******************************************************************************** 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/BRF1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2:27273572-27273652 1.0000 80 chr17:37310059-37310139 1.0000 80 chr1:161493709-161493789 1.0000 80 chr16:14379703-14379783 1.0000 80 chr5:180615923-180616003 1.0000 80 chr2:27273994-27274074 1.0000 80 chr2:131094770-131094850 1.0000 80 chr1:149684150-149684230 1.0000 80 chr16:22207095-22207175 1.0000 80 chr5:180633793-180633873 1.0000 80 chr14:102783356-10278343 1.0000 80 chr1:249167984-249168064 1.0000 80 chr5:180615483-180615563 1.0000 80 chr17:8042827-8042907 1.0000 80 chr12:125412459-12541253 1.0000 80 chr6:26286685-26286765 1.0000 80 chr1:94313077-94313157 1.0000 80 chr7:149388341-149388421 1.0000 80 chr6:27515579-27515659 1.0000 80 chr6:26569019-26569099 1.0000 80 chr8:67025523-67025603 1.0000 80 chr6:27559664-27559744 1.0000 80 chr6:26521373-26521453 1.0000 80 chr17:73029920-73030000 1.0000 80 chr17:36908108-36908188 1.0000 80 chr16:3200618-3200698 1.0000 80 chr1:145399301-145399381 1.0000 80 chr15:66161451-66161531 1.0000 80 chr19:4724738-4724818 1.0000 80 chr2:157257216-157257296 1.0000 80 chr6:28697049-28697129 1.0000 80 chr10:69524196-69524276 1.0000 80 chr8:124169539-124169619 1.0000 80 chr16:22309922-22310002 1.0000 80 chr17:8126211-8126291 1.0000 80 chr1:204476230-204476310 1.0000 80 chr1:222638277-222638357 1.0000 80 chr16:57334454-57334534 1.0000 80 chr1:149298638-149298718 1.0000 80 chr12:98897963-98898043 1.0000 80 chr1:145396959-145397039 1.0000 80 chr11:75946932-75947012 1.0000 80 chr16:686800-686880 1.0000 80 chr19:1383469-1383549 1.0000 80 chr14:23398830-23398910 1.0000 80 chr19:39902895-39902975 1.0000 80 chr6:28908769-28908849 1.0000 80 chr7:149344125-149344205 1.0000 80 chr17:47269805-47269885 1.0000 80 chr5:180649473-180649553 1.0000 80 chr11:75946468-75946548 1.0000 80 chr7:128423422-128423502 1.0000 80 chr15:45493264-45493344 1.0000 80 chr5:140098478-140098558 1.0000 80 chr5:180645341-180645421 1.0000 80 chr6:28775672-28775752 1.0000 80 chr2:70476164-70476244 1.0000 80 chr17:8028989-8029069 1.0000 80 chr6:28710774-28710854 1.0000 80 chr17:8089603-8089683 1.0000 80 chr6:28911484-28911564 1.0000 80 chr1:161591389-161591469 1.0000 80 chr1:167683882-167683962 1.0000 80 chr6:27573513-27573593 1.0000 80 chr7:139025366-139025446 1.0000 80 chr6:28864094-28864174 1.0000 80 chr8:96281964-96282044 1.0000 80 chr1:161391952-161392032 1.0000 80 chr6:28763796-28763876 1.0000 80 chr6:27513397-27513477 1.0000 80 chr7:149404712-149404792 1.0000 80 chr3:45730557-45730637 1.0000 80 chr17:66016082-66016162 1.0000 80 chr1:145395589-145395669 1.0000 80 chr6:26328296-26328376 1.0000 80 chr6:28616054-28616134 1.0000 80 chr16:3232696-3232776 1.0000 80 chr6:27618754-27618834 1.0000 80 chr6:28831528-28831608 1.0000 80 chr6:27261642-27261722 1.0000 80 chr17:37310801-37310881 1.0000 80 chr12:125424267-12542434 1.0000 80 chr13:41634889-41634969 1.0000 80 chr6:28715468-28715548 1.0000 80 chr6:28678296-28678376 