******************************************************************************** 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_Negs.radius75bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2:27152244-27152394 1.0000 150 chr6:88203946-88204096 1.0000 150 chr6:38757546-38757696 1.0000 150 chr6:38856152-38856302 1.0000 150 chr7:92271259-92271409 1.0000 150 chr7:90158496-90158646 1.0000 150 chr7:108272327-108272477 1.0000 150 chr7:69960031-69960181 1.0000 150 chr7:127922155-127922305 1.0000 150 chr7:67296514-67296664 1.0000 150 chr7:71503065-71503215 1.0000 150 chr7:71037117-71037267 1.0000 150 chr7:100578775-100578925 1.0000 150 chr7:106294951-106295101 1.0000 150 chr7:66469114-66469264 1.0000 150 chr7:105413204-105413354 1.0000 150 chr7:68211639-68211789 1.0000 150 chr7:103971079-103971229 1.0000 150 chr7:83097224-83097374 1.0000 150 chr7:70144883-70145033 1.0000 150 chr7:81826318-81826468 1.0000 150 chr7:66763878-66764028 1.0000 150 chr7:83064330-83064480 1.0000 150 chr7:66280364-66280514 1.0000 150 chr7:63499650-63499800 1.0000 150 chr8:122109021-122109171 1.0000 150 chrX:150565944-150566094 1.0000 150 chrX:150846675-150846825 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_Negs.radius75bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATA_Negs.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= 28 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= 4200 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.227 G 0.201 T 0.300 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.227 G 0.201 T 0.300 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 14 sites = 9 llr = 114 E-value = 3.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :24146:16:113: pos.-specific C 78:1::a7:::::: probability G :::834:::a197a matrix T 3:6:2::24:8::: bits 2.3 * * 2.1 * * * 1.9 * * * * 1.6 * * * * Relative 1.4 * * * * * Entropy 1.2 ** * ** * *** (18.2 bits) 0.9 ** * ** ****** 0.7 **** ********* 0.5 ************** 0.2 ************** 0.0 -------------- Multilevel CCTGAACCAGTGGG consensus TAA GG TT A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:127922155-127922305 107 1.30e-07 AGCTGGTAGC CCAGGGCTTGTGGG AAACTCTAAC chr7:68211639-68211789 91 2.19e-07 GGACACCCTG CCTCAACCAGTGGG TAGAAGGTAG chr7:69960031-69960181 76 2.19e-07 AGATTATATT TCAGAACCAGTGAG TAAATGCAGA chr7:83064330-83064480 82 3.12e-07 ATTGACCACA CATGAGCCAGTGAG CAGTTATGAC chr7:105413204-105413354 90 3.63e-07 AAGCTCTGAG CCTGTGCTTGTGGG GTCGTGTGCT chr7:66763878-66764028 115 5.70e-07 TCCCAGAGCC TCAGGACCTGGGGG CGCTGGGTGC chr7:71503065-71503215 40 7.75e-07 GAATTGTGTG TATGTGCCAGTGGG TTTCAAAGAA chr7:103971079-103971229 72 3.35e-06 AAAAACATCT CCTGAACAAGAGAG GCTTTCTGAT chr7:70144883-70145033 15 3.76e-06 AGAATGGATG CCAAGACCTGTAGG CTCATGTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127922155-127922305 1.3e-07 106_[+1]_30 chr7:68211639-68211789 2.2e-07 90_[+1]_46 chr7:69960031-69960181 2.2e-07 75_[+1]_61 chr7:83064330-83064480 3.1e-07 81_[+1]_55 chr7:105413204-105413354 3.6e-07 89_[+1]_47 chr7:66763878-66764028 5.7e-07 114_[+1]_22 chr7:71503065-71503215 7.8e-07 39_[+1]_97 chr7:103971079-103971229 3.3e-06 71_[+1]_65 chr7:70144883-70145033 3.8e-06 14_[+1]_122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=9 chr7:127922155-127922305 ( 107) CCAGGGCTTGTGGG 1 chr7:68211639-68211789 ( 91) CCTCAACCAGTGGG 1 chr7:69960031-69960181 ( 76) TCAGAACCAGTGAG 1 chr7:83064330-83064480 ( 82) CATGAGCCAGTGAG 1 chr7:105413204-105413354 ( 90) CCTGTGCTTGTGGG 1 chr7:66763878-66764028 ( 115) TCAGGACCTGGGGG 1 chr7:71503065-71503215 ( 40) TATGTGCCAGTGGG 1 chr7:103971079-103971229 ( 72) CCTGAACAAGAGAG 1 chr7:70144883-70145033 ( 15) CCAAGACCTGTAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 3836 