******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.6.1 (Release date: Mon Mar 21 15:08:38 EST 2011) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= GATATopEnh.radius75bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr12:32050244-32050394 1.0000 150 chr13:14542965-14543115 1.0000 150 chr14:118194729-11819487 1.0000 150 chr15:66826254-66826404 1.0000 150 chr18:32542546-32542696 1.0000 150 chr18:38494977-38495127 1.0000 150 chr1:134093005-134093155 1.0000 150 chr1:130300211-130300361 1.0000 150 chr3:146405863-146406013 1.0000 150 chr6:88117034-88117184 1.0000 150 chr6:88203106-88203256 1.0000 150 chr7:103861042-103861192 1.0000 150 chr7:97210145-97210295 1.0000 150 chr7:103861054-103861204 1.0000 150 chr7:16295013-16295163 1.0000 150 chr7:111004283-111004433 1.0000 150 chr8:122313387-122313537 1.0000 150 chr9:123958069-123958219 1.0000 150 chrX:7841153-7841303 1.0000 150 chrX:7971480-7971630 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 GATATopEnh.radius75bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATATopEnh.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= 20 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 3000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.232 C 0.269 G 0.258 T 0.241 Background letter frequencies (from dataset with add-one prior applied): A 0.232 C 0.269 G 0.258 T 0.241 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 21 sites = 13 llr = 164 E-value = 6.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 17:21::51515155:7:85: pos.-specific C 81:8::32525:43223::22 probability G ::1::a522:244128:1128 matrix T 229:9:212321222::9211 bits 2.1 1.9 * 1.7 * ** * 1.5 * ** * Relative 1.3 **** * * Entropy 1.1 **** **** * (18.2 bits) 0.8 ****** * **** * 0.6 ****** * **** * 0.4 ******** * * ****** 0.2 ********************* 0.0 --------------------- Multilevel CATCTGGACACACAAGATAAG consensus T CGTTGGGC CC G sequence T CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr3:146405863-146406013 52 4.24e-09 TCTTGTTCTC CATCTGTACAGGGAAGATAAT AGGTCCAGGG chr6:88203106-88203256 79 5.65e-09 CCTATCCGGA CATCTGCAGCCGGTAGATAAG GAAACTTCGT chr7:103861054-103861204 1 2.70e-08 . CATCTGGCCACACACCCTAAG CCTCAGCATG chr7:103861042-103861192 13 2.70e-08 CAGCTGAAAA CATCTGGCCACACACCCTAAG CCTCAGCATG chr12:32050244-32050394 16 3.43e-08 CATCTGTGAA CATCTGGGTCTGTAAGCTAAG AGCCAGAAGG chr14:118194729-11819487 56 2.37e-07 TTCCTTCCAA CATATGTTTTTGCCAGATAAG TAAACAGTGT chr18:32542546-32542696 42 7.75e-07 TCCCTATAAC CCTCTGCAACTACCTGATAAG AGGCTCAGCT chr7:111004283-111004433 63 1.49e-06 CAGATATGGG CTTATGGGCTCACTAGATGGG GCCAGGCCAG chr7:97210145-97210295 77 1.88e-06 TTAGCCACAG AATCTGGAGAAAGATGATTGG AGGCACTGAG chr13:14542965-14543115 16 4.44e-06 GCTGCCTTCT TTTCTGCACTCAAGAGATACC ATGTCTTAGC chr6:88117034-88117184 78 5.08e-06 TTCTTTACCA CATCAGGATACAGAGCATTGC ATGAATTCCG chr1:134093005-134093155 71 6.17e-06 GAGGGCGGGG CTGCTGCGCAGGGCGGCTACG GCCACGCAAT chr15:66826254-66826404 99 1.01e-05 TCTCTGGCCT TATCTGTACTGTTCAGAGATG TTGGAAAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:146405863-146406013 4.2e-09 51_[+1]_78 chr6:88203106-88203256 5.7e-09 78_[+1]_51 chr7:103861054-103861204 2.7e-08 [+1]_129 chr7:103861042-103861192 2.7e-08 12_[+1]_117 chr12:32050244-32050394 3.4e-08 15_[+1]_114 chr14:118194729-11819487 2.4e-07 55_[+1]_74 chr18:32542546-32542696 7.8e-07 41_[+1]_88 chr7:111004283-111004433 1.5e-06 62_[+1]_67 chr7:97210145-97210295 1.9e-06 76_[+1]_53 chr13:14542965-14543115 4.4e-06 15_[+1]_114 chr6:88117034-88117184 5.1e-06 77_[+1]_52 chr1:134093005-134093155 6.2e-06 70_[+1]_59 chr15:66826254-66826404 1e-05 98_[+1]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=13 chr3:146405863-146406013 ( 52) CATCTGTACAGGGAAGATAAT 1 chr6:88203106-88203256 ( 