******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://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 ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/K562/fasta/RankLinear0.6_40/U2AF2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:176120565-176120645 1.0000 80 chr13:91137504-91137584 1.0000 80 chr13:91138495-91138575 1.0000 80 chr7:85823337-85823417 1.0000 80 chr4:97514156-97514236 1.0000 80 chr1:191724820-191724900 1.0000 80 chr1:186918478-186918558 1.0000 80 chr15:37425167-37425247 1.0000 80 chr2:166010212-166010292 1.0000 80 chr6:84246516-84246596 1.0000 80 chr4:134502607-134502687 1.0000 80 chr13:90686822-90686902 1.0000 80 chr6:100301955-100302035 1.0000 80 chr7:136891610-136891690 1.0000 80 chr13:92381360-92381440 1.0000 80 chr10:59174998-59175078 1.0000 80 chr11:122734111-12273419 1.0000 80 chr10:91750123-91750203 1.0000 80 chr7:94147905-94147985 1.0000 80 chr10:84521549-84521629 1.0000 80 chr8:130108757-130108837 1.0000 80 chr7:83612429-83612509 1.0000 80 chr7:113813345-113813425 1.0000 80 chr3:151875304-151875384 1.0000 80 chr13:63409967-63410047 1.0000 80 chr13:81416709-81416789 1.0000 80 chr7:136155831-136155911 1.0000 80 chr21:20674572-20674652 1.0000 80 chr2:183126736-183126816 1.0000 80 chr13:92239497-92239577 1.0000 80 chr2:66048201-66048281 1.0000 80 chr5:65214111-65214191 1.0000 80 chr6:11927145-11927225 1.0000 80 chr21:34044432-34044512 1.0000 80 chr1:188588128-188588208 1.0000 80 chr1:234776631-234776711 1.0000 80 chr1:217638715-217638795 1.0000 80 chr11:13468597-13468677 1.0000 80 chr6:153569218-153569298 1.0000 80 chr20:43187090-43187170 1.0000 80 chr12:11321013-11321093 1.0000 80 chr1:248070209-248070289 1.0000 80 chr5:64571279-64571359 1.0000 80 chr8:102319790-102319870 1.0000 80 chr2:157758871-157758951 1.0000 80 chr3:17748470-17748550 1.0000 80 chr5:28780283-28780363 1.0000 80 chr15:63519973-63520053 1.0000 80 chr8:72276085-72276165 1.0000 80 chr18:2993263-2993343 1.0000 80 chr13:92447457-92447537 1.0000 80 chr17:56756712-56756792 1.0000 80 chr8:83695407-83695487 1.0000 80 chr13:90550047-90550127 1.0000 80 chr13:93320020-93320100 1.0000 80 chr13:91601717-91601797 1.0000 80 chr7:143147042-143147122 1.0000 80 chr13:91179767-91179847 1.0000 80 chr13:92358753-92358833 1.0000 80 chr4:165805398-165805478 1.0000 80 chr13:91054485-91054565 1.0000 80 chr1:190645196-190645276 1.0000 80 chr3:33115882-33115962 1.0000 80 chr17:46482620-46482700 1.0000 80 chr12:39928722-39928802 1.0000 80 chr1:193860027-193860107 1.0000 80 chr3:2293417-2293497 1.0000 80 chr1:26704297-26704377 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/K562/inference_raw/MEME/RankLinear0.6_40_U2AF2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/U2AF2.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 68 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 5440 N= 68 sample: seed= 0 hsfrac= 0 searchsize= 5440 norand= no csites= 1000 Letter frequencies in dataset: A 0.349 C 0.161 G 0.141 T 0.349 Background letter frequencies (from file dataset with add-one prior applied): A 0.348 C 0.161 G 0.141 T 0.349 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RAGAAARA MEME-1 width = 8 sites = 21 llr = 162 E-value = 5.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 69:9985a pos.