******************************************************************************** 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= GATA_No_Function.radius75bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr11:78066028-78066178 1.0000 150 chr11:96941156-96941306 1.0000 150 chr11:96918230-96918380 1.0000 150 chr11:121433465-12143361 1.0000 150 chr16:17638345-17638495 1.0000 150 chr17:4626334-4626484 1.0000 150 chr18:78123162-78123312 1.0000 150 chr1:133825587-133825737 1.0000 150 chr1:155039328-155039478 1.0000 150 chr2:27393862-27394012 1.0000 150 chr2:35336372-35336522 1.0000 150 chr3:21996029-21996179 1.0000 150 chr5:147442057-147442207 1.0000 150 chr6:88190742-88190892 1.0000 150 chr6:38874495-38874645 1.0000 150 chr6:38850125-38850275 1.0000 150 chr7:103827921-103828071 1.0000 150 chr7:128672393-128672543 1.0000 150 chr7:81828551-81828701 1.0000 150 chr7:100684791-100684941 1.0000 150 chr7:66079514-66079664 1.0000 150 chr7:80629499-80629649 1.0000 150 chr7:126396946-126397096 1.0000 150 chr7:126348298-126348448 1.0000 150 chr7:83695929-83696079 1.0000 150 chr7:65300566-65300716 1.0000 150 chr7:83898433-83898583 1.0000 150 chr7:126126668-126126818 1.0000 150 chr7:81371603-81371753 1.0000 150 chr7:103910176-103910326 1.0000 150 chr7:90129365-90129515 1.0000 150 chr8:122306903-122307053 1.0000 150 chr8:122329088-122329238 1.0000 150 chr8:122309313-122309463 1.0000 150 chr9:110668725-110668875 1.0000 150 chr9:96241534-96241684 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 GATA_No_Function.radius75bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATA_No_Function.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= 36 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= 5400 N= 36 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.243 C 0.255 G 0.245 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.243 C 0.255 G 0.245 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 25 llr = 180 E-value = 1.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:7:5a:a pos.-specific C ::::4:2: probability G 1a25::8: matrix T 6:151::: bits 2.0 * * 1.8 * * * 1.6 * * * 1.4 * *** Relative 1.2 * *** Entropy 1.0 * * *** (10.4 bits) 0.8 *** *** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGATAAGA consensus A GGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:126126668-126126818 85 2.70e-05 AAGGAAGCAT TGATAAGA AGTTCAGCAG chr1:155039328-155039478 140 2.70e-05 GATCGAGCCC TGAGAAGA GTC chr6:88190742-88190892 59 5.25e-05 TGGAAGGCAG AGATAAGA AACACCATTT chr3:21996029-21996179 21 5.25e-05 ATGGTGGCCC AGATAAGA CTGTCACAGG chr11:96941156-96941306 142 5.25e-05 TGTTTTTGGA AGATAAGA G chr7:128672393-128672543 76 8.09e-05 AGGCGGGCGC TGAGCAGA CACCTCCTGG chr7:103827921-103828071 72 8.09e-05 CTATCCTGTG TGAGCAGA TTGGCCCTTA chr2:35336372-35336522 78 8.09e-05 GAAACAAGAA TGAGCAGA GGAGGCTGAA chr16:17638345-17638495 96 8.09e-05 TTATCTCCTG TGAGCAGA AGGTACTATA chr7:80629499-80629649 15 1.08e-04 TCCTCTCTGC AGATCAGA TGAAGCTCTG chr6:38874495-38874645 38 1.35e-04 AGAGCCTGAA TGGTAAGA GAGTCCATGC chr11:96918230-96918380 132 1.35e-04 GCTGCTGTAG TGGGAAGA CCAAGATTCT chr8:122306903-122307053 5 2.46e-04 GCAG TGATAACA CAGTGATGGG chr7:83695929-83696079 52 2.46e-04 AGATTAAGTC TGGGCAGA CGCCTAGGCT chr7:100684791-100684941 88 2.46e-04 TTGGCCATGT TGATAACA AGATAACAAA chr18:78123162-78123312 3 3.00e-04 GG GGATAAGA GTAAAGAGGA chr11:78066028-78066178 130 3.00e-04 AAGGGGGTGG GGAGAAGA ACCTCCTAGC chr7:103910176-103910326 141 3.27e-04 TTAAGCCTTG AGAGTAGA AC chr2:27393862-27394012 83 3.27e-04 TGGGACTCCT AGAGTAGA TAAACAGGTG chr7:83898433-83898583 33 4.37e-04 GTGTTCAGTG AGTGAAGA TAACTGTGCC chr7:65300566-65300716 75 4.94e-04 TTCCTCAAAC TGTTCAGA AATATGCTTC chr7:66079514-66079664 37 7.74e-04 CCCCGCCCTC TGGTCACA CCCCCCCTGT chr9:96241534-96241684 90 8.32e-04 AACTGAGGGC TGTGTAGA AATAGCCCCA chr8:122309313-122309463 112 9.69e-04 CGGCTCCCAC AGATAGGA ATTTCTGTGC chr11:121433465-12143361 51 1.05e-03 AGCCCATGAC AGGTCACA AGGACCCTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:126126668-126126818 