e-06 AACTTCACAC TCCTTATCCTC CTGTC chr6:72279647-72279797 11 3.87e-06 TTCTGATACT TCCTTCGCCTC CTGAGTGCTG chrX:150564760-150564910 43 1.40e-05 ACAGTCCCCA CCCTGCTCCTG CCTATCTAGT chr7:79358627-79358777 119 1.57e-05 AGTGCTTCTG TCCTGCTCAGG AGAAAGGCCT chr2:27344010-27344160 46 1.99e-05 CAGCAAACTC TCCTTATCAGC CACCACCATT chr2:168050409-168050559 135 2.61e-05 CCAGCCCCGG CCCTGCGCCCC CGGAT chr4:107008317-107008467 28 2.90e-05 CACAACTCAC TCCTGAGCCCG CTCATTCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:122314990-122315140 7.8e-07 131_[+3]_8 chr11:78069792-78069942 1.2e-06 63_[+3]_76 chr11:78069720-78069870 1.2e-06 135_[+3]_4 chr7:123366187-123366337 3e-06 134_[+3]_5 chr6:72279647-72279797 3.9e-06 10_[+3]_129 chrX:150564760-150564910 1.4e-05 42_[+3]_97 chr7:79358627-79358777 1.6e-05 118_[+3]_21 chr2:27344010-27344160 2e-05 45_[+3]_94 chr2:168050409-168050559 2.6e-05 134_[+3]_5 chr4:107008317-107008467 2.9e-05 27_[+3]_112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=11 seqs=10 chr8:122314990-122315140 ( 132) TCCTTCTCCGC 1 chr11:78069792-78069942 ( 64) TCCTGCTCCAC 1 chr11:78069720-78069870 ( 136) TCCTGCTCCAC 1 chr7:123366187-123366337 ( 135) TCCTTATCCTC 1 chr6:72279647-72279797 ( 11) TCCTTCGCCTC 1 chrX:150564760-150564910 ( 43) CCCTGCTCCTG 1 chr7:79358627-79358777 ( 119) TCCTGCTCAGG 1 chr2:27344010-27344160 ( 46) TCCTTATCAGC 1 chr2:168050409-168050559 ( 135) CCCTGCGCCCC 1 chr4:107008317-107008467 ( 28) TCCTGAGCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 4760 bayes= 9.14381 E= 1.8e+001 -997 -35 -997 182 -997 197 -997 -997 -997 197 -997 -997 -997 -997 -997 214 -997 -997 120 82 23 145 -997 -997 -997 -997 20 162 -997 197 -997 -997 -36 164 -997 -997 -36 -35 20 40 -997 145 20 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 10 E= 1.8e+001 0.000000 0.200000 0.000000 0.800000 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 0.600000 0.400000 0.300000 0.700000 0.000000 0.000000 0.000000 0.000000 0.300000 0.700000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.200000 0.300000 0.300000 0.000000 0.700000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]CCT[GT][CA][TG]C[CA][GTACA][CG] -------------------------------------------------------------------------------- Time 8.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 10 sites = 34 llr = 214 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A 663:1:1461 pos.-specific C 3::9:232:4 probability G :471:84246 matrix T 1:::9:32:: bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 ** Entropy 1.1 ***** (9.1 bits) 0.9 ****** * 0.6 ****** ** 0.4 ****** ** 0.2 ******* ** 0.0 ---------- Multilevel AAGCTGGAAG consensus CGA CCGGC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- chr7:126042281-126042431 59 5.51e-06 TATCAGCAGT AAGCTGGAGG CTTGTCTCCT chr10:117106347-11710649 94 6.67e-06 CACACGTGGC AAGCTGCAGG GTTTTAACAG chr8:36283726-36283876 92 1.10e-05 CATGAGATGC AAGCTGTAAC GTGAGATAAC chr7:125428722-125428872 48 1.99e-05 TAGAATCACA AAGCTGGGAG AGAAGCCACT chr12:86800987-86801137 81 5.13e-05 AATCCCGGGG AGGCTGTGAG CACGGTAAAG chr7:79358627-79358777 62 6.42e-05 TTCCTCGCCC CAGCTGCAAG AGCAGATAAG chr7:127770637-127770787 55 7.73e-05 TAAGTCTGAT AAACTGCAGG TGTGGGAGGA chr7:79742512-79742662 