79) CATCTGCAGCCGGTAGATAAG 1 chr7:103861054-103861204 ( 1) CATCTGGCCACACACCCTAAG 1 chr7:103861042-103861192 ( 13) CATCTGGCCACACACCCTAAG 1 chr12:32050244-32050394 ( 16) CATCTGGGTCTGTAAGCTAAG 1 chr14:118194729-11819487 ( 56) CATATGTTTTTGCCAGATAAG 1 chr18:32542546-32542696 ( 42) CCTCTGCAACTACCTGATAAG 1 chr7:111004283-111004433 ( 63) CTTATGGGCTCACTAGATGGG 1 chr7:97210145-97210295 ( 77) AATCTGGAGAAAGATGATTGG 1 chr13:14542965-14543115 ( 16) TTTCTGCACTCAAGAGATACC 1 chr6:88117034-88117184 ( 78) CATCAGGATACAGAGCATTGC 1 chr1:134093005-134093155 ( 71) CTGCTGCGCAGGGCGGCTACG 1 chr15:66826254-66826404 ( 99) TATCTGTACTGTTCAGAGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2600 bayes= 7.39087 E= 6.2e-005 -159 152 -1035 -65 157 -180 -1035 -6 -1035 -1035 -174 193 -59 165 -1035 -1035 -159 -1035 -1035 193 -1035 -1035 196 -1035 -1035 20 84 -6 121 -80 -16 -165 -159 100 -74 -6 99 -22 -1035 35 -159 78 -16 -6 121 -1035 58 -165 -159 52 58 -65 99 20 -174 -65 121 -80 -74 -65 -1035 -22 158 -1035 157 20 -1035 -1035 -1035 -1035 -174 193 173 -1035 -174 -65 121 -80 -16 -165 -1035 -80 158 -165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 6.2e-005 0.076923 0.769231 0.000000 0.153846 0.692308 0.076923 0.000000 0.230769 0.000000 0.000000 0.076923 0.923077 0.153846 0.846154 0.000000 0.000000 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 1.000000 0.000000 0.000000 0.307692 0.461538 0.230769 0.538462 0.153846 0.230769 0.076923 0.076923 0.538462 0.153846 0.230769 0.461538 0.230769 0.000000 0.307692 0.076923 0.461538 0.230769 0.230769 0.538462 0.000000 0.384615 0.076923 0.076923 0.384615 0.384615 0.153846 0.461538 0.307692 0.076923 0.153846 0.538462 0.153846 0.153846 0.153846 0.000000 0.230769 0.769231 0.000000 0.692308 0.307692 0.000000 0.000000 0.000000 0.000000 0.076923 0.923077 0.769231 0.000000 0.076923 0.153846 0.538462 0.153846 0.230769 0.076923 0.000000 0.153846 0.769231 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AT]TCTG[GCT][AG][CT][ATC][CGT][AG][CG][AC]A[GC][AC]TA[AG]G -------------------------------------------------------------------------------- Time 1.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 23 sites = 7 llr = 125 E-value = 3.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::61:11:::::::::1913:9 pos.-specific C 9:117164366::11a97::7:: probability G 149:1:317141999::117:11 matrix T :6:3:9:3:3:91:::1::1:9: bits 2.1 1.9 * 1.7 * 1.5 * ** * * ** Relative 1.3 * * * ****** * ** Entropy 1.1 *** * * ****** * *** (25.8 bits) 0.8 *** ** * ************* 0.6 ******* *************** 0.4 ******* *************** 0.2 *********************** 0.0 ----------------------- Multilevel CTGACTCCGCCTGGGCCCAGCTA consensus G T GTCTG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------- chr7:103861054-103861204 116 2.46e-14 GAGTGGAGAA CTGACTCCGCCTGGGCCCAGCTA ACCTCCTCTG chr7:103861042-103861192 128 2.46e-14 GAGTGGAGAA CTGACTCCGCCTGGGCCCAGCTA chr7:16295013-16295163 58 5.10e-09 CGGGGCGGCC CGGCCTCCGCCTGGCCCGAGCGA TAACGCTCTG chr7:111004283-111004433 36 7.36e-09 AATTGCTTCC CTGTGTGTCTGTGGGCTCAGATA TGGGCTTATG chrX:7971480-7971630 28 4.88e-08 GCATAGATAA GGGAATCAGCGGGGGCCAGGCTA GGCTTGGGGG chrX:7841153-7841303 75 5.15e-08 CGGTGCACGT CTGTCTATCGGTTGGCCCATCTG AAGTGATGGA chr1:134093005-134093155 117 7.44e-08 CGCCCGCAGC CGCACCGGGTCTGCGCCCAAATA AGGACAGCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103861054-103861204 2.5e-14 115_[+2]_12 chr7:103861042-103861192 2.5e-14 127_[+2] chr7:16295013-16295163 5.1e-09 57_[+2]_70 chr7:111004283-111004433 7.4e-09 35_[+2]_92 chrX:7971480-7971630 4.9e-08 27_[+2]_100 chrX:7841153-7841303 5.2e-08 74_[+2]_53 chr1:134093005-134093155 7.4e-08 116_[+2]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=23 seqs=7 chr7:103861054-103861204 ( 116) CTGACTCCGCCTGGGCCCAGCTA 