******************************************************************************** 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/BDP1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr7:149344108-149344188 1.0000 80 chr17:37310070-37310150 1.0000 80 chr2:131094788-131094868 1.0000 80 chr2:157257210-157257290 1.0000 80 chr5:180615490-180615570 1.0000 80 chr5:180615931-180616011 1.0000 80 chr1:249167986-249168066 1.0000 80 chr17:19411422-19411502 1.0000 80 chr15:26327453-26327533 1.0000 80 chr2:27273999-27274079 1.0000 80 chr17:8042831-8042911 1.0000 80 chr16:22207111-22207191 1.0000 80 chr11:75946471-75946551 1.0000 80 chr12:125412468-12541254 1.0000 80 chr19:4724729-4724809 1.0000 80 chr6:27652539-27652619 1.0000 80 chr12:96429716-96429796 1.0000 80 chr1:161493713-161493793 1.0000 80 chr19:893394-893474 1.0000 80 chr1:149684164-149684244 1.0000 80 chr6:26286666-26286746 1.0000 80 chr11:75946936-75947016 1.0000 80 chr1:145396965-145397045 1.0000 80 chr1:222638275-222638355 1.0000 80 chr8:67025525-67025605 1.0000 80 chr7:149388349-149388429 1.0000 80 chr17:73029923-73030003 1.0000 80 chr6:27573534-27573614 1.0000 80 chr17:37310816-37310896 1.0000 80 chr17:8028992-8029072 1.0000 80 chr6:26569013-26569093 1.0000 80 chr1:145395602-145395682 1.0000 80 chr2:27273565-27273645 1.0000 80 chr17:8089591-8089671 1.0000 80 chr19:45981960-45982040 1.0000 80 chr17:8125631-8125711 1.0000 80 chr8:124169543-124169623 1.0000 80 chr8:67026333-67026413 1.0000 80 chr17:36908103-36908183 1.0000 80 chr14:23398820-23398900 1.0000 80 chr15:45493248-45493328 1.0000 80 chr1:204476236-204476316 1.0000 80 chr16:57334479-57334559 1.0000 80 chr7:149404671-149404751 1.0000 80 chr15:45490894-45490974 1.0000 80 chr12:125411990-12541207 1.0000 80 chr13:95201977-95202057 1.0000 80 chr17:8022374-8022454 1.0000 80 chr14:21093442-21093522 1.0000 80 chr6:27515595-27515675 1.0000 80 chr6:28806288-28806368 1.0000 80 chr1:94313062-94313142 1.0000 80 chr7:149052836-149052916 1.0000 80 chr6:28180728-28180808 1.0000 80 chr6:27763704-27763784 1.0000 80 chr12:98897202-98897282 1.0000 80 chr11:66115504-66115584 1.0000 80 chr6:27559664-27559744 1.0000 80 chr1:149298629-149298709 1.0000 80 chr9:137029697-137029777 1.0000 80 chr10:69524179-69524259 1.0000 80 chr1:145399305-145399385 1.0000 80 chr11:59327885-59327965 1.0000 80 chr16:686813-686893 1.0000 80 chr16:14379681-14379761 1.0000 80 chr6:27473689-27473769 1.0000 80 chr16:3200606-3200686 1.0000 80 chr6:27745563-27745643 1.0000 80 chr5:180614613-180614693 1.0000 80 chr17:8124262-8124342 1.0000 80 chr6:28849084-28849164 1.0000 80 chr17:37025621-37025701 1.0000 80 chr6:27263133-27263213 1.0000 80 chr6:28678293-28678373 1.0000 80 chr3:190595816-190595896 1.0000 80 chr5:180645338-180645418 1.0000 80 chr6:28715459-28715539 1.0000 80 chr6:28775677-28775757 1.0000 80 chrX:18693096-18693176 1.0000 80 chr7:139025371-139025451 1.0000 80 chr6:27471448-27471528 1.0000 80 chr7:128423421-128423501 1.0000 80 chr5:180633782-180633862 1.0000 80 chr14:21077565-21077645 1.0000 80 chr6:27447368-27447448 1.0000 80 chr6:27543776-27543856 1.0000 80 chr6:27513378-27513458 1.0000 80 chr17:8023008-8023088 1.0000 80 chr6:28864108-28864188 1.0000 80 chr19:1383469-1383549 1.0000 80 chr6:27570453-27570533 1.0000 80 chr17:8126222-8126302 1.0000 80 chr6:27261603-27261683 1.0000 80 chr1:167683877-167683957 1.0000 80 chr6:28442394-28442474 1.0000 80 chr15:45492703-45492783 1.0000 80 chr16:57333777-57333857 1.0000 80 chr6:28908758-28908838 