******************************************************************************** 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/ZNF207.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr15:22436268-22436288 1.0000 20 chr19:54693294-54693314 1.0000 20 chr21:33104168-33104188 1.0000 20 chr17:20946134-20946154 1.0000 20 chr8:146127415-146127435 1.0000 20 chr10:102759192-10275921 1.0000 20 chr21:35747825-35747845 1.0000 20 chr1:32538485-32538505 1.0000 20 chr5:154317777-154317797 1.0000 20 chr14:39736742-39736762 1.0000 20 chr1:16940133-16940153 1.0000 20 chr6:52442249-52442269 1.0000 20 chr19:2163585-2163605 1.0000 20 chr2:114737305-114737325 1.0000 20 chr5:179921496-179921516 1.0000 20 chr3:52739808-52739828 1.0000 20 chr6:13712423-13712443 1.0000 20 chr20:55926536-55926556 1.0000 20 chr1:249200506-249200526 1.0000 20 chr17:18529076-18529096 1.0000 20 chr19:7745637-7745657 1.0000 20 chr18:12407959-12407979 1.0000 20 chr17:25680970-25680990 1.0000 20 chr1:205561198-205561218 1.0000 20 chr6:26022302-26022322 1.0000 20 chr5:142783793-142783813 1.0000 20 chr9:131799115-131799135 1.0000 20 chr1:1677849-1677869 1.0000 20 chr19:54663274-54663294 1.0000 20 chr5:65221844-65221864 1.0000 20 chr20:42086777-42086797 1.0000 20 chr1:45769796-45769816 1.0000 20 chr17:78965619-78965639 1.0000 20 chr15:34659861-34659881 1.0000 20 chr6:148668-148688 1.0000 20 chr1:2343867-2343887 1.0000 20 chr17:2296852-2296872 1.0000 20 chr13:22178153-22178173 1.0000 20 chr17:1620099-1620119 1.0000 20 chr9:134378439-134378459 1.0000 20 chr1:113615445-113615465 1.0000 20 chrX:47077935-47077955 1.0000 20 chr18:48724715-48724735 1.0000 20 chr9:95858708-95858728 1.0000 20 chr21:38640158-38640178 1.0000 20 chr5:139145312-139145332 1.0000 20 chr4:120375903-120375923 1.0000 20 chr14:106765540-10676556 1.0000 20 chr1:6052284-6052304 1.0000 20 chr17:20946981-20947001 1.0000 20 chr19:4007399-4007419 1.0000 20 chr9:135753681-135753701 1.0000 20 chr1:62902561-62902581 1.0000 20 chr11:34073203-34073223 1.0000 20 chr18:3261999-3262019 1.0000 20 chr1:115300449-115300469 1.0000 20 chr13:52027757-52027777 1.0000 20 chr9:132372943-132372963 1.0000 20 chr17:80709924-80709944 1.0000 20 chr12:64173838-64173858 1.0000 20 chr19:2611307-2611327 1.0000 20 chr4:6784250-6784270 1.0000 20 chr2:26467585-26467605 1.0000 20 chr14:100751963-10075198 1.0000 20 chr1:6844928-6844948 1.0000 20 chr20:62339301-62339321 1.0000 20 chr2:232478979-232478999 1.0000 20 chr1:16971381-16971401 1.0000 20 chr1:208136949-208136969 1.0000 20 chr3:9773363-9773383 1.0000 20 chr1:153895983-153896003 1.0000 20 chr19:3761739-3761759 1.0000 20 chr16:2563820-2563840 1.0000 20 chr19:59025362-59025382 1.0000 20 chr15:34502281-34502301 1.0000 20 chr1:115053971-115053991 1.0000 20 chr1:155658781-155658801 1.0000 20 chr19:45458236-45458256 1.0000 20 chr8:41435844-41435864 1.0000 20 chr9:106856525-106856545 1.0000 20 chr19:49622191-49622211 1.0000 20 chr16:1359223-1359243 1.0000 20 chr1:156698778-156698798 1.0000 20 chr7:100027676-100027696 1.0000 20 chr9:139010636-139010656 1.0000 20 chr14:75745417-75745437 1.0000 20 chrX:130950941-130950961 1.0000 20 chr16:53164702-53164722 1.0000 20 chr19:6737426-6737446 1.0000 20 chr3:50336537-50336557 1.0000 20 chr17:62915677-62915697 1.0000 20 chr8:66754421-66754441 1.0000 20 chr2:241500357-241500377 1.0000 20 chr19:56652320-56652340 1.0000 20 chr2:65659832-65659852 1.0000 20 chr1:78149265-78149285 1.0000 20 chr8:101734951-101734971 1.0000 20 chr20:37377193-37377213 1.0000 20 chr8:143820915-143820935 1.0000 20 chr5:179125369-179125389 1.0000 20 chr6:32163955-32163975 1.0000 20 