1 chr7:103861042-103861192 ( 128) CTGACTCCGCCTGGGCCCAGCTA 1 chr7:16295013-16295163 ( 58) CGGCCTCCGCCTGGCCCGAGCGA 1 chr7:111004283-111004433 ( 36) CTGTGTGTCTGTGGGCTCAGATA 1 chrX:7971480-7971630 ( 28) GGGAATCAGCGGGGGCCAGGCTA 1 chrX:7841153-7841303 ( 75) CTGTCTATCGGTTGGCCCATCTG 1 chr1:134093005-134093155 ( 117) CGCACCGGGTCTGCGCCCAAATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 23 n= 2560 bayes= 9.1177 E= 3.8e-002 -945 167 -85 -945 -945 -945 73 124 -945 -91 173 -945 130 -91 -945 24 -70 141 -85 -945 -945 -91 -945 183 -70 109 15 -945 -70 67 -85 24 -945 9 147 -945 -945 109 -85 24 -945 109 73 -945 -945 -945 -85 183 -945 -945 173 -76 -945 -91 173 -945 -945 -91 173 -945 -945 189 -945 -945 -945 167 -945 -76 -70 141 -85 -945 188 -945 -85 -945 -70 -945 147 -76 30 141 -945 -945 -945 -945 -85 183 188 -945 -85 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 23 nsites= 7 E= 3.8e-002 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.142857 0.857143 0.000000 0.571429 0.142857 0.000000 0.285714 0.142857 0.714286 0.142857 0.000000 0.000000 0.142857 0.000000 0.857143 0.142857 0.571429 0.285714 0.000000 0.142857 0.428571 0.142857 0.285714 0.000000 0.285714 0.714286 0.000000 0.000000 0.571429 0.142857 0.285714 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.857143 0.142857 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.142857 0.714286 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.714286 0.142857 0.285714 0.714286 0.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TG]G[AT]CT[CG][CT][GC][CT][CG]TGGGCCCAG[CA]TA -------------------------------------------------------------------------------- Time 2.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 25 sites = 8 llr = 136 E-value = 2.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3:8331813a::::::1:311553: pos.-specific C :::815:38:4359:4::63413:a probability G :9:::1:4::5331:636::::38: matrix T 813:6333::153:a:641654::: bits 2.1 * * 1.9 * * * 1.7 * * * 1.5 * * * * Relative 1.3 *** * * ** ** Entropy 1.1 **** * ** *** * ** (24.5 bits) 0.8 ***** * ** *** * ** 0.6 ***** * *** ********* ** 0.4 ***** * ***************** 0.2 ******* ***************** 0.0 ------------------------- Multilevel TGACTCAGCAGTCCTGTGCTTAAGC consensus A TAATTCA CCG CGTACCTCA sequence T GT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:103861054-103861204 40 2.34e-13 TGACTCAGCA TGACTCAGCACTGCTGTGCTCAAGC TAGATGCTGG chr7:103861042-103861192 52 2.34e-13 TGACTCAGCA TGACTCAGCACTGCTGTGCTCAAGC TAGATGCTGG chr6:88117034-88117184 8 1.77e-08 TGATGGC TGTCTCACCATCCCTGGGCCTTCAC AGCCCCTGCC chr14:118194729-11819487 119 1.77e-08 TGCAATTTAA TGACATTACAGCTCTCAGCTTAGGC TGGCGTG chr12:32050244-32050394 103 2.95e-08 GTGTAAGGCT AGAATTATCAGTTCTCGGAATAAAC CACAGAGTCA chr8:122313387-122313537 103 3.61e-08 GGTTTCTGTG TGAACCTCAAGGCCTGTTATCTGGC GGCCGAGGCA chr13:14542965-14543115 110 7.04e-08 ACCACAAAGT ATTCTAATCACTCCTCTTCCATAGC AGCCGTTAAT chrX:7841153-7841303 25 1.07e-07 AGGGCGGAGG TGACAGAGAAGGCGTGTTTTTCCGC CAAACACTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103861054-103861204 2.3e-13 39_[+3]_86 chr7:103861042-103861192 2.3e-13 51_[+3]_74 chr6:88117034-88117184 1.8e-08 7_[+3]_118 chr14:118194729-11819487 1.8e-08 118_[+3]_7 chr12:32050244-32050394 2.9e-08 102_[+3]_23 chr8:122313387-122313537 3.6e-08 102_[+3]_23 chr13:14542965-14543115 7e-08 109_[+3]_16 chrX:7841153-7841303 1.1e-07 24_[+3]_101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=25 seqs=8 chr7:103861054-103861204 ( 40) TGACTCAGCACTGCTGTGCTCAAGC 1 chr7:103861042-103861192 ( 52) TGACTCAGCACTGCTGTGCTCAAGC 1 chr6:88117034-88117184 ( 8) TGTCTCACCATCCCTGGGCCTTCAC 1 chr14:118194729-11819487 ( 119) TGACATTACAGCTCTCAGCTTAGGC 1 chr12:32050244-32050394 ( 103) AGAATTATCAGTTCTCGGAATAAAC 1 