1.0000 80 chr14:21152092-21152172 1.0000 80 chr6:26577250-26577330 1.0000 80 chr14:21149776-21149856 1.0000 80 chr17:8129630-8129710 1.0000 80 chr6:28912272-28912352 1.0000 80 chr16:3225603-3225683 1.0000 80 chr6:52860328-52860408 1.0000 80 chr12:56584074-56584154 1.0000 80 chr7:148638512-148638592 1.0000 80 chr17:8124787-8124867 1.0000 80 chr6:27721244-27721324 1.0000 80 chr6:26538196-26538276 1.0000 80 chr16:3232715-3232795 1.0000 80 chr6:26330586-26330666 1.0000 80 chr5:180649471-180649551 1.0000 80 chr6:28949882-28949962 1.0000 80 chr5:180618760-180618840 1.0000 80 chr1:161591387-161591467 1.0000 80 chr16:22308368-22308448 1.0000 80 chr6:144537612-144537692 1.0000 80 chr12:125424391-12542447 1.0000 80 chr5:156704334-156704414 1.0000 80 chr12:98897946-98898026 1.0000 80 chr16:3202820-3202900 1.0000 80 chr6:26554255-26554335 1.0000 80 chr1:167684806-167684886 1.0000 80 chr17:8024162-8024242 1.0000 80 chr6:26533219-26533299 1.0000 80 chr2:43037611-43037691 1.0000 80 chr6:28918734-28918814 1.0000 80 chr17:66016071-66016151 1.0000 80 chr1:147825615-147825695 1.0000 80 chr10:114667883-11466796 1.0000 80 chr17:73031122-73031202 1.0000 80 chr2:78182138-78182218 1.0000 80 chr19:4724006-4724086 1.0000 80 chr7:149028148-149028228 1.0000 80 chr6:27551302-27551382 1.0000 80 chr7:149292349-149292429 1.0000 80 chr17:37017995-37018075 1.0000 80 chr7:149074678-149074758 1.0000 80 chr21:18827182-18827262 1.0000 80 chr6:28831536-28831616 1.0000 80 chr3:45730567-45730647 1.0000 80 chr6:28703271-28703351 1.0000 80 chr17:8130396-8130476 1.0000 80 chr15:89878215-89878295 1.0000 80 chr5:140098434-140098514 1.0000 80 chr6:27618766-27618846 1.0000 80 chr6:27586031-27586111 1.0000 80 chr6:126101464-126101544 1.0000 80 chr1:161397940-161398020 1.0000 80 chr19:50643558-50643638 1.0000 80 chr13:41634933-41635013 1.0000 80 chr6:28616049-28616129 1.0000 80 chr6:28697025-28697105 1.0000 80 chr6:26553654-26553734 1.0000 80 chr10:12236799-12236879 1.0000 80 chr14:21151354-21151434 1.0000 80 chr19:49535020-49535100 1.0000 80 chr6:27265694-27265774 1.0000 80 chr7:149332696-149332776 1.0000 80 chr19:33667878-33667958 1.0000 80 chr6:27302827-27302907 1.0000 80 chr6:27870350-27870430 1.0000 80 chr2:70476179-70476259 1.0000 80 chr8:96281969-96282049 1.0000 80 chr1:161369568-161369648 1.0000 80 chr6:27688972-27689052 1.0000 80 chr16:3230624-3230704 1.0000 80 chr14:21131446-21131526 1.0000 80 chr6:27599114-27599194 1.0000 80 chr6:28911479-28911559 1.0000 80 chr1:153643644-153643724 1.0000 80 chr17:73030602-73030682 1.0000 80 chr15:66161467-66161547 1.0000 80 chr16:22309927-22310007 1.0000 80 chr17:80452688-80452768 1.0000 80 chr1:148000734-148000814 1.0000 80 chr16:3241927-3242007 1.0000 80 chr7:148680765-148680845 1.0000 80 chr2:47562370-47562450 1.0000 80 chr16:71460310-71460390 1.0000 80 chr16:3207491-3207571 1.0000 80 chr6:27177545-27177625 1.0000 80 chr16:87417685-87417765 1.0000 80 chr6:27446513-27446593 1.0000 80 chr11:35548241-35548321 1.0000 80 chr19:51108130-51108210 1.0000 80 chr14:102783352-10278343 1.0000 80 chr6:28763829-28763909 1.0000 80 chr12:58053921-58054001 1.0000 80 chr1:17004809-17004889 1.0000 80 chr6:27125821-27125901 1.0000 80 chr3:169489933-169490013 1.0000 80 chr6:26705529-26705609 1.0000 80 chr14:21125715-21125795 1.0000 80 chr6:26322951-26323031 1.0000 80 chr13:92975106-92975186 1.0000 80 chr13:45492139-45492219 1.0000 80 chr1:161391958-161392038 1.0000 80 chr6:26572157-26572237 1.0000 80 chr7:149361813-149361893 