2.7e-05 84_[+1]_58 chr1:155039328-155039478 2.7e-05 139_[+1]_3 chr6:88190742-88190892 5.3e-05 58_[+1]_84 chr3:21996029-21996179 5.3e-05 20_[+1]_122 chr11:96941156-96941306 5.3e-05 141_[+1]_1 chr7:128672393-128672543 8.1e-05 75_[+1]_67 chr7:103827921-103828071 8.1e-05 71_[+1]_71 chr2:35336372-35336522 8.1e-05 77_[+1]_65 chr16:17638345-17638495 8.1e-05 95_[+1]_47 chr7:80629499-80629649 0.00011 14_[+1]_128 chr6:38874495-38874645 0.00013 37_[+1]_105 chr11:96918230-96918380 0.00013 131_[+1]_11 chr8:122306903-122307053 0.00025 4_[+1]_138 chr7:83695929-83696079 0.00025 51_[+1]_91 chr7:100684791-100684941 0.00025 87_[+1]_55 chr18:78123162-78123312 0.0003 2_[+1]_140 chr11:78066028-78066178 0.0003 129_[+1]_13 chr7:103910176-103910326 0.00033 140_[+1]_2 chr2:27393862-27394012 0.00033 82_[+1]_60 chr7:83898433-83898583 0.00044 32_[+1]_110 chr7:65300566-65300716 0.00049 74_[+1]_68 chr7:66079514-66079664 0.00077 36_[+1]_106 chr9:96241534-96241684 0.00083 89_[+1]_53 chr8:122309313-122309463 0.00097 111_[+1]_31 chr11:121433465-12143361 0.0011 50_[+1]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=25 chr7:126126668-126126818 ( 85) TGATAAGA 1 chr1:155039328-155039478 ( 140) TGAGAAGA 1 chr6:88190742-88190892 ( 59) AGATAAGA 1 chr3:21996029-21996179 ( 21) AGATAAGA 1 chr11:96941156-96941306 ( 142) AGATAAGA 1 chr7:128672393-128672543 ( 76) TGAGCAGA 1 chr7:103827921-103828071 ( 72) TGAGCAGA 1 chr2:35336372-35336522 ( 78) TGAGCAGA 1 chr16:17638345-17638495 ( 96) TGAGCAGA 1 chr7:80629499-80629649 ( 15) AGATCAGA 1 chr6:38874495-38874645 ( 38) TGGTAAGA 1 chr11:96918230-96918380 ( 132) TGGGAAGA 1 chr8:122306903-122307053 ( 5) TGATAACA 1 chr7:83695929-83696079 ( 52) TGGGCAGA 1 chr7:100684791-100684941 ( 88) TGATAACA 1 chr18:78123162-78123312 ( 3) GGATAAGA 1 chr11:78066028-78066178 ( 130) GGAGAAGA 1 chr7:103910176-103910326 ( 141) AGAGTAGA 1 chr2:27393862-27394012 ( 83) AGAGTAGA 1 chr7:83898433-83898583 ( 33) AGTGAAGA 1 chr7:65300566-65300716 ( 75) TGTTCAGA 1 chr7:66079514-66079664 ( 37) TGGTCACA 1 chr9:96241534-96241684 ( 90) TGTGTAGA 1 chr8:122309313-122309463 ( 112) AGATAGGA 1 chr11:121433465-12143361 ( 51) AGGTCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5148 bayes= 8.17099 E= 1.3e+000 57 -1129 -161 112 -1129 -1129 203 -1129 148 -1129 -29 -110 -1129 -1129 97 102 110 50 -1129 -110 198 -1129 -261 -1129 -1129 -67 178 -1129 204 -1129 -1129 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.3e+000 0.360000 0.000000 0.080000 0.560000 0.000000 0.000000 1.000000 0.000000 0.680000 0.000000 0.200000 0.120000 0.000000 0.000000 0.480000 0.520000 0.520000 0.360000 0.000000 0.120000 0.960000 0.000000 0.040000 0.000000 0.000000 0.160000 0.840000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA]G[AG][TG][AC]AGA -------------------------------------------------------------------------------- Time 3.45 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 8 sites = 35 llr = 213 E-value = 2.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :6::1:3: pos.-specific C 9:1359:1 probability G 1:953::9 matrix T :4:2217: bits 2.0 1.8 1.6 * * 1.4 * * * * Relative 1.2 * * * * Entropy 1.0 *** *** (8.8 bits) 0.8 *** *** 0.6 *** *** 0.4 **** *** 0.2 ******** 0.0 -------- Multilevel CAGGCCTG consensus T CG A sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:81371603-81371753 84 1.52e-05 ATCTCCAAGA CAGGCCTG GGCACCAGGG chr6:88190742-88190892 104 3.11e-05 AAACAATTCC CAGCCCTG TACAACCCCA chr16:17638345-17638495 74 4.72e-05 GGTGACATGC CTGGCCTG GTGCTTATCT chr8:122329088-122329238 123 6.18e-05 TGATGTCATC CAGGGCTG GGGGGAGGGA chr7:103827921-103828071 41 7.86e-05 CTTATATGCT CTGCCCTG GCTCCTGCCC chr7:81828551-81828701 5 9.30e-05 GAAG CAGGCCAG CCTGATACCT chr9:96241534-96241684 52 1.55e-04 CATTCCTGGT CTGGGCTG CCACCTGTGA chr9:110668725-110668875 42 2.01e-04 GCCTAAACCT CAGCTCTG TTCATCCTAG chr7:100684791-100684941 37 2.01e-04 TTACTGCATC CAGCTCTG TGCATCTTTA chr5:147442057-147442207 127 2.01e-04 TTGCCCAGGA CTGGCCAG TGAATGGCAA chr2:27393862-27394012 116 2.01e-04 GGGTGACAAG CTGGCCAG ACAGTCCCCA chr1:133825587-133825737 