chr1:11539066-11539086 1.0000 20 chr15:22461261-22461281 1.0000 20 chr19:2236392-2236412 1.0000 20 chr13:103248881-10324890 1.0000 20 chr4:1341154-1341174 1.0000 20 chr20:47894857-47894877 1.0000 20 chr8:135725450-135725470 1.0000 20 chr10:76995878-76995898 1.0000 20 chr2:242576907-242576927 1.0000 20 chr19:37157765-37157785 1.0000 20 chr5:114961501-114961521 1.0000 20 chr15:35838454-35838474 1.0000 20 chr8:145734103-145734123 1.0000 20 chr2:208031232-208031252 1.0000 20 chr1:1243589-1243609 1.0000 20 chrX:10087735-10087755 1.0000 20 chr5:179050413-179050433 1.0000 20 chr19:8578789-8578809 1.0000 20 chr21:40685698-40685718 1.0000 20 chr16:30969231-30969251 1.0000 20 chr2:42588458-42588478 1.0000 20 chr2:95787548-95787568 1.0000 20 chr2:239197819-239197839 1.0000 20 chr10:75571470-75571490 1.0000 20 chr5:179921285-179921305 1.0000 20 chr6:148872-148892 1.0000 20 chr17:8339506-8339526 1.0000 20 chr22:43583796-43583816 1.0000 20 chr15:22462168-22462188 1.0000 20 chr8:141474617-141474637 1.0000 20 chr2:74405717-74405737 1.0000 20 chr7:105926051-105926071 1.0000 20 chr7:100183698-100183718 1.0000 20 chr3:11314147-11314167 1.0000 20 chr4:1714231-1714251 1.0000 20 chr5:138775189-138775209 1.0000 20 chr16:2390901-2390921 1.0000 20 chr16:69220980-69221000 1.0000 20 chr19:40030814-40030834 1.0000 20 chr3:50358985-50359005 1.0000 20 chr1:153756128-153756148 1.0000 20 chr22:38902734-38902754 1.0000 20 chr14:106873628-10687364 1.0000 20 chr4:981001-981021 1.0000 20 chr21:19191830-19191850 1.0000 20 chr1:24306657-24306677 1.0000 20 chr3:197476686-197476706 1.0000 20 chr8:97274042-97274062 1.0000 20 chr7:2394476-2394496 1.0000 20 chr10:15001910-15001930 1.0000 20 chr16:81040688-81040708 1.0000 20 chr11:125933095-12593311 1.0000 20 chr4:925997-926017 1.0000 20 chr17:73030015-73030035 1.0000 20 chr7:55433807-55433827 1.0000 20 chr1:226595809-226595829 1.0000 20 chr7:21985726-21985746 1.0000 20 chr1:230778177-230778197 1.0000 20 chr9:88897150-88897170 1.0000 20 chr19:18699715-18699735 1.0000 20 chr12:860710-860730 1.0000 20 chr19:489157-489177 1.0000 20 chr4:128982124-128982144 1.0000 20 chr19:488956-488976 1.0000 20 chr17:48278174-48278194 1.0000 20 chr11:75479629-75479649 1.0000 20 chr21:34863981-34864001 1.0000 20 chr10:61666381-61666401 1.0000 20 chr18:77404482-77404502 1.0000 20 chr2:85555265-85555285 1.0000 20 chr9:131580842-131580862 1.0000 20 chr2:70141552-70141572 1.0000 20 chr6:227479-227499 1.0000 20 chr19:56159470-56159490 1.0000 20 chr12:54674853-54674873 1.0000 20 chr19:572553-572573 1.0000 20 chr5:135468900-135468920 1.0000 20 chr12:108155008-10815502 1.0000 20 chr11:124670507-12467052 1.0000 20 chr7:104654789-104654809 1.0000 20 chr1:54411183-54411203 1.0000 20 chr1:2126722-2126742 1.0000 20 chr8:144679628-144679648 1.0000 20 chr9:101984407-101984427 1.0000 20 chr20:35492428-35492448 1.0000 20 chr2:55450703-55450723 1.0000 20 chr17:6915976-6915996 1.0000 20 chr17:79451474-79451494 1.0000 20 chr16:30969031-30969051 1.0000 20 chr19:1407446-1407466 1.0000 20 chr4:10458287-10458307 1.0000 20 chr14:39736539-39736559 1.0000 20 chr7:152134034-152134054 1.0000 20 chr17:34136276-34136296 1.0000 20 chr11:66079467-66079487 1.0000 20 chr14:68141527-68141547 1.0000 20 chrX:347804-347824 1.0000 20 chr11:67169028-67169048 1.0000 20 chr18:12702839-12702859 1.0000 20 chr1:151254252-151254272 1.0000 20 chr19:42772813-42772833 1.0000 20 chr1:231664302-231664322 1.0000 20 chr19:39881563-39881583 1.0000 20 chr2:101869583-101869603 1.0000 20 chr1:1624486-1624506 1.0000 20 chr10:101380778-10138079 1.0000 20 chr8:145158957-145158977 1.0000 20 