1.0000 80 chr6:26305770-26305850 1.0000 80 chr19:39902907-39902987 1.0000 80 chr6:27181689-27181769 1.0000 80 chr17:8042286-8042366 1.0000 80 chr13:93054904-93054984 1.0000 80 chr5:180649047-180649127 1.0000 80 chr1:161582450-161582530 1.0000 80 chr16:70823349-70823429 1.0000 80 chr6:26575734-26575814 1.0000 80 chr6:27117961-27118041 1.0000 80 chrX:47662157-47662237 1.0000 80 chr7:149243551-149243631 1.0000 80 chr6:28456828-28456908 1.0000 80 chr22:37589982-37590062 1.0000 80 chr5:180596526-180596606 1.0000 80 chr12:113552435-11355251 1.0000 80 chr17:8023703-8023783 1.0000 80 chr1:61564892-61564972 1.0000 80 chr6:28779916-28779996 1.0000 80 chr1:17188355-17188435 1.0000 80 chr14:21098683-21098763 1.0000 80 chr6:27129979-27130059 1.0000 80 chr1:149186055-149186135 1.0000 80 chr5:140105659-140105739 1.0000 80 chr13:91795434-91795514 1.0000 80 chr1:17053725-17053805 1.0000 80 chr3:131948004-131948084 1.0000 80 chr14:21081598-21081678 1.0000 80 chr6:27487230-27487310 1.0000 80 chr17:37023811-37023891 1.0000 80 chr13:90850359-90850439 1.0000 80 chr2:157257710-157257790 1.0000 80 chr1:143879880-143879960 1.0000 80 chr17:8090811-8090891 1.0000 80 chr14:32672477-32672557 1.0000 80 chr16:70813014-70813094 1.0000 80 chr5:180634669-180634749 1.0000 80 chr5:135416282-135416362 1.0000 80 chr16:3239548-3239628 1.0000 80 chr14:21078206-21078286 1.0000 80 chr6:27870762-27870842 1.0000 80 chr2:65794566-65794646 1.0000 80 chr7:149305386-149305466 1.0000 80 chr5:180600572-180600652 1.0000 80 chr17:47269804-47269884 1.0000 80 chr10:22518511-22518591 1.0000 80 chr13:90712094-90712174 1.0000 80 chr5:140090795-140090875 1.0000 80 chr14:21099365-21099445 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_BDP1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/BDP1.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= 250 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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.26 C 0.237 G 0.245 T 0.257 Background letter frequencies (from file dataset with add-one prior applied): A 0.26 C 0.237 G 0.245 T 0.257 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCGCCCCC MEME-1 width = 8 sites = 4 llr = 46 E-value = 1.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C aa:aaaaa probability G ::a::::: matrix T :::::::: bits 2.1 ******** 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.2 ******** Entropy 1.0 ******** (16.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCGCCCCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr16:3239548-3239628 31 1.03e-05 TCCGCCCCAG CCGCCCCC AGGATGCTAG chr15:66161467-66161547 51 1.03e-05 TCAGAGAACC CCGCCCCC ATCCACAAAC chr17:66016071-66016151 70 1.03e-05 CATCACGCTC CCGCCCCC GCG chr15:45492703-45492783 38 1.03e-05 GTTGAAAGCC CCGCCCCC TTGCAATGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr16:3239548-3239628 1e-05 30_[+1]_42 chr15:66161467-66161547 1e-05 50_[+1]_22 chr17:66016071-66016151 1e-05 69_[+1]_3 chr15:45492703-45492783 1e-05 37_[+1]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGCCCCC width=8 seqs=4 chr16:3239548-3239628 ( 31) CCGCCCCC 1 chr15:66161467-66161547 ( 51) CCGCCCCC 1 chr17:66016071-66016151 ( 70) CCGCCCCC 1 chr15:45492703-45492783 ( 38) CCGCCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.1553 E= 1.1e+004 -865 207 -865 -865 -865 207 -865 -865 -865 -865 203 -865 -865 207 -865 -865 -865 207 -865 -865 -865 207 -865 -865 -865 207 -865 -865 -865 207 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.1e+004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCCC MEME-1 regular expression -------------------------------------------------------------------------------- CCGCCCCC -------------------------------------------------------------------------------- Time 5.04 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGCCACA MEME-2 width = 8 sites = 6 llr = 67 E-value = 2.