122 2.01e-04 GTCTCTTCAC CAGCTCTG TGTCTGCATT chr2:35336372-35336522 137 2.50e-04 CTGCCAGGGT CTGTCCTG GTCTGC chr7:83898433-83898583 16 2.95e-04 GCCGTATGGG CAGTGCTG TGTTCAGTGA chr7:65300566-65300716 118 4.32e-04 ATGCTACTCA CTGTGCTG AGTGTTCAAT chr7:126348298-126348448 43 4.63e-04 GGGCGGGCTG CAGCTCAG GGTTTATCTC chr11:121433465-12143361 76 4.63e-04 TGGGGATGGC CAGCACTG ACAGGCTTTG chr11:96918230-96918380 101 5.25e-04 TTAGTGGACC CTGGACTG AACTGCCTGG chr11:96941156-96941306 26 5.25e-04 CCTTAGGAAC CTGTCCAG GAGGTATAAG chr6:38874495-38874645 74 5.57e-04 AATTCATTTA GAGCCCTG GTACTAATAA chr8:122309313-122309463 124 7.38e-04 ATAGGAATTT CTGTGCAG TGGGCAGCGA chr7:103910176-103910326 40 7.38e-04 GCTGCTGGCA GAGGCCAG CTGAAGTGCC chr7:90129365-90129515 62 8.13e-04 CGCTGGTTGT CAGCCTTG TAGGGTCAAG chr1:155039328-155039478 98 8.13e-04 CAGACTATCA GAGTCCTG CTGCAAAGAG chr7:80629499-80629649 129 8.74e-04 ATCTGTCTCC CTGGCTTG TCCCCAGACC chr18:78123162-78123312 27 1.14e-03 AGGACGAAGG CAGCCCTC AGCAAGGACT chr11:78066028-78066178 6 1.14e-03 GTTAA GAGGGCAG GAATCCGTGC chr7:126126668-126126818 52 1.25e-03 GCTACAGGCA CAGGTTTG CCTTGCTTTG chr7:128672393-128672543 90 1.25e-03 CAGACACCTC CTGGCCTC CAGCAGGAGC chr7:126396946-126397096 7 1.67e-03 TCGATT CTGTACAG TTCATCCATT chr8:122306903-122307053 94 1.81e-03 TTGGTGGCTG GAGCTCAG ATGCCAGCCA chr3:21996029-21996179 55 2.23e-03 GACCCATGCC CATGGCTG CCTAAGAAAA chr7:66079514-66079664 103 2.39e-03 TCAGTACCGC CACGGCAG TGAGCGCCAC chr6:38850125-38850275 121 2.72e-03 AAATAGAACT CTCCTCTG TGAGTGTTTC chr7:83695929-83696079 63 2.90e-03 GGGCAGACGC CTAGGCTG TCATTTTTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:81371603-81371753 1.5e-05 83_[+2]_59 chr6:88190742-88190892 3.1e-05 103_[+2]_39 chr16:17638345-17638495 4.7e-05 73_[+2]_69 chr8:122329088-122329238 6.2e-05 122_[+2]_20 chr7:103827921-103828071 7.9e-05 40_[+2]_102 chr7:81828551-81828701 9.3e-05 4_[+2]_138 chr9:96241534-96241684 0.00016 51_[+2]_91 chr9:110668725-110668875 0.0002 41_[+2]_101 chr7:100684791-100684941 0.0002 36_[+2]_106 chr5:147442057-147442207 0.0002 126_[+2]_16 chr2:27393862-27394012 0.0002 115_[+2]_27 chr1:133825587-133825737 0.0002 121_[+2]_21 chr2:35336372-35336522 0.00025 136_[+2]_6 chr7:83898433-83898583 0.0003 15_[+2]_127 chr7:65300566-65300716 0.00043 117_[+2]_25 chr7:126348298-126348448 0.00046 42_[+2]_100 chr11:121433465-12143361 0.00046 75_[+2]_67 chr11:96918230-96918380 0.00052 100_[+2]_42 chr11:96941156-96941306 0.00052 25_[+2]_117 chr6:38874495-38874645 0.00056 73_[+2]_69 chr8:122309313-122309463 0.00074 123_[+2]_19 chr7:103910176-103910326 0.00074 39_[+2]_103 chr7:90129365-90129515 0.00081 61_[+2]_81 chr1:155039328-155039478 0.00081 97_[+2]_45 chr7:80629499-80629649 0.00087 128_[+2]_14 chr18:78123162-78123312 0.0011 26_[+2]_116 chr11:78066028-78066178 0.0011 5_[+2]_137 chr7:126126668-126126818 0.0012 51_[+2]_91 chr7:128672393-128672543 0.0012 89_[+2]_53 chr7:126396946-126397096 0.0017 6_[+2]_136 chr8:122306903-122307053 0.0018 93_[+2]_49 chr3:21996029-21996179 0.0022 54_[+2]_88 chr7:66079514-66079664 0.0024 102_[+2]_40 chr6:38850125-38850275 0.0027 120_[+2]_22 chr7:83695929-83696079 0.0029 62_[+2]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=8 seqs=35 chr7:81371603-81371753 ( 84) CAGGCCTG 1 chr6:88190742-88190892 ( 104) CAGCCCTG 1 chr16:17638345-17638495 ( 74) CTGGCCTG 1 chr8:122329088-122329238 ( 123) CAGGGCTG 1 chr7:103827921-103828071 ( 41) CTGCCCTG 1 chr7:81828551-81828701 ( 5) CAGGCCAG 1 chr9:96241534-96241684 ( 52) CTGGGCTG 1 chr9:110668725-110668875 ( 42) CAGCTCTG 1 chr7:100684791-100684941 ( 37) CAGCTCTG 1 chr5:147442057-147442207 ( 127) CTGGCCAG 1 chr2:27393862-27394012 ( 116) CTGGCCAG 1 chr1:133825587-133825737 ( 122) CAGCTCTG 1 chr2:35336372-35336522 ( 137) CTGTCCTG 1 chr7:83898433-83898583 ( 16) CAGTGCTG 1 chr7:65300566-65300716 ( 118) CTGTGCTG 1 chr7:126348298-126348448 ( 43) CAGCTCAG 1 chr11:121433465-12143361 ( 76) CAGCACTG 1 chr11:96918230-96918380 ( 101) CTGGACTG 1 chr11:96941156-96941306 ( 26) CTGTCCAG 1 chr6:38874495-38874645 ( 74) GAGCCCTG 1 