1.0000 80 chr6:28849101-28849181 1.0000 80 chr17:37025619-37025699 1.0000 80 chr17:8022328-8022408 1.0000 80 chr1:16872488-16872568 1.0000 80 chr17:8129597-8129677 1.0000 80 chr6:28912288-28912368 1.0000 80 chr11:59327853-59327933 1.0000 80 chr6:27473681-27473761 1.0000 80 chr2:43037609-43037689 1.0000 80 chr12:98897206-98897286 1.0000 80 chr17:45213584-45213664 1.0000 80 chr6:27688955-27689035 1.0000 80 chr17:80452666-80452746 1.0000 80 chr14:21131432-21131512 1.0000 80 chr5:180649045-180649125 1.0000 80 chr13:31248163-31248243 1.0000 80 chr16:22308379-22308459 1.0000 80 chr6:27263140-27263220 1.0000 80 chr6:144537599-144537679 1.0000 80 chr5:180618745-180618825 1.0000 80 chr11:68227644-68227724 1.0000 80 chr17:8042266-8042346 1.0000 80 chr21:18827174-18827254 1.0000 80 chr17:8124254-8124334 1.0000 80 chr17:8023010-8023090 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_BRF1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/BRF1.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= 110 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= 8800 N= 110 sample: seed= 0 hsfrac= 0 searchsize= 8800 norand= no csites= 1000 Letter frequencies in dataset: A 0.238 C 0.262 G 0.265 T 0.235 Background letter frequencies (from file dataset with add-one prior applied): A 0.238 C 0.262 G 0.265 T 0.235 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TAGCTCAG MEME-1 width = 8 sites = 9 llr = 93 E-value = 2.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a:2::a: pos.-specific C :::7:a:: probability G ::a::::a matrix T a::1a::: bits 2.1 ** * * 1.9 *** **** 1.7 *** **** 1.5 *** **** Relative 1.3 *** **** Entropy 1.0 *** **** (14.8 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TAGCTCAG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:28715468-28715548 60 1.51e-05 AGGgcctgga tagctcag ttggtagaac chr6:27261642-27261722 36 1.51e-05 GTCggccggt tagctcag ttggttagag chr7:149404712-149404792 55 1.51e-05 TCAgggggta tagctcag gggtagagca chr5:140098478-140098558 42 1.51e-05 GGGCTGGCTT TAGCTCAG CGGTTACTTC chr6:28697049-28697129 50 1.51e-05 TCAgggggtg tagctcag tggtagagcg chr2:157257216-157257296 72 1.51e-05 CTGggggatg tagctcag t chr1:149298638-149298718 32 2.88e-05 ATGAAAATCT TAGATCAG CCGTTTCTAT chr1:149684150-149684230 54 2.88e-05 ATGAAAATCT TAGATCAG CCGTTTCTAT chr6:27263140-27263220 59 4.23e-05 TAGGAAATGC TAGTTCAG CTTCAggttc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:28715468-28715548 1.5e-05 59_[+1]_13 chr6:27261642-27261722 1.5e-05 35_[+1]_37 chr7:149404712-149404792 1.5e-05 54_[+1]_18 chr5:140098478-140098558 1.5e-05 41_[+1]_31 chr6:28697049-28697129 1.5e-05 49_[+1]_23 chr2:157257216-157257296 1.5e-05 71_[+1]_1 chr1:149298638-149298718 2.9e-05 31_[+1]_41 chr1:149684150-149684230 2.9e-05 53_[+1]_19 chr6:27263140-27263220 4.2e-05 58_[+1]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TAGCTCAG width=8 seqs=9 chr6:28715468-28715548 ( 60) TAGCTCAG 1 chr6:27261642-27261722 ( 36) TAGCTCAG 1 chr7:149404712-149404792 ( 55) TAGCTCAG 1 chr5:140098478-140098558 ( 42) TAGCTCAG 