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:::a:a pos.-specific C :::aa:a: probability G a:a::::: matrix T :::::::: bits 2.1 * *** * 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.2 ******** Entropy 1.0 ******** (16.1 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAGCCACA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:21125715-21125795 48 1.40e-05 CAAACAGAGG GAGCCACA TCCCTGGAAT chr19:49535020-49535100 7 1.40e-05 CGGTCG GAGCCACA ATAGCTCGGG chr19:50643558-50643638 2 1.40e-05 G GAGCCACA GTGGCTCCGG chr12:98897946-98898026 67 1.40e-05 GAAACTGCGC GAGCCACA GCCCAG chr3:190595816-190595896 6 1.40e-05 GGCCG GAGCCACA ATGGCTCCGG chr6:27652539-27652619 4 1.40e-05 acg gagccACA GCCGAGAAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:21125715-21125795 1.4e-05 47_[+2]_25 chr19:49535020-49535100 1.4e-05 6_[+2]_66 chr19:50643558-50643638 1.4e-05 1_[+2]_71 chr12:98897946-98898026 1.4e-05 66_[+2]_6 chr3:190595816-190595896 1.4e-05 5_[+2]_67 chr6:27652539-27652619 1.4e-05 3_[+2]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGCCACA width=8 seqs=6 chr14:21125715-21125795 ( 48) GAGCCACA 1 chr19:49535020-49535100 ( 7) GAGCCACA 1 chr19:50643558-50643638 ( 2) GAGCCACA 1 chr12:98897946-98898026 ( 67) GAGCCACA 1 chr3:190595816-190595896 ( 6) GAGCCACA 1 chr6:27652539-27652619 ( 4) GAGCCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.229 E= 2.8e+004 -923 -923 203 -923 194 -923 -923 -923 -923 -923 203 -923 -923 207 -923 -923 -923 207 -923 -923 194 -923 -923 -923 -923 207 -923 -923 194 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 2.8e+004 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 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCCACA MEME-2 regular expression -------------------------------------------------------------------------------- GAGCCACA -------------------------------------------------------------------------------- Time 8.89 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCCCGCC MEME-3 width = 8 sites = 2 llr = 23 E-value = 4.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :aaaa:aa probability G a::::a:: matrix T :::::::: bits 2.1 ******** 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.2 ******** Entropy 1.0 ******** (16.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCCCCGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr19:39902907-39902987 58 1.06e-05 TCACCGGAGG GCCCCGCC TTGTGTTATA chr16:22207111-22207191 53 1.06e-05 TGACGGAGGC GCCCCGCC CTCAAAGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:39902907-39902987 1.1e-05 57_[+3]_15 chr16:22207111-22207191 1.1e-05 52_[+3]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCCCGCC width=8 seqs=2 chr19:39902907-39902987 ( 58) GCCCCGCC 1 chr16:22207111-22207191 ( 53) GCCCCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 4.8e+004 -765 -765 202 -765 -765 207 -765 -765 -765 207 -765 -765 -765 207 -765 -765 -765 207 -765 -765 -765 -765 202 -765 -765 207 -765 -765 -765 207 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.8e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCGCC MEME-3 