bayes= 9.58158 E= 3.9e-002 -982 155 -982 15 -29 177 -982 -982 71 -982 -982 89 -128 -103 195 -982 71 -982 73 -43 103 -982 114 -982 -982 214 -982 -982 -128 155 -982 -43 103 -982 -982 56 -982 -982 231 -982 -128 -982 -85 137 -128 -982 214 -982 30 -982 173 -982 -982 -982 231 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 9 E= 3.9e-002 0.000000 0.666667 0.000000 0.333333 0.222222 0.777778 0.000000 0.000000 0.444444 0.000000 0.000000 0.555556 0.111111 0.111111 0.777778 0.000000 0.444444 0.000000 0.333333 0.222222 0.555556 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.666667 0.000000 0.222222 0.555556 0.000000 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.111111 0.777778 0.111111 0.000000 0.888889 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CA][TA]G[AGT][AG]C[CT][AT]GTG[GA]G -------------------------------------------------------------------------------- Time 2.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 25 sites = 5 llr = 106 E-value = 1.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2644:2::2:::24:8:6:::4:8: pos.-specific C 84::2:846a:424::a:a82:228 probability G ::6:8:2::::622a:::::228:: matrix T :::6:8:62:a:4::2:4:264::2 bits 2.3 * 2.1 * * * * 1.9 * * * * 1.6 * ** * * * * Relative 1.4 * * * ** * * ** * * Entropy 1.2 * * *** *** *** ** *** (30.7 bits) 0.9 ******** *** ****** *** 0.7 ************ ****** *** 0.5 ************ ************ 0.2 ************ ************ 0.0 ------------------------- Multilevel CAGTGTCTCCTGTAGACACCTAGAC consensus ACAACAGCA CAC T T TCTCCT sequence T CG GG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:83064330-83064480 36 3.70e-12 CCAAGTGAGA CAGAGTCTCCTCTAGACACCTGGCC CATATCATCT chr7:81826318-81826468 83 2.06e-11 TCAGCCTGGA CAGTGTCCACTGCCGACTCCTACAC TGAGAAATAA chr8:122109021-122109171 104 1.37e-10 AGCTCAGGCT CCGTGTCTTCTGAGGACACTGTGAC AAGATCGGTC chr6:88203946-88204096 109 3.80e-10 AATTCAATTT AAATCTCTCCTGGCGACTCCTAGAT CCTATATAGG chr7:66280364-66280514 8 6.57e-10 TGGCTGG CCAAGAGCCCTCTAGTCACCCTGAC TCACATTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:83064330-83064480 3.7e-12 35_[+2]_90 chr7:81826318-81826468 2.1e-11 82_[+2]_43 chr8:122109021-122109171 1.4e-10 103_[+2]_22 chr6:88203946-88204096 3.8e-10 108_[+2]_17 chr7:66280364-66280514 6.6e-10 7_[+2]_118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=25 seqs=5 chr7:83064330-83064480 ( 36) CAGAGTCTCCTCTAGACACCTGGCC 1 chr7:81826318-81826468 ( 83) CAGTGTCCACTGCCGACTCCTACAC 1 chr8:122109021-122109171 ( 104) CCGTGTCTTCTGAGGACACTGTGAC 1 chr6:88203946-88204096 ( 109) AAATCTCTCCTGGCGACTCCTAGAT 1 chr7:66280364-66280514 ( 8) CCAAGAGCCCTCTAGTCACCCTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 3528 bayes= 9.71253 E= 1.0e+001 -44 181 -897 -897 114 81 -897 -897 56 -897 158 -897 56 -897 -897 100 -897 -18 199 -897 -44 -897 -897 141 -897 181 -1 -897 -897 81 -897 100 -44 140 -897 -59 -897 213 -897 -897 -897 -897 -897 173 -897 81 158 -897 -44 -18 -1 41 56 81 -1 -897 -897 -897 231 -897 156 -897 -897 -59 -897 213 -897 -897 114 -897 -897 41 -897 213 -897 -897 -897 181 -897 -59 -897 -18 -1 100 56 -897 -1 41 -897 -18 199 -897 156 -18 -897 -897 -897 181 -897 -59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 5 E= 1.0e+001 0.200000 0.800000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.400000 0.000000 0.600000 0.200000 0.600000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.200000 0.200000 0.400000 0.400000 0.400000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.200000 0.600000 0.400000 0.000000 0.200000 0.400000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][AC][GA][TA][GC][TA][CG][TC][CAT]CT[GC][TACGA][ACG]G[AT]C[AT]C[CT][TCG][ATG][GC][AC][CT] -------------------------------------------------------------------------------- Time 4.