******************************************************************************** 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/GM12878/fasta/RankLinear0.6_10/TBP.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr6:28456863-28456883 1.0000 20 chr6:28180770-28180790 1.0000 20 chr6:28510980-28511000 1.0000 20 chr6:27487269-27487289 1.0000 20 chr6:27515623-27515643 1.0000 20 chr6:28806313-28806333 1.0000 20 chr6:27618795-27618815 1.0000 20 chr6:28849118-28849138 1.0000 20 chr6:28616082-28616102 1.0000 20 chr6:28442420-28442440 1.0000 20 chr6:26572183-26572203 1.0000 20 chr20:6727791-6727811 1.0000 20 chr6:27129992-27130012 1.0000 20 chr14:21093486-21093506 1.0000 20 chr15:26327468-26327488 1.0000 20 chr6:27471485-27471505 1.0000 20 chr6:28912314-28912334 1.0000 20 chr6:26577292-26577312 1.0000 20 chr2:131094792-131094812 1.0000 20 chr14:21101120-21101140 1.0000 20 chr6:26327775-26327795 1.0000 20 chr6:28908788-28908808 1.0000 20 chr15:79152886-79152906 1.0000 20 chr17:17863495-17863515 1.0000 20 chr6:26553690-26553710 1.0000 20 chr6:27551319-27551339 1.0000 20 chr6:27300861-27300881 1.0000 20 chr6:27759218-27759238 1.0000 20 chr1:222638306-222638326 1.0000 20 chr14:21151392-21151412 1.0000 20 chr6:26305825-26305845 1.0000 20 chr17:73031178-73031198 1.0000 20 chr7:33080534-33080554 1.0000 20 chr14:21099410-21099430 1.0000 20 chr6:28918763-28918783 1.0000 20 chr11:59319194-59319214 1.0000 20 chr16:71460367-71460387 1.0000 20 chr6:27652564-27652584 1.0000 20 chr6:26556730-26556750 1.0000 20 chr5:135416284-135416304 1.0000 20 chr16:3202859-3202879 1.0000 20 chr6:27059481-27059501 1.0000 20 chr6:26323004-26323024 1.0000 20 chr6:26183940-26183960 1.0000 20 chr17:8125641-8125661 1.0000 20 chr14:21078254-21078274 1.0000 20 chr6:27470780-27470800 1.0000 20 chr6:28697055-28697075 1.0000 20 chr6:27248136-27248156 1.0000 20 chr6:27203243-27203263 1.0000 20 chr6:27473711-27473731 1.0000 20 chr6:27763732-27763752 1.0000 20 chr6:27559689-27559709 1.0000 20 chr6:27636321-27636341 1.0000 20 chr6:28641700-28641720 1.0000 20 chr6:28921138-28921158 1.0000 20 chr12:125412006-12541202 1.0000 20 chr17:8029030-8029050 1.0000 20 chr6:26330624-26330644 1.0000 20 chr6:27638437-27638457 1.0000 20 chr6:28626067-28626087 1.0000 20 chr14:21077588-21077608 1.0000 20 chr1:145397962-145397982 1.0000 20 chr1:145396998-145397018 1.0000 20 chr6:27513429-27513449 1.0000 20 chr6:27599164-27599184 1.0000 20 chr6:26331761-26331781 1.0000 20 chr1:161591461-161591481 1.0000 20 chr6:27258364-27258384 1.0000 20 chr6:26286704-26286724 1.0000 20 chr12:125406387-12540640 1.0000 20 chr5:94417354-94417374 1.0000 20 chr6:27446547-27446567 1.0000 20 chr6:26555461-26555481 1.0000 20 chr17:8023040-8023060 1.0000 20 chr16:3208894-3208914 1.0000 20 chr12:56584109-56584129 1.0000 20 chr14:21098676-21098696 1.0000 20 chr6:26328324-26328344 1.0000 20 chr6:27463552-27463572 1.0000 20 chr7:148660346-148660366 1.0000 20 chr6:28557121-28557141 1.0000 20 chr7:148680774-148680794 1.0000 20 chrX:18693109-18693129 1.0000 20 chr5:140098468-140098488 1.0000 20 chr6:26595065-26595085 1.0000 20 chr17:8042863-8042883 1.0000 20 chr12:14520122-14520142 1.0000 20 chr14:58706701-58706721 1.0000 20 chr11:59327902-59327922 1.0000 20 chr17:8124265-8124285 1.0000 20 chr6:27521286-27521306 1.0000 20 chr6:27560686-27560706 1.0000 20 chr15:45493292-45493312 1.0000 20 chr5:180615948-180615968 1.0000 20 chr1:161582514-161582534 1.0000 20 chr1:161397959-161397979 1.0000 20 chr12:85925314-85925334 1.0000 20 