******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-suite.org . ******************************************************************************** ******************************************************************************** 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= /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.AluYe5.MemeChipResults/seqs-centered ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:1280182-1280482 1.0000 100 chr1:1470417-1470499 1.0000 82 chr1:1798925-1799219 1.0000 100 chr1:1855419-1855723 1.0000 100 chr1:10501316-10501600 1.0000 100 chr1:11993454-11993761 1.0000 100 chr1:13372159-13372454 1.0000 100 chr1:15815344-15815404 1.0000 60 chr1:16503462-16503509 1.0000 47 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.AluYe5.MemeChipResults/seqs-centered -oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.AluYe5.MemeChipResults/meme_out -mod anr -nmotifs 10 -minw 5 -maxw 50 -bfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.AluYe5.MemeChipResults/background -dna -revcomp -nostatus model: mod= anr nmotifs= 10 evt= inf object function= E-value of product of p-values width: minw= 5 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 45 wnsites= 0.8 theta: 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= 789 N= 9 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.247 C 0.253 G 0.253 T 0.247 Background letter frequencies (from /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.AluYe5.MemeChipResults/background): A 0.219 C 0.281 G 0.281 T 0.219 ******************************************************************************** ******************************************************************************** MOTIF ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 width = 39 sites = 6 llr = 291 E-value = 2.1e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A a::::5:::::a::aaaaa:a:a8aaa8::8::2322:: pos.-specific C :aaaa::a:a::a::::::::a::::::22::88:::7: probability G :::::5:::::::::::::::::2:::2::2a2:78828 matrix T ::::::a:a:a::a:::::a::::::::88:::::::22 bits 2.2 * * * ** ******** * *** 2.0 * * * ** ******** * *** 1.8 ***** ***************** *** * 1.5 ***** ************************** Relative 1.3 ***** ************************** * ** * Entropy 1.1 ************************************* * (70.0 bits) 0.9 ************************************* * 0.7 *************************************** 0.4 *************************************** 0.2 *************************************** 0.0 --------------------------------------- Multilevel ACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGCG consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------------------------- chr1:1798925-1799219 - 55 1.02e-24 CGGTGAA ACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGCG AGGTGGCGGG chr1:13372159-13372454 + 8 4.15e-24 tggtgaa accccgtctctactaaaaatacaaaaaattagccaggcg aggtggcggg chr1:11993454-11993761 + 1 4.95e-24 . accccatctctactaaaaatacaaaaaattagccgggtg aggtggcggg chr1:1855419-1855723 + 3 1.02e-23 aa accccatctctactaaaaatacaaaaaattagcagggcg aggtggcagg chr1:1280182-1280482 + 5 3.06e-22 tgaa accccgtctctactaaaaatacagaaaattagccagacg tggtggcggg chr1:10501316-10501600 - 50 1.35e-19 ACACGGTGAA ACCCCGTCTCTACTAAAAATACAAAAAGCCGGGCGAGGT GGCGGGCGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:1798925-1799219 1e-24 54_[-1]_7 chr1:13372159-13372454 4.2e-24 7_[+1]_54 chr1:11993454-11993761 4.9e-24 [+1]_61 chr1:1855419-1855723 1e-23 2_[+1]_59 chr1:1280182-1280482 3.1e-22 4_[+1]_57 chr1:10501316-10501600 1.3e-19 49_[-1]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG width=39 seqs=6 chr1:1798925-1799219 ( 55) ACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGCG 1 chr1:13372159-13372454 ( 8) ACCCCGTCTCTACTAAAAATACAAAAAATTAGCCAGGCG 1 chr1:11993454-11993761 ( 1) ACCCCATCTCTACTAAAAATACAAAAAATTAGCCGGGTG 1 chr1:1855419-1855723 ( 3) ACCCCATCTCTACTAAAAATACAAAAAATTAGCAGGGCG 1 chr1:1280182-1280482 ( 5) ACCCCGTCTCTACTAAAAATACAGAAAATTAGCCAGACG 1 chr1:10501316-10501600 ( 50) ACCCCGTCTCTACTAAAAATACAAAAAGCCGGGCGAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 447 bayes= 6.65236 E= 2.1e-050 219 -923 -923 -923 -923 183 -923 -923 -923 183 -923 -923 -923 183 -923 -923 -923 183 -923 -923 119 -923 83 -923 -923 -923 -923 219 -923 183 -923 -923 -923 -923 -923 219 -923 183 -923 -923 -923 -923 -923 219 219 -923 -923 -923 -923 183 -923 -923 -923 -923 -923 219 219 -923 -923 -923 219 -923 -923 -923 219 -923 -923 -923 219 -923 -923 -923 219 -923 -923 -923 -923 -923 -923 219 219 -923 -923 -923 -923 183 -923 -923 219 -923 -923 -923 192 -923 -75 -923 219 -923 -923 -923 219 -923 -923 -923 219 -923 -923 -923 192 -923 -75 -923 -923 -75 -923 192 -923 -75 -923 192 192 -923 -75 -923 -923 -923 183 -923 -923 157 -75 -923 -39 157 -923 -923 60 -923 125 -923 -39 -923 157 -923 -39 -923 157 -923 -923 125 -75 -39 -923 -923 157 -39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 6 E= 2.1e-050 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 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 0.833333 0.000000 0.166667 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.666667 0.166667 0.166667 0.000000 0.000000 0.833333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCRTCTCTACTAAAAATACAAAAAATTAGCCRGGCG MEME-1 regular expression -------------------------------------------------------------------------------- ACCCC[AG]TCTCTACTAAAAATACAAAAAATTAGCC[GA]GGCG -------------------------------------------------------------------------------- Time 0.57 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 width = 36 sites = 6 llr = 265 E-value = 4.9e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::a:::::a2:2a:::322a::::28:::8::a pos.-specific C aa::::::aaa::8::a:8::::::a:::::a:::: probability G :::a::a:::::82:::::588:aa::82aa:2aa: matrix T ::a:a::a::::::8::a22::::::a::::::::: bits 2.2 * ** * * * * * * * 2.0 * ** * * * * * * * 1.8 ************ *** ***** *** *** 1.5 ************ **** ***** ******** Relative 1.3 ************* ***** **************** Entropy 1.1 ******************* **************** (63.7 bits) 0.9 ******************* **************** 0.7 ************************************ 0.4 ************************************ 0.2 ************************************ 0.0 ------------------------------------ Multilevel CCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGA consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------------ chr1:10501316-10501600 - 6 5.57e-22 GTGGCGGGCG CCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGA GAATG chr1:1280182-1280482 + 56 7.27e-21 gtggcgggcg cctgtagtcccaggtactcaggaggctgaggcagga gaatggcgt chr1:1855419-1855723 + 54 8.70e-21 gtggcaggcg cctgtagtcccagctactcgggaggctgaggcggga gaatggctgg chr1:1798925-1799219 - 7 1.95e-20 GTGGCGGGCA CCTGTAGTCCCAGCTACTCAAAAGGCTGAGGCAGGA GAATGG chr1:13372159-13372454 + 59 5.09e-20 gtggcgggca cctgtagtcccaacaactctggaggctgaggcagga gaatgg chr1:11993454-11993761 + 52 8.62e-20 gtggcgggcg cctgtagtcccagctacttgggaggctagggcagga gaatggtgtg -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:10501316-10501600 5.6e-22 5_[-2]_59 chr1:1280182-1280482 7.3e-21 55_[+2]_9 chr1:1855419-1855723 8.7e-21 53_[+2]_11 chr1:1798925-1799219 2e-20 6_[-2]_58 chr1:13372159-13372454 5.1e-20 58_[+2]_6 chr1:11993454-11993761 8.6e-20 51_[+2]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA width=36 seqs=6 chr1:10501316-10501600 ( 6) CCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGA 1 chr1:1280182-1280482 ( 56) CCTGTAGTCCCAGGTACTCAGGAGGCTGAGGCAGGA 1 chr1:1855419-1855723 ( 54) CCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGA 1 chr1:1798925-1799219 ( 7) CCTGTAGTCCCAGCTACTCAAAAGGCTGAGGCAGGA 1 chr1:13372159-13372454 ( 59) CCTGTAGTCCCAACAACTCTGGAGGCTGAGGCAGGA 1 chr1:11993454-11993761 ( 52) CCTGTAGTCCCAGCTACTTGGGAGGCTAGGGCAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 36 n= 474 bayes= 6.73779 E= 4.9e-044 -923 183 -923 -923 -923 183 -923 -923 -923 -923 -923 219 -923 -923 183 -923 -923 -923 -923 219 219 -923 -923 -923 -923 -923 183 -923 -923 -923 -923 219 -923 183 -923 -923 -923 183 -923 -923 -923 183 -923 -923 219 -923 -923 -923 -39 -923 157 -923 -923 157 -75 -923 -39 -923 -923 192 219 -923 -923 -923 -923 183 -923 -923 -923 -923 -923 219 -923 157 -923 -39 60 -923 83 -39 -39 -923 157 -923 -39 -923 157 -923 219 -923 -923 -923 -923 -923 183 -923 -923 -923 183 -923 -923 183 -923 -923 -923 -923 -923 219 -39 -923 157 -923 192 -923 -75 -923 -923 -923 183 -923 -923 -923 183 -923 -923 183 -923 -923 192 -923 -75 -923 -923 -923 183 -923 -923 -923 183 -923 219 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 36 nsites= 6 E= 4.9e-044 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.000000 0.833333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.333333 0.000000 0.500000 0.166667 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.000000 0.166667 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 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAGTCCCAGCTACTCRGGAGGCTGAGGCAGGA MEME-2 regular expression -------------------------------------------------------------------------------- CCTGTAGTCCCAGCTACTC[GA]GGAGGCTGAGGCAGGA -------------------------------------------------------------------------------- Time 0.84 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 width = 43 sites = 3 llr = 141 E-value = 3.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::3:::::3733:733:::::73::::::::a:7::::a::: pos.-specific C :::::::::::::7::::333737:::7:aaa:::a::::::: probability G ::::::::3737333777:::3:::a::7::::a3::aa:a:a matrix T aaa7aaaa7:::3::::3777:::a:a33:::::::a::::a: bits 2.2 *** **** * * * * * * 2.0 *** **** * * * * * * 1.8 *** **** *** ***** ******** 1.5 *** **** *** ***** ******** Relative 1.3 ******** *** ***** ******** Entropy 1.1 ************ ******* ********************* (67.9 bits) 0.9 ************ ****************************** 0.7 ************ ****************************** 0.4 ******************************************* 0.2 ******************************************* 0.0 ------------------------------------------- Multilevel TTTTTTTTTGAGACAGGGTTTCACTGTCGCCCAGACTGGAGTG consensus A GAGAGGGAATCCCGCA TT G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------------------- chr1:1470417-1470499 + 22 2.25e-24 tttttttttt tttttttttgagacagagtctcactgtcgcccagactggagtg cagtgatgag chr1:16503462-16503509 + 3 4.17e-24 tt tttttttttgaggcagggtttcactgtctcccaggctggagtg ca chr1:15815344-15815404 - 6 2.87e-20 TTATTATTTA TTTATTTTGAGATGGAGTCTCGCATGTTGCCCAGACTGGAGTG CAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:1470417-1470499 2.3e-24 21_[+3]_18 chr1:16503462-16503509 4.2e-24 2_[+3]_2 chr1:15815344-15815404 2.9e-20 5_[-3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG width=43 seqs=3 chr1:1470417-1470499 ( 22) TTTTTTTTTGAGACAGAGTCTCACTGTCGCCCAGACTGGAGTG 1 chr1:16503462-16503509 ( 3) TTTTTTTTTGAGGCAGGGTTTCACTGTCTCCCAGGCTGGAGTG 1 chr1:15815344-15815404 ( 6) TTTATTTTGAGATGGAGTCTCGCATGTTGCCCAGACTGGAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 43 n= 411 bayes= 6.74359 E= 3.8e-002 -823 -823 -823 219 -823 -823 -823 219 -823 -823 -823 219 60 -823 -823 160 -823 -823 -823 219 -823 -823 -823 219 -823 -823 -823 219 -823 -823 -823 219 -823 -823 25 160 60 -823 124 -823 160 -823 25 -823 60 -823 124 -823 60 -823 25 60 -823 124 25 -823 160 -823 25 -823 60 -823 124 -823 60 -823 124 -823 -823 -823 124 60 -823 25 -823 160 -823 25 -823 160 -823 25 -823 160 -823 124 25 -823 160 25 -823 -823 60 124 -823 -823 -823 -823 -823 219 -823 -823 183 -823 -823 -823 -823 219 -823 124 -823 60 -823 -823 124 60 -823 183 -823 -823 -823 183 -823 -823 -823 183 -823 -823 219 -823 -823 -823 -823 -823 183 -823 160 -823 25 -823 -823 183 -823 -823 -823 -823 -823 219 -823 -823 183 -823 -823 -823 183 -823 219 -823 -823 -823 -823 -823 183 -823 -823 -823 -823 219 -823 -823 183 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 43 nsites= 3 E= 3.8e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.333333 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 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 1.000000 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 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTWTTTTKRRRDSRRRKYYYSMMTGTYKCCCAGRCTGGAGTG MEME-3 regular expression -------------------------------------------------------------------------------- TTT[TA]TTTT[TG][GA][AG][GA][AGT][CG][AG][GA][GA][GT][TC][TC][TC][CG][AC][CA]TGT[CT][GT]CCCAG[AG]CTGGAGTG -------------------------------------------------------------------------------- Time 1.07 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGGCGGGC MEME-4 width = 9 sites = 6 llr = 63 E-value = 4.