-specific C :::1:::: probability G 41a:125: matrix T :::::::: bits 2.8 * 2.5 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 * * (11.1 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel AAGAAAGA consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:64571279-64571359 14 1.43e-05 aagaaagaaa gagaaaga aagGGATCAT chr3:151875304-151875384 17 1.43e-05 ggaggaaaga gagaaaga gaaaaTGTTG chr1:186918478-186918558 14 1.43e-05 aagaaagaaa gagaaaga aagaaaagaa chr12:39928722-39928802 18 5.54e-05 gaaagaaaga aagaaaga aagaaaACAA chr3:33115882-33115962 12 5.54e-05 gaaagaaaga aagaaaga atattacaca chr8:102319790-102319870 13 5.54e-05 gagaaaaaga aagaaaga aaagagaaaA chr12:11321013-11321093 31 5.54e-05 agaaaaaaga aagaaaga aagagaaaag chr17:56756712-56756792 52 9.65e-05 AGCGTGTGTG GAGAAAAA AATGACCATT chr13:63409967-63410047 17 1.17e-04 AATCAACGTT AAGAAGGA GCAACCAGTA chr11:122734111-12273419 1 1.17e-04 . GAGCAAGA CTATTAGCCT chr20:43187090-43187170 22 1.26e-04 ATAATTGTAA GAGAGAGA AAATCATCTT chr13:91601717-91601797 64 2.44e-04 aaatcgaaat aagaaaaa gtttaaaag chr13:93320020-93320100 26 2.44e-04 TTCATGTGTT GAGCAGGA TATAGCTCAA chr21:34044432-34044512 62 2.44e-04 ATAACTAAAA AAGAAAAA TTTTATCTCA chr2:183126736-183126816 3 2.77e-04 AA GGGAAAAA CATCAGATAT chr7:83612429-83612509 29 2.77e-04 TAAATTCTTT GGGAAAAA TAGATTAAGT chr13:92381360-92381440 42 3.51e-04 AAAGTTGAAT AAGAAGAA GTTTTCATAA chr15:37425167-37425247 14 3.51e-04 AAAGTATTTT AAGAAGAA TTAATCTAAT chr10:91750123-91750203 12 4.25e-04 actcaaataa aggaaaaa tattttatgt chr2:66048201-66048281 4 4.79e-04 aac aagcaaaa aaaataaata chr7:94147905-94147985 20 5.49e-04 AAAGAAGACA AAGAGAAA ATATCACCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:64571279-64571359 1.4e-05 13_[+1]_59 chr3:151875304-151875384 1.4e-05 16_[+1]_56 chr1:186918478-186918558 1.4e-05 13_[+1]_59 chr12:39928722-39928802 5.5e-05 17_[+1]_55 chr3:33115882-33115962 5.5e-05 11_[+1]_61 chr8:102319790-102319870 5.5e-05 12_[+1]_60 chr12:11321013-11321093 5.5e-05 30_[+1]_42 chr17:56756712-56756792 9.7e-05 51_[+1]_21 chr13:63409967-63410047 0.00012 16_[+1]_56 chr11:122734111-12273419 0.00012 [+1]_72 chr20:43187090-43187170 0.00013 21_[+1]_51 chr13:91601717-91601797 0.00024 63_[+1]_9 chr13:93320020-93320100 0.00024 25_[+1]_47 chr21:34044432-34044512 0.00024 61_[+1]_11 chr2:183126736-183126816 0.00028 2_[+1]_70 chr7:83612429-83612509 0.00028 28_[+1]_44 chr13:92381360-92381440 0.00035 41_[+1]_31 chr15:37425167-37425247 0.00035 13_[+1]_59 chr10:91750123-91750203 0.00043 11_[+1]_61 chr2:66048201-66048281 0.00048 3_[+1]_69 chr7:94147905-94147985 0.00055 19_[+1]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAGAAARA width=8 seqs=21 chr5:64571279-64571359 ( 14) GAGAAAGA 1 chr3:151875304-151875384 ( 17) GAGAAAGA 1 chr1:186918478-186918558 ( 14) GAGAAAGA 1 chr12:39928722-39928802 ( 18) AAGAAAGA 1 chr3:33115882-33115962 ( 12) AAGAAAGA 1 chr8:102319790-102319870 ( 13) AAGAAAGA 1 chr12:11321013-11321093 ( 31) AAGAAAGA 1 chr17:56756712-56756792 ( 52) GAGAAAAA 1 chr13:63409967-63410047 ( 17) AAGAAGGA 1 chr11:122734111-12273419 ( 1) GAGCAAGA 1 chr20:43187090-43187170 ( 22) GAGAGAGA 1 chr13:91601717-91601797 ( 64) AAGAAAAA 1 chr13:93320020-93320100 ( 26) GAGCAGGA 1 chr21:34044432-34044512 ( 62) AAGAAAAA 1 chr2:183126736-183126816 ( 3) GGGAAAAA 1 chr7:83612429-83612509 ( 29) GGGAAAAA 1 chr13:92381360-92381440 ( 42) AAGAAGAA 1 chr15:37425167-37425247 ( 14) AAGAAGAA 1 chr10:91750123-91750203 ( 12) AGGAAAAA 1 chr2:66048201-66048281 ( 4) AAGCAAAA 1 chr7:94147905-94147985 ( 20) AAGAGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 