chr8:145754414-145754434 1.0000 20 chr20:35807725-35807745 1.0000 20 chr9:68726348-68726368 1.0000 20 chr14:39901477-39901497 1.0000 20 chr10:32635893-32635913 1.0000 20 chr2:100106874-100106894 1.0000 20 chr10:49879896-49879916 1.0000 20 chr1:212458911-212458931 1.0000 20 chr9:140135099-140135119 1.0000 20 chr15:41408590-41408610 1.0000 20 chr9:131580642-131580662 1.0000 20 chr19:35739785-35739805 1.0000 20 chr22:21336274-21336294 1.0000 20 chr19:984415-984435 1.0000 20 chr19:36249155-36249175 1.0000 20 chr16:31084838-31084858 1.0000 20 chr19:14317792-14317812 1.0000 20 chr10:135122337-13512235 1.0000 20 chr9:115095545-115095565 1.0000 20 chr16:31470844-31470864 1.0000 20 chr14:106765331-10676535 1.0000 20 chr10:70660625-70660645 1.0000 20 chr16:84220732-84220752 1.0000 20 chr19:1848647-1848667 1.0000 20 chr4:110354752-110354772 1.0000 20 chr2:43037624-43037644 1.0000 20 chr1:150336223-150336243 1.0000 20 chr1:16971182-16971202 1.0000 20 chr6:2765767-2765787 1.0000 20 chr6:31620551-31620571 1.0000 20 chr10:99094540-99094560 1.0000 20 chr8:87520692-87520712 1.0000 20 chr11:64902161-64902181 1.0000 20 chr13:111368312-11136833 1.0000 20 chr2:128145345-128145365 1.0000 20 chr8:145550563-145550583 1.0000 20 chr7:10979941-10979961 1.0000 20 chrX:52964036-52964056 1.0000 20 chr11:67397126-67397146 1.0000 20 chr19:2427960-2427980 1.0000 20 chr12:46121464-46121484 1.0000 20 chr20:60877780-60877800 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_ZNF207/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/ZNF207.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 0.147 C 0.35 G 0.358 T 0.145 Background letter frequencies (from file dataset with add-one prior applied): A 0.147 C 0.35 G 0.358 T 0.145 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCTKTYTT MEME-1 width = 8 sites = 17 llr = 139 E-value = 1.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::11: pos.-specific C 98::2631 probability G :::42::: matrix T 12a66469 bits 2.8 * 2.5 * * 2.2 * * 2.0 * * Relative 1.7 * * Entropy 1.4 ** * (11.8 bits) 1.1 ***** ** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCTTTCTT consensus T G TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:54674853-54674873 5 1.61e-06 TTGT CTTTTTTT AAACCTTG chr19:42772813-42772833 4 2.36e-05 CGA CTTTTTCT CCTCGCCGG chr14:106873628-10687364 4 2.36e-05 CCT CCTGTCTT GAGAGACCT chr7:105926051-105926071 8 2.36e-05 TCCTGAC CCTGTCTT TAAGA chr15:34659861-34659881 12 3.02e-05 AGGCGGACCA CCTTTCCT T chr14:106765540-10676556 12 3.91e-05 CCTAAGCACC CCTTGTTT C chr16:30969031-30969051 1 4.18e-05 . CTTTTCCT CAGGGACTAG chr8:66754421-66754441 11 5.87e-05 GCGACAGTAG CCTTCCTT GT chr9:131799115-131799135 11 5.87e-05 CGAGAGGGTG CCTTGCTT GG chr19:572553-572573 13 6.03e-05 GCCTCCGCCG CTTTTTAT chr14:39901477-39901497 4 7.52e-05 GCC TCTGTCTT CTCAAACTC chr7:152134034-152134054 10 8.47e-05 TCGCCGAGG TCTTTCCT CGT chr1:156698778-156698798 7 8.47e-05 ACTCTT CCTGTTCT GCCTGC chr15:22461261-22461281 11 1.40e-04 CTGAACCTCC CCTGGTTT CC chr7:10979941-10979961 5 1.79e-04 AATG CCTTCATT GCCGTGCC chr1:24306657-24306677 8 2.25e-04 CGGAGTA CCTGCCTT GTACC chr3:50358985-50359005 13 2.25e-04 GTGTGGTCCA CCTTTCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:54674853-54674873 1.6e-06 4_[+1]_8 chr19:42772813-42772833 2.4e-05 3_[+1]_9 chr14:106873628-10687364 2.4e-05 3_[+1]_9 chr7:105926051-105926071 2.4e-05 7_[+1]_5 chr15:34659861-34659881 3e-05 11_[+1]_1 chr14:106765540-10676556 3.9e-05 11_[+1]_1 chr16:30969031-30969051 4.2e-05 [+1]_12 chr8:66754421-66754441 5.9e-05 10_[+1]_2 chr9:131799115-131799135 5.9e-05 10_[+1]_2 chr19:572553-572573 