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 15 sites = 5 llr = 74 E-value = 1.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::422:a4:2:::6: pos.-specific C :::626::::42a:: probability G aa6224:6a46:::a matrix T ::::4::::4:8:4: bits 2.3 ** * * 2.1 ** * * * 1.9 ** * * * * 1.6 ** * * * * Relative 1.4 ** * * * * Entropy 1.2 *** **** *** * (21.3 bits) 0.9 *** **** ***** 0.7 **** **** ***** 0.5 **** ********** 0.2 **** ********** 0.0 --------------- Multilevel GGGCTCAGGGGTCAG consensus AAAG A TCC T sequence GC A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- chr7:90158496-90158646 14 2.73e-08 GTAAACCACC GGGCACAGGGGCCAG CACCTTTTAT chr7:103971079-103971229 108 5.62e-08 TCTCCCTTGA GGACTGAGGTCTCAG AGCACAATCT chr7:105413204-105413354 121 5.62e-08 GCTGTAACTG GGGCTGAAGTGTCTG AGGCAAAGCA chr2:27152244-27152394 6 1.89e-07 AAGGG GGAGCCAAGGGTCAG AGGCTCAAAG chr7:66280364-66280514 113 3.26e-07 CAATATGCAA GGGAGCAGGACTCTG TGTCTGCAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:90158496-90158646 2.7e-08 13_[+3]_122 chr7:103971079-103971229 5.6e-08 107_[+3]_28 chr7:105413204-105413354 5.6e-08 120_[+3]_15 chr2:27152244-27152394 1.9e-07 5_[+3]_130 chr7:66280364-66280514 3.3e-07 112_[+3]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=5 chr7:90158496-90158646 ( 14) GGGCACAGGGGCCAG 1 chr7:103971079-103971229 ( 108) GGACTGAGGTCTCAG 1 chr7:105413204-105413354 ( 121) GGGCTGAAGTGTCTG 1 chr2:27152244-27152394 ( 6) GGAGCCAAGGGTCAG 1 chr7:66280364-66280514 ( 113) GGGAGCAGGACTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 3808 bayes= 9.00449 E= 1.6e+002 -897 -897 231 -897 -897 -897 231 -897 56 -897 158 -897 -44 140 -1 -897 -44 -18 -1 41 -897 140 99 -897 188 -897 -897 -897 56 -897 158 -897 -897 -897 231 -897 -44 -897 99 41 -897 81 158 -897 -897 -18 -897 141 -897 213 -897 -897 114 -897 -897 41 -897 -897 231 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 1.6e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.600000 0.200000 0.000000 0.200000 0.200000 0.200000 0.400000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.400000 0.400000 0.000000 0.400000 0.600000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GG[GA][CAG][TACGA][CG]A[GA]G[GTA][GC][TC]C[AT]G -------------------------------------------------------------------------------- Time 6.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 25 sites = 12 llr = 160 E-value = 2.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A ::1::31211::2::31:54511:: pos.-specific C 6:153:1333:33731283515884 probability G 41831:31:1:323:233:1231:: matrix T :9:2685476a43:755:3:32:36 bits 2.3 2.1 1.9 1.6 * Relative 1.4 ** * * * * Entropy 1.2 *** * * * ** (19.3 bits) 0.9 *** * * ** * *** 0.7 ****** * * ** * * *** 0.5 ******* * ** ** *** **** 0.2 ************ ************ 0.0 ------------------------- Multilevel CTGCTTTTTTTTCCTTTCACACCCT consensus G GCAGCCC GTGCAGGCATG TC sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:100578775-100578925 67 4.32e-10 TCTGGGAAAT GTGCTTTCTTTTCCCTGCAATGCCT GGCATTATTT chr6:38856152-38856302 86 3.16e-09 CTGATGAGAT CTGCTTCCTATGCCTTTCAAACCCT TGGTTCAAGT chr7:81826318-81826468 47 1.60e-08 AAAGTTTTCT CTGGTATTATTTCCTTCCAAACCCT GTCAGCCTGG chr7:66280364-66280514 40 8.57e-08 GACTCACATT GTGGCTGTTTTCTCTGAGAATCCCC TTCCTAAAGC chr7:92271259-92271409 25 8.57e-08 CAACTAATTT GTGCTTGTTCTTCCTATCTCATGCC TTTAATATTG chr7:66469114-66469264 44 2.89e-07 GTTAGAACCT CTGCCTGTTCTCAGCTCCCCGGCTT CCTTCCGTGC chr6:38757546-38757696 3 8.19e-07 AG GGGCTAGCTTTTTCCATGTCAACCT AGTAGTCAAG chr7:105413204-105413354 55 8.81e-07 CTCGGAAAGG CTGGCTTACTTGGGCAGGACGGCTC AAGCTCTGAG chr7:67296514-67296664 15 8.81e-07 TCTTTTCTGG CTCCTTTATTTTTGTGTCAGCCCCC AAGACATTCT