1 chr6:28697049-28697129 ( 50) TAGCTCAG 1 chr2:157257216-157257296 ( 72) TAGCTCAG 1 chr1:149298638-149298718 ( 32) TAGATCAG 1 chr1:149684150-149684230 ( 54) TAGATCAG 1 chr6:27263140-27263220 ( 59) TAGTTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8030 bayes= 9.93409 E= 2.7e+001 -982 -982 -982 209 207 -982 -982 -982 -982 -982 192 -982 -10 135 -982 -108 -982 -982 -982 209 -982 193 -982 -982 207 -982 -982 -982 -982 -982 192 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 2.7e+001 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.222222 0.666667 0.000000 0.111111 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 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCTCAG MEME-1 regular expression -------------------------------------------------------------------------------- TAG[CA]TCAG -------------------------------------------------------------------------------- Time 1.68 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAATAKA MEME-2 width = 8 sites = 11 llr = 105 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 Description -------------------------------------------------------------------------------- Simplified A aaaa:a:7 pos.-specific C ::::1:2: probability G ::::::3: matrix T ::::9:53 bits 2.1 **** * 1.9 **** * 1.7 ****** 1.5 ****** Relative 1.3 ****** * Entropy 1.0 ****** * (13.8 bits) 0.8 ****** * 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAATATA consensus GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:28678296-28678376 43 1.00e-05 AGCCAGTTAT AAAATATA GCAAAAAAGC chr5:140098478-140098558 7 1.00e-05 GTCAAG AAAATATA ATCCGGAGAT chr1:149684150-149684230 33 1.00e-05 CCTGCACGGC AAAATATA ACCATGAAAA chr17:8023010-8023090 10 2.14e-05 AAGACACGC AAAATAGA ATGTCCAGTA chr6:28864094-28864174 42 2.14e-05 TTTTTGCACT AAAATAGA GATCAACAAG chr17:8022328-8022408 41 3.13e-05 AATCTGTGCC AAAATATT CTATGCTGCA chr6:28831528-28831608 24 3.13e-05 AACGTGGGCC AAAATATT TCTATGACCT chr12:98897206-98897286 55 4.25e-05 GCTGTCTGAG AAAATACA CAGCCTAACG chr6:28775672-28775752 43 4.25e-05 TCATTTCTTC AAAATACA GAAACTGCCA chr7:139025366-139025446 39 5.36e-05 ACCAAAGAGG AAAATAGT TGAATATGTT chr1:149298638-149298718 11 7.59e-05 CCTGCGCGGC AAAACATA ACCATGAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:28678296-28678376 1e-05 42_[+2]_30 chr5:140098478-140098558 1e-05 6_[+2]_66 chr1:149684150-149684230 1e-05 32_[+2]_40 chr17:8023010-8023090 2.1e-05 9_[+2]_63 chr6:28864094-28864174 2.1e-05 41_[+2]_31 chr17:8022328-8022408 3.1e-05 40_[+2]_32 chr6:28831528-28831608 3.1e-05 23_[+2]_49 chr12:98897206-98897286 4.2e-05 54_[+2]_18 chr6:28775672-28775752 4.2e-05 42_[+2]_30 chr7:139025366-139025446 5.4e-05 38_[+2]_34 chr1:149298638-149298718 7.6e-05 10_[+2]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAATAKA width=8 seqs=11 chr6:28678296-28678376 ( 43) AAAATATA 1 chr5:140098478-140098558 ( 7) AAAATATA 1 chr1:149684150-149684230 ( 33) AAAATATA 1 chr17:8023010-8023090 ( 10) AAAATAGA 1 chr6:28864094-28864174 ( 42) AAAATAGA 1 chr17:8022328-8022408 ( 41) AAAATATT 1 