6e-05 12_[+1] chr14:39901477-39901497 7.5e-05 3_[+1]_9 chr7:152134034-152134054 8.5e-05 9_[+1]_3 chr1:156698778-156698798 8.5e-05 6_[+1]_6 chr15:22461261-22461281 0.00014 10_[+1]_2 chr7:10979941-10979961 0.00018 4_[+1]_8 chr1:24306657-24306677 0.00022 7_[+1]_5 chr3:50358985-50359005 0.00022 12_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCTKTYTT width=8 seqs=17 chr12:54674853-54674873 ( 5) CTTTTTTT 1 chr19:42772813-42772833 ( 4) CTTTTTCT 1 chr14:106873628-10687364 ( 4) CCTGTCTT 1 chr7:105926051-105926071 ( 8) CCTGTCTT 1 chr15:34659861-34659881 ( 12) CCTTTCCT 1 chr14:106765540-10676556 ( 12) CCTTGTTT 1 chr16:30969031-30969051 ( 1) CTTTTCCT 1 chr8:66754421-66754441 ( 11) CCTTCCTT 1 chr9:131799115-131799135 ( 11) CCTTGCTT 1 chr19:572553-572573 ( 13) CTTTTTAT 1 chr14:39901477-39901497 ( 4) TCTGTCTT 1 chr7:152134034-152134054 ( 10) TCTTTCCT 1 chr1:156698778-156698798 ( 7) CCTGTTCT 1 chr15:22461261-22461281 ( 11) CCTGGTTT 1 chr7:10979941-10979961 ( 5) CCTTCATT 1 chr1:24306657-24306677 ( 8) CCTGCCTT 1 chr3:50358985-50359005 ( 13) CCTTTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.36909 E= 1.0e-001 -1073 133 -1073 -30 -1073 113 -1073 70 -1073 -1073 -1073 279 -1073 -1073 -2 216 -1073 -99 -102 216 -132 75 -1073 128 -132 -25 -1073 216 -1073 -257 -1073 270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 17 E= 1.0e-001 0.000000 0.882353 0.000000 0.117647 0.000000 0.764706 0.000000 0.235294 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.352941 0.647059 0.000000 0.176471 0.176471 0.647059 0.058824 0.588235 0.000000 0.352941 0.058824 0.294118 0.000000 0.647059 0.000000 0.058824 0.000000 0.941176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTKTYTT MEME-1 regular expression -------------------------------------------------------------------------------- C[CT]T[TG]T[CT][TC]T -------------------------------------------------------------------------------- Time 2.23 secs. ******************************************************************************** ******************************************************************************** MOTIF TGAWTWAT MEME-2 width = 8 sites = 2 llr = 26 E-value = 2.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::a5:5a: pos.-specific C :::::::: probability G :a:::::: matrix T a::5a5:a bits 2.8 * * * ** 2.5 * * * ** 2.2 * * * ** 2.0 * * * ** Relative 1.7 * ****** Entropy 1.4 ******** (18.9 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TGAATAAT consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr10:15001910-15001930 11 2.01e-06 ACACAGTTAG TGATTTAT GG chr16:69220980-69221000 9 2.01e-06 TGGCCTCA TGAATAAT GAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:15001910-15001930 2e-06 10_[+2]_2 chr16:69220980-69221000 2e-06 8_[+2]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGAWTWAT width=8 seqs=2 chr10:15001910-15001930 ( 11) TGATTTAT 1 chr16:69220980-69221000 ( 9) TGAATAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.7e+002 -765 -765 -765 278 -765 -765 148 -765 276 -765 -765 -765 176 -765 -765 178 -765 -765 -765 278 176 -765 -765 178 276 -765 -765 -765 -765 -765 -765 278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.7e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGAWTWAT MEME-2 regular expression -------------------------------------------------------------------------------- TGA[AT]T[AT]AT -------------------------------------------------------------------------------- Time 2.98 secs. ******************************************************************************** ******************************************************************************** MOTIF CTGVAAAA MEME-3 width = 8 sites = 5 llr = 52 E-value = 8.