chr7:108272327-108272477 38 1.65e-06 CTCAATGCCA CTATCTTTCCTGACTTGCCAACCTT CTAATACAGG chr7:66763878-66764028 84 1.76e-06 GAAGAGGAGC GTGTTAAGCTTGGCTTTCTCATCCC AGAGCCTCAG chr2:27152244-27152394 39 3.08e-06 AGGAACTAGC CTGGGTTCTGTCTGTCTCCCTCACT GTGTGATCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:100578775-100578925 4.3e-10 66_[+4]_59 chr6:38856152-38856302 3.2e-09 85_[+4]_40 chr7:81826318-81826468 1.6e-08 46_[+4]_79 chr7:66280364-66280514 8.6e-08 39_[+4]_86 chr7:92271259-92271409 8.6e-08 24_[+4]_101 chr7:66469114-66469264 2.9e-07 43_[+4]_82 chr6:38757546-38757696 8.2e-07 2_[+4]_123 chr7:105413204-105413354 8.8e-07 54_[+4]_71 chr7:67296514-67296664 8.8e-07 14_[+4]_111 chr7:108272327-108272477 1.6e-06 37_[+4]_88 chr7:66763878-66764028 1.8e-06 83_[+4]_42 chr2:27152244-27152394 3.1e-06 38_[+4]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=25 seqs=12 chr7:100578775-100578925 ( 67) GTGCTTTCTTTTCCCTGCAATGCCT 1 chr6:38856152-38856302 ( 86) CTGCTTCCTATGCCTTTCAAACCCT 1 chr7:81826318-81826468 ( 47) CTGGTATTATTTCCTTCCAAACCCT 1 chr7:66280364-66280514 ( 40) GTGGCTGTTTTCTCTGAGAATCCCC 1 chr7:92271259-92271409 ( 25) GTGCTTGTTCTTCCTATCTCATGCC 1 chr7:66469114-66469264 ( 44) CTGCCTGTTCTCAGCTCCCCGGCTT 1 chr6:38757546-38757696 ( 3) GGGCTAGCTTTTTCCATGTCAACCT 1 chr7:105413204-105413354 ( 55) CTGGCTTACTTGGGCAGGACGGCTC 1 chr7:67296514-67296664 ( 15) CTCCTTTATTTTTGTGTCAGCCCCC 1 chr7:108272327-108272477 ( 38) CTATCTTTCCTGACTTGCCAACCTT 1 chr7:66763878-66764028 ( 84) GTGTTAAGCTTGGCTTTCTCATCCC 1 chr2:27152244-27152394 ( 39) CTGGGTTCTGTCTGTCTCCCTCACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 3528 bayes= 7.85241 E= 2.8e+002 -1023 136 105 -1023 -1023 -1023 -127 161 -170 -145 205 -1023 -1023 114 73 -85 -1023 55 -127 96 -12 -1023 -1023 132 -170 -145 73 73 -70 55 -127 47 -170 14 -1023 115 -170 14 -127 96 -1023 -1023 -1023 173 -1023 14 73 47 -70 55 -27 15 -1023 155 73 -1023 -1023 55 -1023 115 -12 -145 -27 73 -170 -45 31 73 -1023 172 31 -1023 88 14 -1023 -26 62 114 -127 -1023 88 -145 -27 -26 -170 114 31 -85 -170 187 -127 -1023 -1023 172 -1023 -26 -1023 87 -1023 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 12 E= 2.8e+002 0.000000 0.583333 0.416667 0.000000 0.000000 0.000000 0.083333 0.916667 0.083333 0.083333 0.833333 0.000000 0.000000 0.500000 0.333333 0.166667 0.000000 0.333333 0.083333 0.583333 0.250000 0.000000 0.000000 0.750000 0.083333 0.083333 0.333333 0.500000 0.166667 0.333333 0.083333 0.416667 0.083333 0.250000 0.000000 0.666667 0.083333 0.250000 0.083333 0.583333 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.333333 0.416667 0.166667 0.333333 0.166667 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.250000 0.083333 0.166667 0.500000 0.083333 0.166667 0.250000 0.500000 0.000000 0.750000 0.250000 0.000000 0.500000 0.250000 0.000000 0.250000 0.416667 0.500000 0.083333 0.000000 0.500000 0.083333 0.166667 0.250000 0.083333 0.500000 0.250000 0.166667 0.083333 0.833333 0.083333 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.416667 0.000000 0.583333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- [CG]TG[CG][TC][TA][TG][TC][TC][TC]T[TGC][CT][CG][TC][TA][TG][CG][ACT][CA][AT][CG]C[CT][TC] -------------------------------------------------------------------------------- Time 7.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 21 sites = 4 llr = 78 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A :a::3:553:583::::::a: pos.