******************************************************************************** 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.radius25bp.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2:27152294-27152344 1.0000 50 chr6:38856202-38856252 1.0000 50 chr6:88203996-88204046 1.0000 50 chr6:38757596-38757646 1.0000 50 chr7:68211689-68211739 1.0000 50 chr7:63499700-63499750 1.0000 50 chr7:108272377-108272427 1.0000 50 chr7:105413254-105413304 1.0000 50 chr7:103971129-103971179 1.0000 50 chr7:106295001-106295051 1.0000 50 chr7:71037167-71037217 1.0000 50 chr7:71503115-71503165 1.0000 50 chr7:67296564-67296614 1.0000 50 chr7:69960081-69960131 1.0000 50 chr7:127922205-127922255 1.0000 50 chr7:66469164-66469214 1.0000 50 chr7:90158546-90158596 1.0000 50 chr7:83097274-83097324 1.0000 50 chr7:66280414-66280464 1.0000 50 chr7:81826368-81826418 1.0000 50 chr7:66763928-66763978 1.0000 50 chr7:100578825-100578875 1.0000 50 chr7:92271309-92271359 1.0000 50 chr7:83064380-83064430 1.0000 50 chr7:70144933-70144983 1.0000 50 chr8:122109071-122109121 1.0000 50 chrX:150565994-150566044 1.0000 50 chrX:150846725-150846775 1.0000 50 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme GATA_Negs.radius25bp.fa -maxw 25 -dna -nmotifs 10 -maxsize 200000 -o GATA_Negs.radius25bp.meme.maxw25 model: mod= zoops nmotifs= 10 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 25 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 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= 1400 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.223 G 0.193 T 0.304 Background letter frequencies (from dataset with add-one prior applied): A 0.281 C 0.223 G 0.193 T 0.303 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 8 sites = 8 llr = 69 E-value = 4.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 934:9::: pos.-specific C ::5a:3:: probability G 181::8:a matrix T ::::1:a: bits 2.4 * 2.1 * * 1.9 * * 1.7 * ** Relative 1.4 ** * *** Entropy 1.2 ** ***** (12.5 bits) 0.9 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AGCCAGTG consensus AA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:83064380-83064430 36 8.55e-06 ACCACACATG AGCCAGTG AGCAGTT chr6:38757596-38757646 3 1.93e-05 CA AGACAGTG ATATTACCTA chr7:66280414-66280464 22 3.66e-05 CCCTTCCTAA AGCCACTG TACATGTTGG chr7:69960081-69960131 30 4.91e-05 TATATTTCAG AACCAGTG AGTAAATGCA chrX:150565994-150566044 11 9.23e-05 CAGCTATACA AAACAGTG TTACATTTCC chr7:105413254-105413304 38 9.23e-05 TCAAGCTCTG AGCCTGTG CTTGT chr7:81826368-81826418 30 9.97e-05 CTGTCAGCCT GGACAGTG TCCACTGCCG chr6:88203996-88204046 15 1.20e-04 GTGCAGTAAA AGGCACTG AGTGTTTAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:83064380-83064430 8.6e-06 35_[+1]_7 chr6:38757596-38757646 1.9e-05 2_[+1]_40 chr7:66280414-66280464 3.7e-05 21_[+1]_21 chr7:69960081-69960131 4.9e-05 29_[+1]_13 chrX:150565994-150566044 9.2e-05 10_[+1]_32 chr7:105413254-105413304 9.2e-05 37_[+1]_5 chr7:81826368-81826418 0.0001 29_[+1]_13 chr6:88203996-88204046 0.00012 14_[+1]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=8 seqs=8 chr7:83064380-83064430 ( 36) AGCCAGTG 1 chr6:38757596-38757646 ( 3) AGACAGTG 1 chr7:66280414-66280464 ( 22) AGCCACTG 1 chr7:69960081-69960131 ( 30) AACCAGTG 1 chrX:150565994-150566044 ( 11) AAACAGTG 1 chr7:105413254-105413304 ( 38) AGCCTGTG 1 chr7:81826368-81826418 ( 30) GGACAGTG 1 chr6:88203996-88204046 ( 15) AGGCACTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1204 bayes= 7.224 E= 4.2e+000 164 -965 -63 -965 -17 -965 196 -965 42 116 -63 -965 -965 216 -965 -965 164 -965 -965 -128 -965 17 196 -965 -965 -965 -965 172 -965 -965 237 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 4.2e+000 0.875000 0.000000 0.125000 0.000000 0.250000 0.000000 0.750000 0.000000 0.375000 0.500000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[GA][CA]CA[GC]TG -------------------------------------------------------------------------------- Time 0.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 14 sites = 5 llr = 67 E-value = 7.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :64a22::::::a: pos.-specific C 44::24aa:::8:: probability G 6:6:22:::a62:4 matrix T ::::42::a:4::6 bits 2.4 * 2.1 ** * 1.9 * ** * * 1.7 * **** * Relative 1.4 * * **** ** Entropy 1.2 * ** ******* (19.4 bits) 0.9 **** ******** 0.7 **** ******** 0.5 **** ******** 0.2 **** ********* 0.0 -------------- Multilevel GAGATCCCTGGCAT consensus CCA AA TG G sequence CG GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr7:90158546-90158596 27 1.78e-07 CAATAGCTAA GAGACACCTGGCAT TGATCTCTGG chr7:100578825-100578875 33 2.13e-07 TCTTTTCCCT GCAATGCCTGGCAT TATT chr8:122109071-122109121 2 2.43e-07 G CAGAGCCCTGTCAT GGTGTCAGCA chr7:70144933-70144983 23 6.99e-07 TTAGATTCCA GAGATTCCTGGGAG GTGAAGTTAA chr7:81826368-81826418 13 1.18e-06 TTATTTCCTT CCAAACCCTGTCAG CCTGGACAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:90158546-90158596 1.8e-07 26_[+2]_10 chr7:100578825-100578875 2.1e-07 32_[+2]_4 chr8:122109071-122109121 2.4e-07 1_[+2]_35 chr7:70144933-70144983 7e-07 22_[+2]_14 chr7:81826368-81826418 1.2e-06 12_[+2]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=5 chr7:90158546-90158596 ( 27) GAGACACCTGGCAT 1 chr7:100578825-100578875 ( 33) GCAATGCCTGGCAT 1 chr8:122109071-122109121 ( 2) CAGAGCCCTGTCAT 1 chr7:70144933-70144983 ( 23) GAGATTCCTGGGAG 1 chr7:81826368-81826418 ( 13) CCAAACCCTGTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1036 bayes= 7.11894 E= 7.9e+000 -897 84 163 -897 109 84 -897 -897 51 -897 163 -897 183 -897 -897 -897 -49 -16 5 40 -49 84 5 -60 -897 216 -897 -897 -897 216 -897 -897 -897 -897 -897 172 -897 -897 237 -897 -897 -897 163 40 -897 184 5 -897 183 -897 -897 -897 -897 -897 105 98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 5 E= 7.9e+000 0.000000 0.400000 0.600000 0.000000 0.600000 0.400000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.200000 0.400000 0.200000 0.400000 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][AC][GA]A[TACGA][CAGTA]CCTG[GT][CG]A[TG] -------------------------------------------------------------------------------- Time 0.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 13 sites = 4 llr = 54 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3:a:3::88583: pos.-specific C :::3::a:3:::a probability G 8a:58a:::338: matrix T :::3:::3:3::: bits 2.4 * * 2.1 * ** * 1.9 ** ** * 1.7 ** ** * Relative 1.4 *** *** ** Entropy 1.2 *** *** * *** (19.5 bits) 0.9 *** ***** *** 0.7 ********* *** 0.5 ************* 0.2 ************* 0.0 ------------- Multilevel GGAGGGCAAAAGC consensus A CA TCGGA sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- chr8:122109071-122109121 34 1.09e-07 CATCCTTCCA AGAGGGCAAGAGC TCAG chr7:90158546-90158596 11 1.92e-07 CAAAAAACAT GGAGAGCAATAGC TAAGAGACAC chr7:105413254-105413304 21 3.97e-07 TACTTGGGCA