chr6:28831528-28831608 ( 24) AAAATATT 1 chr12:98897206-98897286 ( 55) AAAATACA 1 chr6:28775672-28775752 ( 43) AAAATACA 1 chr7:139025366-139025446 ( 39) AAAATAGT 1 chr1:149298638-149298718 ( 11) AAAACATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8030 bayes= 10.5373 E= 1.3e+002 207 -1010 -1010 -1010 207 -1010 -1010 -1010 207 -1010 -1010 -1010 207 -1010 -1010 -1010 -1010 -153 -1010 195 207 -1010 -1010 -1010 -1010 -53 4 121 161 -1010 -1010 21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 1.3e+002 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 0.090909 0.000000 0.909091 1.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.272727 0.545455 0.727273 0.000000 0.000000 0.272727 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATAKA MEME-2 regular expression -------------------------------------------------------------------------------- AAAATA[TG][AT] -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** MOTIF WCTWTTAT MEME-3 width = 8 sites = 7 llr = 71 E-value = 7.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 4::4::a: pos.-specific C :a:::::: probability G :::::::: matrix T 6:a6aa:a bits 2.1 * **** 1.9 ** **** 1.7 ** **** 1.5 ** **** Relative 1.3 ** **** Entropy 1.0 ******** (14.6 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCTTTTAT consensus A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:28616054-28616134 25 1.05e-05 TTCTGTGGCT TCTTTTAT GACCGAATTG chr12:125412459-12541253 23 1.05e-05 ACTGCGATGC TCTTTTAT CCTCCTGGTC chr5:180645341-180645421 25 3.18e-05 TTACTCTATG ACTTTTAT AAGTGTTATA chr1:145396959-145397039 65 3.18e-05 ATTTCGTGCT ACTTTTAT TTGGCCAG chr1:149298638-149298718 45 3.18e-05 ATCAGCCGTT TCTATTAT AGTTTCCAAA chr1:149684150-149684230 67 3.18e-05 ATCAGCCGTT TCTATTAT AGTTTC chr6:28831528-28831608 45 4.25e-05 ATGACCTGTT ACTATTAT CGGTCGTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:28616054-28616134 1.1e-05 24_[+3]_48 chr12:125412459-12541253 1.1e-05 22_[+3]_50 chr5:180645341-180645421 3.2e-05 24_[+3]_48 chr1:145396959-145397039 3.2e-05 64_[+3]_8 chr1:149298638-149298718 3.2e-05 44_[+3]_28 chr1:149684150-149684230 3.2e-05 66_[+3]_6 chr6:28831528-28831608 4.3e-05 44_[+3]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WCTWTTAT width=8 seqs=7 chr6:28616054-28616134 ( 25) TCTTTTAT 1 chr12:125412459-12541253 ( 23) TCTTTTAT 1 chr5:180645341-180645421 ( 25) ACTTTTAT 1 chr1:145396959-145397039 ( 65) ACTTTTAT 1 chr1:149298638-149298718 ( 45) TCTATTAT 1 chr1:149684150-149684230 ( 67) TCTATTAT 1 chr6:28831528-28831608 ( 45) ACTATTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8030 bayes= 10.0063 E= 7.6e+003 85 -945 -945 128 -945 193 -945 -945 -945 -945 -945 209 85 -945 -945 128 -945 -945 -945 209 -945 -945 -945 209 207 -945 -945 -945 -945 -945 -945 209 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 7.6e+003 0.428571 0.000000 0.000000 0.571429 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCTWTTAT MEME-3 regular expression -------------------------------------------------------------------------------- [TA]CT[TA]TTAT -------------------------------------------------------------------------------- Time 4.04 secs. ******************************************************************************** ******************************************************************************** MOTIF AACCATTA MEME-4 width = 8 sites = 8 llr = 78 E-value = 8.