96 9.44e-05 GCTACAAAAG AAGCTCCAAG TTTCTCTGGA chr1:151953775-151953925 69 9.44e-05 GGAGAAGCCG AGGCTGGTGG GGGAATGGTT chrX:150549776-150549926 64 1.10e-04 TAATGGTGAT AAGCTCTAGG GGCTTTATCT chr11:78069720-78069870 67 1.49e-04 AGCACGTGCT AGGCTGCTAC CCTGATAGTG chr7:109115127-109115277 67 2.13e-04 TGTTTGGGGA CAGCTGGCAG TCCGATAAGG chrX:150564760-150564910 113 2.42e-04 CACAGAAGCA AGGCTCTAAC ATGGACAGGA chr9:45803540-45803690 40 2.71e-04 GCAGATGCTG AGACTGGGGG CCACATGAAG chr7:66196788-66196938 124 3.06e-04 TCCCCGCTGT AGACTGTTGG GTATAGATAG chr7:128301163-128301313 127 3.06e-04 AGGATGAAAT AAACTGGCAC TTTTAATGAA chr7:125472297-125472447 98 5.45e-04 GCTCAAAGAT AAGCTGAGAC AGATGGTGTA chr6:72279647-72279797 86 5.45e-04 ATTACACCTA CGGCTCGAGG GCAAGCACTT chr4:107008317-107008467 86 5.45e-04 GACTGGGGTG TGGCTGTAAC TGGGGAAGCA chr7:103865818-103865968 109 5.92e-04 CCCTTCTTGA TAGCTGGCAG CTAGCATCAG chr8:80493895-80494045 138 6.96e-04 GGCCTTCCTA AGGCTGACAG ACA chr11:78069792-78069942 129 6.96e-04 ACAGGCTCTC TGGCTGGTAG AGATATCTCT chr7:123366187-123366337 69 8.89e-04 ACAACTCCTG AGACTCTCAG GGCAGACTCT chr6:88189747-88189897 44 8.89e-04 GCTGTATAAT AGACTCCGGG GAGATAGGAA chr2:27344010-27344160 7 8.89e-04 ATCAAT AAGCAGGAAC TGCTCAGACC chr5:84811644-84811794 115 9.60e-04 ATGGCATATT CAGCTCTTGC TGAATTAATC chr4:155788382-155788532 9 9.60e-04 ACACATTC AAACTGCAGA ATTGTTCCAG chr2:168050409-168050559 46 1.18e-03 CGGCTGTTCC CGGCTCTGGC CGCTGCGATA chr8:122314990-122315140 3 1.35e-03 TG CAGGTGGAGC CCGAGAGGGG chr7:127091403-127091553 91 1.63e-03 GGTGCGGAAG CAACTGCAAA TGGGGGACTG chr7:120980099-120980249 53 1.98e-03 GTTAGACTTG AAGATGTGAC ACCTTCATCT chr7:111179533-111179683 14 2.22e-03 TGATAAGGTA CGGGTGCTGG GCCTCTTCTG chr2:27389674-27389824 85 2.89e-03 CACCCCTGGA AAACAGCCAC ACAGGCAGAG chr1:86479304-86479454 70 3.21e-03 TGTCCTTGGG CAAGTGGGGC TTGCAGGTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:126042281-126042431 5.5e-06 58_[+4]_82 chr10:117106347-11710649 6.7e-06 93_[+4]_47 chr8:36283726-36283876 1.1e-05 91_[+4]_49 chr7:125428722-125428872 2e-05 47_[+4]_93 chr12:86800987-86801137 5.1e-05 80_[+4]_60 chr7:79358627-79358777 6.4e-05 61_[+4]_79 chr7:127770637-127770787 7.7e-05 54_[+4]_86 chr7:79742512-79742662 9.4e-05 95_[+4]_45 chr1:151953775-151953925 9.4e-05 68_[+4]_72 chrX:150549776-150549926 0.00011 63_[+4]_77 chr11:78069720-78069870 0.00015 66_[+4]_74 chr7:109115127-109115277 0.00021 66_[+4]_74 chrX:150564760-150564910 0.00024 112_[+4]_28 chr9:45803540-45803690 0.00027 39_[+4]_101 chr7:66196788-66196938 0.00031 123_[+4]_17 chr7:128301163-128301313 0.00031 126_[+4]_14 chr7:125472297-125472447 0.00055 97_[+4]_43 chr6:72279647-72279797 0.00055 85_[+4]_55 chr4:107008317-107008467 0.00055 85_[+4]_55 chr7:103865818-103865968 0.00059 108_[+4]_32 chr8:80493895-80494045 0.0007 137_[+4]_3 chr11:78069792-78069942 0.0007 128_[+4]_12 chr7:123366187-123366337 0.00089 68_[+4]_72 chr6:88189747-88189897 0.00089 43_[+4]_97 chr2:27344010-27344160 0.00089 6_[+4]_134 chr5:84811644-84811794 0.00096 114_[+4]_26 chr4:155788382-155788532 0.00096 8_[+4]_132 chr2:168050409-168050559 0.0012 45_[+4]_95 chr8:122314990-122315140 0.0013 2_[+4]_138 chr7:127091403-127091553 0.0016 90_[+4]_50 chr7:120980099-120980249 