chr8:122309313-122309463 ( 124) CTGTGCAG 1 chr7:103910176-103910326 ( 40) GAGGCCAG 1 chr7:90129365-90129515 ( 62) CAGCCTTG 1 chr1:155039328-155039478 ( 98) GAGTCCTG 1 chr7:80629499-80629649 ( 129) CTGGCTTG 1 chr18:78123162-78123312 ( 27) CAGCCCTC 1 chr11:78066028-78066178 ( 6) GAGGGCAG 1 chr7:126126668-126126818 ( 52) CAGGTTTG 1 chr7:128672393-128672543 ( 90) CTGGCCTC 1 chr7:126396946-126397096 ( 7) CTGTACAG 1 chr8:122306903-122307053 ( 94) GAGCTCAG 1 chr3:21996029-21996179 ( 55) CATGGCTG 1 chr7:66079514-66079664 ( 103) CACGGCAG 1 chr6:38850125-38850275 ( 121) CTCCTCTG 1 chr7:83695929-83696079 ( 63) CTAGGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5148 bayes= 7.29383 E= 2.1e+001 -1177 175 -78 -1177 123 -1177 -1177 74 -309 -216 185 -317 -1177 43 90 -36 -150 84 7 -36 -1177 184 -1177 -158 37 -1177 -1177 141 -1177 -216 195 -1177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 2.1e+001 0.000000 0.857143 0.142857 0.000000 0.571429 0.000000 0.000000 0.428571 0.028571 0.057143 0.885714 0.028571 0.000000 0.342857 0.457143 0.200000 0.085714 0.457143 0.257143 0.200000 0.000000 0.914286 0.000000 0.085714 0.314286 0.000000 0.000000 0.685714 0.000000 0.057143 0.942857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT]G[GCT][CGT]C[TA]G -------------------------------------------------------------------------------- Time 6.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 14 sites = 7 llr = 91 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :6:13::133117: pos.-specific C a3::::a7:::9:: probability G :19979::179::a matrix T ::1::1:16:::3: bits 2.0 * * * 1.8 * * * 1.6 * * * 1.4 * ** ** ** * Relative 1.2 * ***** ***** Entropy 1.0 * ***** ***** (18.7 bits) 0.8 * ****** ***** 0.6 ************** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel CAGGGGCCTGGCAG consensus C A AA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:128672393-128672543 101 2.05e-08 TGGCCTCCAG CAGGAGCCTGGCAG TGTTCATTTA chr1:133825587-133825737 98 2.05e-08 ATGCAAGGAA CAGGGGCCTGGCTG GTCTCTTCAC chr8:122309313-122309463 80 3.06e-08 TTTGCATCCT CCGGGGCCAGGCAG TGCACTATCG chr6:88190742-88190892 137 6.51e-07 GGGCAGCCTC CGGGAGCCGGGCAG chr7:81371603-81371753 97 2.71e-06 GCCTGGGCAC CAGGGGCTTAGATG GATCATATCT chr7:81828551-81828701 41 2.85e-06 TATTATCTTC CAGAGTCCTGACAG CAAACCGTGG chr9:96241534-96241684 115 3.45e-06 CCACCCCTCG CCTGGGCAAAGCAG GATAGCTGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:128672393-128672543 2.1e-08 100_[+3]_36 chr1:133825587-133825737 2.1e-08 97_[+3]_39 chr8:122309313-122309463 3.1e-08 79_[+3]_57 chr6:88190742-88190892 6.5e-07 136_[+3] chr7:81371603-81371753 2.7e-06 96_[+3]_40 chr7:81828551-81828701 2.8e-06 40_[+3]_96 chr9:96241534-96241684 3.4e-06 114_[+3]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=7 chr7:128672393-128672543 ( 101) CAGGAGCCTGGCAG 1 chr1:133825587-133825737 ( 98) CAGGGGCCTGGCTG 1 chr8:122309313-122309463 ( 80) CCGGGGCCAGGCAG 1 chr6:88190742-88190892 ( 137) CGGGAGCCGGGCAG 1 chr7:81371603-81371753 ( 97) CAGGGGCTTAGATG 1 chr7:81828551-81828701 ( 41) CAGAGTCCTGACAG 1 chr9:96241534-96241684 ( 115) CCTGGGCAAAGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 4932 bayes= 9.3022 E= 1.5e+002 -945 197 -945 -945 123 16 -78 -945 -945 -945 181 -85 -77 -945 181 -945 23 -945 154 -945 -945 -945 181 -85 -945 197 -945 -945 -77 149 -945 -85 23 -945 -78 115 23 -945 154 -945 -77 -945 181 -945 -77 175 -945 -945 155 -945 -945 15 -945 -945 203 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 7 E= 1.5e+002 0.000000 1.000000 0.000000 0.000000 0.571429 0.285714 0.142857 0.000000 0.000000 0.000000 0.857143 0.142857 0.142857 0.000000 0.857143 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.142857 0.714286 0.000000 0.142857 0.285714 0.000000 0.142857 0.571429 0.285714 0.000000 0.714286 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.857143 0.000000 0.000000 0.714286 0.000000 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC]GG[GA]GCC[TA][GA]GC[AT]G -------------------------------------------------------------------------------- Time 9.