-specific C ::333a:::::::38:::3:: probability G a::35::58a3:3833a83:a matrix T ::85::5:::335::8:35:: bits 2.3 * * * * 2.1 * * * * * 1.9 ** * * * ** 1.6 ** * * * ** Relative 1.4 ** * ** ** ** ** Entropy 1.2 ** * *** ***** ** (28.3 bits) 0.9 *** * *** * ***** ** 0.7 *** ****** * ***** ** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GATTGCAAGGAATGCTGGTAG consensus CCA TGA GTACGG TC sequence GC T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- chr6:88203946-88204096 35 5.20e-11 TATGACTATT GATTGCTAGGAATGCTGTTAG TGCAGTAAAA chr7:66469114-66469264 14 4.90e-10 CATGACCTGT GATGGCTGGGGAGGGGGGCAG TTAGAACCTC chr7:127922155-127922305 85 1.19e-09 GGATGGCAAA GACCACAAGGTAAGCTGGTAG CCCAGGGCTT chr7:70144883-70145033 66 2.67e-09 CATGTCATTA GATTCCAGAGATTCCTGGGAG GTGAAGTTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:88203946-88204096 5.2e-11 34_[+5]_95 chr7:66469114-66469264 4.9e-10 13_[+5]_116 chr7:127922155-127922305 1.2e-09 84_[+5]_45 chr7:70144883-70145033 2.7e-09 65_[+5]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=21 seqs=4 chr6:88203946-88204096 ( 35) GATTGCTAGGAATGCTGTTAG 1 chr7:66469114-66469264 ( 14) GATGGCTGGGGAGGGGGGCAG 1 chr7:127922155-127922305 ( 85) GACCACAAGGTAAGCTGGTAG 1 chr7:70144883-70145033 ( 66) GATTCCAGAGATTCCTGGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3640 bayes= 9.82814 E= 1.0e+003 -865 -865 231 -865 188 -865 -865 -865 -865 14 -865 132 -865 14 31 73 -12 14 131 -865 -865 213 -865 -865 88 -865 -865 73 88 -865 131 -865 -12 -865 190 -865 -865 -865 231 -865 88 -865 31 -26 147 -865 -865 -26 -12 -865 31 73 -865 14 190 -865 -865 172 31 -865 -865 -865 31 132 -865 -865 231 -865 -865 -865 190 -26 -865 14 31 73 188 -865 -865 -865 -865 -865 231 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.0e+003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.250000 0.500000 0.250000 0.250000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.250000 0.250000 0.000000 0.250000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.250000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- GA[TC][TCG][GAC]C[AT][AG][GA]G[AGT][AT][TAG][GC][CG][TG]G[GT][TCG]AG -------------------------------------------------------------------------------- Time 9.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 14 sites = 4 llr = 61 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A :a3::::::8:53: pos.-specific C a:3:aaa5a3853a probability G ::3a::::::3::: matrix T ::3::::5::::5: bits 2.3 * 2.1 * **** * * 1.9 ** **** * * 1.6 ** **** * * Relative 1.4 ** **** * * * Entropy 1.2 ** **** *** * (21.9 bits) 0.9 ** ********* * 0.7 ** ********* * 0.5 ** *********** 0.2 ** *********** 0.0 -------------- Multilevel CAAGCCCCCACATC consensus C T CGCA sequence G C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:68211639-68211789 131 4.73e-09 ACATAAGCTT CAGGCCCCCACATC CATGCA chr7:81826318-81826468 18 3.45e-08 AGGCCTAAAA CACGCCCCCACCCC CTTAAAAAGT chr7:67296514-67296664 71 1.71e-07 AAGCCCTTAT CAAGCCCTCAGATC TAGCCAAATG chr7:63499650-63499800 119 2.52e-07 TAATATCACT CATGCCCTCCCCAC ACATATGTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:68211639-68211789 4.7e-09 130_[+6]_6 chr7:81826318-81826468 3.5e-08 17_[+6]_119 chr7:67296514-67296664 1.7e-07 70_[+6]_66 chr7:63499650-63499800 2.5e-07 118_[+6]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=14 seqs=4 chr7:68211639-68211789 ( 131) CAGGCCCCCACATC 1 chr7:81826318-81826468 ( 18) CACGCCCCCACCCC 1 chr7:67296514-67296664 ( 71) CAAGCCCTCAGATC 1 chr7:63499650-63499800 ( 119) CATGCCCTCCCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 3836 bayes= 10.6414 E= 1.1e+003 -865 213 -865 -865 188 -865 -865 -865 -12 14 31 -26 -865 -865 231 -865 -865 213 -865 -865 -865 213 -865 -865 -865 213 -865 -865 -865 113 -865 73 -865 213 -865 -865 147 14 -865 -865 -865 172 31 -865 88 113 -865 -865 -12 14 -865 73 -865 213 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 4 E= 1.1e+003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.250000 0.250000 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 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.500000 0.500000 0.