GGACGGCTCAAGC TCTGAGCCTG chr7:127922205-127922255 25 6.72e-07 TGTATGAAGT GGATGGCAAAGAC CACAAGGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:122109071-122109121 1.1e-07 33_[+3]_4 chr7:90158546-90158596 1.9e-07 10_[+3]_27 chr7:105413254-105413304 4e-07 20_[+3]_17 chr7:127922205-127922255 6.7e-07 24_[+3]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=13 seqs=4 chr8:122109071-122109121 ( 34) AGAGGGCAAGAGC 1 chr7:90158546-90158596 ( 11) GGAGAGCAATAGC 1 chr7:105413254-105413304 ( 21) GGACGGCTCAAGC 1 chr7:127922205-127922255 ( 25) GGATGGCAAAGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 1064 bayes= 8.04985 E= 1.1e+002 -17 -865 196 -865 -865 -865 237 -865 183 -865 -865 -865 -865 16 137 -28 -17 -865 196 -865 -865 -865 237 -865 -865 216 -865 -865 142 -865 -865 -28 142 16 -865 -865 83 -865 37 -28 142 -865 37 -865 -17 -865 196 -865 -865 216 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 4 E= 1.1e+002 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]GA[GCT][GA]GC[AT][AC][AGT][AG][GA]C -------------------------------------------------------------------------------- Time 1.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 14 sites = 6 llr = 71 E-value = 4.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A 355a:3:::::::: pos.-specific C ::::2355a::58: probability G 755:2225::2::: matrix T ::::723::a852a bits 2.4 2.1 * 1.9 * * 1.7 * ** * Relative 1.4 * ** ** Entropy 1.2 **** **** ** (17.1 bits) 0.9 **** ******* 0.7 ***** ******* 0.5 ***** ******** 0.2 ***** ******** 0.0 -------------- Multilevel GAAATACCCTTCCT consensus AGG CTG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- chr6:38856202-38856252 31 1.52e-07 CCAGTCTGAT GAGATCTGCTTCCT ATGCCT chr7:66280414-66280464 6 4.72e-07 CTCTG AGAATCCCCTTCCT AAAGCCACTG chr7:100578825-100578875 12 1.38e-06 TCGGCTCTGG GAAATGTGCTTTCT TTTCCCTGCA chr7:68211689-68211739 30 2.05e-06 GGGTTTGATA GGGACACCCTGCCT CAACCAG chr7:106295001-106295051 5 5.84e-06 TCTT GGAATTCCCTTTTT AGAGTCACTT chr7:103971129-103971179 29 6.16e-06 TCTCCTGAAC AAGAGAGGCTTTCT GATTCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:38856202-38856252 1.5e-07 30_[+4]_6 chr7:66280414-66280464 4.7e-07 5_[+4]_31 chr7:100578825-100578875 1.4e-06 11_[+4]_25 chr7:68211689-68211739 2e-06 29_[+4]_7 chr7:106295001-106295051 5.8e-06 4_[+4]_32 chr7:103971129-103971179 6.2e-06 28_[+4]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=14 seqs=6 chr6:38856202-38856252 ( 31) GAGATCTGCTTCCT 1 chr7:66280414-66280464 ( 6) AGAATCCCCTTCCT 1 chr7:100578825-100578875 ( 12) GAAATGTGCTTTCT 1 chr7:68211689-68211739 ( 30) GGGACACCCTGCCT 1 chr7:106295001-106295051 ( 5) GGAATTCCCTTTTT 1 chr7:103971129-103971179 ( 29) AAGAGAGGCTTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1036 bayes= 7.87316 E= 4.1e+002 25 -923 179 -923 83 -923 137 -923 83 -923 137 -923 183 -923 -923 -923 -923 -42 -21 113 25 58 -21 -86 -923 116 -21 14 -923 116 137 -923 -923 216 -923 -923 -923 -923 -923 172 -923 -923 -21 146 -923 116 -923 72 -923 190 -923 -86 -923 -923 -923 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 6 E= 4.1e+002 0.333333 0.000000 0.666667 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.333333 0.333333 0.166667 0.166667 0.000000 0.500000 0.166667 0.333333 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.500000 0.000000 0.500000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- [GA][AG][AG]AT[AC][CT][CG]CTT[CT]CT -------------------------------------------------------------------------------- Time 1.65 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 25 sites = 5 llr = 92 E-value = 8.