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 9a::a::a pos.-specific C ::8a:3:: probability G ::3::::: matrix T 1::::8a: bits 2.1 * * ** 1.9 * ** ** 1.7 * ** ** 1.5 ** ** ** Relative 1.3 ** ***** Entropy 1.0 ******** (14.1 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AACCATTA consensus G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:27513397-27513477 27 1.22e-05 CGCTCCACTC AACCATTA TAAGTTCACC chr15:66161451-66161531 1 1.22e-05 . aaccatta caccatggaa chr6:27515579-27515659 4 1.22e-05 gct aaccatta caccatggaa chr16:22308379-22308459 42 2.45e-05 GCAAAAGCAA AAGCATTA AGTAGCTTTC chr2:27273572-27273652 37 2.45e-05 AGGTTGCGGT AAGCATTA GAGGGCTATC chr6:27618754-27618834 6 3.80e-05 gtgat aaccacta cactacggaa chr7:149344125-149344205 14 3.80e-05 TGTCTCTACT AACCACTA TAAACCTGTA chr11:59327853-59327933 67 5.00e-05 AAGACTCTGT TACCATTA TGCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:27513397-27513477 1.2e-05 26_[+4]_46 chr15:66161451-66161531 1.2e-05 [+4]_72 chr6:27515579-27515659 1.2e-05 3_[+4]_69 chr16:22308379-22308459 2.4e-05 41_[+4]_31 chr2:27273572-27273652 2.4e-05 36_[+4]_36 chr6:27618754-27618834 3.8e-05 5_[+4]_67 chr7:149344125-149344205 3.8e-05 13_[+4]_59 chr11:59327853-59327933 5e-05 66_[+4]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AACCATTA width=8 seqs=8 chr6:27513397-27513477 ( 27) AACCATTA 1 chr15:66161451-66161531 ( 1) AACCATTA 1 chr6:27515579-27515659 ( 4) AACCATTA 1 chr16:22308379-22308459 ( 42) AAGCATTA 1 chr2:27273572-27273652 ( 37) AAGCATTA 1 chr6:27618754-27618834 ( 6) AACCACTA 1 chr7:149344125-149344205 ( 14) AACCACTA 1 chr11:59327853-59327933 ( 67) TACCATTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8030 bayes= 9.96975 E= 8.7e+003 188 -965 -965 -91 207 -965 -965 -965 -965 152 -8 -965 -965 193 -965 -965 207 -965 -965 -965 -965 -7 -965 167 -965 -965 -965 209 207 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 8.7e+003 0.875000 0.000000 0.000000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACCATTA MEME-4 regular expression -------------------------------------------------------------------------------- AA[CG]CA[TC]TA -------------------------------------------------------------------------------- Time 5.35 secs. ******************************************************************************** ******************************************************************************** MOTIF ATTTTTTY MEME-5 width = 8 sites = 3 llr = 33 E-value = 1.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::::::: pos.