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 14 sites = 5 llr = 69 E-value = 6.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A 2682::82a:682a pos.-specific C ::::a8:8:::::: probability G 8426::2::a428: matrix T :::2:2:::::::: bits 2.0 * ** * 1.8 * ** * 1.6 * ** * 1.4 * ** * Relative 1.2 * * ****** *** Entropy 1.0 *** ********** (19.9 bits) 0.8 *** ********** 0.6 ************** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel GAAGCCACAGAAGA consensus AGGA TGA GGA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:126396946-126397096 136 3.90e-08 CTCATTCTCG GAAGCCACAGAAAA A chr2:35336372-35336522 93 2.31e-07 AGAGGAGGCT GAAGCTGCAGAAGA GGCGCCTCTA chr1:155039328-155039478 5 2.31e-07 AGTA GGAACCAAAGAAGA CAACAAGTAC chr7:80629499-80629649 32 4.39e-07 ATGAAGCTCT GAGGCCACAGGGGA ACCACAGGGA chr8:122329088-122329238 87 4.80e-07 GAGCAGGCTC AGATCCACAGGAGA ATTTAAAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:126396946-126397096 3.9e-08 135_[+4]_1 chr2:35336372-35336522 2.3e-07 92_[+4]_44 chr1:155039328-155039478 2.3e-07 4_[+4]_132 chr7:80629499-80629649 4.4e-07 31_[+4]_105 chr8:122329088-122329238 4.8e-07 86_[+4]_50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=14 seqs=5 chr7:126396946-126397096 ( 136) GAAGCCACAGAAAA 1 chr2:35336372-35336522 ( 93) GAAGCTGCAGAAGA 1 chr1:155039328-155039478 ( 5) GGAACCAAAGAAGA 1 chr7:80629499-80629649 ( 32) GAGGCCACAGGGGA 1 chr8:122329088-122329238 ( 87) AGATCCACAGGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 4932 bayes= 10.1963 E= 6.2e+002 -28 -897 171 -897 130 -897 71 -897 172 -897 -29 -897 -28 -897 129 -36 -897 197 -897 -897 -897 165 -897 -36 172 -897 -29 -897 -28 165 -897 -897 204 -897 -897 -897 -897 -897 203 -897 130 -897 71 -897 172 -897 -29 -897 -28 -897 171 -897 204 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 5 E= 6.2e+002 0.200000 0.000000 0.800000 0.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.600000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- [GA][AG][AG][GAT]C[CT][AG][CA]AG[AG][AG][GA]A -------------------------------------------------------------------------------- Time 12.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 21 sites = 5 llr = 91 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A 882:22:2662:::a48:82: pos.-specific C 22:::6462::2:a:6:a:2a probability G ::8a62:2:228a::::::6: matrix T ::::2:6:226:::::2:2:: bits 2.0 * *** * * 1.8 * *** * * 1.6 * *** * * 1.4 * *** * * Relative 1.2 **** **** *** * Entropy 1.0 **** * ******** * (26.3 bits) 0.8 **** * ******** * 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AAGGGCTCAATGGCACACAGC consensus CCA AACACGAC AT TA sequence TG GTTG C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr7:103910176-103910326 84 1.14e-11 GGATAAAGTT AAGGGCTCAATCGCAAACAGC CCGTTGCTTT chr11:96941156-96941306 94 1.35e-09 TACCCCCCTT AAGGGATGTATGGCACACTGC CCTAACCACC chr18:78123162-78123312 38 2.22e-09 AGCCCTCAGC AAGGACTCATTGGCAATCAAC AGAAATGAGG chr7:126126668-126126818 20 6.23e-09 GTTGACCTGC CAGGGGCAAGAGGCACACAGC AGCTACAGGC chr2:27393862-27394012 124 2.20e-08 AGCTGGCCAG ACAGTCCCCAGGGCACACACC AAGGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103910176-103910326 1.1e-11 83_[+5]_46 chr11:96941156-96941306 1.4e-09 93_[+5]_36 chr18:78123162-78123312 2.2e-09 37_[+5]_92 chr7:126126668-126126818 6.2e-09 19_[+5]_110 chr2:27393862-27394012 2.2e-08 123_[+5]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=21 seqs=5 chr7:103910176-103910326 ( 84) AAGGGCTCAATCGCAAACAGC 1 chr11:96941156-96941306 ( 94) AAGGGATGTATGGCACACTGC 1 chr18:78123162-78123312 ( 38) AAGGACTCATTGGCAATCAAC 1 chr7:126126668-126126818 ( 20) CAGGGGCAAGAGGCACACAGC 1 chr2:27393862-27394012 ( 124) ACAGTCCCCAGGGCACACACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4680 bayes= 10.1206 E= 1.3e+003 172 -35 -897 -897 172 -35 -897 -897 -28 -897 171 -897 -897 -897 203 -897 -28 -897 129 -36 -28 123 -29 -897 -897 65 -897 122 -28 123 -29 -897 130 -35 -897 -36 130 -897 -29 -36 -28 -897 -29 122 -897 -35 171 -897 -897 -897 203 -897 -897 197 -897 -897 204 -897 -897 -897 72 123 -897 -897 172 -897 -897 -36 -897 197 -897 -897 172 -897 -897 -36 -28 -35 129 -897 -897 197 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.3e+003 0.800000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.600000 0.200000 0.200000 0.600000 0.200000 0.000000 0.000000 0.400000 0.000000 0.600000 0.200000 0.600000 0.200000 0.000000 0.600000 0.200000 0.000000 0.200000 0.600000 0.000000 0.200000 0.200000 0.200000 0.000000 0.200000 0.600000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.200000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- [AC][AC][GA]G[GAT][CAG][TC][CAG][ACT][AGT][TAG][GC]GCA[CA][AT]C[AT][GAC]C -------------------------------------------------------------------------------- Time 14.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 15 sites = 3 llr = 49 E-value = 5.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A :77a7:77a3aa:3a pos.-specific C :33::::::3::::: probability G a:::3a33::::a7: matrix T :::::::::3::::: bits 2.0 * * * * *** * 1.8 * * * * *** * 1.6 * * * * *** * 1.4 * * * * *** * Relative 1.2 * * * * *** * Entropy 1.0 ********* ***** (23.4 bits) 0.8 ********* ***** 0.6 ********* ***** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GAAAAGAAAAAAGGA consensus CC G GG C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr2:35336372-35336522 63 7.11e-09 CGCTGGGGCA GAAAAGAAACAAGAA TGAGCAGAGG chr1:155039328-155039478 108 4.43e-08 GAGTCCTGCT GCAAAGAGATAAGGA CCATTCTGAT chr7:80629499-80629649 103 7.14e-08 ACTCTCCTCA GACAGGGAAAAAGGA TATCTGTCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:35336372-35336522 7.1e-09 62_[+6]_73 chr1:155039328-155039478 4.4e-08 107_[+6]_28 chr7:80629499-80629649 7.1e-08 102_[+6]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=15 seqs=3 chr2:35336372-35336522 ( 63) GAAAAGAAACAAGAA 1 chr1:155039328-155039478 ( 108) GCAAAGAGATAAGGA 1 chr7:80629499-80629649 ( 103) GACAGGGAAAAAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4896 bayes= 11.1192 E= 5.8e+003 -823 -823 203 -823 145 39 -823 -823 145 39 -823 -823 204 -823 -823 -823 145 -823 44 -823 -823 -823 203 -823 145 -823 44 -823 145 -823 44 -823 204 -823 -823 -823 45 39 -823 37 204 -823 -823 -823 204 -823 -823 -823 -823 -823 203 -823 45 -823 144 -823 204 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3 E= 5.8e+003 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 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 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- G[AC][AC]A[AG]G[AG][AG]A[ACT]AAG[GA]A -------------------------------------------------------------------------------- Time 17.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 25 sites = 5 llr = 102 E-value = 2.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A ::a:48:4428:6::::66:62:42 pos.-specific C :a:4:::24422::2424482:2:: probability G a::6::a424::4:8:2::2::6:8 matrix T ::::62:::::8:a:66:::2826: bits 2.0 *** * * 1.8 *** * * 1.6 *** * * 1.4 *** * * Relative 1.2 *** ** ** ** * * * Entropy 1.0 ******* ****** *** * ** (29.6 bits) 0.8 ******* ****** *** * ** 0.6 ******* *************** 0.4 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel GCAGTAGAACATATGTTAACATGTG consensus CAT GCGCCG CCCCCGCACAA sequence CGA G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:126126668-126126818 99 6.32e-12 AAGAAGTTCA GCAGTAGCAGATATGCTAACAAGTG TGTCTAATGT chr16:17638345-17638495 6 2.37e-11 GGCAG GCACAAGGCCACATGTTCCCATGTG TGAGCTGGTG chr7:83695929-83696079 89 3.24e-10 CTATCGAGCA GCAGATGGCGCTGTGTTAACCTGAG CAAGATTACC chr7:126348298-126348448 83 4.77e-10 TTCCTTCCTT GCAGTAGAAAATGTGCCCACATTTA AACCCTTGGT chr8:122306903-122307053 34 3.02e-09 GCGATAACGG GCACTAGAGCATATCTGACGTTCAG GCGGGTCCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:126126668-126126818 6.3e-12 98_[+7]_27 chr16:17638345-17638495 2.4e-11 5_[+7]_120 chr7:83695929-83696079 3.2e-10 88_[+7]_37 chr7:126348298-126348448 4.8e-10 82_[+7]_43 chr8:122306903-122307053 3e-09 33_[+7]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=25 seqs=5 chr7:126126668-126126818 ( 