0.002 52_[+4]_88 chr7:111179533-111179683 0.0022 13_[+4]_127 chr2:27389674-27389824 0.0029 84_[+4]_56 chr1:86479304-86479454 0.0032 69_[+4]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=10 seqs=34 chr7:126042281-126042431 ( 59) AAGCTGGAGG 1 chr10:117106347-11710649 ( 94) AAGCTGCAGG 1 chr8:36283726-36283876 ( 92) AAGCTGTAAC 1 chr7:125428722-125428872 ( 48) AAGCTGGGAG 1 chr12:86800987-86801137 ( 81) AGGCTGTGAG 1 chr7:79358627-79358777 ( 62) CAGCTGCAAG 1 chr7:127770637-127770787 ( 55) AAACTGCAGG 1 chr7:79742512-79742662 ( 96) AAGCTCCAAG 1 chr1:151953775-151953925 ( 69) AGGCTGGTGG 1 chrX:150549776-150549926 ( 64) AAGCTCTAGG 1 chr11:78069720-78069870 ( 67) AGGCTGCTAC 1 chr7:109115127-109115277 ( 67) CAGCTGGCAG 1 chrX:150564760-150564910 ( 113) AGGCTCTAAC 1 chr9:45803540-45803690 ( 40) AGACTGGGGG 1 chr7:66196788-66196938 ( 124) AGACTGTTGG 1 chr7:128301163-128301313 ( 127) AAACTGGCAC 1 chr7:125472297-125472447 ( 98) AAGCTGAGAC 1 chr6:72279647-72279797 ( 86) CGGCTCGAGG 1 chr4:107008317-107008467 ( 86) TGGCTGTAAC 1 chr7:103865818-103865968 ( 109) TAGCTGGCAG 1 chr8:80493895-80494045 ( 138) AGGCTGACAG 1 chr11:78069792-78069942 ( 129) TGGCTGGTAG 1 chr7:123366187-123366337 ( 69) AGACTCTCAG 1 chr6:88189747-88189897 ( 44) AGACTCCGGG 1 chr2:27344010-27344160 ( 7) AAGCAGGAAC 1 chr5:84811644-84811794 ( 115) CAGCTCTTGC 1 chr4:155788382-155788532 ( 9) AAACTGCAGA 1 chr2:168050409-168050559 ( 46) CGGCTCTGGC 1 chr8:122314990-122315140 ( 3) CAGGTGGAGC 1 chr7:127091403-127091553 ( 91) CAACTGCAAA 1 chr7:120980099-120980249 ( 53) AAGATGTGAC 1 chr7:111179533-111179683 ( 14) CGGGTGCTGG 1 chr2:27389674-27389824 ( 85) AAACAGCCAC 1 chr1:86479304-86479454 ( 70) CAAGTGGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 4794 bayes= 7.19931 E= 2.6e+001 133 5 -1173 -136 120 -1173 66 -1173 20 -1173 144 -1173 -312 179 -156 -1173 -212 -1173 -1173 205 -1173 -12 155 -1173 -212 20 44 37 68 -53 -15 -36 112 -1173 76 -1173 -212 58 110 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 34 E= 2.6e+001 0.647059 0.264706 0.000000 0.088235 0.588235 0.000000 0.411765 0.000000 0.294118 0.000000 0.705882 0.000000 0.029412 0.882353 0.088235 0.000000 0.058824 0.000000 0.000000 0.941176 0.000000 0.235294 0.764706 0.000000 0.058824 0.294118 0.352941 0.294118 0.411765 0.176471 0.235294 0.176471 0.558824 0.000000 0.441176 0.000000 0.058824 0.382353 0.558824 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- [AC][AG][GA]CT[GC][GCT][AG][AG][GC] -------------------------------------------------------------------------------- Time 11.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 17 sites = 5 llr = 84 E-value = 3.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A 22::22642::::2::: pos.-specific C ::4:::::44::8:::: probability G :8:::2464::::::aa matrix T 8:6a86:::6aa28a:: bits 2.1 * ** * 1.9 * ** *** 1.7 * ** *** 1.5 * ** *** Relative 1.3 ** ** ******* Entropy 1.1 ***** ** ******** (24.4 bits) 0.9 ***** ** ******** 0.6 ******** ******** 0.4 ***************** 0.2 ***************** 0.0 ----------------- Multilevel TGTTTTAGCTTTCTTGG consensus AAC AAGAGC TA sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- chr7:125472297-125472447 34 1.71e-10 CCAACAGAAA