9.38761 E= 5.0e+001 71 -1104 160 -1104 130 -1104 2 -1104 -1104 -1104 282 -1104 130 -17 -1104 -1104 138 -1104 -57 -1104 122 -1104 43 -1104 45 -1104 189 -1104 152 -1104 -1104 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 5.0e+001 0.571429 0.000000 0.428571 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.904762 0.000000 0.095238 0.000000 0.809524 0.000000 0.190476 0.000000 0.476190 0.000000 0.523810 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGAAARA MEME-1 regular expression -------------------------------------------------------------------------------- [AG]AGAAA[GA]A -------------------------------------------------------------------------------- Time 1.27 secs. ******************************************************************************** ******************************************************************************** MOTIF GARGGGTG MEME-2 width = 8 sites = 2 llr = 25 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a5::::: pos.-specific C :::::::: probability G a:5aaa:a matrix T ::::::a: bits 2.8 * *** * 2.5 * *** * 2.3 * *** * 2.0 * *** * Relative 1.7 * *** * Entropy 1.4 ** ***** (18.3 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GAAGGGTG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:56756712-56756792 24 9.54e-07 CACCAACCAC GAGGGGTG TGAGACCAAA chr1:248070209-248070289 51 3.31e-06 ttgataacca gaagggtg tgctGAAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:56756712-56756792 9.5e-07 23_[+2]_49 chr1:248070209-248070289 3.3e-06 50_[+2]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GARGGGTG width=8 seqs=2 chr17:56756712-56756792 ( 24) GAGGGGTG 1 chr1:248070209-248070289 ( 51) GAAGGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 11.2767 E= 1.8e+003 -765 -765 282 -765 152 -765 -765 -765 52 -765 182 -765 -765 -765 282 -765 -765 -765 282 -765 -765 -765 282 -765 -765 -765 -765 151 -765 -765 282 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.8e+003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARGGGTG MEME-2 regular expression -------------------------------------------------------------------------------- GA[AG]GGGTG -------------------------------------------------------------------------------- Time 1.99 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCYCWGC MEME-3 width = 8 sites = 2 llr = 25 E-value = 6.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::5:: pos.-specific C :aa5a::a probability G a:::::a: matrix T :::5:5:: bits 2.8 * * 2.5 *** * ** 2.3 *** * ** 2.0 *** * ** Relative 1.7 *** * ** Entropy 1.4 *** * ** (17.8 bits) 1.1 ***** ** 0.8 ***** ** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCCCCAGC consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:234776631-234776711 20 1.50e-06 taactcaacc gcccctgc tttcttaaag chr8:102319790-102319870 41 4.75e-06 Agatcctcca gcctcagc ctcccaagta -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:234776631-234776711 1.5e-06 19_[+3]_53 chr8:102319790-102319870 4.7e-06 40_[+3]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCYCWGC width=8 seqs=2 chr1:234776631-234776711 ( 20) GCCCCTGC 1 chr8:102319790-102319870 ( 41) GCCTCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 10.4282 E= 6.7e+003 -765 -765 282 -765 -765 263 -765 -765 -765 263 -765 -765 -765 163 -765 52 -765 263 -765 -765 52 -765 -765 52 -765 -765 282 -765 -765 263 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.7e+003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCYCWGC MEME-3 regular expression -------------------------------------------------------------------------------- GCC[CT]C[AT]GC -------------------------------------------------------------------------------- Time 2.72 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCTGTGT MEME-4 width = 8 sites = 4 llr = 42 E-value = 8.