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A 2::::2::: pos.-specific C ::::a:::a probability G 8:aa:7aa: matrix T :a:::2::: bits 2.2 * 2.0 * 1.8 **** *** 1.5 **** *** Relative 1.3 ***** *** Entropy 1.1 ***** *** (15.1 bits) 0.9 ***** *** 0.7 ********* 0.4 ********* 0.2 ********* 0.0 --------- Multilevel GTGGCGGGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------- chr1:13372159-13372454 + 49 8.51e-06 gccaggcgag gtggcgggc acctgtagtc chr1:11993454-11993761 + 42 8.51e-06 gccgggtgag gtggcgggc gcctgtagtc chr1:1798925-1799219 - 44 8.51e-06 GCCGGGCGAG GTGGCGGGC ACCTGTAGTC chr1:1280182-1280482 + 46 8.51e-06 gccagacgtg gtggcgggc gcctgtagtc chr1:1855419-1855723 + 44 2.18e-05 gcagggcgag gtggcaggc gcctgtagtc chr1:1855419-1855723 + 92 3.88e-05 aggcgggaga atggctggc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:13372159-13372454 8.5e-06 48_[+4]_43 chr1:11993454-11993761 8.5e-06 41_[+4]_50 chr1:1798925-1799219 8.5e-06 43_[-4]_48 chr1:1280182-1280482 8.5e-06 45_[+4]_46 chr1:1855419-1855723 2.2e-05 43_[+4]_39_[+4] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGGCGGGC width=9 seqs=6 chr1:13372159-13372454 ( 49) GTGGCGGGC 1 chr1:11993454-11993761 ( 42) GTGGCGGGC 1 chr1:1798925-1799219 ( 44) GTGGCGGGC 1 chr1:1280182-1280482 ( 46) GTGGCGGGC 1 chr1:1855419-1855723 ( 44) GTGGCAGGC 1 chr1:1855419-1855723 ( 92) ATGGCTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 717 bayes= 6.54446 E= 4.6e+001 -39 -923 157 -923 -923 -923 -923 219 -923 -923 183 -923 -923 -923 183 -923 -923 183 -923 -923 -39 -923 125 -39 -923 -923 183 -923 -923 -923 183 -923 -923 183 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 6 E= 4.6e+001 0.166667 0.000000 0.833333 0.000000 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 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCGGGC MEME-4 regular expression -------------------------------------------------------------------------------- GTGGCGGGC -------------------------------------------------------------------------------- Time 1.20 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTWTTWTTT MEME-5 width = 11 sites = 2 llr = 31 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::5::5::: pos.-specific C ::::::::::: probability G ::::::::::: matrix T aaaa5aa5aaa bits 2.2 **** ** *** 2.0 **** ** *** 1.8 **** ** *** 1.5 **** ** *** Relative 1.3 **** ** *** Entropy 1.1 *********** (22.1 bits) 0.9 *********** 0.7 *********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel TTTTATTATTT consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------- chr1:15815344-15815404 - 50 2.22e-07 . TTTTATTATTT ATTTATTTTG chr1:1470417-1470499 + 9 2.22e-07 tttctggc ttttttttttt tttttttttt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:15815344-15815404 2.2e-07 49_[-5] chr1:1470417-1470499 2.2e-07 8_[+5]_63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTWTTWTTT width=11 seqs=2 chr1:15815344-15815404 ( 50) TTTTATTATTT 1 chr1:1470417-1470499 ( 9) TTTTTTTTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 699 bayes= 8.44501 E= 1.7e+003 -765 -765 -765 218 -765 -765 -765 218 -765 -765 -765 218 -765 -765 -765 218 119 -765 -765 119 -765 -765 -765 218 -765 -765 -765 218 119 -765 -765 119 -765 -765 -765 218 -765 -765 -765 218 -765 -765 -765 218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2 E= 1.7e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWTTWTTT MEME-5 regular expression -------------------------------------------------------------------------------- TTTT[AT]TT[AT]TTT -------------------------------------------------------------------------------- Time 1.35 secs. ******************************************************************************** ******************************************************************************** MOTIF GAATG MEME-6 width = 5 sites = 2 llr = 14 E-value = 3.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAATG MEME-6 Description -------------------------------------------------------------------------------- Simplified A :aa:: pos.