chr7:148638527-148638547 1.0000 20 chr6:27205448-27205468 1.0000 20 chr6:28574893-28574913 1.0000 20 chr5:180600610-180600630 1.0000 20 chr6:27573540-27573560 1.0000 20 chr17:29877059-29877079 1.0000 20 chr11:59323854-59323874 1.0000 20 chr6:27648968-27648988 1.0000 20 chr5:180634713-180634733 1.0000 20 chr17:37025629-37025649 1.0000 20 chr1:46799545-46799565 1.0000 20 chr4:84035897-84035917 1.0000 20 chr5:108063452-108063472 1.0000 20 chr6:26554313-26554333 1.0000 20 chr17:8130413-8130433 1.0000 20 chr12:104301573-10430159 1.0000 20 chr6:126101479-126101499 1.0000 20 chr6:27145085-27145105 1.0000 20 chr4:156536506-156536526 1.0000 20 chr4:111115211-111115231 1.0000 20 chr17:73029965-73029985 1.0000 20 chr10:16933861-16933881 1.0000 20 chrX:73072571-73072591 1.0000 20 chr17:37023859-37023879 1.0000 20 chr6:26312068-26312088 1.0000 20 chr1:161391974-161391994 1.0000 20 chr11:44581373-44581393 1.0000 20 chr17:8129684-8129704 1.0000 20 chr13:41634958-41634978 1.0000 20 chr17:8089622-8089642 1.0000 20 chr2:121832986-121833006 1.0000 20 chr3:4793324-4793344 1.0000 20 chr18:20714529-20714549 1.0000 20 chr6:27125845-27125865 1.0000 20 chr6:28909465-28909485 1.0000 20 chr17:8023730-8023750 1.0000 20 chr6:26521442-26521462 1.0000 20 chr14:21131472-21131492 1.0000 20 chr17:57905510-57905530 1.0000 20 chr6:28505319-28505339 1.0000 20 chr6:27263182-27263202 1.0000 20 chr5:133773026-133773046 1.0000 20 chr1:228645625-228645645 1.0000 20 chr5:180633832-180633852 1.0000 20 chr12:125412493-12541251 1.0000 20 chr17:36908123-36908143 1.0000 20 chr6:26044059-26044079 1.0000 20 chr7:34797698-34797718 1.0000 20 chr12:29581852-29581872 1.0000 20 chr6:28831554-28831574 1.0000 20 chr8:67026381-67026401 1.0000 20 chr13:99959665-99959685 1.0000 20 chr6:28775696-28775716 1.0000 20 chr1:145395616-145395636 1.0000 20 chr11:59333950-59333970 1.0000 20 chr5:140105740-140105760 1.0000 20 chr3:133144234-133144254 1.0000 20 chr17:19411448-19411468 1.0000 20 chr17:33700657-33700677 1.0000 20 chr5:180645365-180645385 1.0000 20 chr12:8088742-8088762 1.0000 20 chr10:112262001-11226202 1.0000 20 chr10:22518535-22518555 1.0000 20 chr16:3232720-3232740 1.0000 20 chr7:148684393-148684413 1.0000 20 chr18:60984403-60984423 1.0000 20 chr6:28611189-28611209 1.0000 20 chr5:180614655-180614675 1.0000 20 chr14:22984561-22984581 1.0000 20 chr17:37018035-37018055 1.0000 20 chr6:27261632-27261652 1.0000 20 chr6:26311468-26311488 1.0000 20 chr10:14227429-14227449 1.0000 20 chr1:149859726-149859746 1.0000 20 chr1:234738689-234738709 1.0000 20 chr2:30454380-30454400 1.0000 20 chr1:161493733-161493753 1.0000 20 chr14:21152122-21152142 1.0000 20 chr17:37310837-37310857 1.0000 20 chrX:153190999-153191019 1.0000 20 chr14:20937544-20937564 1.0000 20 chr17:73030609-73030629 1.0000 20 chr6:27640337-27640357 1.0000 20 chr4:54561836-54561856 1.0000 20 chr1:204476255-204476275 1.0000 20 chrX:106960306-106960326 1.0000 20 chr6:26533245-26533265 1.0000 20 chr14:21149795-21149815 1.0000 20 chr6:26538257-26538277 1.0000 20 chr2:161993427-161993447 1.0000 20 chr1:94313095-94313115 1.0000 20 chr17:8126246-8126266 1.0000 20 chr5:159886256-159886276 1.0000 20 chr16:3200647-3200667 1.0000 20 chr6:26033870-26033890 1.0000 20 chr16:22207124-22207144 1.0000 20 chr16:3239599-3239619 1.0000 20 chr16:3207497-3207517 1.0000 20 chr15:45018998-45019018 1.0000 20 chr6:28949455-28949475 1.0000 20 chr17:8022425-8022445 1.0000 20 chr1:16171436-16171456 1.0000 20 chr6:27265728-27265748 1.0000 20 chr6:33043724-33043744 1.0000 