TGTTTTGGCTTTCTTGG GCCAATGCCA chr4:155788382-155788532 33 2.50e-09 TTCCAGGAAT TGTTTTAGGCTTTTTGG TTTCAAAGGA chrX:150549776-150549926 108 7.69e-09 CAGCCTTGAG TGCTTTAGCCTTCATGG CCAGGCAGTC chr7:109115127-109115277 131 4.07e-08 GCCTCTCGGC AGTTTAGAATTTCTTGG GTC chr9:45803540-45803690 97 6.68e-08 AAACCCCAGC TACTAGAAGTTTCTTGG TGCTTAAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:125472297-125472447 1.7e-10 33_[+5]_100 chr4:155788382-155788532 2.5e-09 32_[+5]_101 chrX:150549776-150549926 7.7e-09 107_[+5]_26 chr7:109115127-109115277 4.1e-08 130_[+5]_3 chr9:45803540-45803690 6.7e-08 96_[+5]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=17 seqs=5 chr7:125472297-125472447 ( 34) TGTTTTGGCTTTCTTGG 1 chr4:155788382-155788532 ( 33) TGTTTTAGGCTTTTTGG 1 chrX:150549776-150549926 ( 108) TGCTTTAGCCTTCATGG 1 chr7:109115127-109115277 ( 131) AGTTTAGAATTTCTTGG 1 chr9:45803540-45803690 ( 97) TACTAGAAGTTTCTTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 4556 bayes= 10.7742 E= 3.1e+001 -36 -897 -897 182 -36 -897 161 -897 -897 64 -897 140 -897 -897 -897 214 -36 -897 -897 182 -36 -897 -38 140 122 -897 62 -897 64 -897 120 -897 -36 64 62 -897 -897 64 -897 140 -897 -897 -897 214 -897 -897 -897 214 -897 164 -897 -18 -36 -897 -897 182 -897 -897 -897 214 -897 -897 194 -897 -897 -897 194 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 5 E= 3.1e+001 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.600000 0.600000 0.000000 0.400000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.400000 0.400000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- [TA][GA][TC]T[TA][TAG][AG][GA][CGA][TC]TT[CT][TA]TGG -------------------------------------------------------------------------------- Time 14.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 8 sites = 9 llr = 87 E-value = 7.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A :6:a:9a1 pos.-specific C a::::1:: probability G ::a::::9 matrix T :4::a::: bits 2.1 * 1.9 * *** * 1.7 * *** * 1.5 * ****** Relative 1.3 * ****** Entropy 1.1 ******** (13.9 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CAGATAAG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:79358627-79358777 74 1.70e-05 GCTGCAAGAG CAGATAAG ATTGCAGAGG chr7:127770637-127770787 41 1.70e-05 AGGGAGCTAG CAGATAAG TCTGATAAAC chr5:84811644-84811794 79 1.70e-05 TTTGTCGGCA CAGATAAG CCTATTGCAT chr9:45803540-45803690 123 3.21e-05 GTGCTTAAAA CTGATAAG TCAAGAAAAG chr7:109115127-109115277 40 3.21e-05 GCTGCCCCAG CTGATAAG GACGGGTATT chr7:111179533-111179683 3 3.21e-05 CT CTGATAAG GTACGGGTGC chr11:78069720-78069870 51 3.21e-05 CCCTGCAGGC CTGATAAG CACGTGCTAG chr4:107008317-107008467 63 6.58e-05 GATCCTCTCC CAGATAAA GGCAGGACTG chr12:86800987-86801137 57 6.58e-05 CACACACTCA CAGATCAG CAACCAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:79358627-79358777 1.7e-05 73_[+6]_69 chr7:127770637-127770787 1.7e-05 40_[+6]_102 chr5:84811644-84811794 1.7e-05 78_[+6]_64 chr9:45803540-45803690 3.2e-05 122_[+6]_20 chr7:109115127-109115277 3.2e-05 39_[+6]_103 chr7:111179533-111179683 3.2e-05 2_[+6]_140 chr11:78069720-78069870 3.2e-05 50_[+6]_92 chr4:107008317-107008467 6.6e-05 62_[+6]_80 chr12:86800987-86801137 6.6e-05 56_[+6]_86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=8 