regular expression -------------------------------------------------------------------------------- GCCCCGCC -------------------------------------------------------------------------------- Time 12.74 secs. ******************************************************************************** ******************************************************************************** MOTIF GTCCTTTC MEME-4 width = 8 sites = 5 llr = 56 E-value = 1.5e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::aa:::a probability G a::::::: matrix T :a::aaa: bits 2.1 * ** * 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.2 ******** Entropy 1.0 ******** (16.1 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GTCCTTTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:26575734-26575814 61 1.42e-05 AGGGCTAGGG GTCctttc gatagctcag chr6:28911479-28911559 59 1.42e-05 CCCCTTTCCA GTCCTTTC ATTCCCATTC chr19:50643558-50643638 31 1.42e-05 TGTCGGGGCT GTCCTttc ttccctttct chr2:78182138-78182218 26 1.42e-05 TGTTGGGGCT GTCCTTTC TTCCCTTTGA chr3:190595816-190595896 35 1.42e-05 TGTCGCGGCT GTCCTTTC ATCCCTTTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:26575734-26575814 1.4e-05 60_[+4]_12 chr6:28911479-28911559 1.4e-05 58_[+4]_14 chr19:50643558-50643638 1.4e-05 30_[+4]_42 chr2:78182138-78182218 1.4e-05 25_[+4]_47 chr3:190595816-190595896 1.4e-05 34_[+4]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTCCTTTC width=8 seqs=5 chr6:26575734-26575814 ( 61) GTCCTTTC 1 chr6:28911479-28911559 ( 59) GTCCTTTC 1 chr19:50643558-50643638 ( 31) GTCCTTTC 1 chr2:78182138-78182218 ( 26) GTCCTTTC 1 chr3:190595816-190595896 ( 35) GTCCTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.2675 E= 1.5e+005 -897 -897 203 -897 -897 -897 -897 196 -897 207 -897 -897 -897 207 -897 -897 -897 -897 -897 196 -897 -897 -897 196 -897 -897 -897 196 -897 207 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.5e+005 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTCCTTTC MEME-4 regular expression -------------------------------------------------------------------------------- GTCCTTTC -------------------------------------------------------------------------------- Time 16.58 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCGCATG MEME-5 width = 8 sites = 7 llr = 74 E-value = 2.0e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C ::a:a::: probability G :a:a::3a matrix T a:::::7: bits 2.1 **** * 1.9 ****** * 1.7 ****** * 1.5 ****** * Relative 1.2 ****** * Entropy 1.0 ******** (15.3 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGCGCATG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:27599114-27599194 59 1.42e-05 CTCTGTAGAG TGCGCATG GCCAAGCAAA chr19:33667878-33667958 18 1.42e-05 GCCGAATGTG TGCGCATG CGCGCGGCCC chr16:57334479-57334559 43 1.42e-05 TTCTGCAATA TGCGCATG CGTAGTGGGC chr8:124169543-124169623 52 1.42e-05 GCTGGTCTGC TGCGCATG CCCACTTTTA chr16:22207111-22207191 70 1.42e-05 CCTCAAAGTT TGCGCATG CTC chr19:1383469-1383549 16 2.77e-05 GCGCCTTCCC TGCGCAGG CGCAGTCGTT chr17:37310070-37310150 32 2.77e-05 GTGGTATTGC TGCGCAGG CGCTGTGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:27599114-27599194 1.4e-05 58_[+5]_14 chr19:33667878-33667958 1.4e-05 17_[+5]_55 chr16:57334479-57334559 1.4e-05 42_[+5]_30 chr8:124169543-124169623 1.4e-05 51_[+5]_21 chr16:22207111-22207191 1.4e-05 69_[+5]_3 chr19:1383469-1383549 2.8e-05 15_[+5]_57 chr17:37310070-37310150 2.8e-05 31_[+5]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCGCATG width=8 seqs=7 chr6:27599114-27599194 ( 59) TGCGCATG 1 chr19:33667878-33667958 ( 18) TGCGCATG 1 chr16:57334479-57334559 ( 43) TGCGCATG 1 chr8:124169543-124169623 ( 52) TGCGCATG 1 chr16:22207111-22207191 ( 70) TGCGCATG 1 chr19:1383469-1383549 ( 16) TGCGCAGG 1 chr17:37310070-37310150 ( 32) TGCGCAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.1915 E= 2.0e+005 -945 -945 -945 196 -945 -945 203 -945 -945 207 -945 -945 -945 -945 203 -945 -945 207 -945 -945 194 -945 -945 -945 -945 -945 22 147 -945 -945 203 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.0e+005 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGCATG MEME-5 regular expression -------------------------------------------------------------------------------- TGCGCA[TG]G -------------------------------------------------------------------------------- Time 20.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:149344108-149344188 1.44e-01 80 chr17:37310070-37310150 4.42e-02 31_[+5(2.77e-05)]_41 chr2:131094788-131094868 9.09e-02 80 chr2:157257210-157257290 8.22e-01 80 chr5:180615490-180615570 9.38e-01 80 chr5:180615931-180616011 9.62e-01 80 chr1:249167986-249168066 9.91e-01 80 chr17:19411422-19411502 3.92e-01 80 chr15:26327453-26327533 2.16e-02 80 chr2:27273999-27274079 9.03e-01 80 chr17:8042831-8042911 6.71e-01 80 chr16:22207111-22207191 2.18e-05 52_[+3(1.06e-05)]_9_[+5(1.42e-05)]_\ 3 chr11:75946471-75946551 3.13e-01 80 chr12:125412468-12541254 5.29e-02 80 chr19:4724729-4724809 5.71e-01 80 chr6:27652539-27652619 1.19e-01 3_[+2(1.40e-05)]_69 chr12:96429716-96429796 6.06e-01 80 chr1:161493713-161493793 4.89e-01 80 chr19:893394-893474 9.76e-01 80 chr1:149684164-149684244 9.52e-01 80 chr6:26286666-26286746 7.24e-01 80 chr11:75946936-75947016 6.75e-01 80 chr1:145396965-145397045 6.99e-01 80 chr1:222638275-222638355 8.52e-01 80 chr8:67025525-67025605 8.53e-01 80 chr7:149388349-149388429 9.65e-01 80 chr17:73029923-73030003 3.72e-01 80 chr6:27573534-27573614 5.34e-01 80 chr17:37310816-37310896 9.83e-01 80 chr17:8028992-8029072 2.14e-01 80 chr6:26569013-26569093 6.29e-01 80 chr1:145395602-145395682 9.53e-01 80 chr2:27273565-27273645 9.98e-01 80 chr17:8089591-8089671 3.48e-01 80 chr19:45981960-45982040 3.78e-01 80 chr17:8125631-8125711 4.77e-01 80 chr8:124169543-124169623 1.16e-01 51_[+5(1.42e-05)]_21 chr8:67026333-67026413 5.12e-01 80 chr17:36908103-36908183 9.20e-01 80 chr14:23398820-23398900 1.49e-01 80 chr15:45493248-45493328 6.71e-01 80 chr1:204476236-204476316 7.47e-01 80 chr16:57334479-57334559 2.23e-02 42_[+5(1.42e-05)]_30 chr7:149404671-149404751 4.84e-01 80 chr15:45490894-45490974 3.40e-01 80 chr12:125411990-12541207 1.00e+00 80 chr13:95201977-95202057 6.07e-01 80 chr17:8022374-8022454 8.21e-01 80 chr14:21093442-21093522 9.33e-01 80 chr6:27515595-27515675 3.23e-01 80 chr6:28806288-28806368 9.38e-01 80 chr1:94313062-94313142 5.52e-01 80 chr7:149052836-149052916 3.06e-02 80 chr6:28180728-28180808 1.00e+00 80 chr6:27763704-27763784 4.44e-01 80 chr12:98897202-98897282 8.77e-01 80 chr11:66115504-66115584 9.80e-01 80 chr6:27559664-27559744 7.16e-01 80 chr1:149298629-149298709 7.08e-01 80 chr9:137029697-137029777 3.88e-01 80 chr10:69524179-69524259 9.67e-03 80 chr1:145399305-145399385 9.05e-01 80 chr11:59327885-59327965 9.98e-01 80 chr16:686813-686893 7.29e-02 80 chr16:14379681-14379761 1.67e-01 80 chr6:27473689-27473769 8.40e-01 80 chr16:3200606-3200686 3.96e-01 80 chr6:27745563-27745643 9.71e-01 80 chr5:180614613-180614693 8.85e-03 80 chr17:8124262-8124342 8.36e-02 