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :2:48aa8 pos.-specific C a::2:::: probability G ::a42::: matrix T :8:::::2 bits 2.8 ** 2.5 ** 2.2 ** 2.0 * *** Relative 1.7 * **** Entropy 1.4 *** **** (14.9 bits) 1.1 *** **** 0.8 *** **** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTGAAAAA consensus A GG T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:31620551-31620571 5 1.25e-06 ATGC CTGAAAAA CAGTCACC chr19:14317792-14317812 13 4.28e-06 CGCCTCCTCC CTGGAAAA chr18:77404482-77404502 6 6.78e-06 ATGAG CAGAAAAA CCTTGTT chr10:70660625-70660645 5 2.60e-05 CCGG CTGCAAAT GGCGAGGC chr19:56652320-56652340 7 3.34e-05 TGCATT CTGGGAAA TGTAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:31620551-31620571 1.2e-06 4_[+3]_8 chr19:14317792-14317812 4.3e-06 12_[+3] chr18:77404482-77404502 6.8e-06 5_[+3]_7 chr10:70660625-70660645 2.6e-05 4_[+3]_8 chr19:56652320-56652340 3.3e-05 6_[+3]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGVAAAA width=8 seqs=5 chr6:31620551-31620571 ( 5) CTGAAAAA 1 chr19:14317792-14317812 ( 13) CTGGAAAA 1 chr18:77404482-77404502 ( 6) CAGAAAAA 1 chr10:70660625-70660645 ( 5) CTGCAAAT 1 chr19:56652320-56652340 ( 7) CTGGGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.77541 E= 8.7e+002 -897 151 -897 -897 44 -897 -897 246 -897 -897 148 -897 144 -81 16 -897 244 -897 -84 -897 276 -897 -897 -897 276 -897 -897 -897 244 -897 -897 46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 8.7e+002 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGVAAAA MEME-3 regular expression -------------------------------------------------------------------------------- C[TA]G[AGC][AG]AA[AT] -------------------------------------------------------------------------------- Time 3.98 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTKTGGT MEME-4 width = 8 sites = 2 llr = 25 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::::: probability G :::5:aa: matrix T aaa5a::a bits 2.8 *** * * 2.5 *** * * 2.2 *** * * 2.0 *** * * Relative 1.7 *** * * Entropy 1.4 *** **** (18.0 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TTTGTGGT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr19:2163585-2163605 12 1.19e-06 GAAATTCGGA TTTTTGGT T chr15:22462168-22462188 5 4.13e-06 CCCC TTTGTGGT CCTGAGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:2163585-2163605 1.2e-06 11_[+4]_1 chr15:22462168-22462188 4.1e-06 4_[+4]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTKTGGT width=8 seqs=2 chr19:2163585-2163605 ( 12) TTTTTGGT 1 chr15:22462168-22462188 ( 5) TTTGTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.1e+003 -765 -765 -765 278 -765 -765 -765 278 -765 -765 -765 278 -765 -765 48 178 -765 -765 -765 278 -765 -765 148 -765 -765 -765 148 -765 -765 -765 -765 278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.1e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 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 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTKTGGT MEME-4 regular expression -------------------------------------------------------------------------------- TTT[GT]TGGT -------------------------------------------------------------------------------- Time 7.26 secs. ******************************************************************************** ******************************************************************************** MOTIF STTCCACT MEME-5 width = 8 sites = 3 llr = 34 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C 3::aa:a: probability G 7::::::: matrix T :aa::::a bits 2.8 ** * * 2.5 ** * * 2.2 ** * * 2.0 ** * * Relative 1.7 ** * * Entropy 1.4 ******* (16.2 bits) 1.1 ******* 0.8 ******* 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GTTCCACT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:1624486-1624506 13 6.88e-06 CGCCCGGGCC GTTCCACT chr1:1677849-1677869 4 6.88e-06 GCC GTTCCACT GAAGGCAGA chr2:65659832-65659852 4 1.36e-05 TGG CTTCCACT CCCGGGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:1624486-1624506 6.9e-06 12_[+5] chr1:1677849-1677869 6.9e-06 3_[+5]_9 chr2:65659832-65659852 1.4e-05 3_[+5]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STTCCACT width=8 seqs=3 chr1:1624486-1624506 ( 13) GTTCCACT 1 chr1:1677849-1677869 ( 4) GTTCCACT 1 chr2:65659832-65659852 ( 4) CTTCCACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.73854 E= 1.7e+003 -823 -7 90 -823 -823 -823 -823 278 -823 -823 -823 278 -823 151 -823 -823 -823 151 -823 -823 276 -823 -823 -823 -823 151 -823 -823 -823 -823 -823 278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.7e+003 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTCCACT MEME-5 regular expression -------------------------------------------------------------------------------- [GC]TTCCACT -------------------------------------------------------------------------------- Time 10.60 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:22436268-22436288 7.70e-01 20 chr19:54693294-54693314 8.49e-01 20 chr21:33104168-33104188 9.96e-01 20 chr17:20946134-20946154 8.21e-01 20 chr8:146127415-146127435 4.58e-03 20 chr10:102759192-10275921 1.22e-02 20 chr21:35747825-35747845 9.74e-01 20 chr1:32538485-32538505 1.87e-01 20 chr5:154317777-154317797 6.27e-01 20 chr14:39736742-39736762 7.62e-02 20 chr1:16940133-16940153 4.24e-01 20 chr6:52442249-52442269 9.96e-01 20 chr19:2163585-2163605 2.51e-05 11_[+4(1.19e-06)]_1 chr2:114737305-114737325 3.58e-01 20 chr5:179921496-179921516 9.76e-01 20 chr3:52739808-52739828 8.94e-01 20 chr6:13712423-13712443 9.51e-01 20 chr20:55926536-55926556 7.13e-01 20 chr1:249200506-249200526 6.73e-01 20 chr17:18529076-18529096 1.65e-02 20 chr19:7745637-7745657 6.63e-01 20 chr18:12407959-12407979 5.50e-01 20 chr17:25680970-25680990 1.00e+00 20 chr1:205561198-205561218 1.89e-01 20 chr6:26022302-26022322 2.33e-01 20 chr5:142783793-142783813 1.06e-03 20 chr9:131799115-131799135 2.75e-02 10_[+1(5.87e-05)]_2 chr1:1677849-1677869 3.78e-03 3_[+5(6.88e-06)]_9 chr19:54663274-54663294 9.40e-01 20 chr5:65221844-65221864 4.15e-01 20 chr20:42086777-42086797 7.20e-01 20 chr1:45769796-45769816 2.80e-01 20 chr17:78965619-78965639 1.00e+00 20 chr15:34659861-34659881 6.47e-03 11_[+1(3.02e-05)]_1 chr6:148668-148688 7.30e-01 20 chr1:2343867-2343887 3.28e-01 20 chr17:2296852-2296872 8.91e-01 20 chr13:22178153-22178173 9.86e-01 20 chr17:1620099-1620119 9.26e-01 20 chr9:134378439-134378459 5.16e-02 20 chr1:113615445-113615465 6.82e-01 20 chrX:47077935-47077955 8.30e-02 20 chr18:48724715-48724735 2.65e-01 20 chr9:95858708-95858728 5.47e-01 20 chr21:38640158-38640178 2.90e-01 20 chr5:139145312-139145332 6.08e-01 20 chr4:120375903-120375923 3.19e-01 20 chr14:106765540-10676556 1.85e-02 11_[+1(3.91e-05)]_1 chr1:6052284-6052304 9.82e-01 20 chr17:20946981-20947001 3.22e-02 20 chr19:4007399-4007419 1.72e-02 20 chr9:135753681-135753701 9.68e-01 20 chr1:62902561-62902581 8.02e-01 20 chr11:34073203-34073223 6.21e-01 20 chr18:3261999-3262019 9.84e-01 20 chr1:115300449-115300469 2.31e-03 20 chr13:52027757-52027777 1.00e+00 20 chr9:132372943-132372963 7.74e-01 20 chr17:80709924-80709944 9.99e-01 20 chr12:64173838-64173858 9.92e-01 20 chr19:2611307-2611327 7.89e-01 20 chr4:6784250-6784270 9.99e-01 20 