seqs=9 chr7:79358627-79358777 ( 74) CAGATAAG 1 chr7:127770637-127770787 ( 41) CAGATAAG 1 chr5:84811644-84811794 ( 79) CAGATAAG 1 chr9:45803540-45803690 ( 123) CTGATAAG 1 chr7:109115127-109115277 ( 40) CTGATAAG 1 chr7:111179533-111179683 ( 3) CTGATAAG 1 chr11:78069720-78069870 ( 51) CTGATAAG 1 chr4:107008317-107008467 ( 63) CAGATAAA 1 chr12:86800987-86801137 ( 57) CAGATCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4862 bayes= 9.92392 E= 7.4e+001 -982 197 -982 -982 111 -982 -982 97 -982 -982 194 -982 196 -982 -982 -982 -982 -982 -982 214 179 -120 -982 -982 196 -982 -982 -982 -120 -982 177 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 7.4e+001 0.000000 1.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.888889 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- C[AT]GATAAG -------------------------------------------------------------------------------- Time 16.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 25 sites = 3 llr = 78 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A :::3:::::::37a::::::a:33: pos.-specific C a373:::7::::3:7:7a3::::3a probability G ::3:a3:3:a:3:::::::a:::3: matrix T :7:3:7a:a:a3::3a3:7::a7:: bits 2.1 * * * * * 1.9 * * * *** * * * *** * 1.7 * * * *** * * * *** * 1.5 * * * *** * * * *** * Relative 1.3 * * * *** * * * *** * Entropy 1.1 *** ******* *********** * (37.6 bits) 0.9 *** ******* *********** * 0.6 *** ******* *********** * 0.4 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel CTCAGTTCTGTAAACTCCTGATTAC consensus CGC G G GC T T C AC sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:128301163-128301313 4 6.98e-14 CAG CTCCGTTCTGTAAACTTCTGATTCC TGAGGACTGC chr6:72279647-72279797 56 2.11e-12 TGCTGCCACG CCCAGGTCTGTGAACTCCCGATTAC ACCTACGGCT chr7:111179533-111179683 65 4.35e-12 AGAGAGCATC CTGTGTTGTGTTCATTCCTGATAGC GTCAAGATGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:128301163-128301313 7e-14 3_[+7]_122 chr6:72279647-72279797 2.1e-12 55_[+7]_70 chr7:111179533-111179683 4.3e-12 64_[+7]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=25 seqs=3 chr7:128301163-128301313 ( 4) CTCCGTTCTGTAAACTTCTGATTCC 1 chr6:72279647-72279797 ( 56) CCCAGGTCTGTGAACTCCCGATTAC 1 chr7:111179533-111179683 ( 65) CTGTGTTGTGTTCATTCCTGATAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 4284 bayes= 10.9265 E= 1.5e+003 -823 196 -823 -823 -823 38 -823 155 -823 138 35 -823 38 38 -823 55 -823 -823 193 -823 -823 -823 35 155 -823 -823 -823 214 -823 138 35 -823 -823 -823 -823 214 -823 -823 193 -823 -823 -823 -823 214 38 -823 35 55 138 38 -823 -823 196 -823 -823 -823 -823 138 -823 55 -823 -823 -823 214 -823 138 -823 55 -823 196 -823 -823 -823 38 -823 155 -823 -823 193 -823 196 -823 -823 -823 -823 -823 -823 214 38 -823 -823 155 38 38 35 -823 -823 196 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 3 E= 1.5e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 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 0.333333 0.000000 0.333333 0.333333 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- C[TC][CG][ACT]G[TG]T[CG]TGT[AGT][AC]A[CT]T[CT]C[TC]GAT[TA][ACG]C -------------------------------------------------------------------------------- Time 18.