20 chr6:27870354-27870374 1.0000 20 chr11:75946959-75946979 1.0000 20 chr6:27745616-27745636 1.0000 20 chr8:23021535-23021555 1.0000 20 chr14:88471484-88471504 1.0000 20 chr6:28911503-28911523 1.0000 20 chr16:3225648-3225668 1.0000 20 chr18:13567600-13567620 1.0000 20 chr7:50159840-50159860 1.0000 20 chr14:69289121-69289141 1.0000 20 chr2:188312995-188313015 1.0000 20 chr17:8124882-8124902 1.0000 20 chr2:157394703-157394723 1.0000 20 chr12:9913492-9913512 1.0000 20 chr8:67025564-67025584 1.0000 20 chr14:23120277-23120297 1.0000 20 chr1:204475640-204475660 1.0000 20 chr4:47495562-47495582 1.0000 20 chr19:4724738-4724758 1.0000 20 chr17:8090874-8090894 1.0000 20 chr2:25585019-25585039 1.0000 20 chr3:169489971-169489991 1.0000 20 chr11:75946519-75946539 1.0000 20 chr13:95201996-95202016 1.0000 20 chr5:67569791-67569811 1.0000 20 chr15:68132448-68132468 1.0000 20 chr16:87417716-87417736 1.0000 20 chr6:27198431-27198451 1.0000 20 chr12:98897994-98898014 1.0000 20 chr17:39835037-39835057 1.0000 20 chr9:113018773-113018793 1.0000 20 chr2:70476211-70476231 1.0000 20 chr3:186739615-186739635 1.0000 20 chr6:26319417-26319437 1.0000 20 chr6:28763833-28763853 1.0000 20 chr12:11805664-11805684 1.0000 20 chr17:37310084-37310104 1.0000 20 chr7:114194302-114194322 1.0000 20 chr10:50396520-50396540 1.0000 20 chr15:66161485-66161505 1.0000 20 chr1:22108827-22108847 1.0000 20 chr14:21082049-21082069 1.0000 20 chr9:85341480-85341500 1.0000 20 chr10:112115207-11211522 1.0000 20 chr19:893389-893409 1.0000 20 chr17:36105059-36105079 1.0000 20 chr12:11806540-11806560 1.0000 20 chr6:143770898-143770918 1.0000 20 ******************************************************************************** ******************************************************************************** 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/GM12878/inference_raw/MEME/RankLinear0.6_10_TBP/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/TBP.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= 5000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.29 C 0.199 G 0.208 T 0.303 Background letter frequencies (from file dataset with add-one prior applied): A 0.29 C 0.199 G 0.208 T 0.303 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGAGGTAG MEME-1 width = 8 sites = 4 llr = 44 E-value = 2.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3:a:::a: pos.-specific C :::::::: probability G 8a:aa::a matrix T :::::a:: bits 2.3 * ** * 2.1 * ** * 1.9 **** ** 1.6 ******* Relative 1.4 ******** Entropy 1.2 ******** (15.7 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGAGGTAG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:26033870-26033890 13 9.92e-06 TATACTGACT GGAGGTAG chr16:71460367-71460387 2 9.92e-06 A GGAGGTAG CAAGCTTGTC chr17:73031178-73031198 11 9.92e-06 GGCCTCTCTA GGAGGTAG CT chr6:27471485-27471505 5 2.38e-05 TATT AGAGGTAG TCAAAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:26033870-26033890 9.9e-06 12_[+1] chr16:71460367-71460387 9.9e-06 1_[+1]_11 chr17:73031178-73031198 9.9e-06 10_[+1]_2 chr6:27471485-27471505 2.4e-05 4_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGGTAG width=8 seqs=4 chr6:26033870-26033890 ( 13) GGAGGTAG 1 chr16:71460367-71460387 ( 2) GGAGGTAG 1 chr17:73031178-73031198 ( 11) GGAGGTAG 1 chr6:27471485-27471505 ( 5) AGAGGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.66445 E= 2.1e+003 -21 -865 185 -865 -865 -865 226 -865 178 -865 -865 -865 -865 -865 226 -865 -865 -865 226 -865 -865 -865 -865 172 178 -865 -865 -865 -865 -865 226 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 2.1e+003 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGTAG MEME-1 regular expression -------------------------------------------------------------------------------- [GA]GAGGTAG -------------------------------------------------------------------------------- Time 2.27 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGCTHCA MEME-2 width = 8 sites = 5 llr = 51 E-value = 5.