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::3:: pos.-specific C 3a8::::3 probability G 8:3:a:a: matrix T :::a:8:8 bits 2.8 * * 2.5 * * * 2.3 * * * 2.0 *** * * Relative 1.7 *** * * Entropy 1.4 ***** * (15.3 bits) 1.1 ***** * 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCCTGTGT consensus C G A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:217638715-217638795 71 3.09e-06 gagatggtct gcctgtgt cc chr17:56756712-56756792 43 7.22e-06 GAGACCAAAA GCGTGTGT GGAGAAAAAA chr4:134502607-134502687 60 1.03e-05 CAATTTAATT GCCTGAGT TTTCCtcttt chr2:66048201-66048281 48 1.81e-05 aatacagcat ccctgtgc taaccaccat -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:217638715-217638795 3.1e-06 70_[+4]_2 chr17:56756712-56756792 7.2e-06 42_[+4]_30 chr4:134502607-134502687 1e-05 59_[+4]_13 chr2:66048201-66048281 1.8e-05 47_[+4]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCTGTGT width=8 seqs=4 chr1:217638715-217638795 ( 71) GCCTGTGT 1 chr17:56756712-56756792 ( 43) GCGTGTGT 1 chr4:134502607-134502687 ( 60) GCCTGAGT 1 chr2:66048201-66048281 ( 48) CCCTGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 10.2761 E= 8.8e+003 -865 63 241 -865 -865 263 -865 -865 -865 221 82 -865 -865 -865 -865 152 -865 -865 282 -865 -48 -865 -865 110 -865 -865 282 -865 -865 63 -865 110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 8.8e+003 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTGTGT MEME-4 regular expression -------------------------------------------------------------------------------- [GC]C[CG]TG[TA]G[TC] -------------------------------------------------------------------------------- Time 3.48 secs. ******************************************************************************** ******************************************************************************** MOTIF ARGGCTGS MEME-5 width = 8 sites = 2 llr = 24 E-value = 9.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 Description -------------------------------------------------------------------------------- Simplified A a5:::::: pos.-specific C ::::a::5 probability G :5aa::a5 matrix T :::::a:: bits 2.8 ** * 2.5 *** * 2.3 *** * 2.0 *** * Relative 1.7 *** ** Entropy 1.4 * ****** (17.0 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel AAGGCTGC consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:248070209-248070289 22 1.09e-06 aacccaggaa agggctgg aatctgataa chr15:63519973-63520053 16 8.09e-06 ATTGTTCACC AAGGCTGC TTTTGCCCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:248070209-248070289 1.1e-06 21_[+5]_51 chr15:63519973-63520053 8.1e-06 15_[+5]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ARGGCTGS width=8 seqs=2 chr1:248070209-248070289 ( 22) AGGGCTGG 1 chr15:63519973-63520053 ( 16) AAGGCTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 11.2767 E= 9.1e+003 152 -765 -765 -765 52 -765 182 -765 -765 -765 282 -765 -765 -765 282 -765 -765 263 -765 -765 -765 -765 -765 151 -765 -765 282 -765 -765 163 182 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 9.1e+003 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGCTGS MEME-5 regular expression -------------------------------------------------------------------------------- A[AG]GGCTG[CG] -------------------------------------------------------------------------------- Time 4.