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- CA[ACGTA]GCCC[CT]C[AC][CG][AC][TAC]C -------------------------------------------------------------------------------- Time 11.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 13 sites = 5 llr = 68 E-value = 9.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A 8:6::6a:a:::4 pos.-specific C :::2a4:6::a:6 probability G :a28:::2:8::: matrix T 2:2::::2:2:a: bits 2.3 * 2.1 * * * 1.9 * * * * * 1.6 * ** * * ** Relative 1.4 * ** * **** Entropy 1.2 ** ** * ***** (19.6 bits) 0.9 ** **** ***** 0.7 ** ********** 0.5 ************* 0.2 ************* 0.0 ------------- Multilevel AGAGCAACAGCTC consensus T GC C G T A sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- chr7:127922155-127922305 50 1.87e-07 ATCTATCGAA AGAGCAACATCTC TGTGTATGAA chr8:122109021-122109171 86 2.14e-07 TCCTTCCAAG AGGGCAAGAGCTC AGGCTCCGTG chr7:90158496-90158646 63 2.41e-07 AAAAACATGG AGAGCAATAGCTA AGAGACACCT chr6:38856152-38856302 121 3.50e-07 TGGTTCAAGT AGACCCACAGCTA ATTGTTCTTA chr2:27152244-27152394 95 6.38e-07 TTAACTTTTC TGTGCCACAGCTC CTTTGTCTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127922155-127922305 1.9e-07 49_[+7]_88 chr8:122109021-122109171 2.1e-07 85_[+7]_52 chr7:90158496-90158646 2.4e-07 62_[+7]_75 chr6:38856152-38856302 3.5e-07 120_[+7]_17 chr2:27152244-27152394 6.4e-07 94_[+7]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=13 seqs=5 chr7:127922155-127922305 ( 50) AGAGCAACATCTC 1 chr8:122109021-122109171 ( 86) AGGGCAAGAGCTC 1 chr7:90158496-90158646 ( 63) AGAGCAATAGCTA 1 chr6:38856152-38856302 ( 121) AGACCCACAGCTA 1 chr2:27152244-27152394 ( 95) TGTGCCACAGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 3864 bayes= 10.5364 E= 9.2e+002 156 -897 -897 -59 -897 -897 231 -897 114 -897 -1 -59 -897 -18 199 -897 -897 213 -897 -897 114 81 -897 -897 188 -897 -897 -897 -897 140 -1 -59 188 -897 -897 -897 -897 -897 199 -59 -897 213 -897 -897 -897 -897 -897 173 56 140 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 5 E= 9.2e+002 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.400000 0.600000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- [AT]G[AGT][GC]C[AC]A[CGT]A[GT]CT[CA] -------------------------------------------------------------------------------- Time 12.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 14 sites = 7 llr = 84 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A 17::41:39:4::a pos.-specific C 9:9a13311:1aa: probability G ::1::1:1:::::: matrix T :3::4474:a4::: bits 2.3 2.1 * ** 1.9 * *** 1.6 * ** * *** Relative 1.4 * ** ** *** Entropy 1.2 * ** ** *** (17.4 bits) 0.9 **** * ** *** 0.7 **** * ** *** 0.5 ***** * ****** 0.2 ***** * ****** 0.0 -------------- Multilevel CACCATTTATACCA consensus T TCCA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:90158496-90158646 29 2.67e-07 CAGGGGCCAG CACCTTTTATCCCA GTCTGTCTCA chr7:69960031-69960181 4 3.27e-07 TAA CACCTCTCATACCA TAACCCTGCC chr7:68211639-68211789 5 6.89e-07 AGCA CACCTGTGATTCCA GCCTTGGAAG chr7:92271259-92271409 104 8.98e-07 ATTATTTTCC CTCCATCTATTCCA ACATCCTGAG chr7:66469114-66469264 109 2.38e-06 AACAAGCATT CTCCATTTCTACCA CTATTGGTGT chrX:150565944-150566094 125 3.78e-06 ATCTCTAGAT AACCAATAATACCA AATTCAAATA chr6:38856152-38856302 60 5.81e-06 TTCCAGCATG CAGCCCCAATTCCA GTCTGATGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:90158496-90158646 2.7e-07 28_[+8]_108 chr7:69960031-69960181 3.3e-07 3_[+8]_133 chr7:68211639-68211789 6.9e-07 4_[+8]_132 chr7:92271259-92271409 9e-07 103_[+8]_33 chr7:66469114-66469264 2.4e-06 108_[+8]_28 chrX:150565944-150566094 3.8e-06 124_[+8]_12 chr6:38856152-38856302 5.8e-06 59_[+8]_77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=14 