99) GCAGTAGCAGATATGCTAACAAGTG 1 chr16:17638345-17638495 ( 6) GCACAAGGCCACATGTTCCCATGTG 1 chr7:83695929-83696079 ( 89) GCAGATGGCGCTGTGTTAACCTGAG 1 chr7:126348298-126348448 ( 83) GCAGTAGAAAATGTGCCCACATTTA 1 chr8:122306903-122307053 ( 34) GCACTAGAGCATATCTGACGTTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 4536 bayes= 10.7679 E= 2.6e+004 -897 -897 203 -897 -897 197 -897 -897 204 -897 -897 -897 -897 65 129 -897 72 -897 -897 122 172 -897 -897 -36 -897 -897 203 -897 72 -35 71 -897 72 65 -29 -897 -28 65 71 -897 172 -35 -897 -897 -897 -35 -897 164 130 -897 71 -897 -897 -897 -897 196 -897 -35 171 -897 -897 65 -897 122 -897 -35 -29 122 130 65 -897 -897 130 65 -897 -897 -897 165 -29 -897 130 -35 -897 -36 -28 -897 -897 164 -897 -35 129 -36 72 -897 -897 122 -28 -897 171 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 5 E= 2.6e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.400000 0.000000 0.000000 0.600000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.400000 0.400000 0.200000 0.000000 0.200000 0.400000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.200000 0.600000 0.600000 0.400000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.600000 0.200000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.200000 0.600000 0.200000 0.400000 0.000000 0.000000 0.600000 0.200000 0.000000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- GCA[GC][TA][AT]G[AGC][ACG][CGA][AC][TC][AG]T[GC][TC][TCG][AC][AC][CG][ACT][TA][GCT][TA][GA] -------------------------------------------------------------------------------- Time 19.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 8 sites = 2 llr = 22 E-value = 3.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A :aaaaa:a pos.-specific C a::::::: probability G :::::::: matrix T ::::::a: bits 2.0 ******** 1.8 ******** 1.6 ******** 1.4 ******** Relative 1.2 ******** Entropy 1.0 ******** (16.2 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CAAAAATA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:122306903-122307053 126 1.35e-05 GATTTATAGC CAAAAATA ATAGGACTTT chr6:38850125-38850275 108 1.35e-05 ATCCTATTTA CAAAAATA GAACTCTCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:122306903-122307053 1.3e-05 125_[+8]_17 chr6:38850125-38850275 1.3e-05 107_[+8]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=8 seqs=2 chr8:122306903-122307053 ( 126) CAAAAATA 1 chr6:38850125-38850275 ( 108) CAAAAATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5148 bayes= 11.3292 E= 3.4e+004 -765 197 -765 -765 203 -765 -765 -765 203 -765 -765 -765 203 -765 -765 -765 203 -765 -765 -765 203 -765 -765 -765 -765 -765 -765 195 203 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.4e+004 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- CAAAAATA -------------------------------------------------------------------------------- Time 22.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 9 sites = 2 llr = 25 E-value = 2.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A ::aa:aa:: pos.-specific C :a::::::: probability G a:::a::aa matrix T ::::::::: bits 2.0 ********* 1.8 ********* 1.6 ********* 1.4 ********* Relative 1.2 ********* Entropy 1.0 ********* (18.3 bits) 0.8 ********* 0.6 ********* 0.4 ********* 0.2 ********* 0.0 --------- Multilevel GCAAGAAGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- chr7:126348298-126348448 16 3.20e-06 CAGGTTCCTT GCAAGAAGG CAGACGTCGG chr11:78066028-78066178 115 3.20e-06 AGCTGTCTTA GCAAGAAGG GGGTGGGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:126348298-126348448 3.2e-06 15_[+9]_126 chr11:78066028-78066178 3.2e-06 114_[+9]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=9 seqs=2 chr7:126348298-126348448 ( 16) GCAAGAAGG 1 chr11:78066028-78066178 ( 115) GCAAGAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 5112 bayes= 11.3191 E= 2.4e+004 -765 -765 202 -765 -765 197 -765 -765 203 -765 -765 -765 203 -765 -765 -765 -765 -765 202 -765 203 -765 -765 -765 203 -765 -765 -765 -765 -765 202 -765 -765 -765 202 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 2 E= 2.4e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- GCAAGAAGG -------------------------------------------------------------------------------- Time 24.