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 20 sites = 6 llr = 100 E-value = 2.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A 22::83a::782::2:::83 pos.-specific C ::38:::::2:::782:a:: probability G :332:7:572:7a3::5::7 matrix T 853:2::53:22:::85:2: bits 2.1 1.9 * * * 1.7 * * * 1.5 * * * * * Relative 1.3 * ** * * * ** ** Entropy 1.1 * ****** * ******** (24.2 bits) 0.9 * ****** * ******** 0.6 ** ***************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TTCCAGAGGAAGGCCTGCAG consensus GG A TT G T A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- chr4:155788382-155788532 50 7.32e-10 GGCTTTTTGG TTTCAAAGGAAGGGCTGCAA TATGCTTGTG chr7:79358627-79358777 83 1.05e-09 GCAGATAAGA TTGCAGAGGAAGGGCTTCTG CCGTACAGTG chr7:127770637-127770787 125 6.98e-09 GAACTGAAGA TTCCAGAGTGTGGCCTGCAG ATGTGT chr4:107008317-107008467 101 1.49e-08 GTAACTGGGG AAGCAGATGCAGGCCTGCAG TATTTGTGAT chr7:123366187-123366337 38 4.75e-08 GACCTTGACT TGCCAAATGAAAGCACTCAG AACAACTCCT chr5:84811644-84811794 11 5.68e-08 GTTGAAAATA TGTGTGATTAATGCCTTCAA CTATTATCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:155788382-155788532 7.3e-10 49_[+8]_81 chr7:79358627-79358777 1.1e-09 82_[+8]_48 chr7:127770637-127770787 7e-09 124_[+8]_6 chr4:107008317-107008467 1.5e-08 100_[+8]_30 chr7:123366187-123366337 4.7e-08 37_[+8]_93 chr5:84811644-84811794 5.7e-08 10_[+8]_120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=20 seqs=6 chr4:155788382-155788532 ( 50) TTTCAAAGGAAGGGCTGCAA 1 chr7:79358627-79358777 ( 83) TTGCAGAGGAAGGGCTTCTG 1 chr7:127770637-127770787 ( 125) TTCCAGAGTGTGGCCTGCAG 1 chr4:107008317-107008467 ( 101) AAGCAGATGCAGGCCTGCAG 1 chr7:123366187-123366337 ( 38) TGCCAAATGAAAGCACTCAG 1 chr5:84811644-84811794 ( 11) TGTGTGATTAATGCCTTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4454 bayes= 9.98196 E= 2.9e+003 -62 -923 -923 188 -62 -923 35 114 -923 38 35 55 -923 170 -65 -923 170 -923 -923 -44 38 -923 135 -923 196 -923 -923 -923 -923 -923 94 114 -923 -923 135 55 138 -62 -65 -923 170 -923 -923 -44 -62 -923 135 -44 -923 -923 194 -923 -923 138 35 -923 -62 170 -923 -923 -923 -62 -923 188 -923 -923 94 114 -923 197 -923 -923 170 -923 -923 -44 38 -923 135 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 2.9e+003 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.333333 0.500000 0.000000 0.333333 0.333333 0.333333 0.000000 0.833333 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.666667 0.333333 0.666667 0.166667 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.333333 0.000000 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- T[TG][CGT]CA[GA]A[GT][GT]AAGG[CG]CT[GT]CA[GA] -------------------------------------------------------------------------------- Time 20.48 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 8 sites = 10 llr = 88 E-value = 4.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A :3:a:::: pos.