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:::4:a pos.-specific C :::a:2a: probability G a:a::::: matrix T ::::a4:: bits 2.3 * ** * 2.1 * ** * 1.9 **** ** 1.6 ***** ** Relative 1.4 ***** ** Entropy 1.2 ***** ** (14.8 bits) 0.9 ***** ** 0.7 ***** ** 0.5 ***** ** 0.2 ******** 0.0 -------- Multilevel GAGCTACA consensus T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr9:113018773-113018793 8 2.59e-05 CCAAACA GAGCTTCA AGACT chr2:25585019-25585039 4 2.59e-05 GAG GAGCTTCA GAAATGCTG chr6:28626067-28626087 6 2.59e-05 ccact gagctaca tccccAC chr6:26553690-26553710 13 2.59e-05 CAACTAGGGA GAGCTACA chr5:67569791-67569811 7 3.46e-05 AACACA GAGCTCCA GCAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:113018773-113018793 2.6e-05 7_[+2]_5 chr2:25585019-25585039 2.6e-05 3_[+2]_9 chr6:28626067-28626087 2.6e-05 5_[+2]_7 chr6:26553690-26553710 2.6e-05 12_[+2] chr5:67569791-67569811 3.5e-05 6_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGCTHCA width=8 seqs=5 chr9:113018773-113018793 ( 8) GAGCTTCA 1 chr2:25585019-25585039 ( 4) GAGCTTCA 1 chr6:28626067-28626087 ( 6) GAGCTACA 1 chr6:26553690-26553710 ( 13) GAGCTACA 1 chr5:67569791-67569811 ( 7) GAGCTCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.59397 E= 5.4e+002 -897 -897 226 -897 178 -897 -897 -897 -897 -897 226 -897 -897 233 -897 -897 -897 -897 -897 172 46 1 -897 40 -897 233 -897 -897 178 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 5.4e+002 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 0.000000 0.000000 1.000000 0.400000 0.200000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCTHCA MEME-2 regular expression -------------------------------------------------------------------------------- GAGCT[ATC]CA -------------------------------------------------------------------------------- Time 3.08 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCACCTS MEME-3 width = 8 sites = 2 llr = 23 E-value = 3.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::a:::: pos.-specific C aaa:aa:5 probability G :::::::5 matrix T ::::::a: bits 2.3 *** ** 2.1 *** ** 1.9 ****** 1.6 ******* Relative 1.4 ******** Entropy 1.2 ******** (16.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCACCTC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:159886256-159886276 10 5.46e-06 ACACTGCCT CCCACCTC TTA chr13:41634958-41634978 11 1.12e-05 ACTGCCGTGA CCCACCTG AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:159886256-159886276 5.5e-06 9_[+3]_3 chr13:41634958-41634978 1.1e-05 10_[+3]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCACCTS width=8 seqs=2 chr5:159886256-159886276 ( 10) CCCACCTC 1 chr13:41634958-41634978 ( 11) CCCACCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 3.2e+003 -765 232 -765 -765 -765 232 -765 -765 -765 232 -765 -765 178 -765 -765 -765 -765 232 -765 -765 -765 232 -765 -765 -765 -765 -765 172 -765 133 126 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.2e+003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCTS MEME-3 regular expression -------------------------------------------------------------------------------- CCCACCT[CG] -------------------------------------------------------------------------------- Time 4.01 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCTCTWA MEME-4 width = 8 sites = 14 llr = 110 E-value = 6.