chr2:26467585-26467605 9.46e-01 20 chr14:100751963-10075198 8.64e-02 20 chr1:6844928-6844948 6.41e-01 20 chr20:62339301-62339321 9.83e-01 20 chr2:232478979-232478999 1.00e+00 20 chr1:16971381-16971401 3.97e-01 20 chr1:208136949-208136969 9.99e-01 20 chr3:9773363-9773383 7.90e-01 20 chr1:153895983-153896003 1.09e-01 20 chr19:3761739-3761759 9.74e-01 20 chr16:2563820-2563840 9.92e-01 20 chr19:59025362-59025382 6.73e-01 20 chr15:34502281-34502301 6.68e-01 20 chr1:115053971-115053991 1.22e-01 20 chr1:155658781-155658801 9.66e-01 20 chr19:45458236-45458256 1.87e-01 20 chr8:41435844-41435864 9.99e-01 20 chr9:106856525-106856545 6.41e-01 20 chr19:49622191-49622211 9.18e-01 20 chr16:1359223-1359243 6.84e-01 20 chr1:156698778-156698798 1.48e-03 6_[+1(8.47e-05)]_6 chr7:100027676-100027696 9.88e-01 20 chr9:139010636-139010656 9.33e-01 20 chr14:75745417-75745437 9.92e-01 20 chrX:130950941-130950961 4.43e-01 20 chr16:53164702-53164722 9.83e-01 20 chr19:6737426-6737446 8.52e-01 20 chr3:50336537-50336557 7.68e-01 20 chr17:62915677-62915697 9.95e-01 20 chr8:66754421-66754441 2.59e-03 10_[+1(5.87e-05)]_2 chr2:241500357-241500377 9.84e-01 20 chr19:56652320-56652340 9.39e-04 6_[+3(3.34e-05)]_6 chr2:65659832-65659852 6.06e-03 3_[+5(1.36e-05)]_9 chr1:78149265-78149285 1.00e+00 20 chr8:101734951-101734971 9.94e-01 20 chr20:37377193-37377213 5.48e-01 20 chr8:143820915-143820935 1.00e+00 20 chr5:179125369-179125389 1.66e-01 20 chr6:32163955-32163975 9.90e-01 20 chr1:11539066-11539086 9.99e-01 20 chr15:22461261-22461281 1.32e-03 20 chr19:2236392-2236412 5.10e-01 20 chr13:103248881-10324890 8.29e-01 20 chr4:1341154-1341174 6.32e-01 20 chr20:47894857-47894877 4.70e-01 20 chr8:135725450-135725470 9.54e-01 20 chr10:76995878-76995898 6.12e-01 20 chr2:242576907-242576927 9.95e-01 20 chr19:37157765-37157785 8.79e-01 20 chr5:114961501-114961521 9.48e-01 20 chr15:35838454-35838474 8.80e-01 20 chr8:145734103-145734123 1.00e+00 20 chr2:208031232-208031252 1.00e+00 20 chr1:1243589-1243609 3.94e-01 20 chrX:10087735-10087755 3.87e-03 20 chr5:179050413-179050433 7.45e-02 20 chr19:8578789-8578809 3.93e-01 20 chr21:40685698-40685718 5.94e-01 20 chr16:30969231-30969251 4.11e-01 20 chr2:42588458-42588478 3.83e-01 20 chr2:95787548-95787568 7.96e-01 20 chr2:239197819-239197839 9.53e-01 20 chr10:75571470-75571490 8.98e-01 20 chr5:179921285-179921305 7.73e-01 20 chr6:148872-148892 9.55e-02 20 chr17:8339506-8339526 1.09e-01 20 chr22:43583796-43583816 1.44e-01 20 chr15:22462168-22462188 4.25e-03 4_[+4(4.13e-06)]_8 chr8:141474617-141474637 6.44e-01 20 chr2:74405717-74405737 9.18e-01 20 chr7:105926051-105926071 6.29e-04 7_[+1(2.36e-05)]_5 chr7:100183698-100183718 9.84e-01 20 chr3:11314147-11314167 2.00e-01 20 chr4:1714231-1714251 6.68e-01 20 chr5:138775189-138775209 1.00e+00 20 chr16:2390901-2390921 4.39e-02 20 chr16:69220980-69221000 4.72e-04 8_[+2(2.01e-06)]_4 chr19:40030814-40030834 4.06e-02 20 chr3:50358985-50359005 2.19e-03 20 chr1:153756128-153756148 1.44e-01 20 chr22:38902734-38902754 9.35e-02 20 chr14:106873628-10687364 1.17e-03 3_[+1(2.36e-05)]_9 chr4:981001-981021 1.81e-01 20 chr21:19191830-19191850 2.02e-01 20 chr1:24306657-24306677 6.06e-03 20 chr3:197476686-197476706 9.90e-01 20 chr8:97274042-97274062 9.76e-01 20 chr7:2394476-2394496 1.00e+00 20 chr10:15001910-15001930 3.09e-04 10_[+2(2.01e-06)]_2 chr16:81040688-81040708 1.00e+00 20 chr11:125933095-12593311 3.02e-01 20 chr4:925997-926017 7.18e-01 20 chr17:73030015-73030035 1.15e-01 20 chr7:55433807-55433827 9.92e-01 20 chr1:226595809-226595829 8.33e-01 20 chr7:21985726-21985746 7.43e-01 20 chr1:230778177-230778197 2.29e-01 