chr8:122313387-122313537 ( 103) TGAACCTCAAGGCCTGTTATCTGGC 1 chr13:14542965-14543115 ( 110) ATTCTAATCACTCCTCTTCCATAGC 1 chrX:7841153-7841303 ( 25) TGACAGAGAAGGCGTGTTTTTCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 2520 bayes= 8.29462 E= 2.5e-001 11 -965 -965 163 -965 -965 176 -95 169 -965 -965 5 11 148 -965 -965 11 -110 -965 137 -89 90 -104 5 169 -965 -965 5 -89 -10 54 5 11 148 -965 -965 210 -965 -965 -965 -965 48 96 -95 -965 -10 -4 105 -965 90 -4 5 -965 170 -104 -965 -965 -965 -965 205 -965 48 128 -965 -89 -965 -4 137 -965 -965 128 64 11 122 -965 -95 -89 -10 -965 137 -89 48 -965 105 110 -110 -965 64 110 -10 -4 -965 11 -965 154 -965 -965 189 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 8 E= 2.5e-001 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.875000 0.125000 0.750000 0.000000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.250000 0.125000 0.000000 0.625000 0.125000 0.500000 0.125000 0.250000 0.750000 0.000000 0.000000 0.250000 0.125000 0.250000 0.375000 0.250000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.500000 0.125000 0.000000 0.250000 0.250000 0.500000 0.000000 0.500000 0.250000 0.250000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.625000 0.000000 0.125000 0.000000 0.250000 0.625000 0.000000 0.000000 0.625000 0.375000 0.250000 0.625000 0.000000 0.125000 0.125000 0.250000 0.000000 0.625000 0.125000 0.375000 0.000000 0.500000 0.500000 0.125000 0.000000 0.375000 0.500000 0.250000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]G[AT][CA][TA][CT][AT][GCT][CA]A[GC][TCG][CGT]CT[GC][TG][GT][CA][TC][TC][AT][ACG][GA]C -------------------------------------------------------------------------------- Time 3.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 25 sites = 4 llr = 96 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A 8:8:3:::3:3:8:8a::::38a:a pos.-specific C :::338:::5:a353:::a3:::8: probability G 3a335::885::::::aa::5:::: matrix T :::5:3a3::8::5:::::833:3: bits 2.1 * * * * 1.9 * * * **** * * 1.7 * * * **** * * 1.5 * * * **** * * Relative 1.3 *** *** *** ****** ** * Entropy 1.1 *** **** ********** **** (34.7 bits) 0.8 *** *************** **** 0.6 *** *************** **** 0.4 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel AGATGCTGGCTCACAAGGCTGAACA consensus G GCAT TAGA CTC CAT T sequence GC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:103861054-103861204 66 3.03e-15 TGCTCAAGCT AGATGCTGGCTCACAAGGCTGAACA CACCCACAGG chr7:103861042-103861192 78 3.03e-15 TGCTCAAGCT AGATGCTGGCTCACAAGGCTGAACA CACCCACAGG chr9:123958069-123958219 35 1.00e-10 TGCTTCTTTG GGACACTGAGACCTAAGGCCTAACA TGTCTGTTTG chr15:66826254-66826404 126 1.32e-10 GATGTTGGAA AGGGCTTTGGTCATCAGGCTATATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103861054-103861204 3e-15 65_[+4]_60 chr7:103861042-103861192 3e-15 77_[+4]_48 chr9:123958069-123958219 1e-10 34_[+4]_91 chr15:66826254-66826404 1.3e-10 125_[+4] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=25 seqs=4 chr7:103861054-103861204 ( 66) AGATGCTGGCTCACAAGGCTGAACA 1 chr7:103861042-103861192 ( 78) AGATGCTGGCTCACAAGGCTGAACA 1 chr9:123958069-123958219 ( 35) GGACACTGAGACCTAAGGCCTAACA 1 chr15:66826254-66826404 ( 126) AGGGCTTTGGTCATCAGGCTATATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 2520 bayes= 10.0348 E= 3.5e+000 169 -865 -4 -865 -865 -865 195 -865 169 -865 -4 -865 -865 -10 -4 105 11 -10 95 -865 -865 148 -865 5 -865 -865 -865 205 -865 -865 154 5 11 -865 154 -865 -865 89 95 -865 11 -865 -865 163 -865 189 -865 -865 169 -10 -865 -865 -865 89 -865 105 169 -10 -865 -865 210 -865 -865 -865 -865 -865 195 -865 -865 -865 195 -865 -865 189 -865 -865 -865 -10 -865 163 11 -865 95 5 169 -865 -865 5 210 -865 -865 -865 -865 148 -865 5 210 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 4 E= 3.5e+000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.250000 0.500000 0.250000 0.250000 0.500000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.750000 0.000000 0.000000 0.500000 0.500000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 0.500000 0.250000 0.750000 0.000000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- [AG]G[AG][TCG][GAC][CT]T[GT][GA][CG][TA]C[AC][CT][AC]AGGC[TC][GAT][AT]A[CT]A -------------------------------------------------------------------------------- Time 4.