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::4a pos.-specific C 2:a3a2:: probability G 1:::::1: matrix T 6a:7:85: bits 2.3 * * 2.1 * * 1.9 * * * 1.6 ** * * Relative 1.4 ** * * Entropy 1.2 ** ** * (11.3 bits) 0.9 ***** * 0.7 ****** * 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTCTCTTA consensus C C CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:28505319-28505339 11 2.93e-05 TAAGAGCATC TTCTCTTA TA chr6:26556730-26556750 5 2.93e-05 TGTA TTCTCTTA GTGTATTG chr8:67026381-67026401 5 5.74e-05 ACCC TTCTCTAA AGGAACAG chr15:79152886-79152906 8 5.74e-05 AACACTT TTCTCTAA CTgcc chr12:125412006-12541202 7 1.14e-04 GTAGCT TTCCCTAA ACACTT chr19:4724738-4724758 6 1.54e-04 TTAAA TTCTCCTA TAGAGAT chr6:27248136-27248156 4 1.54e-04 TTT TTCTCCTA GGAGAAGAA chr18:13567600-13567620 8 1.72e-04 AAGAGTT CTCTCTAA ACTGC chr1:161493733-161493753 2 2.23e-04 T GTCTCTTA AAGCTCACTA chr6:27648968-27648988 2 2.23e-04 G CTCCCTTA CCTTGAAACA chr6:27258364-27258384 7 2.23e-04 TTAATT CTCCCTTA ACGAAG chr6:27759218-27759238 4 2.49e-04 ATT TTCCCTGA ATTCTTTCA chr6:33043724-33043744 5 2.81e-04 CATG GTCTCTAA TATTTCAA chr17:8125641-8125661 4 3.45e-04 CCT TTCTCCGA ATCCTTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:28505319-28505339 2.9e-05 10_[+4]_2 chr6:26556730-26556750 2.9e-05 4_[+4]_8 chr8:67026381-67026401 5.7e-05 4_[+4]_8 chr15:79152886-79152906 5.7e-05 7_[+4]_5 chr12:125412006-12541202 0.00011 6_[+4]_6 chr19:4724738-4724758 0.00015 5_[+4]_7 chr6:27248136-27248156 0.00015 3_[+4]_9 chr18:13567600-13567620 0.00017 7_[+4]_5 chr1:161493733-161493753 0.00022 1_[+4]_11 chr6:27648968-27648988 0.00022 1_[+4]_11 chr6:27258364-27258384 0.00022 6_[+4]_6 chr6:27759218-27759238 0.00025 3_[+4]_9 chr6:33043724-33043744 0.00028 4_[+4]_8 chr17:8125641-8125661 0.00035 3_[+4]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCTCTWA width=8 seqs=14 chr6:28505319-28505339 ( 11) TTCTCTTA 1 chr6:26556730-26556750 ( 5) TTCTCTTA 1 chr8:67026381-67026401 ( 5) TTCTCTAA 1 chr15:79152886-79152906 ( 8) TTCTCTAA 1 chr12:125412006-12541202 ( 7) TTCCCTAA 1 chr19:4724738-4724758 ( 6) TTCTCCTA 1 chr6:27248136-27248156 ( 4) TTCTCCTA 1 chr18:13567600-13567620 ( 8) CTCTCTAA 1 chr1:161493733-161493753 ( 2) GTCTCTTA 1 chr6:27648968-27648988 ( 2) CTCCCTTA 1 chr6:27258364-27258384 ( 7) CTCCCTTA 1 chr6:27759218-27759238 ( 4) TTCCCTGA 1 chr6:33043724-33043744 ( 5) GTCTCTAA 1 chr17:8125641-8125661 ( 4) TTCTCCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.4605 E= 6.6e+003 -1045 11 -54 108 -1045 -1045 -1045 172 -1045 233 -1045 -1045 -1045 52 -1045 123 -1045 233 -1045 -1045 -1045 11 -1045 137 30 -1045 -54 72 179 -1045 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 6.6e+003 0.000000 0.214286 0.142857 0.642857 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.214286 0.000000 0.785714 0.357143 0.000000 0.142857 0.500000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTCTWA MEME-4 regular expression -------------------------------------------------------------------------------- [TC]TC[TC]C[TC][TA]A -------------------------------------------------------------------------------- Time 4.81 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCACAMC MEME-5 width = 8 sites = 2 llr = 23 E-value = 2.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a:a5: pos.