-specific C :::::::3 probability G :::::::: matrix T :aaaaaa7 bits 2.1 ******* 1.9 ******* 1.7 ******* 1.5 ******* Relative 1.3 ******* Entropy 1.0 ******** (15.7 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ATTTTTTT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:27688955-27689035 51 9.42e-06 CAAGGCAATC ATTTTTTT ATAACAACAA chr17:45213584-45213664 47 9.42e-06 AGCTAGCACT ATTTTTTT GGCCATCTTT chr1:161591389-161591469 29 1.99e-05 AGTGCTGAGC ATTTTTTC TTCAGTGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:27688955-27689035 9.4e-06 50_[+5]_22 chr17:45213584-45213664 9.4e-06 46_[+5]_26 chr1:161591389-161591469 2e-05 28_[+5]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATTTTTTY width=8 seqs=3 chr6:27688955-27689035 ( 51) ATTTTTTT 1 chr17:45213584-45213664 ( 47) ATTTTTTT 1 chr1:161591389-161591469 ( 29) ATTTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8030 bayes= 11.8333 E= 1.6e+004 207 -823 -823 -823 -823 -823 -823 209 -823 -823 -823 209 -823 -823 -823 209 -823 -823 -823 209 -823 -823 -823 209 -823 -823 -823 209 -823 35 -823 150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.6e+004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.333333 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTTY MEME-5 regular expression -------------------------------------------------------------------------------- ATTTTTT[TC] -------------------------------------------------------------------------------- Time 6.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:27273572-27273652 2.93e-02 36_[+4(2.45e-05)]_36 chr17:37310059-37310139 8.75e-01 80 chr1:161493709-161493789 2.72e-01 80 chr16:14379703-14379783 9.95e-01 80 chr5:180615923-180616003 4.04e-01 80 chr2:27273994-27274074 6.50e-01 80 chr2:131094770-131094850 9.84e-01 80 chr1:149684150-149684230 5.22e-07 32_[+2(1.00e-05)]_13_[+1(2.88e-05)]_\ 5_[+3(3.18e-05)]_6 chr16:22207095-22207175 9.86e-01 80 chr5:180633793-180633873 8.58e-01 80 chr14:102783356-10278343 9.90e-01 80 chr1:249167984-249168064 8.97e-01 80 chr5:180615483-180615563 2.00e-01 80 chr17:8042827-8042907 2.10e-01 80 chr12:125412459-12541253 2.82e-02 22_[+3(1.05e-05)]_50 chr6:26286685-26286765 6.56e-01 80 chr1:94313077-94313157 8.57e-01 80 chr7:149388341-149388421 6.53e-02 80 chr6:27515579-27515659 5.21e-03 3_[+4(1.22e-05)]_69 chr6:26569019-26569099 9.59e-01 80 chr8:67025523-67025603 6.24e-01 80 chr6:27559664-27559744 1.96e-01 80 chr6:26521373-26521453 4.09e-01 80 chr17:73029920-73030000 8.59e-01 80 chr17:36908108-36908188 1.00e+00 80 chr16:3200618-3200698 1.70e-01 80 chr1:145399301-145399381 5.33e-01 80 chr15:66161451-66161531 9.39e-02 [+4(1.22e-05)]_72 chr19:4724738-4724818 3.01e-01 80 chr2:157257216-157257296 2.90e-02 71_[+1(1.51e-05)]_1 chr6:28697049-28697129 6.58e-04 49_[+1(1.51e-05)]_23 chr10:69524196-69524276 5.27e-01 80 chr8:124169539-124169619 4.65e-01 80 chr16:22309922-22310002 1.91e-01 80 chr17:8126211-8126291 8.94e-01 80 chr1:204476230-204476310 5.24e-01 80 chr1:222638277-222638357 4.14e-01 80 chr16:57334454-57334534 9.88e-01 80 chr1:149298638-149298718 2.82e-06 10_[+2(7.59e-05)]_13_[+1(2.88e-05)]_\ 5_[+3(3.18e-05)]_28 chr12:98897963-98898043 7.79e-01 80 chr1:145396959-145397039 2.97e-02 64_[+3(3.18e-05)]_8 chr11:75946932-75947012 9.64e-01 80 chr16:686800-686880 