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A 8:2::::84826:6488:26:4:2: pos.-specific C 22::8:222:::::4::64::::4: probability G :62a::::42:::::22::2:22:: matrix T :26:2a8:::84a42::442a484a bits 2.4 * 2.1 * 1.9 * 1.7 * * * * * Relative 1.4 *** * * * Entropy 1.2 * ***** * * ** * * * (26.6 bits) 0.9 * ***** ** * *** * * * 0.7 ** *********** *** * * * 0.5 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel AGTGCTTAAATATAAAACCATATCT consensus CCA T CCGGAT TCGGTTG TGT sequence TG C T AT G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- chr7:69960081-69960131 2 3.53e-10 T AGGGCTTACATATAAGATTATATTT CAGAACCAGT chrX:150846725-150846775 18 5.64e-10 ATGAGCTAAT ACAGCTTAAATATTCAACAATGTCT GGAACGTT chr6:88203996-88204046 23 1.59e-09 AAAGGCACTG AGTGTTTAGATTTTAAACTGTAGTT AAA chr7:66469164-66469214 24 3.51e-09 GGCTTCCTTC CGTGCTTAGGATTACAATCTTTTCT AA chr7:92271309-92271359 6 1.01e-08 TTAAT ATTGCTCCAATATATAGCCATTTAT CATCAGCATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:69960081-69960131 3.5e-10 1_[+5]_24 chrX:150846725-150846775 5.6e-10 17_[+5]_8 chr6:88203996-88204046 1.6e-09 22_[+5]_3 chr7:66469164-66469214 3.5e-09 23_[+5]_2 chr7:92271309-92271359 1e-08 5_[+5]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=25 seqs=5 chr7:69960081-69960131 ( 2) AGGGCTTACATATAAGATTATATTT 1 chrX:150846725-150846775 ( 18) ACAGCTTAAATATTCAACAATGTCT 1 chr6:88203996-88204046 ( 23) AGTGTTTAGATTTTAAACTGTAGTT 1 chr7:66469164-66469214 ( 24) CGTGCTTAGGATTACAATCTTTTCT 1 chr7:92271309-92271359 ( 6) ATTGCTCCAATATATAGCCATTTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 728 bayes= 7.42906 E= 8.0e+002 151 -16 -897 -897 -897 -16 163 -60 -49 -897 5 98 -897 -897 237 -897 -897 184 -897 -60 -897 -897 -897 172 -897 -16 -897 140 151 -16 -897 -897 51 -16 105 -897 151 -897 5 -897 -49 -897 -897 140 109 -897 -897 40 -897 -897 -897 172 109 -897 -897 40 51 84 -897 -60 151 -897 5 -897 151 -897 5 -897 -897 143 -897 40 -49 84 -897 40 109 -897 5 -60 -897 -897 -897 172 51 -897 5 40 -897 -897 5 140 -49 84 -897 40 -897 -897 -897 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 5 E= 8.0e+002 0.800000 0.200000 0.000000 0.000000 0.000000 0.200000 0.600000 0.200000 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.800000 0.200000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.000000 0.800000 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.600000 0.000000 0.000000 0.400000 0.400000 0.400000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.600000 0.000000 0.400000 0.200000 0.400000 0.000000 0.400000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.400000 0.000000 0.200000 0.400000 0.000000 0.000000 0.200000 0.800000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- [AC][GCT][TAG]G[CT]T[TC][AC][AGC][AG][TA][AT]T[AT][ACT][AG][AG][CT][CTA][AGT]T[ATG][TG][CTA]T -------------------------------------------------------------------------------- Time 1.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 9 sites = 2 llr = 25 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A a::::a::a pos.