-specific C 54:::a:4 probability G 5::::::6 matrix T :3a:a:a: bits 2.1 * * * 1.9 ***** 1.7 ***** 1.5 ***** Relative 1.3 ***** Entropy 1.1 ****** (12.7 bits) 0.9 * ****** 0.6 * ****** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCTATCTG consensus GA C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:88189747-88189897 75 2.65e-05 ATGGCCGCGC GCTATCTG CGTCGCCATG chr2:27344010-27344160 143 2.65e-05 CGGAAACTCA CCTATCTG chr2:168050409-168050559 69 5.00e-05 TGCGATAGAG CTTATCTG GCGGGTGTCA chr1:86479304-86479454 54 5.00e-05 ATTTCAGGAA GTTATCTG TCCTTGGGCA chrX:150564760-150564910 90 1.02e-04 ATGTGACAGT CCTATCTC AGAACCACAG chr8:122314990-122315140 100 1.02e-04 GCCAGGGCAG GCTATCTC GGTGGCGGCA chr7:128301163-128301313 88 1.02e-04 CCCAAGCCAC CATATCTG ACCCCACACA chr1:151953775-151953925 99 1.02e-04 ACAGCCTCAG CATATCTG CCTGCAGGCC chr7:125472297-125472447 143 1.25e-04 GGACAAGATT GTTATCTC chr11:78069792-78069942 140 1.51e-04 GGCTGGTAGA GATATCTC TGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:88189747-88189897 2.6e-05 74_[+9]_68 chr2:27344010-27344160 2.6e-05 142_[+9] chr2:168050409-168050559 5e-05 68_[+9]_74 chr1:86479304-86479454 5e-05 53_[+9]_89 chrX:150564760-150564910 0.0001 89_[+9]_53 chr8:122314990-122315140 0.0001 99_[+9]_43 chr7:128301163-128301313 0.0001 87_[+9]_55 chr1:151953775-151953925 0.0001 98_[+9]_44 chr7:125472297-125472447 0.00013 142_[+9] chr11:78069792-78069942 0.00015 139_[+9]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=8 seqs=10 chr6:88189747-88189897 ( 75) GCTATCTG 1 chr2:27344010-27344160 ( 143) CCTATCTG 1 chr2:168050409-168050559 ( 69) CTTATCTG 1 chr1:86479304-86479454 ( 54) GTTATCTG 1 chrX:150564760-150564910 ( 90) CCTATCTC 1 chr8:122314990-122315140 ( 100) GCTATCTC 1 chr7:128301163-128301313 ( 88) CATATCTG 1 chr1:151953775-151953925 ( 99) CATATCTG 1 chr7:125472297-125472447 ( 143) GTTATCTC 1 chr11:78069792-78069942 ( 140) GATATCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4862 bayes= 9.86728 E= 4.3e+003 -997 97 94 -997 23 65 -997 40 -997 -997 -997 214 196 -997 -997 -997 -997 -997 -997 214 -997 197 -997 -997 -997 -997 -997 214 -997 65 120 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 4.3e+003 0.000000 0.500000 0.500000 0.000000 0.300000 0.400000 0.000000 0.300000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.600000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- [CG][CAT]TATCT[GC] -------------------------------------------------------------------------------- Time 22.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 13 sites = 2 llr = 34 E-value = 4.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A ::::::5:a::a: pos.-specific C :::::::::5a:a probability G ::::a:::::::: matrix T aaaa:a5a:5::: bits 2.1 **** * * 1.9 ****** ** *** 1.7 ****** ** *** 1.5 ****** ** *** Relative 1.3 ****** ** *** Entropy 1.1 ************* (24.7 bits) 0.9 ************* 0.6 ************* 0.4 ************* 0.2 ************* 0.0 ------------- Multilevel TTTTGTATACCAC consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- chr7:120980099-120980249 113 2.57e-08 ACCAAACGTA TTTTGTTTACCAC TCAGTAGACC chr10:117106347-11710649 74 2.57e-08 CCACTTTGCC TTTTGTATATCAC ACGTGGCAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:120980099-120980249 2.6e-08 112_[+10]_25 chr10:117106347-11710649 2.6e-08 73_[+10]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=13 seqs=2 chr7:120980099-120980249 ( 113) TTTTGTTTACCAC 1 chr10:117106347-11710649 ( 74) TTTTGTATATCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 4692 bayes= 11.1954 E= 4.8e+003 -765 -765 -765 213 -765 -765 -765 213 -765 -765 -765 213 -765 -765 -765 213 -765 -765 193 -765 -765 -765 -765 213 96 -765 -765 114 -765 -765 -765 213 196 -765 -765 -765 -765 96 -765 114 -765 196 -765 -765 196 -765 -765 -765 -765 196 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 2 E= 4.8e+003 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 1.000000 0.000000 0.000000 1.000000 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 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- TTTTGT[AT]TA[CT]CAC -------------------------------------------------------------------------------- Time 24.60 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:117106347-11710649 2.50e-12 25_[+1(5.30e-07)]_27_[+10(2.57e-08)]_7_[+4(6.67e-06)]_10_[+2(1.42e-09)]_12 chr11:78069720-78069870 1.61e-20 50_[+6(3.21e-05)]_22_[+2(4.22e-12)]_4_[+1(2.79e-11)]_5_[+3(1.22e-06)]_4 chr11:78069792-78069942 4.17e-16 8_[+2(4.22e-12)]_4_[+1(2.79e-11)]_5_[+3(1.22e-06)]_76 chr12:86800987-86801137 2.82e-05 21_[+1(1.03e-07)]_14_[+6(6.58e-05)]_16_[+4(5.13e-05)]_60 chr1:86479304-86479454 1.68e-01 53_[+9(5.00e-05)]_89 chr1:151953775-151953925 1.25e-01 68_[+4(9.44e-05)]_72 chr2:168050409-168050559 8.24e-05 68_[+9(5.00e-05)]_14_[+2(5.85e-07)]_19_[+3(2.61e-05)]_5 chr2:27344010-27344160 4.26e-03 45_[+3(1.99e-05)]_86_[+9(2.65e-05)] chr2:27389674-27389824 3.40e-02 108_[+1(1.28e-06)]_21 chr4:107008317-107008467 3.03e-06 27_[+3(2.90e-05)]_24_[+6(6.58e-05)]_30_[+8(1.49e-08)]_30 chr4:155788382-155788532 2.61e-08 32_[+5(2.50e-09)]_[+8(7.32e-10)]_81 chr5:84811644-84811794 5.87e-05 10_[+8(5.68e-08)]_48_[+6(1.70e-05)]_64 chr6:72279647-72279797 2.60e-08 10_[+3(3.87e-06)]_34_[+7(2.11e-12)]_70 chr6:88189747-88189897 9.61e-02 74_[+9(2.65e-05)]_68 chr7:128301163-128301313 1.04e-08 3_[+7(6.98e-14)]_122 chr7:111179533-111179683 2.48e-12 2_[+6(3.21e-05)]_54_[+7(4.35e-12)]_6_[+2(1.44e-08)]_30 chr7:127770637-127770787 1.25e-08 13_[+2(2.71e-07)]_2_[+6(1.70e-05)]_6_[+4(7.73e-05)]_60_[+8(6.98e-09)]_6 chr7:79358627-79358777 1.69e-11 14_[+1(5.39e-08)]_26_[+4(6.42e-05)]_2_[+6(1.70e-05)]_1_[+8(1.05e-09)]_16_[+3(1.57e-05)]_21 chr7:120980099-120980249 6.46e-07 68_[+2(4.94e-07)]_19_[+10(2.57e-08)]_25 chr7:126042281-126042431 3.57e-02 58_[+4(5.51e-06)]_82 chr7:103865818-103865968 5.55e-09 21_[+1(5.94e-08)]_34_[+2(2.27e-08)]_49 chr7:127091403-127091553 4.35e-02 51_[+2(1.21e-07)]_74 chr7:125472297-125472447 9.16e-07 33_[+5(1.71e-10)]_100 chr7:109115127-109115277 1.86e-08 7_[+2(3.26e-07)]_7_[+6(3.21e-05)]_83_[+5(4.07e-08)]_3 chr7:123366187-123366337 9.52e-06 37_[+8(4.75e-08)]_77_[+3(3.02e-06)]_5 chr7:125428722-125428872 2.60e-01 47_[+4(1.99e-05)]_93 chr7:66196788-66196938 3.36e-03 92_[+1(1.05e-06)]_37 chr7:79742512-79742662 1.91e-02 95_[+4(9.44e-05)]_45 chr8:80493895-80494045 1.43e-06 16_[+1(2.15e-07)]_28_[+2(4.86e-08)]_60 chr8:122314990-122315140 6.35e-03 131_[+3(7.84e-07)]_8 chr8:36283726-36283876 2.46e-01 91_[+4(1.10e-05)]_49 chr9:45803540-45803690 5.00e-06 96_[+5(6.68e-08)]_9_[+6(3.21e-05)]_20 chrX:150549776-150549926 2.24e-09 7_[+1(8.63e-08)]_79_[+5(7.69e-09)]_26 chrX:150564760-150564910 7.44e-05 5_[+1(9.45e-08)]_16_[+3(1.40e-05)]_97 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************