59_[+3(7.61e-05)]_13 chr6:28849084-28849164 2.34e-01 80 chr17:37025621-37025701 7.48e-01 80 chr6:27263133-27263213 9.87e-01 80 chr6:28678293-28678373 1.00e+00 80 chr3:190595816-190595896 1.51e-04 5_[+2(1.40e-05)]_21_[+4(1.42e-05)]_\ 38 chr5:180645338-180645418 9.67e-01 80 chr6:28715459-28715539 9.95e-01 80 chr6:28775677-28775757 2.63e-01 80 chrX:18693096-18693176 6.13e-04 72_[+3(1.06e-05)] chr7:139025371-139025451 6.20e-01 80 chr6:27471448-27471528 5.79e-01 80 chr7:128423421-128423501 8.56e-01 80 chr5:180633782-180633862 5.79e-01 80 chr14:21077565-21077645 6.44e-01 80 chr6:27447368-27447448 8.33e-01 80 chr6:27543776-27543856 9.99e-01 80 chr6:27513378-27513458 5.65e-01 80 chr17:8023008-8023088 9.97e-01 80 chr6:28864108-28864188 8.86e-01 80 chr19:1383469-1383549 6.55e-04 15_[+5(2.77e-05)]_57 chr6:27570453-27570533 9.96e-01 80 chr17:8126222-8126302 3.88e-01 80 chr6:27261603-27261683 7.29e-01 80 chr1:167683877-167683957 4.50e-01 80 chr6:28442394-28442474 9.63e-01 80 chr15:45492703-45492783 4.32e-04 37_[+1(1.03e-05)]_35 chr16:57333777-57333857 3.18e-01 80 chr6:28908758-28908838 9.25e-01 80 chr14:21152092-21152172 9.58e-01 80 chr6:26577250-26577330 9.76e-01 80 chr14:21149776-21149856 5.25e-01 80 chr17:8129630-8129710 8.97e-01 80 chr6:28912272-28912352 9.84e-01 80 chr16:3225603-3225683 7.57e-01 80 chr6:52860328-52860408 5.56e-01 80 chr12:56584074-56584154 5.74e-01 80 chr7:148638512-148638592 7.31e-01 80 chr17:8124787-8124867 2.03e-01 80 chr6:27721244-27721324 1.85e-01 80 chr6:26538196-26538276 9.93e-01 80 chr16:3232715-3232795 9.53e-01 80 chr6:26330586-26330666 4.14e-01 80 chr5:180649471-180649551 6.52e-01 80 chr6:28949882-28949962 6.11e-01 80 chr5:180618760-180618840 1.43e-01 80 chr1:161591387-161591467 9.09e-01 80 chr16:22308368-22308448 8.63e-01 80 chr6:144537612-144537692 8.45e-01 80 chr12:125424391-12542447 6.45e-01 80 chr5:156704334-156704414 4.71e-01 80 chr12:98897946-98898026 1.75e-02 66_[+2(1.40e-05)]_6 chr16:3202820-3202900 3.61e-01 80 chr6:26554255-26554335 1.00e+00 80 chr1:167684806-167684886 5.61e-01 80 chr17:8024162-8024242 1.68e-02 80 chr6:26533219-26533299 9.65e-01 80 chr2:43037611-43037691 1.78e-02 80 chr6:28918734-28918814 5.59e-01 80 chr17:66016071-66016151 9.37e-03 69_[+1(1.03e-05)]_3 chr1:147825615-147825695 9.65e-01 80 chr10:114667883-11466796 8.73e-01 80 chr17:73031122-73031202 4.10e-01 80 chr2:78182138-78182218 8.07e-03 25_[+4(1.42e-05)]_47 chr19:4724006-4724086 8.65e-01 80 chr7:149028148-149028228 9.84e-01 80 chr6:27551302-27551382 1.00e+00 80 chr7:149292349-149292429 2.66e-01 80 chr17:37017995-37018075 5.66e-01 80 chr7:149074678-149074758 7.84e-01 80 chr21:18827182-18827262 9.50e-01 80 chr6:28831536-28831616 8.98e-01 80 chr3:45730567-45730647 9.83e-01 80 chr6:28703271-28703351 9.66e-01 80 chr17:8130396-8130476 9.98e-01 80 chr15:89878215-89878295 8.04e-01 80 chr5:140098434-140098514 9.06e-01 80 chr6:27618766-27618846 9.98e-01 80 chr6:27586031-27586111 9.86e-01 80 chr6:126101464-126101544 9.99e-01 80 chr1:161397940-161398020 9.95e-01 80 chr19:50643558-50643638 4.24e-04 1_[+2(1.40e-05)]_21_[+4(1.42e-05)]_\ 42 chr13:41634933-41635013 2.99e-01 80 chr6:28616049-28616129 8.84e-01 80 chr6:28697025-28697105 9.98e-01 80 chr6:26553654-26553734 6.33e-01 80 chr10:12236799-12236879 2.81e-01 80 chr14:21151354-21151434 8.98e-01 80 chr19:49535020-49535100 2.40e-03 6_[+2(1.40e-05)]_66 chr6:27265694-27265774 1.00e+00 80 chr7:149332696-149332776 7.11e-01 80 chr19:33667878-33667958 4.44e-02 17_[+5(1.42e-05)]_55 