******************************************************************************** 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/LARP7.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:859191-859211 1.0000 20 chr16:56659564-56659584 1.0000 20 chr1:856649-856669 1.0000 20 chr16:56716255-56716275 1.0000 20 chr16:56691750-56691770 1.0000 20 chr12:129308119-12930813 1.0000 20 chr9:132805119-132805139 1.0000 20 chr15:59041624-59041644 1.0000 20 chr1:16825424-16825444 1.0000 20 chr6:2245679-2245699 1.0000 20 chr16:56642351-56642371 1.0000 20 chr10:112258062-11225808 1.0000 20 chr16:47177548-47177568 1.0000 20 chr1:51984655-51984675 1.0000 20 chr10:112679509-11267952 1.0000 20 chr18:46478007-46478027 1.0000 20 chr12:12714820-12714840 1.0000 20 chr10:69644724-69644744 1.0000 20 chr9:123963689-123963709 1.0000 20 chr10:81107467-81107487 1.0000 20 chr11:119077088-11907710 1.0000 20 chr2:128459534-128459554 1.0000 20 chr11:74460209-74460229 1.0000 20 chr7:43622990-43623010 1.0000 20 chr5:179160072-179160092 1.0000 20 chr7:151216500-151216520 1.0000 20 chr4:185746877-185746897 1.0000 20 chr10:99400664-99400684 1.0000 20 chr17:76777643-76777663 1.0000 20 chr4:146101207-146101227 1.0000 20 chr4:15656835-15656855 1.0000 20 chr1:15736500-15736520 1.0000 20 chr2:65283817-65283837 1.0000 20 chr5:139028065-139028085 1.0000 20 chr22:36783765-36783785 1.0000 20 chr1:172502396-172502416 1.0000 20 chr2:11886562-11886582 1.0000 20 chr9:131644651-131644671 1.0000 20 chr19:10829018-10829038 1.0000 20 chr3:150264100-150264120 1.0000 20 chr2:174830480-174830500 1.0000 20 chr1:32403795-32403815 1.0000 20 chr10:181876-181896 1.0000 20 chr7:99516869-99516889 1.0000 20 chr1:173991163-173991183 1.0000 20 chr14:50360085-50360105 1.0000 20 chr16:4675070-4675090 1.0000 20 chr19:16187441-16187461 1.0000 20 chr3:47205067-47205087 1.0000 20 chr8:76319585-76319605 1.0000 20 chr1:9189012-9189032 1.0000 20 chr15:79049401-79049421 1.0000 20 chr10:22292362-22292382 1.0000 20 chr1:224371145-224371165 1.0000 20 chr17:37910342-37910362 1.0000 20 chr5:130599821-130599841 1.0000 20 chr4:6718093-6718113 1.0000 20 chr3:25706072-25706092 1.0000 20 chr6:157802315-157802335 1.0000 20 chr4:83294839-83294859 1.0000 20 chr2:178129303-178129323 1.0000 20 chr16:68119544-68119564 1.0000 20 chr17:46985967-46985987 1.0000 20 chr17:42296759-42296779 1.0000 20 chr17:4046058-4046078 1.0000 20 chr9:128003343-128003363 1.0000 20 chr4:1341209-1341229 1.0000 20 chr16:30346590-30346610 1.0000 20 chr2:88926720-88926740 1.0000 20 chr5:156693431-156693451 1.0000 20 chr16:1832332-1832352 1.0000 20 chr1:198126269-198126289 1.0000 20 chr11:13299559-13299579 1.0000 20 chr15:90645513-90645533 1.0000 20 chr4:113153093-113153113 1.0000 20 chr3:196594997-196595017 1.0000 20 chr3:178866398-178866418 1.0000 20 chr17:76164723-76164743 1.0000 20 chr16:88878823-88878843 1.0000 20 chr5:55290653-55290673 1.0000 20 chr7:6414345-6414365 