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 15 sites = 9 llr = 107 E-value = 3.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A 19:::32313612:: pos.-specific C 7:::121::::::22 probability G 2:aa91779729388 matrix T :1:::3::::2:4:: bits 2.1 1.9 ** 1.7 *** 1.5 **** * * Relative 1.3 **** * * ** Entropy 1.1 **** *** * ** (17.2 bits) 0.8 **** **** * ** 0.6 ***** ****** ** 0.4 ***** ********* 0.2 *************** 0.0 --------------- Multilevel CAGGGAGGGGAGTGG consensus G TAA AG GCC sequence C T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr7:103861054-103861204 97 2.16e-09 AACACACCCA CAGGGTGGGGAGTGG AGAACTGACT chr7:103861042-103861192 109 2.16e-09 AACACACCCA CAGGGTGGGGAGTGG AGAACTGACT chr1:130300211-130300361 9 7.76e-07 GGAGAAAG AAGGGAGAGGGGTGG GCAATCTGCT chr7:16295013-16295163 100 1.47e-06 GGTTTGGAAC CAGGGCGGGAAGTCC TTCCTGAAGT chr18:32542546-32542696 132 2.37e-06 TCAGCATATG GAGGGAGGGAAAAGG CTCT chrX:7971480-7971630 70 3.44e-06 GAGCCCATTG CAGGCGGGGGTGGGG TGTCCGGGTT chr18:38494977-38495127 103 5.48e-06 GCAGAGCCCT CAGGGCAGAGTGAGG ACTTTGCCCT chrX:7841153-7841303 6 8.29e-06 AACGT GAGGGTAAGAGGGCG GAGGTGACAG chr1:134093005-134093155 52 1.03e-05 CCCGCCCTGG CTGGGACAGGAGGGC GGGGCTGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103861054-103861204 2.2e-09 96_[+5]_39 chr7:103861042-103861192 2.2e-09 108_[+5]_27 chr1:130300211-130300361 7.8e-07 8_[+5]_127 chr7:16295013-16295163 1.5e-06 99_[+5]_36 chr18:32542546-32542696 2.4e-06 131_[+5]_4 chrX:7971480-7971630 3.4e-06 69_[+5]_66 chr18:38494977-38495127 5.5e-06 102_[+5]_33 chrX:7841153-7841303 8.3e-06 5_[+5]_130 chr1:134093005-134093155 1e-05 51_[+5]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=15 seqs=9 chr7:103861054-103861204 ( 97) CAGGGTGGGGAGTGG 1 chr7:103861042-103861192 ( 109) CAGGGTGGGGAGTGG 1 chr1:130300211-130300361 ( 9) AAGGGAGAGGGGTGG 1 chr7:16295013-16295163 ( 100) CAGGGCGGGAAGTCC 1 chr18:32542546-32542696 ( 132) GAGGGAGGGAAAAGG 1 chrX:7971480-7971630 ( 70) CAGGCGGGGGTGGGG 1 chr18:38494977-38495127 ( 103) CAGGGCAGAGTGAGG 1 chrX:7841153-7841303 ( 6) GAGGGTAAGAGGGCG 1 chr1:134093005-134093155 ( 52) CTGGGACAGGAGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2720 bayes= 8.36941 E= 3.7e+000 -106 131 -21 -982 193 -982 -982 -112 -982 -982 196 -982 -982 -982 196 -982 -982 -127 179 -982 52 -27 -121 47 -6 -127 137 -982 52 -982 137 -982 -106 -982 179 -982 52 -982 137 -982 126 -982 -21 -12 -106 -982 179 -982 -6 -982 37 88 -982 -27 159 -982 -982 -27 159 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 3.7e+000 0.111111 0.666667 0.222222 0.000000 0.888889 0.000000 0.000000 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.333333 0.222222 0.111111 0.333333 0.222222 0.111111 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.111111 0.000000 0.888889 0.000000 0.333333 0.000000 0.666667 0.000000 0.555556 0.000000 0.222222 0.222222 0.111111 0.000000 0.888889 0.000000 0.222222 0.000000 0.333333 0.444444 0.000000 0.222222 0.777778 0.000000 0.000000 0.222222 0.777778 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- [CG]AGGG[ATC][GA][GA]G[GA][AGT]G[TGA][GC][GC] -------------------------------------------------------------------------------- Time 5.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 19 sites = 3 llr = 63 E-value = 1.