chr6:27302827-27302907 7.26e-01 80 chr6:27870350-27870430 1.00e+00 80 chr2:70476179-70476259 3.45e-02 80 chr8:96281969-96282049 9.46e-01 80 chr1:161369568-161369648 8.99e-01 80 chr6:27688972-27689052 9.94e-01 80 chr16:3230624-3230704 9.72e-01 80 chr14:21131446-21131526 8.85e-01 80 chr6:27599114-27599194 1.13e-02 58_[+5(1.42e-05)]_14 chr6:28911479-28911559 1.07e-02 58_[+4(1.42e-05)]_14 chr1:153643644-153643724 9.98e-01 80 chr17:73030602-73030682 6.12e-01 80 chr15:66161467-66161547 4.22e-04 50_[+1(1.03e-05)]_22 chr16:22309927-22310007 1.00e+00 80 chr17:80452688-80452768 3.59e-01 80 chr1:148000734-148000814 3.07e-01 80 chr16:3241927-3242007 8.40e-01 80 chr7:148680765-148680845 9.45e-01 80 chr2:47562370-47562450 6.04e-01 80 chr16:71460310-71460390 2.12e-01 80 chr16:3207491-3207571 7.48e-01 80 chr6:27177545-27177625 4.09e-01 80 chr16:87417685-87417765 1.65e-01 80 chr6:27446513-27446593 7.29e-01 80 chr11:35548241-35548321 9.32e-01 80 chr19:51108130-51108210 2.25e-01 80 chr14:102783352-10278343 5.52e-01 80 chr6:28763829-28763909 4.77e-01 80 chr12:58053921-58054001 9.42e-01 80 chr1:17004809-17004889 6.77e-01 80 chr6:27125821-27125901 6.67e-02 80 chr3:169489933-169490013 7.87e-01 80 chr6:26705529-26705609 9.90e-01 80 chr14:21125715-21125795 4.59e-02 47_[+2(1.40e-05)]_25 chr6:26322951-26323031 1.00e+00 80 chr13:92975106-92975186 9.95e-01 80 chr13:45492139-45492219 1.10e-01 80 chr1:161391958-161392038 5.99e-01 80 chr6:26572157-26572237 9.49e-01 80 chr7:149361813-149361893 8.33e-01 80 chr6:26305770-26305850 3.92e-01 80 chr19:39902907-39902987 2.22e-03 57_[+3(1.06e-05)]_15 chr6:27181689-27181769 8.52e-01 80 chr17:8042286-8042366 3.73e-02 80 chr13:93054904-93054984 8.22e-01 80 chr5:180649047-180649127 9.86e-01 80 chr1:161582450-161582530 1.00e+00 80 chr16:70823349-70823429 5.39e-01 80 chr6:26575734-26575814 1.58e-01 60_[+4(1.42e-05)]_12 chr6:27117961-27118041 9.52e-01 80 chrX:47662157-47662237 6.63e-01 80 chr7:149243551-149243631 1.00e+00 80 chr6:28456828-28456908 1.70e-01 80 chr22:37589982-37590062 7.41e-01 80 chr5:180596526-180596606 8.34e-01 80 chr12:113552435-11355251 2.86e-01 80 chr17:8023703-8023783 8.76e-01 80 chr1:61564892-61564972 9.35e-01 80 chr6:28779916-28779996 1.00e+00 80 chr1:17188355-17188435 8.77e-01 80 chr14:21098683-21098763 8.95e-01 80 chr6:27129979-27130059 9.78e-01 80 chr1:149186055-149186135 9.63e-01 80 chr5:140105659-140105739 8.85e-01 80 chr13:91795434-91795514 9.97e-01 80 chr1:17053725-17053805 9.27e-01 80 chr3:131948004-131948084 7.69e-01 80 chr14:21081598-21081678 6.13e-01 80 chr6:27487230-27487310 9.99e-01 80 chr17:37023811-37023891 3.58e-01 80 chr13:90850359-90850439 4.24e-01 80 chr2:157257710-157257790 6.80e-01 80 chr1:143879880-143879960 2.69e-01 80 chr17:8090811-8090891 8.63e-01 80 chr14:32672477-32672557 9.77e-02 80 chr16:70813014-70813094 6.82e-01 80 chr5:180634669-180634749 9.97e-01 80 chr5:135416282-135416362 9.01e-01 80 chr16:3239548-3239628 9.36e-03 30_[+1(1.03e-05)]_42 chr14:21078206-21078286 9.95e-01 80 chr6:27870762-27870842 9.60e-01 80 chr2:65794566-65794646 2.99e-01 80 chr7:149305386-149305466 9.93e-01 80 chr5:180600572-180600652 5.94e-01 80 chr17:47269804-47269884 6.40e-01 80 chr10:22518511-22518591 7.01e-01 80 chr13:90712094-90712174 9.97e-01 80 chr5:140090795-140090875 8.75e-01 80 chr14:21099365-21099445 2.60e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n08.farnam.hpc.yale.internal ********************************************************************************