-specific C aaa:a:5a probability G :::::::: matrix T :::::::: bits 2.3 *** * * 2.1 *** * * 1.9 ****** * 1.6 ****** * Relative 1.4 ****** * Entropy 1.2 ******** (16.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCACAAC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr16:3207497-3207517 2 5.22e-06 T CCCACACC TCTGTTGGAG chr5:133773026-133773046 11 1.28e-05 CTCTCAGTTT CCCACAAC CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr16:3207497-3207517 5.2e-06 1_[+5]_11 chr5:133773026-133773046 1.3e-05 10_[+5]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCACAMC width=8 seqs=2 chr16:3207497-3207517 ( 2) CCCACACC 1 chr5:133773026-133773046 ( 11) CCCACAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.9e+003 -765 232 -765 -765 -765 232 -765 -765 -765 232 -765 -765 178 -765 -765 -765 -765 232 -765 -765 178 -765 -765 -765 78 133 -765 -765 -765 232 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.9e+003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACAMC MEME-5 regular expression -------------------------------------------------------------------------------- CCCACA[AC]C -------------------------------------------------------------------------------- Time 5.66 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:28456863-28456883 6.06e-01 20 chr6:28180770-28180790 5.96e-02 20 chr6:28510980-28511000 9.96e-01 20 chr6:27487269-27487289 4.75e-01 20 chr6:27515623-27515643 9.81e-01 20 chr6:28806313-28806333 9.55e-01 20 chr6:27618795-27618815 3.01e-01 20 chr6:28849118-28849138 4.98e-01 20 chr6:28616082-28616102 3.38e-01 20 chr6:28442420-28442440 9.71e-01 20 chr6:26572183-26572203 1.28e-01 20 chr20:6727791-6727811 3.27e-01 20 chr6:27129992-27130012 9.83e-01 20 chr14:21093486-21093506 7.25e-01 20 chr15:26327468-26327488 6.70e-01 20 chr6:27471485-27471505 1.94e-02 4_[+1(2.38e-05)]_8 chr6:28912314-28912334 8.66e-01 20 chr6:26577292-26577312 1.49e-02 20 chr2:131094792-131094812 9.62e-01 20 chr14:21101120-21101140 9.98e-01 20 chr6:26327775-26327795 9.81e-01 20 chr6:28908788-28908808 9.60e-01 20 chr15:79152886-79152906 2.91e-02 7_[+4(5.74e-05)]_5 chr17:17863495-17863515 5.74e-01 20 chr6:26553690-26553710 1.14e-02 12_[+2(2.59e-05)] chr6:27551319-27551339 1.00e+00 20 chr6:27300861-27300881 7.71e-01 20 chr6:27759218-27759238 1.28e-01 20 chr1:222638306-222638326 8.91e-01 20 chr14:21151392-21151412 8.13e-01 20 chr6:26305825-26305845 7.73e-01 20 chr17:73031178-73031198 1.02e-03 10_[+1(9.92e-06)]_2 chr7:33080534-33080554 6.08e-01 20 chr14:21099410-21099430 8.08e-01 20 chr6:28918763-28918783 4.22e-01 20 chr11:59319194-59319214 8.51e-01 20 chr16:71460367-71460387 2.01e-02 1_[+1(9.92e-06)]_11 chr6:27652564-27652584 8.24e-01 20 chr6:26556730-26556750 9.52e-02 4_[+4(2.93e-05)]_8 chr5:135416284-135416304 4.66e-01 20 chr16:3202859-3202879 3.75e-01 20 chr6:27059481-27059501 3.68e-01 20 chr6:26323004-26323024 4.83e-01 20 chr6:26183940-26183960 4.29e-01 20 chr17:8125641-8125661 4.95e-02 20 chr14:21078254-21078274 6.74e-01 20 chr6:27470780-27470800 8.59e-01 20 chr6:28697055-28697075 8.38e-01 20 chr6:27248136-27248156 4.78e-02 20 chr6:27203243-27203263 9.11e-01 20 chr6:27473711-27473731 9.33e-01 20 chr6:27763732-27763752 6.81e-01 20 chr6:27559689-27559709 7.73e-01 20 chr6:27636321-27636341 6.59e-01 20 chr6:28641700-28641720 8.94e-01 20 chr6:28921138-28921158 8.18e-01 20 chr12:125412006-12541202 7.98e-03 20 chr17:8029030-8029050 6.95e-02 20 chr6:26330624-26330644 5.28e-01 20 chr6:27638437-27638457 8.42e-01 20 chr6:28626067-28626087 