-specific C ::::a:::: probability G :a:a::a:: matrix T ::a::::a: bits 2.4 * * * 2.1 * ** * 1.9 ** **** * 1.7 ********* Relative 1.4 ********* Entropy 1.2 ********* (18.2 bits) 0.9 ********* 0.7 ********* 0.5 ********* 0.2 ********* 0.0 --------- Multilevel AGTGCAGTA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- chr7:103971129-103971179 2 3.27e-06 C AGTGCAGTA CAAAAACATC chr6:88203996-88204046 4 3.27e-06 GTT AGTGCAGTA AAAGGCACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:103971129-103971179 3.3e-06 1_[+6]_40 chr6:88203996-88204046 3.3e-06 3_[+6]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=9 seqs=2 chr7:103971129-103971179 ( 2) AGTGCAGTA 1 chr6:88203996-88204046 ( 4) AGTGCAGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 1176 bayes= 9.19722 E= 1.0e+003 183 -765 -765 -765 -765 -765 237 -765 -765 -765 -765 172 -765 -765 237 -765 -765 216 -765 -765 183 -765 -765 -765 -765 -765 237 -765 -765 -765 -765 172 183 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 2 E= 1.0e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 regular expression -------------------------------------------------------------------------------- AGTGCAGTA -------------------------------------------------------------------------------- Time 2.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 8 sites = 4 llr = 38 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A :a::a:3: pos.-specific C a::a:33a probability G ::a:::3: matrix T :::::83: bits 2.4 * 2.1 * ** * 1.9 ***** * 1.7 ***** * Relative 1.4 ***** * Entropy 1.2 ***** * (13.6 bits) 0.9 ****** * 0.7 ****** * 0.5 ****** * 0.2 ****** * 0.0 -------- Multilevel CAGCATAC consensus CC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:38856202-38856252 3 9.88e-06 TC CAGCATGC AGCCCCAATT chr8:122109071-122109121 21 2.13e-05 GTCATGGTGT CAGCATCC TTCCAAGAGG chr7:92271309-92271359 34 3.57e-05 CATTTATCAT CAGCATAC CTATTATTT chrX:150565994-150566044 41 8.89e-05 ATAATCCATT CAGCACTC CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:38856202-38856252 9.9e-06 2_[+7]_40 chr8:122109071-122109121 2.1e-05 20_[+7]_22 chr7:92271309-92271359 3.6e-05 33_[+7]_9 chrX:150565994-150566044 8.9e-05 40_[+7]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=8 seqs=4 chr6:38856202-38856252 ( 3) CAGCATGC 1 chr8:122109071-122109121 ( 21) CAGCATCC 1 chr7:92271309-92271359 ( 34) CAGCATAC 1 chrX:150565994-150566044 ( 41) CAGCACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1204 bayes= 8.22882 E= 1.6e+003 -865 216 -865 -865 183 -865 -865 -865 -865 -865 237 -865 -865 216 -865 -865 183 -865 -865 -865 -865 16 -865 130 -17 16 37 -28 -865 216 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.6e+003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.250000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 regular expression -------------------------------------------------------------------------------- CAGCA[TC][ACGTA]C -------------------------------------------------------------------------------- Time 2.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 8 sites = 4 llr = 38 E-value = 3.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A 5aaaa:a: pos.