8.82e-01 80 chr19:1383469-1383549 9.24e-01 80 chr14:23398830-23398910 2.90e-01 80 chr19:39902895-39902975 9.68e-01 80 chr6:28908769-28908849 2.98e-01 80 chr7:149344125-149344205 7.25e-02 13_[+4(3.80e-05)]_59 chr17:47269805-47269885 9.99e-01 80 chr5:180649473-180649553 2.24e-01 80 chr11:75946468-75946548 4.04e-01 80 chr7:128423422-128423502 5.99e-01 80 chr15:45493264-45493344 8.32e-01 80 chr5:140098478-140098558 5.21e-04 6_[+2(1.00e-05)]_27_[+1(1.51e-05)]_\ 31 chr5:180645341-180645421 4.40e-02 24_[+3(3.18e-05)]_48 chr6:28775672-28775752 2.99e-03 42_[+2(4.25e-05)]_30 chr2:70476164-70476244 6.08e-03 9_[+4(8.93e-05)]_63 chr17:8028989-8029069 2.82e-01 80 chr6:28710774-28710854 3.65e-01 80 chr17:8089603-8089683 1.00e+00 80 chr6:28911484-28911564 8.19e-01 80 chr1:161591389-161591469 2.16e-02 [+5(4.01e-05)]_20_[+5(1.99e-05)]_44 chr1:167683882-167683962 9.61e-01 80 chr6:27573513-27573593 5.32e-01 80 chr7:139025366-139025446 1.13e-01 38_[+2(5.36e-05)]_34 chr6:28864094-28864174 2.54e-03 41_[+2(2.14e-05)]_31 chr8:96281964-96282044 3.84e-01 80 chr1:161391952-161392032 4.71e-01 80 chr6:28763796-28763876 8.18e-01 80 chr6:27513397-27513477 5.86e-03 26_[+4(1.22e-05)]_46 chr7:149404712-149404792 4.76e-02 54_[+1(1.51e-05)]_18 chr3:45730557-45730637 3.26e-01 80 chr17:66016082-66016162 9.97e-01 80 chr1:145395589-145395669 3.35e-01 80 chr6:26328296-26328376 8.51e-02 80 chr6:28616054-28616134 5.54e-03 24_[+3(1.05e-05)]_48 chr16:3232696-3232776 1.00e+00 80 chr6:27618754-27618834 1.94e-01 5_[+4(3.80e-05)]_67 chr6:28831528-28831608 8.03e-05 23_[+2(3.13e-05)]_13_[+3(4.25e-05)]_\ 28 chr6:27261642-27261722 3.76e-02 35_[+1(1.51e-05)]_37 chr17:37310801-37310881 6.41e-01 80 chr12:125424267-12542434 3.69e-01 80 chr13:41634889-41634969 5.35e-01 80 chr6:28715468-28715548 8.19e-02 59_[+1(1.51e-05)]_13 chr6:28678296-28678376 1.43e-02 42_[+2(1.00e-05)]_30 chr6:28849101-28849181 8.29e-01 80 chr17:37025619-37025699 4.79e-01 80 chr17:8022328-8022408 6.66e-02 40_[+2(3.13e-05)]_32 chr1:16872488-16872568 1.19e-01 80 chr17:8129597-8129677 3.77e-01 80 chr6:28912288-28912368 4.13e-01 80 chr11:59327853-59327933 5.71e-02 66_[+4(5.00e-05)]_6 chr6:27473681-27473761 9.47e-01 80 chr2:43037609-43037689 9.74e-01 80 chr12:98897206-98897286 1.51e-01 54_[+2(4.25e-05)]_18 chr17:45213584-45213664 4.61e-05 46_[+5(9.42e-06)]_26 chr6:27688955-27689035 7.88e-04 50_[+5(9.42e-06)]_22 chr17:80452666-80452746 9.32e-01 80 chr14:21131432-21131512 9.45e-01 80 chr5:180649045-180649125 6.25e-01 80 chr13:31248163-31248243 9.58e-01 80 chr16:22308379-22308459 2.08e-02 41_[+4(2.45e-05)]_31 chr6:27263140-27263220 1.21e-01 58_[+1(4.23e-05)]_14 chr6:144537599-144537679 9.88e-01 80 chr5:180618745-180618825 6.98e-01 80 chr11:68227644-68227724 6.22e-01 80 chr17:8042266-8042346 9.33e-01 80 chr21:18827174-18827254 8.39e-02 80 chr17:8124254-8124334 1.71e-01 80 chr17:8023010-8023090 1.30e-01 9_[+2(2.14e-05)]_63 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n09.farnam.hpc.yale.internal ********************************************************************************