-specific C ::::: probability G a:::a matrix T :::a: bits 2.2 *** 2.0 *** 1.8 ***** 1.5 ***** Relative 1.3 ***** Entropy 1.1 ***** (10.2 bits) 0.9 ***** 0.7 ***** 0.4 ***** 0.2 ***** 0.0 ----- Multilevel GAATG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----- chr1:10501316-10501600 - 1 8.29e-04 TGAGGCAGGA GAATG chr1:1798925-1799219 - 2 8.29e-04 TGAGGCAGGA GAATG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:10501316-10501600 0.00083 [-6]_95 chr1:1798925-1799219 0.00083 1_[-6]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAATG width=5 seqs=2 chr1:10501316-10501600 ( 1) GAATG 1 chr1:1798925-1799219 ( 2) GAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 5 n= 753 bayes= 8.55267 E= 3.8e+004 -765 -765 183 -765 218 -765 -765 -765 218 -765 -765 -765 -765 -765 -765 218 -765 -765 183 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 5 nsites= 2 E= 3.8e+004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-6 regular expression -------------------------------------------------------------------------------- GAATG -------------------------------------------------------------------------------- Time 1.44 secs. ******************************************************************************** ******************************************************************************** MOTIF GAATG MEME-7 width = 5 sites = 2 llr = 14 E-value = 3.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAATG MEME-7 Description -------------------------------------------------------------------------------- Simplified A :aa:: pos.-specific C ::::: probability G a:::a matrix T :::a: bits 2.2 *** 2.0 *** 1.8 ***** 1.5 ***** Relative 1.3 ***** Entropy 1.1 ***** (10.2 bits) 0.9 ***** 0.7 ***** 0.4 ***** 0.2 ***** 0.0 ----- Multilevel GAATG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----- chr1:13372159-13372454 + 95 8.29e-04 tgaggcagga gaatg g chr1:1280182-1280482 + 92 8.29e-04 tgaggcagga gaatg gcgt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:13372159-13372454 0.00083 94_[+7]_1 chr1:1280182-1280482 0.00083 91_[+7]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAATG width=5 seqs=2 chr1:13372159-13372454 ( 95) GAATG 1 chr1:1280182-1280482 ( 92) GAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 5 n= 753 bayes= 8.55267 E= 3.8e+004 -765 -765 183 -765 218 -765 -765 -765 218 -765 -765 -765 -765 -765 -765 218 -765 -765 183 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 5 nsites= 2 E= 3.8e+004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATG MEME-7 regular expression -------------------------------------------------------------------------------- GAATG -------------------------------------------------------------------------------- Time 1.56 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGAA MEME-8 width = 5 sites = 2 llr = 14 E-value = 3.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGAA MEME-8 Description -------------------------------------------------------------------------------- Simplified A :::aa pos.-specific C ::::: probability G a:a:: matrix T :a::: bits 2.2 * ** 2.0 * ** 1.8 ***** 1.5 ***** Relative 1.3 ***** Entropy 1.1 ***** (10.2 bits) 0.9 ***** 0.7 ***** 0.4 ***** 0.2 ***** 0.0 ----- Multilevel GTGAA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAA MEME-8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----- chr1:13372159-13372454 + 3 8.29e-04 tg gtgaa accccgtctc chr1:11993454-11993761 + 95 8.29e-04 ggagaatggt gtgaa c -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAA MEME-8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:13372159-13372454 0.00083 2_[+8]_93 chr1:11993454-11993761 0.00083 94_[+8]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAA MEME-8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGAA width=5 seqs=2 chr1:13372159-13372454 ( 3) GTGAA 1 chr1:11993454-11993761 ( 95) GTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAA MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 5 n= 753 bayes= 8.55267 E= 3.8e+004 -765 -765 183 -765 -765 -765 -765 218 -765 -765 183 -765 218 -765 -765 -765 218 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAA MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 5 nsites= 2 E= 3.8e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAA MEME-8 regular expression -------------------------------------------------------------------------------- GTGAA -------------------------------------------------------------------------------- Time 1.68 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCAC MEME-9 width = 5 sites = 2 llr = 14 E-value = 3.