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A a7a3:7::::33:7a:a7a pos.-specific C ::::a:7::::7a:::::: probability G :::7::3:3::::::a:3: matrix T :3:::3:a7a7::3::::: bits 2.1 * * * * * * * 1.9 * * * * * * *** * 1.7 * * * * * * *** * 1.5 * * * * * * *** * Relative 1.3 *** ** * * ***** * Entropy 1.1 ******************* (30.4 bits) 0.8 ******************* 0.6 ******************* 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel AAAGCACTTTTCCAAGAAA consensus T A TG G AA T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- chr7:97210145-97210295 27 5.14e-11 GAAGTTATGC AAAACTCTTTTCCAAGAAA TGCCTTGCCC chr13:14542965-14543115 80 2.87e-10 TGGGAGTCAC ATAGCACTGTTCCTAGAAA TACCACAAAG chr1:130300211-130300361 81 3.61e-10 GCTGCTGATA AAAGCAGTTTAACAAGAGA CTTGGGGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:97210145-97210295 5.1e-11 26_[+6]_105 chr13:14542965-14543115 2.9e-10 79_[+6]_52 chr1:130300211-130300361 3.6e-10 80_[+6]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=19 seqs=3 chr7:97210145-97210295 ( 27) AAAACTCTTTTCCAAGAAA 1 chr13:14542965-14543115 ( 80) ATAGCACTGTTCCTAGAAA 1 chr1:130300211-130300361 ( 81) AAAGCAGTTTAACAAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 2640 bayes= 10.2276 E= 1.4e+002 210 -823 -823 -823 152 -823 -823 46 210 -823 -823 -823 52 -823 137 -823 -823 189 -823 -823 152 -823 -823 46 -823 131 37 -823 -823 -823 -823 205 -823 -823 37 146 -823 -823 -823 205 52 -823 -823 146 52 131 -823 -823 -823 189 -823 -823 152 -823 -823 46 210 -823 -823 -823 -823 -823 195 -823 210 -823 -823 -823 152 -823 37 -823 210 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 3 E= 1.4e+002 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- A[AT]A[GA]C[AT][CG]T[TG]T[TA][CA]C[AT]AGA[AG]A -------------------------------------------------------------------------------- Time 6.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 15 sites = 3 llr = 50 E-value = 2.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A 7a:::3::a3a7aaa pos.-specific C :::3::3:::::::: probability G 3::::33:::::::: matrix T ::a7a33a:7:3::: bits 2.1 ** * ** * *** 1.9 ** * ** * *** 1.7 ** * ** * *** 1.5 ** * ** * *** Relative 1.3 ** * ** ***** Entropy 1.1 ***** ******** (24.2 bits) 0.8 ***** ******** 0.6 ***** ******** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AATTTACTATAAAAA consensus G C GG A T sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr15:66826254-66826404 11 9.15e-09 CAGCAGGCTG AATTTAGTATATAAA ACACAGTAAA chr1:130300211-130300361 26 2.00e-08 AGGGGTGGGC AATCTGCTATAAAAA TACACCCACA chr6:88203106-88203256 26 2.73e-08 TCATTTGAGT GATTTTTTAAAAAAA TGTCCTTTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:66826254-66826404 9.1e-09 10_[+7]_125 chr1:130300211-130300361 2e-08 25_[+7]_110 chr6:88203106-88203256 2.7e-08 25_[+7]_110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=15 seqs=3 chr15:66826254-66826404 ( 11) AATTTAGTATATAAA 1 chr1:130300211-130300361 ( 26) AATCTGCTATAAAAA 1 chr6:88203106-88203256 ( 26) GATTTTTTAAAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2720 bayes= 9.48137 E= 2.9e+002 152 -823 37 -823 210 -823 -823 -823 -823 -823 -823 205 -823 31 -823 146 -823 -823 -823 205 52 -823 37 46 -823 31 37 46 -823 -823 -823 205 210 -823 -823 -823 52 -823 -823 146 210 -823 -823 -823 152 -823 -823 46 210 -823 -823 -823 210 -823 -823 -823 210 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3 E= 2.9e+002 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- [AG]AT[TC]T[AGT][CGT]TA[TA]A[AT]AAA -------------------------------------------------------------------------------- Time 6.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 15 sites = 6 llr = 80 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A 823:2:::5:::::8 pos.