seqs=7 chr7:90158496-90158646 ( 29) CACCTTTTATCCCA 1 chr7:69960031-69960181 ( 4) CACCTCTCATACCA 1 chr7:68211639-68211789 ( 5) CACCTGTGATTCCA 1 chr7:92271259-92271409 ( 104) CTCCATCTATTCCA 1 chr7:66469114-66469264 ( 109) CTCCATTTCTACCA 1 chrX:150565944-150566094 ( 125) AACCAATAATACCA 1 chr6:38856152-38856302 ( 60) CAGCCCCAATTCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 3836 bayes= 8.93898 E= 1.8e+003 -92 191 -945 -945 140 -945 -945 -7 -945 191 -49 -945 -945 214 -945 -945 66 -67 -945 51 -92 33 -49 51 -945 33 -945 125 8 -67 -49 51 166 -67 -945 -945 -945 -945 -945 173 66 -67 -945 51 -945 214 -945 -945 -945 214 -945 -945 188 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 7 E= 1.8e+003 0.142857 0.857143 0.000000 0.000000 0.714286 0.000000 0.000000 0.285714 0.000000 0.857143 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.142857 0.000000 0.428571 0.142857 0.285714 0.142857 0.428571 0.000000 0.285714 0.000000 0.714286 0.285714 0.142857 0.142857 0.428571 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.428571 0.142857 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- C[AT]CC[AT][TC][TC][TA]AT[AT]CCA -------------------------------------------------------------------------------- Time 14.18 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 25 sites = 2 llr = 60 E-value = 2.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A ::::a:5:::55::5:5::a:5::: pos.-specific C ::aa:::::55::::5::a::55aa probability G aa:::a:a5::5:a555a::a:5:: matrix T ::::::5:55::a:::::::::::: bits 2.3 ** * * * * * 2.1 **** * * * ** * ** 1.9 ****** * * **** ** 1.6 ****** * ** **** ** Relative 1.4 ****** * ** **** ** Entropy 1.2 ****** * ********** *** (42.9 bits) 0.9 ****** ****************** 0.7 ************************* 0.5 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel GGCCAGAGGCAATGACAGCAGACCC consensus T TTCG GGG CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:127922155-127922305 4 3.61e-14 CAG GGCCAGTGTCAGTGGCGGCAGCCCC CAGGGAAGGA chr8:122109021-122109171 34 7.02e-14 AGGTGATCAT GGCCAGAGGTCATGAGAGCAGAGCC CTGTCATGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127922155-127922305 3.6e-14 3_[+9]_122 chr8:122109021-122109171 7e-14 33_[+9]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=25 seqs=2 chr7:127922155-127922305 ( 4) GGCCAGTGTCAGTGGCGGCAGCCCC 1 chr8:122109021-122109171 ( 34) GGCCAGAGGTCATGAGAGCAGAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 3528 bayes= 10.7838 E= 2.5e+003 -765 -765 231 -765 -765 -765 231 -765 -765 213 -765 -765 -765 213 -765 -765 188 -765 -765 -765 -765 -765 231 -765 88 -765 -765 73 -765 -765 231 -765 -765 -765 131 73 -765 113 -765 73 88 113 -765 -765 88 -765 131 -765 -765 -765 -765 173 -765 -765 231 -765 88 -765 131 -765 -765 113 131 -765 88 -765 131 -765 -765 -765 231 -765 -765 213 -765 -765 188 -765 -765 -765 -765 -765 231 -765 88 113 -765 -765 -765 113 131 -765 -765 213 -765 -765 -765 213 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 2 E= 2.5e+003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.500000 0.500000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- GGCCAG[AT]G[GT][CT][AC][AG]TG[AG][CG][AG]GCAG[AC][CG]CC -------------------------------------------------------------------------------- Time 15.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 12 sites = 5 llr = 65 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A a6::64:8:::: pos.