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 15 sites = 2 llr = 39 E-value = 4.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A aaa::::::5:a::: pos.-specific C :::aa:::::::aaa probability G :::::5:aa5a:::: matrix T :::::5a:::::::: bits 2.0 ***** *** ***** 1.8 ***** *** ***** 1.6 ***** *** ***** 1.4 ***** *** ***** Relative 1.2 ***** *** ***** Entropy 1.0 *************** (28.1 bits) 0.8 *************** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AAACCGTGGAGACCC consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr7:81828551-81828701 56 1.70e-09 TCCTGACAGC AAACCGTGGAGACCC TGACAACCCC chr7:81371603-81371753 132 3.48e-09 CATAAGGTTG AAACCTTGGGGACCC TTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:81828551-81828701 1.7e-09 55_[+10]_80 chr7:81371603-81371753 3.5e-09 131_[+10]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=15 seqs=2 chr7:81828551-81828701 ( 56) AAACCGTGGAGACCC 1 chr7:81371603-81371753 ( 132) AAACCTTGGGGACCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4896 bayes= 11.2568 E= 4.4e+004 203 -765 -765 -765 203 -765 -765 -765 203 -765 -765 -765 -765 197 -765 -765 -765 197 -765 -765 -765 -765 103 96 -765 -765 -765 195 -765 -765 202 -765 -765 -765 202 -765 104 -765 103 -765 -765 -765 202 -765 203 -765 -765 -765 -765 197 -765 -765 -765 197 -765 -765 -765 197 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2 E= 4.4e+004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- AAACC[GT]TGG[AG]GACCC -------------------------------------------------------------------------------- Time 27.49 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:78066028-78066178 1.74e-02 114_[+9(3.20e-06)]_27 chr11:96941156-96941306 8.02e-05 93_[+5(1.35e-09)]_27_[+1(5.25e-05)]_1 chr11:96918230-96918380 1.61e-01 150 chr11:121433465-12143361 8.05e-03 47_[+6(1.07e-05)]_88 chr16:17638345-17638495 1.88e-06 5_[+7(2.37e-11)]_43_[+2(4.72e-05)]_14_[+1(8.09e-05)]_47 chr17:4626334-4626484 1.00e+00 150 chr18:78123162-78123312 1.78e-07 6_[+4(9.70e-05)]_17_[+5(2.22e-09)]_92 chr1:133825587-133825737 2.75e-04 76_[+3(7.53e-05)]_7_[+3(2.05e-08)]_39 chr1:155039328-155039478 7.42e-08 4_[+4(2.31e-07)]_89_[+6(4.43e-08)]_17_[+1(2.70e-05)]_3 chr2:27393862-27394012 1.34e-04 123_[+5(2.20e-08)]_6 chr2:35336372-35336522 1.73e-09 62_[+6(7.11e-09)]_[+1(8.09e-05)]_7_[+4(2.31e-07)]_44 chr3:21996029-21996179 3.03e-03 20_[+1(5.25e-05)]_122 chr5:147442057-147442207 3.52e-01 150 chr6:88190742-88190892 2.42e-05 58_[+1(5.25e-05)]_37_[+2(3.11e-05)]_25_[+3(6.51e-07)] chr6:38874495-38874645 1.59e-01 150 chr6:38850125-38850275 4.13e-01 107_[+8(1.35e-05)]_35 chr7:103827921-103828071 5.63e-02 40_[+2(7.86e-05)]_23_[+1(8.09e-05)]_71 chr7:128672393-128672543 1.31e-04 68_[+3(7.53e-05)]_18_[+3(2.05e-08)]_36 chr7:81828551-81828701 2.15e-07 4_[+2(9.30e-05)]_28_[+3(2.85e-06)]_1_[+10(1.70e-09)]_80 chr7:100684791-100684941 9.00e-02 150 chr7:66079514-66079664 6.44e-01 150 chr7:80629499-80629649 1.10e-07 31_[+4(4.39e-07)]_57_[+6(7.14e-08)]_33 chr7:126396946-126397096 1.57e-02 135_[+4(3.90e-08)]_1 chr7:126348298-126348448 1.28e-06 15_[+9(3.20e-06)]_58_[+7(4.77e-10)]_43 chr7:83695929-83696079 4.70e-06 88_[+7(3.24e-10)]_37 chr7:65300566-65300716 1.17e-02 150 chr7:83898433-83898583 3.14e-01 150 chr7:126126668-126126818 2.25e-12 19_[+5(6.23e-09)]_44_[+1(2.70e-05)]_6_[+7(6.32e-12)]_27 chr7:81371603-81371753 1.49e-06 83_[+2(1.52e-05)]_5_[+3(2.71e-06)]_21_[+10(3.48e-09)]_4 chr7:103910176-103910326 1.51e-06 83_[+5(1.14e-11)]_46 chr7:90129365-90129515 9.43e-01 150 chr8:122306903-122307053 1.91e-06 33_[+7(3.02e-09)]_67_[+8(1.35e-05)]_17 chr8:122329088-122329238 9.05e-03 86_[+4(4.80e-07)]_22_[+2(6.18e-05)]_20 chr8:122309313-122309463 4.58e-03 79_[+3(3.06e-08)]_57 chr9:110668725-110668875 7.42e-01 150 chr9:96241534-96241684 1.12e-03 45_[+3(1.17e-05)]_55_[+3(3.45e-06)]_22 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************