20 chr9:88897150-88897170 9.28e-01 20 chr19:18699715-18699735 9.07e-01 20 chr12:860710-860730 6.75e-01 20 chr19:489157-489177 5.65e-01 20 chr4:128982124-128982144 9.79e-01 20 chr19:488956-488976 9.85e-01 20 chr17:48278174-48278194 3.07e-01 20 chr11:75479629-75479649 2.10e-01 20 chr21:34863981-34864001 9.49e-01 20 chr10:61666381-61666401 8.55e-01 20 chr18:77404482-77404502 5.37e-03 5_[+3(6.78e-06)]_7 chr2:85555265-85555285 9.92e-01 20 chr9:131580842-131580862 9.71e-01 20 chr2:70141552-70141572 9.52e-01 20 chr6:227479-227499 5.16e-01 20 chr19:56159470-56159490 6.43e-01 20 chr12:54674853-54674873 4.96e-05 4_[+1(1.61e-06)]_8 chr19:572553-572573 8.56e-04 12_[+1(6.03e-05)] chr5:135468900-135468920 7.03e-01 20 chr12:108155008-10815502 2.18e-01 20 chr11:124670507-12467052 9.88e-01 20 chr7:104654789-104654809 2.65e-01 20 chr1:54411183-54411203 3.11e-01 20 chr1:2126722-2126742 9.97e-01 20 chr8:144679628-144679648 9.68e-01 20 chr9:101984407-101984427 2.74e-01 20 chr20:35492428-35492448 9.97e-01 20 chr2:55450703-55450723 9.09e-01 20 chr17:6915976-6915996 7.94e-01 20 chr17:79451474-79451494 9.94e-01 20 chr16:30969031-30969051 2.92e-05 [+1(4.18e-05)]_12 chr19:1407446-1407466 8.97e-01 20 chr4:10458287-10458307 9.34e-01 20 chr14:39736539-39736559 1.04e-01 20 chr7:152134034-152134054 1.60e-03 9_[+1(8.47e-05)]_3 chr17:34136276-34136296 1.37e-02 20 chr11:66079467-66079487 7.24e-01 20 chr14:68141527-68141547 1.85e-01 10_[+3(8.51e-05)]_2 chrX:347804-347824 9.55e-01 20 chr11:67169028-67169048 6.16e-01 20 chr18:12702839-12702859 9.95e-01 20 chr1:151254252-151254272 2.12e-03 20 chr19:42772813-42772833 2.30e-04 3_[+1(2.36e-05)]_9 chr1:231664302-231664322 1.00e+00 20 chr19:39881563-39881583 8.55e-01 20 chr2:101869583-101869603 1.00e+00 20 chr1:1624486-1624506 1.37e-02 12_[+5(6.88e-06)] chr10:101380778-10138079 7.32e-01 20 chr8:145158957-145158977 9.79e-01 20 chr8:145754414-145754434 9.87e-01 20 chr20:35807725-35807745 3.67e-01 20 chr9:68726348-68726368 4.61e-01 20 chr14:39901477-39901497 1.33e-04 3_[+1(7.52e-05)]_9 chr10:32635893-32635913 2.12e-01 20 chr2:100106874-100106894 4.55e-01 20 chr10:49879896-49879916 2.69e-02 20 chr1:212458911-212458931 9.72e-01 20 chr9:140135099-140135119 6.91e-01 20 chr15:41408590-41408610 9.23e-01 20 chr9:131580642-131580662 6.92e-01 20 chr19:35739785-35739805 5.76e-02 20 chr22:21336274-21336294 4.62e-01 20 chr19:984415-984435 4.39e-02 20 chr19:36249155-36249175 9.11e-01 20 chr16:31084838-31084858 9.93e-01 20 chr19:14317792-14317812 2.12e-03 12_[+3(4.28e-06)] chr10:135122337-13512235 9.99e-01 20 chr9:115095545-115095565 9.93e-01 20 chr16:31470844-31470864 4.10e-01 20 chr14:106765331-10676535 4.57e-01 20 chr10:70660625-70660645 1.65e-02 4_[+3(2.60e-05)]_8 chr16:84220732-84220752 9.24e-01 20 chr19:1848647-1848667 9.46e-01 20 chr4:110354752-110354772 9.98e-01 20 chr2:43037624-43037644 9.60e-01 20 chr1:150336223-150336243 8.91e-01 20 chr1:16971182-16971202 6.74e-01 20 chr6:2765767-2765787 9.94e-01 20 chr6:31620551-31620571 4.45e-04 4_[+3(1.25e-06)]_8 chr10:99094540-99094560 9.99e-01 20 chr8:87520692-87520712 7.18e-01 20 chr11:64902161-64902181 3.03e-01 20 chr13:111368312-11136833 2.22e-01 20 chr2:128145345-128145365 1.00e+00 20 chr8:145550563-145550583 6.21e-01 20 chr7:10979941-10979961 9.23e-03 20 chrX:52964036-52964056 1.00e+00 20 chr11:67397126-67397146 6.68e-01 20 chr19:2427960-2427980 1.04e-01 20 chr12:46121464-46121484 9.63e-01 20 chr20:60877780-60877800 8.93e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n09.farnam.hpc.yale.internal ********************************************************************************