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:176120565-176120645 5.68e-01 80 chr13:91137504-91137584 7.09e-01 80 chr13:91138495-91138575 6.97e-01 80 chr7:85823337-85823417 8.43e-01 80 chr4:97514156-97514236 7.87e-01 80 chr1:191724820-191724900 1.85e-01 80 chr1:186918478-186918558 7.56e-02 3_[+1(5.54e-05)]_2_[+1(1.43e-05)]_5_\ [+1(5.54e-05)]_[+1(5.54e-05)]_9_[+1(5.54e-05)]_3_[+1(5.54e-05)]_10 chr15:37425167-37425247 5.90e-01 80 chr2:166010212-166010292 1.06e-01 80 chr6:84246516-84246596 9.99e-01 80 chr4:134502607-134502687 3.28e-02 59_[+4(1.03e-05)]_13 chr13:90686822-90686902 7.90e-01 80 chr6:100301955-100302035 2.83e-02 80 chr7:136891610-136891690 1.00e+00 80 chr13:92381360-92381440 2.96e-01 80 chr10:59174998-59175078 6.52e-01 80 chr11:122734111-12273419 9.75e-03 80 chr10:91750123-91750203 5.43e-01 80 chr7:94147905-94147985 3.47e-01 80 chr10:84521549-84521629 9.64e-01 80 chr8:130108757-130108837 5.03e-01 80 chr7:83612429-83612509 1.28e-01 80 chr7:113813345-113813425 1.26e-01 80 chr3:151875304-151875384 1.50e-03 1_[+1(2.01e-05)]_7_[+1(1.43e-05)]_\ 56 chr13:63409967-63410047 3.13e-02 80 chr13:81416709-81416789 1.09e-01 80 chr7:136155831-136155911 9.75e-01 80 chr21:20674572-20674652 3.82e-01 80 chr2:183126736-183126816 3.99e-01 80 chr13:92239497-92239577 9.10e-01 80 chr2:66048201-66048281 6.85e-04 47_[+4(1.81e-05)]_25 chr5:65214111-65214191 5.91e-01 80 chr6:11927145-11927225 1.44e-01 80 chr21:34044432-34044512 1.65e-02 80 chr1:188588128-188588208 9.05e-01 80 chr1:234776631-234776711 7.97e-05 19_[+3(1.50e-06)]_53 chr1:217638715-217638795 1.10e-03 70_[+4(3.09e-06)]_2 chr11:13468597-13468677 9.29e-01 80 chr6:153569218-153569298 9.82e-01 80 chr20:43187090-43187170 1.72e-01 80 chr12:11321013-11321093 7.71e-03 26_[+1(5.54e-05)]_[+1(5.54e-05)]_38 chr1:248070209-248070289 9.86e-07 21_[+5(1.09e-06)]_21_[+2(3.31e-06)]_\ 22 chr5:64571279-64571359 4.98e-02 3_[+1(5.54e-05)]_2_[+1(1.43e-05)]_\ 59 chr8:102319790-102319870 6.13e-05 8_[+1(5.54e-05)]_7_[+1(9.65e-05)]_9_\ [+3(4.75e-06)]_32 chr2:157758871-157758951 6.31e-01 80 chr3:17748470-17748550 9.66e-01 80 chr5:28780283-28780363 1.00e+00 80 chr15:63519973-63520053 3.87e-05 15_[+5(8.09e-06)]_57 chr8:72276085-72276165 6.26e-01 80 chr18:2993263-2993343 9.97e-01 80 chr13:92447457-92447537 9.94e-01 80 chr17:56756712-56756792 1.24e-07 23_[+2(9.54e-07)]_11_[+4(7.22e-06)]_\ 1_[+1(9.65e-05)]_21 chr8:83695407-83695487 2.94e-01 80 chr13:90550047-90550127 2.79e-03 38_[+5(3.63e-05)]_34 chr13:93320020-93320100 4.09e-02 80 chr13:91601717-91601797 1.12e-01 80 chr7:143147042-143147122 9.45e-01 80 chr13:91179767-91179847 3.04e-01 80 chr13:92358753-92358833 9.61e-01 80 chr4:165805398-165805478 2.68e-01 80 chr13:91054485-91054565 3.18e-01 80 chr1:190645196-190645276 2.11e-01 80 chr3:33115882-33115962 1.53e-01 3_[+1(5.54e-05)]_[+1(5.54e-05)]_61 chr17:46482620-46482700 3.43e-01 80 chr12:39928722-39928802 1.78e-02 1_[+1(5.54e-05)]_[+1(5.54e-05)]_\ [+1(5.54e-05)]_55 chr1:193860027-193860107 8.56e-01 80 chr3:2293417-2293497 3.12e-01 80 chr1:26704297-26704377 1.19e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n08.farnam.hpc.yale.internal ********************************************************************************