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCAC MEME-9 Description -------------------------------------------------------------------------------- Simplified A :::a: pos.-specific C ::a:a probability G ::::: matrix T aa::: bits 2.2 ** * 2.0 ** * 1.8 ***** 1.5 ***** Relative 1.3 ***** Entropy 1.1 ***** (10.2 bits) 0.9 ***** 0.7 ***** 0.4 ***** 0.2 ***** 0.0 ----- Multilevel TTCAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAC MEME-9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----- chr1:10501316-10501600 + 89 8.29e-04 gagacggggt ttcac cgtgtta chr1:1798925-1799219 + 94 8.29e-04 gagatggggt ttcac cg -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAC MEME-9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:10501316-10501600 0.00083 88_[+9]_7 chr1:1798925-1799219 0.00083 93_[+9]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAC MEME-9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCAC width=5 seqs=2 chr1:10501316-10501600 ( 89) TTCAC 1 chr1:1798925-1799219 ( 94) TTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 5 n= 753 bayes= 8.55267 E= 3.8e+004 -765 -765 -765 218 -765 -765 -765 218 -765 183 -765 -765 218 -765 -765 -765 -765 183 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 5 nsites= 2 E= 3.8e+004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAC MEME-9 regular expression -------------------------------------------------------------------------------- TTCAC -------------------------------------------------------------------------------- Time 1.80 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGWGAT MEME-10 width = 7 sites = 2 llr = 18 E-value = 4.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 Description -------------------------------------------------------------------------------- Simplified A :a:5:a: pos.-specific C a:::::: probability G ::a:a:: matrix T :::5::a bits 2.2 * ** 2.0 * ** 1.8 *** *** 1.5 *** *** Relative 1.3 *** *** Entropy 1.1 ******* (13.3 bits) 0.9 ******* 0.7 ******* 0.4 ******* 0.2 ******* 0.0 ------- Multilevel CAGAGAT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- chr1:1470417-1470499 - 75 1.02e-04 G CAGAGAT CTCATCACTG chr1:1470417-1470499 + 65 1.02e-04 gactggagtg cagtgat gagatctctg -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:1470417-1470499 0.0001 64_[+10]_3_[-10]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGWGAT width=7 seqs=2 chr1:1470417-1470499 ( 75) CAGAGAT 1 chr1:1470417-1470499 ( 65) CAGTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 735 bayes= 8.51767 E= 4.4e+004 -765 183 -765 -765 218 -765 -765 -765 -765 -765 183 -765 119 -765 -765 119 -765 -765 183 -765 218 -765 -765 -765 -765 -765 -765 218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 2 E= 4.4e+004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGWGAT MEME-10 regular expression -------------------------------------------------------------------------------- CAG[AT]GAT -------------------------------------------------------------------------------- Time 1.89 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:1280182-1280482 5.35e-32 4_[+1(3.06e-22)]_2_[+4(8.51e-06)]_1_\ [+2(7.27e-21)]_9 chr1:1470417-1470499 8.40e-22 8_[+5(2.22e-07)]_2_[+3(2.25e-24)]_\ 18 chr1:1798925-1799219 5.07e-37 6_[-2(1.95e-20)]_1_[-4(8.51e-06)]_2_\ [-1(1.02e-24)]_7 chr1:1855419-1855723 1.49e-34 2_[+1(1.02e-23)]_2_[+4(2.18e-05)]_1_\ [+2(8.70e-21)]_2_[+4(3.88e-05)] chr1:10501316-10501600 4.58e-33 5_[-2(5.57e-22)]_8_[-1(1.35e-19)]_\ 12 chr1:11993454-11993761 6.36e-36 [+1(4.95e-24)]_2_[+4(8.51e-06)]_1_\ [+2(8.62e-20)]_13 chr1:13372159-13372454 5.60e-36 7_[+1(4.15e-24)]_2_[+4(8.51e-06)]_1_\ [+2(5.09e-20)]_6 chr1:15815344-15815404 1.65e-15 5_[-3(2.87e-20)]_1_[-5(2.22e-07)] chr1:16503462-16503509 1.00e-20 2_[+3(4.17e-24)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: surya ********************************************************************************