-specific C :8:2:::732:a::2 probability G :::8:8:3:78:27: matrix T 2:7:82a:222:83: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * ** * Relative 1.3 ** **** *** * Entropy 1.1 ******** ***** (19.3 bits) 0.8 ******** ***** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel ACTGTGTCAGGCTGA consensus A GC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr8:122313387-122313537 60 2.02e-09 TGTTATCTAG ACTGTGTCCGGCTGA CTAATCTTGC chr18:32542546-32542696 73 4.83e-08 AGGCTCAGCT ACTGTTTCAGGCTTA TCAGAGGCAG chr12:32050244-32050394 129 3.11e-07 GGAATAAACC ACAGAGTCACGCTGA CGTGGAG chr1:130300211-130300361 64 3.96e-07 GCAGTTGGTT AATGTGTGCTGCTGA TAAAAGCAGT chrX:7971480-7971630 104 1.69e-06 TGAAGCGTCT TCTCTGTCAGGCTTC CATTTGAGAC chr14:118194729-11819487 80 1.89e-06 AGATAAGTAA ACAGTGTGTGTCGGA AATGAAAAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:122313387-122313537 2e-09 59_[+8]_76 chr18:32542546-32542696 4.8e-08 72_[+8]_63 chr12:32050244-32050394 3.1e-07 128_[+8]_7 chr1:130300211-130300361 4e-07 63_[+8]_72 chrX:7971480-7971630 1.7e-06 103_[+8]_32 chr14:118194729-11819487 1.9e-06 79_[+8]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=15 seqs=6 chr8:122313387-122313537 ( 60) ACTGTGTCCGGCTGA 1 chr18:32542546-32542696 ( 73) ACTGTTTCAGGCTTA 1 chr12:32050244-32050394 ( 129) ACAGAGTCACGCTGA 1 chr1:130300211-130300361 ( 64) AATGTGTGCTGCTGA 1 chrX:7971480-7971630 ( 104) TCTCTGTCAGGCTTC 1 chr14:118194729-11819487 ( 80) ACAGTGTGTGTCGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2720 bayes= 9.26955 E= 1.6e+003 184 -923 -923 -53 -48 163 -923 -923 52 -923 -923 146 -923 -69 169 -923 -48 -923 -923 179 -923 -923 169 -53 -923 -923 -923 205 -923 131 37 -923 110 31 -923 -53 -923 -69 137 -53 -923 -923 169 -53 -923 189 -923 -923 -923 -923 -63 179 -923 -923 137 47 184 -69 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6 E= 1.6e+003 0.833333 0.000000 0.000000 0.166667 0.166667 0.833333 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.500000 0.333333 0.000000 0.166667 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.666667 0.333333 0.833333 0.166667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- AC[TA]GTGT[CG][AC]GGCT[GT]A -------------------------------------------------------------------------------- Time 7.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 11 sites = 3 llr = 42 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A a::7:::a::a pos.-specific C ::::a:7::a: probability G ::a:::::a:: matrix T :a:3:a3:::: bits 2.1 ** * * * 1.9 *** ** **** 1.7 *** ** **** 1.5 *** ** **** Relative 1.3 ****** **** Entropy 1.1 *********** (20.3 bits) 0.8 *********** 0.6 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel ATGACTCAGCA consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr7:103861054-103861204 29 2.18e-07 AAGCCTCAGC ATGACTCAGCA TGACTCAGCA chr7:103861042-103861192 41 2.18e-07 AAGCCTCAGC ATGACTCAGCA TGACTCAGCA chr13:14542965-14543115 37 8.43e-07 AAGAGATACC ATGTCTTAGCA ACCCTCCAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103861054-103861204 2.2e-07 28_[+9]_111 chr7:103861042-103861192 2.2e-07 40_[+9]_99 chr13:14542965-14543115 8.4e-07 36_[+9]_103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=11 seqs=3 chr7:103861054-103861204 ( 29) ATGACTCAGCA 1 chr7:103861042-103861192 ( 41) ATGACTCAGCA 1 chr13:14542965-14543115 ( 37) ATGTCTTAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2800 bayes= 9.52325 E= 1.8e+003 210 -823 -823 -823 -823 -823 -823 205 -823 -823 195 -823 152 -823 -823 46 -823 189 -823 -823 -823 -823 -823 205 -823 131 -823 46 210 -823 -823 -823 -823 -823 195 -823 -823 189 -823 -823 210 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 3 E= 1.8e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- ATG[AT]CT[CT]AGCA -------------------------------------------------------------------------------- Time 8.