-specific C 3::::a:: probability G 3::::::: matrix T :::::::a bits 2.4 2.1 * 1.9 ****** 1.7 ******* Relative 1.4 ******* Entropy 1.2 ******* (13.6 bits) 0.9 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AAAAACAT consensus C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:90158546-90158596 3 3.33e-05 CA AAAAACAT GGAGAGCAAT chr7:103971129-103971179 12 3.33e-05 AGTGCAGTAC AAAAACAT CTCCTGAACA chr7:70144933-70144983 1 5.61e-05 . GAAAACAT GTCATTAGAT chr7:66763928-66763978 16 8.25e-05 TTGTGCGTCC CAAAACAT GAAGAGGAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:90158546-90158596 3.3e-05 2_[+8]_40 chr7:103971129-103971179 3.3e-05 11_[+8]_31 chr7:70144933-70144983 5.6e-05 [+8]_42 chr7:66763928-66763978 8.3e-05 15_[+8]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=8 seqs=4 chr7:90158546-90158596 ( 3) AAAAACAT 1 chr7:103971129-103971179 ( 12) AAAAACAT 1 chr7:70144933-70144983 ( 1) GAAAACAT 1 chr7:66763928-66763978 ( 16) CAAAACAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1204 bayes= 8.22882 E= 3.0e+003 83 16 37 -865 183 -865 -865 -865 183 -865 -865 -865 183 -865 -865 -865 183 -865 -865 -865 -865 216 -865 -865 183 -865 -865 -865 -865 -865 -865 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 3.0e+003 0.500000 0.250000 0.250000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 regular expression -------------------------------------------------------------------------------- [ACG]AAAACAT -------------------------------------------------------------------------------- Time 2.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 8 sites = 2 llr = 22 E-value = 2.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A :5:::::: pos.-specific C a:a::a:a probability G :::aa::: matrix T :5::::a: bits 2.4 ** 2.1 * **** * 1.9 * **** * 1.7 * ****** Relative 1.4 * ****** Entropy 1.2 * ****** (15.9 bits) 0.9 * ****** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CACGGCTC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:108272377-108272427 38 7.84e-06 TTCTGTTATT CACGGCTC CATAC chr7:100578825-100578875 1 1.63e-05 . CTCGGCTC TGGGAAATGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:108272377-108272427 7.8e-06 37_[+9]_5 chr7:100578825-100578875 1.6e-05 [+9]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=8 seqs=2 chr7:108272377-108272427 ( 38) CACGGCTC 1 chr7:100578825-100578875 ( 1) CTCGGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1204 bayes= 7.45991 E= 2.4e+003 -765 216 -765 -765 83 -765 -765 72 -765 216 -765 -765 -765 -765 237 -765 -765 -765 237 -765 -765 216 -765 -765 -765 -765 -765 172 -765 216 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.4e+003 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 regular expression -------------------------------------------------------------------------------- C[AT]CGGCTC -------------------------------------------------------------------------------- Time 3.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 11 sites = 6 llr = 59 E-value = 2.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A a:5:2:3::2: pos.-specific C :83:2:3::22 probability G ::::3:3:a:8 matrix T :22a3a:a:7: bits 2.4 * 2.1 * 1.9 * * 1.7 * * * ** * Relative 1.4 ** * * ** * Entropy 1.2 ** * * ** * (14.2 bits) 0.9 ** * * ** * 0.7 ** * * ** * 0.5 **** ****** 0.2 **** ****** 0.0 ----------- Multilevel ACATGTATGTG consensus C T C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr7:127922205-127922255 6 3.94e-06 GAGCA ACATCTCTGTG TATGAAGTGG chr7:66763928-66763978 2 8.65e-06 C ACATTTGTGCG TCCCAAAACA chr2:27152294-27152344 38 1.17e-05 AAGTTAATTA ACTTTTCTGTG CC chrX:150846725-150846775 2 1.28e-05 C ACCTGTATGAG CTAATACAGC chr7:63499700-63499750 14 2.18e-05 GTATATATAT ATATGTATGTG TATACATATA chr6:38757596-38757646 16 3.93e-05 CAGTGATATT ACCTATGTGTC GCTTTGCTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:127922205-127922255 3.9e-06 5_[+10]_34 chr7:66763928-66763978 8.7e-06 1_[+10]_38 chr2:27152294-27152344 1.2e-05 37_[+10]_2 chrX:150846725-150846775 1.3e-05 1_[+10]_38 chr7:63499700-63499750 2.2e-05 13_[+10]_26 chr6:38757596-38757646 3.9e-05 15_[+10]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=11 seqs=6 chr7:127922205-127922255 ( 6) ACATCTCTGTG 1 chr7:66763928-66763978 ( 2) ACATTTGTGCG 1 chr2:27152294-27152344 ( 38) ACTTTTCTGTG 1 chrX:150846725-150846775 ( 2) ACCTGTATGAG 1 chr7:63499700-63499750 ( 14) ATATGTATGTG 1 chr6:38757596-38757646 ( 16) ACCTATGTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1120 bayes= 6.30378 E= 2.8e+003 183 -923 -923 -923 -923 190 -923 -86 83 58 -923 -86 -923 -923 -923 172 -75 -42 79 14 -923 -923 -923 172 25 58 79 -923 -923 -923 -923 172 -923 -923 237 -923 -75 -42 -923 113 -923 -42 211 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6 E= 2.8e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.166667 0.166667 0.333333 0.333333 0.000000 0.000000 0.000000 1.000000 0.333333 0.333333 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.166667 0.000000 0.666667 0.000000 0.166667 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 regular expression -------------------------------------------------------------------------------- AC[AC]T[GT]T[ACG]TGTG -------------------------------------------------------------------------------- Time 3.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:27152294-27152344 5.19e-02 37_[+10(1.17e-05)]_2 chr6:38856202-38856252 3.92e-05 2_[+7(9.88e-06)]_20_[+4(1.52e-07)]_6 chr6:88203996-88204046 7.63e-08 3_[+6(3.27e-06)]_10_[+5(1.59e-09)]_3 chr6:38757596-38757646 1.02e-02 2_[+1(1.93e-05)]_5_[+10(3.93e-05)]_24 chr7:68211689-68211739 5.43e-02 29_[+4(2.05e-06)]_7 chr7:63499700-63499750 3.81e-01 13_[+10(2.18e-05)]_26 chr7:108272377-108272427 3.60e-02 37_[+9(7.84e-06)]_5 chr7:105413254-105413304 5.11e-07 20_[+3(3.97e-07)]_4_[+1(9.23e-05)]_5 chr7:103971129-103971179 2.76e-06 1_[+6(3.27e-06)]_1_[+8(3.33e-05)]_9_[+4(6.16e-06)]_8 chr7:106295001-106295051 8.49e-02 4_[+4(5.84e-06)]_32 chr7:71037167-71037217 5.35e-01 50 chr7:71503115-71503165 4.82e-01 50 chr7:67296564-67296614 8.05e-01 50 chr7:69960081-69960131 2.83e-07 1_[+5(3.53e-10)]_3_[+1(4.91e-05)]_13 chr7:127922205-127922255 1.54e-04 5_[+10(3.94e-06)]_8_[+3(6.72e-07)]_13 chr7:66469164-66469214 1.89e-05 23_[+5(3.51e-09)]_2 chr7:90158546-90158596 1.40e-08 2_[+8(3.33e-05)]_[+3(1.92e-07)]_3_[+2(1.78e-07)]_10 chr7:83097274-83097324 6.02e-01 50 chr7:66280414-66280464 8.17e-04 5_[+4(4.72e-07)]_2_[+1(3.66e-05)]_21 chr7:81826368-81826418 6.85e-04 12_[+2(1.18e-06)]_3_[+1(9.97e-05)]_13 chr7:66763928-66763978 2.91e-03 1_[+10(8.65e-06)]_3_[+8(8.25e-05)]_27 chr7:100578825-100578875 1.14e-06 [+9(1.63e-05)]_3_[+4(1.38e-06)]_7_[+2(2.13e-07)]_4 chr7:92271309-92271359 1.63e-04 5_[+5(1.01e-08)]_3_[+7(3.57e-05)]_9 chr7:83064380-83064430 2.70e-02 35_[+1(8.55e-06)]_7 chr7:70144933-70144983 1.27e-03 [+8(5.61e-05)]_14_[+2(6.99e-07)]_14 chr8:122109071-122109121 5.38e-08 1_[+2(2.43e-07)]_5_[+7(2.13e-05)]_5_[+3(1.09e-07)]_4 chrX:150565994-150566044 1.41e-02 10_[+1(9.23e-05)]_22_[+7(8.89e-05)]_2 chrX:150846725-150846775 1.87e-06 1_[+10(1.28e-05)]_5_[+5(5.64e-10)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: pongo ********************************************************************************