-specific C ::::4::2::a: probability G :4:8::a::8:: matrix T ::a2:6::a2:a bits 2.3 * 2.1 * * 1.9 * * * 1.6 * * * * ** Relative 1.4 * ** * **** Entropy 1.2 **** ****** (18.6 bits) 0.9 ************ 0.7 ************ 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel AATGATGATGCT consensus G TCA C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ chr7:92271259-92271409 133 8.05e-08 CTGAGTTACA AATGATGATGCT CTCCAC chr7:69960031-69960181 92 4.45e-07 CCAGTGAGTA AATGCAGATGCT CCAGAAAGTG chr6:38856152-38856302 32 7.67e-07 GCTTGTCCTC AGTGCTGCTGCT AAGAGATTCC chr7:108272327-108272477 126 1.32e-06 TTGAGACTTC AGTGATGATTCT GTCTCTACCT chr7:83097224-83097374 16 1.74e-06 TGATCAGGCT AATTAAGATGCT GTCGTGAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:92271259-92271409 8.1e-08 132_[+10]_6 chr7:69960031-69960181 4.5e-07 91_[+10]_47 chr6:38856152-38856302 7.7e-07 31_[+10]_107 chr7:108272327-108272477 1.3e-06 125_[+10]_13 chr7:83097224-83097374 1.7e-06 15_[+10]_123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=12 seqs=5 chr7:92271259-92271409 ( 133) AATGATGATGCT 1 chr7:69960031-69960181 ( 92) AATGCAGATGCT 1 chr6:38856152-38856302 ( 32) AGTGCTGCTGCT 1 chr7:108272327-108272477 ( 126) AGTGATGATTCT 1 chr7:83097224-83097374 ( 16) AATTAAGATGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 3892 bayes= 8.13458 E= 2.3e+003 188 -897 -897 -897 114 -897 99 -897 -897 -897 -897 173 -897 -897 199 -59 114 81 -897 -897 56 -897 -897 100 -897 -897 231 -897 156 -18 -897 -897 -897 -897 -897 173 -897 -897 199 -59 -897 213 -897 -897 -897 -897 -897 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 2.3e+003 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.600000 0.400000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- A[AG]T[GT][AC][TA]G[AC]T[GT]CT -------------------------------------------------------------------------------- Time 17.12 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:27152244-27152394 7.26e-08 5_[+3(1.89e-07)]_18_[+4(3.08e-06)]_31_[+7(6.38e-07)]_43 chr6:88203946-88204096 5.05e-10 34_[+5(5.20e-11)]_53_[+2(3.80e-10)]_17 chr6:38757546-38757696 2.12e-03 2_[+4(8.19e-07)]_123 chr6:38856152-38856302 1.11e-11 31_[+10(7.67e-07)]_16_[+8(5.81e-06)]_12_[+4(3.16e-09)]_10_[+7(3.50e-07)]_17 chr7:92271259-92271409 5.55e-07 24_[+4(8.57e-08)]_54_[+8(8.98e-07)]_15_[+10(8.05e-08)]_6 chr7:90158496-90158646 2.46e-09 13_[+3(2.73e-08)]_[+8(2.67e-07)]_20_[+7(2.41e-07)]_75 chr7:108272327-108272477 5.82e-05 37_[+4(1.65e-06)]_63_[+10(1.32e-06)]_13 chr7:69960031-69960181 2.94e-08 3_[+8(3.27e-07)]_58_[+1(2.19e-07)]_2_[+10(4.45e-07)]_47 chr7:127922155-127922305 1.87e-20 3_[+9(3.61e-14)]_21_[+7(1.87e-07)]_22_[+5(1.19e-09)]_1_[+1(1.30e-07)]_30 chr7:67296514-67296664 1.87e-05 14_[+4(8.81e-07)]_31_[+6(1.71e-07)]_66 chr7:71503065-71503215 4.82e-04 39_[+1(7.75e-07)]_97 chr7:71037117-71037267 2.65e-01 150 chr7:100578775-100578925 2.22e-04 66_[+4(4.32e-10)]_59 chr7:106294951-106295101 5.65e-01 150 chr7:66469114-66469264 1.06e-10 13_[+5(4.90e-10)]_9_[+4(2.89e-07)]_40_[+8(2.38e-06)]_28 chr7:105413204-105413354 1.59e-08 54_[+4(8.81e-07)]_10_[+1(3.63e-07)]_17_[+3(5.62e-08)]_15 chr7:68211639-68211789 2.60e-10 4_[+8(6.89e-07)]_72_[+1(2.19e-07)]_26_[+6(4.73e-09)]_6 chr7:103971079-103971229 3.99e-06 71_[+1(3.35e-06)]_22_[+3(5.62e-08)]_28 chr7:83097224-83097374 1.29e-01 15_[+10(1.74e-06)]_123 chr7:70144883-70145033 3.04e-05 14_[+1(3.76e-06)]_37_[+5(2.67e-09)]_64 chr7:81826318-81826468 1.29e-13 17_[+6(3.45e-08)]_15_[+4(1.60e-08)]_11_[+2(2.06e-11)]_43 chr7:66763878-66764028 7.74e-06 83_[+4(1.76e-06)]_6_[+1(5.70e-07)]_22 chr7:83064330-83064480 4.43e-11 35_[+2(3.70e-12)]_21_[+1(3.12e-07)]_55 chr7:66280364-66280514 6.07e-13 7_[+2(6.57e-10)]_7_[+4(8.57e-08)]_48_[+3(3.26e-07)]_23 chr7:63499650-63499800 5.85e-02 118_[+6(2.52e-07)]_18 chr8:122109021-122109171 1.34e-18 33_[+9(7.02e-14)]_27_[+7(2.14e-07)]_5_[+2(1.37e-10)]_22 chrX:150565944-150566094 1.32e-01 124_[+8(3.78e-06)]_12 chrX:150846675-150846825 9.96e-01 150 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************