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 20 sites = 2 llr = 47 E-value = 7.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A :a5a5:5:a::a5:5:a5:a pos.-specific C ::::5a:::5::::5:::a: probability G ::::::::::::5a:::::: matrix T a:5:::5a:5a::::a:5:: bits 2.1 ** * ** ** ** * 1.9 ** * * ** ** * ** ** 1.7 ** * * ** ** * ** ** 1.5 ** * * ** ** * ** ** Relative 1.3 ** * * ** ** * ** ** Entropy 1.1 ******************** (33.8 bits) 0.8 ******************** 0.6 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TAAAACATACTAAGATAACA consensus T C T T G C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- chr12:32050244-32050394 60 2.32e-11 CTCCATCTCC TATACCATATTAAGATATCA GCGATTCCCA chr9:123958069-123958219 124 4.72e-11 GCTATATCTT TAAAACTTACTAGGCTAACA TCTCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:32050244-32050394 2.3e-11 59_[+10]_71 chr9:123958069-123958219 4.7e-11 123_[+10]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=20 seqs=2 chr12:32050244-32050394 ( 60) TATACCATATTAAGATATCA 1 chr9:123958069-123958219 ( 124) TAAAACTTACTAGGCTAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2620 bayes= 10.3542 E= 7.6e+003 -765 -765 -765 205 210 -765 -765 -765 110 -765 -765 105 210 -765 -765 -765 110 89 -765 -765 -765 189 -765 -765 110 -765 -765 105 -765 -765 -765 205 210 -765 -765 -765 -765 89 -765 105 -765 -765 -765 205 210 -765 -765 -765 110 -765 95 -765 -765 -765 195 -765 110 89 -765 -765 -765 -765 -765 205 210 -765 -765 -765 110 -765 -765 105 -765 189 -765 -765 210 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2 E= 7.6e+003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- TA[AT]A[AC]C[AT]TA[CT]TA[AG]G[AC]TA[AT]CA -------------------------------------------------------------------------------- Time 9.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:32050244-32050394 1.42e-16 15_[+1(3.43e-08)]_23_[+10(2.32e-11)]_23_[+3(2.95e-08)]_1_[+8(3.11e-07)]_7 chr13:14542965-14543115 1.04e-11 15_[+1(4.44e-06)]_[+9(8.43e-07)]_32_[+6(2.87e-10)]_11_[+3(7.04e-08)]_16 chr14:118194729-11819487 6.48e-10 55_[+1(2.37e-07)]_3_[+8(1.89e-06)]_24_[+3(1.77e-08)]_7 chr15:66826254-66826404 2.19e-13 10_[+7(9.15e-09)]_73_[+1(1.01e-05)]_6_[+4(1.32e-10)] chr18:32542546-32542696 1.55e-07 41_[+1(7.75e-07)]_10_[+8(4.83e-08)]_12_[+5(2.89e-05)]_17_[+5(2.37e-06)]_4 chr18:38494977-38495127 2.25e-02 102_[+5(5.48e-06)]_33 chr1:134093005-134093155 5.55e-05 51_[+5(1.03e-05)]_4_[+1(6.17e-06)]_25_[+2(7.44e-08)]_11 chr1:130300211-130300361 2.07e-13 8_[+5(7.76e-07)]_2_[+7(2.00e-08)]_23_[+8(3.96e-07)]_2_[+6(3.61e-10)]_51 chr3:146405863-146406013 1.06e-03 51_[+1(4.24e-09)]_78 chr6:88117034-88117184 2.63e-06 7_[+3(1.77e-08)]_45_[+1(5.08e-06)]_52 chr6:88203106-88203256 9.15e-06 25_[+7(2.73e-08)]_38_[+1(5.65e-09)]_51 chr7:103861042-103861192 3.49e-39 12_[+1(2.70e-08)]_7_[+9(2.18e-07)]_[+3(2.34e-13)]_1_[+4(3.03e-15)]_6_[+5(2.16e-09)]_4_[+2(2.46e-14)] chr7:97210145-97210295 2.57e-07 26_[+6(5.14e-11)]_31_[+1(1.88e-06)]_53 chr7:103861054-103861204 3.82e-39 [+1(2.70e-08)]_7_[+9(2.18e-07)]_[+3(2.34e-13)]_1_[+4(3.03e-15)]_6_[+5(2.16e-09)]_4_[+2(2.46e-14)]_12 chr7:16295013-16295163 4.89e-05 57_[+2(5.10e-09)]_19_[+5(1.47e-06)]_36 chr7:111004283-111004433 8.81e-06 14_[+1(4.43e-05)]_[+2(7.36e-09)]_4_[+1(1.49e-06)]_67 chr8:122313387-122313537 6.70e-08 59_[+8(2.02e-09)]_28_[+3(3.61e-08)]_23 chr9:123958069-123958219 5.27e-10 34_[+4(1.00e-10)]_64_[+10(4.72e-11)]_7 chrX:7841153-7841303 1.46e-07 5_[+5(8.29e-06)]_4_[+3(1.07e-07)]_25_[+2(5.15e-08)]_53 chrX:7971480-7971630 9.21e-07 27_[+2(4.88e-08)]_19_[+5(3.44e-06)]_19_[+8(1.69e-06)]_32 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************