1.40e-03 5_[+2(2.59e-05)]_7 chr14:21077588-21077608 9.39e-01 20 chr1:145397962-145397982 3.02e-01 20 chr1:145396998-145397018 9.54e-01 20 chr6:27513429-27513449 8.48e-02 20 chr6:27599164-27599184 7.77e-01 20 chr6:26331761-26331781 8.82e-01 20 chr1:161591461-161591481 3.33e-01 20 chr6:27258364-27258384 1.66e-02 20 chr6:26286704-26286724 4.12e-01 20 chr12:125406387-12540640 8.13e-01 20 chr5:94417354-94417374 9.03e-01 20 chr6:27446547-27446567 9.59e-01 20 chr6:26555461-26555481 4.32e-01 20 chr17:8023040-8023060 7.28e-01 20 chr16:3208894-3208914 5.46e-01 20 chr12:56584109-56584129 4.73e-02 20 chr14:21098676-21098696 9.31e-01 20 chr6:26328324-26328344 5.86e-01 20 chr6:27463552-27463572 1.86e-01 20 chr7:148660346-148660366 9.88e-01 20 chr6:28557121-28557141 3.94e-01 20 chr7:148680774-148680794 6.56e-01 20 chrX:18693109-18693129 9.99e-01 20 chr5:140098468-140098488 1.66e-01 20 chr6:26595065-26595085 9.63e-01 20 chr17:8042863-8042883 4.24e-01 20 chr12:14520122-14520142 7.18e-01 20 chr14:58706701-58706721 9.58e-01 20 chr11:59327902-59327922 6.01e-01 20 chr17:8124265-8124285 9.72e-01 20 chr6:27521286-27521306 7.16e-01 20 chr6:27560686-27560706 6.82e-02 20 chr15:45493292-45493312 4.27e-01 20 chr5:180615948-180615968 9.97e-01 20 chr1:161582514-161582534 8.20e-01 20 chr1:161397959-161397979 9.99e-01 20 chr12:85925314-85925334 5.54e-01 20 chr7:148638527-148638547 2.17e-01 20 chr6:27205448-27205468 9.55e-01 20 chr6:28574893-28574913 8.91e-01 20 chr5:180600610-180600630 5.05e-01 20 chr6:27573540-27573560 9.70e-01 20 chr17:29877059-29877079 5.92e-02 20 chr11:59323854-59323874 9.37e-01 20 chr6:27648968-27648988 3.88e-03 20 chr5:180634713-180634733 4.12e-01 20 chr17:37025629-37025649 7.84e-02 20 chr1:46799545-46799565 8.68e-01 20 chr4:84035897-84035917 2.58e-01 20 chr5:108063452-108063472 4.86e-01 20 chr6:26554313-26554333 7.12e-01 20 chr17:8130413-8130433 5.08e-01 20 chr12:104301573-10430159 9.26e-01 20 chr6:126101479-126101499 5.85e-01 20 chr6:27145085-27145105 9.89e-01 20 chr4:156536506-156536526 1.60e-01 20 chr4:111115211-111115231 6.78e-01 20 chr17:73029965-73029985 6.81e-01 20 chr10:16933861-16933881 5.01e-01 20 chrX:73072571-73072591 4.83e-01 20 chr17:37023859-37023879 8.87e-01 20 chr6:26312068-26312088 9.94e-01 20 chr1:161391974-161391994 3.29e-01 20 chr11:44581373-44581393 7.88e-01 20 chr17:8129684-8129704 1.34e-01 20 chr13:41634958-41634978 1.51e-03 10_[+3(1.12e-05)]_2 chr17:8089622-8089642 5.37e-01 20 chr2:121832986-121833006 2.77e-01 20 chr3:4793324-4793344 2.96e-01 20 chr18:20714529-20714549 5.86e-01 20 chr6:27125845-27125865 6.97e-01 20 chr6:28909465-28909485 6.59e-02 20 chr17:8023730-8023750 9.80e-02 20 chr6:26521442-26521462 4.70e-01 20 chr14:21131472-21131492 2.42e-01 20 chr17:57905510-57905530 2.33e-01 20 chr6:28505319-28505339 4.28e-03 10_[+4(2.93e-05)]_2 chr6:27263182-27263202 9.66e-01 20 chr5:133773026-133773046 3.24e-04 10_[+5(1.28e-05)]_2 chr1:228645625-228645645 7.75e-01 20 chr5:180633832-180633852 2.23e-01 20 chr12:125412493-12541251 2.92e-01 20 chr17:36908123-36908143 7.50e-01 20 chr6:26044059-26044079 9.65e-01 20 chr7:34797698-34797718 3.48e-01 20 chr12:29581852-29581872 6.96e-01 20 chr6:28831554-28831574 3.89e-01 20 chr8:67026381-67026401 1.35e-03 4_[+4(5.74e-05)]_8 chr13:99959665-99959685 8.23e-01 20 chr6:28775696-28775716 5.20e-01 20 chr1:145395616-145395636 9.02e-01 20 chr11:59333950-59333970 9.01e-01 20 chr5:140105740-140105760 7.30e-01 20 chr3:133144234-133144254 5.25e-01 20 chr17:19411448-19411468 5.63e-01 20 chr17:33700657-33700677 9.91e-01 20 chr5:180645365-180645385 7.89e-01 20 chr12:8088742-8088762 3.81e-01 20 chr10:112262001-11226202 4.14e-02 20 chr10:22518535-22518555 8.04e-01 20 chr16:3232720-3232740 6.83e-01 20 chr7:148684393-148684413 4.58e-01 20 chr18:60984403-60984423 9.78e-01 20 chr6:28611189-28611209 4.01e-01 20 chr5:180614655-180614675 3.44e-01 20 chr14:22984561-22984581 5.85e-01 20 chr17:37018035-37018055 3.13e-01 20 chr6:27261632-27261652 7.41e-01 20 chr6:26311468-26311488 3.83e-01 20 chr10:14227429-14227449 6.16e-01 20 chr1:149859726-149859746 3.61e-01 20 chr1:234738689-234738709 2.46e-01 20 chr2:30454380-30454400 4.93e-01 20 chr1:161493733-161493753 4.97e-02 20 chr14:21152122-21152142 8.69e-01 20 chr17:37310837-37310857 5.13e-01 20 chrX:153190999-153191019 8.06e-03 20 chr14:20937544-20937564 2.83e-01 20 chr17:73030609-73030629 4.08e-03 20 chr6:27640337-27640357 4.65e-01 20 chr4:54561836-54561856 6.83e-01 20 chr1:204476255-204476275 5.63e-01 20 chrX:106960306-106960326 2.42e-01 20 chr6:26533245-26533265 9.48e-01 20 chr14:21149795-21149815 3.54e-01 20 chr6:26538257-26538277 8.63e-01 20 chr2:161993427-161993447 9.55e-04 20 chr1:94313095-94313115 6.94e-01 20 chr17:8126246-8126266 1.89e-01 20 chr5:159886256-159886276 1.20e-04 9_[+3(5.46e-06)]_3 chr16:3200647-3200667 1.98e-01 20 chr6:26033870-26033890 3.48e-02 12_[+1(9.92e-06)] chr16:22207124-22207144 9.21e-02 20 chr16:3239599-3239619 1.18e-02 20 chr16:3207497-3207517 1.07e-04 1_[+5(5.22e-06)]_11 chr15:45018998-45019018 3.08e-01 20 chr6:28949455-28949475 5.85e-01 20 chr17:8022425-8022445 6.19e-02 20 chr1:16171436-16171456 5.82e-01 20 chr6:27265728-27265748 7.60e-01 20 chr6:33043724-33043744 2.09e-01 20 chr6:27870354-27870374 9.90e-01 20 chr11:75946959-75946979 9.48e-01 20 chr6:27745616-27745636 1.96e-01 20 chr8:23021535-23021555 8.02e-01 20 chr14:88471484-88471504 2.41e-01 20 chr6:28911503-28911523 5.59e-02 20 chr16:3225648-3225668 8.12e-01 20 chr18:13567600-13567620 2.19e-02 20 chr7:50159840-50159860 2.61e-01 20 chr14:69289121-69289141 5.76e-01 20 chr2:188312995-188313015 9.53e-01 20 chr17:8124882-8124902 3.63e-01 20 chr2:157394703-157394723 2.46e-01 20 chr12:9913492-9913512 4.34e-01 20 chr8:67025564-67025584 1.65e-01 20 chr14:23120277-23120297 3.42e-01 20 chr1:204475640-204475660 2.38e-01 20 chr4:47495562-47495582 9.07e-01 20 chr19:4724738-4724758 8.90e-02 20 chr17:8090874-8090894 9.27e-01 20 chr2:25585019-25585039 2.22e-02 3_[+2(2.59e-05)]_9 chr3:169489971-169489991 6.73e-01 20 chr11:75946519-75946539 8.36e-01 20 chr13:95201996-95202016 7.04e-01 20 chr5:67569791-67569811 2.11e-03 6_[+2(3.46e-05)]_6 chr15:68132448-68132468 9.28e-01 20 chr16:87417716-87417736 4.41e-01 20 chr6:27198431-27198451 9.74e-01 20 chr12:98897994-98898014 8.79e-01 20 chr17:39835037-39835057 1.20e-01 20 chr9:113018773-113018793 1.01e-02 7_[+2(2.59e-05)]_5 chr2:70476211-70476231 9.37e-01 20 chr3:186739615-186739635 5.21e-01 20 chr6:26319417-26319437 8.41e-01 20 chr6:28763833-28763853 9.53e-01 20 chr12:11805664-11805684 2.39e-01 20 chr17:37310084-37310104 8.10e-01 20 chr7:114194302-114194322 9.99e-01 20 chr10:50396520-50396540 1.37e-01 20 chr15:66161485-66161505 3.08e-01 20 chr1:22108827-22108847 3.50e-01 20 chr14:21082049-21082069 9.11e-01 20 chr9:85341480-85341500 2.98e-01 20 chr10:112115207-11211522 7.13e-01 20 chr19:893389-893409 7.01e-01 20 chr17:36105059-36105079 7.27e-02 20 chr12:11806540-11806560 8.94e-01 20 chr6:143770898-143770918 8.51e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************