1.0000 20 chr16:11836465-11836485 1.0000 20 chr16:88877805-88877825 1.0000 20 chr15:40226425-40226445 1.0000 20 chr10:86088637-86088657 1.0000 20 chr17:28088259-28088279 1.0000 20 chr12:39836824-39836844 1.0000 20 chr11:65838036-65838056 1.0000 20 chr14:64971726-64971746 1.0000 20 chr19:39340430-39340450 1.0000 20 chr11:63606805-63606825 1.0000 20 chr10:3827149-3827169 1.0000 20 chr6:3119134-3119154 1.0000 20 chr9:74525816-74525836 1.0000 20 chr17:20946150-20946170 1.0000 20 chr7:33148886-33148906 1.0000 20 chr14:45366843-45366863 1.0000 20 chr5:132072961-132072981 1.0000 20 chr3:39194878-39194898 1.0000 20 chr16:88729279-88729299 1.0000 20 chr10:112257283-11225730 1.0000 20 chr4:110481537-110481557 1.0000 20 chr5:114961456-114961476 1.0000 20 chr4:184425418-184425438 1.0000 20 chr1:1285087-1285107 1.0000 20 chr6:149638368-149638388 1.0000 20 chr9:36400534-36400554 1.0000 20 chr15:60884060-60884080 1.0000 20 chr5:95067030-95067050 1.0000 20 chr4:156874905-156874925 1.0000 20 chr20:62886909-62886929 1.0000 20 chr1:167522828-167522848 1.0000 20 chr6:160148851-160148871 1.0000 20 chr17:54910870-54910890 1.0000 20 chr16:31154059-31154079 1.0000 20 chr16:30670799-30670819 1.0000 20 chr16:87417257-87417277 1.0000 20 chr5:142783122-142783142 1.0000 20 chr17:73892751-73892771 1.0000 20 chr6:139013696-139013716 1.0000 20 chr15:63414311-63414331 1.0000 20 chr1:117909560-117909580 1.0000 20 chr21:45662498-45662518 1.0000 20 chr19:54693195-54693215 1.0000 20 chr20:3870223-3870243 1.0000 20 chr19:1491266-1491286 1.0000 20 chr10:88854403-88854423 1.0000 20 chr19:45579630-45579650 1.0000 20 chr5:77071859-77071879 1.0000 20 chr15:78441940-78441960 1.0000 20 chr9:140095022-140095042 1.0000 20 chr5:179719394-179719414 1.0000 20 chr4:79860472-79860492 1.0000 20 chr9:71320189-71320209 1.0000 20 chr10:64564652-64564672 1.0000 20 chr5:178287220-178287240 1.0000 20 chr13:31774185-31774205 1.0000 20 chr3:128902686-128902706 1.0000 20 chr3:182511632-182511652 1.0000 20 chr4:71705308-71705328 1.0000 20 chr12:862395-862415 1.0000 20 chr19:10679412-10679432 1.0000 20 chr2:232573521-232573541 1.0000 20 chr12:104850842-10485086 1.0000 20 chr6:70577319-70577339 1.0000 20 chr15:65116325-65116345 1.0000 20 chr7:138145371-138145391 1.0000 20 chr22:38240094-38240114 1.0000 20 chr17:29298193-29298213 1.0000 20 chr1:43232435-43232455 1.0000 20 chr3:118959590-118959610 1.0000 20 chr2:114341545-114341565 1.0000 20 chr10:104402360-10440238 1.0000 20 chr6:116422015-116422035 1.0000 20 chr6:37138067-37138087 1.0000 20 chr1:25072054-25072074 1.0000 20 chr2:232572654-232572674 1.0000 20 chr2:208634391-208634411 1.0000 20 chr14:105767144-10576716 1.0000 20 chr17:79875801-79875821 1.0000 20 chr2:223289406-223289426 1.0000 20 chr1:211752517-211752537 1.0000 20 chr15:43425987-43426007 1.0000 20 chr4:147097053-147097073 1.0000 20 chr13:78271963-78271983 1.0000 20 chr11:64948866-64948886 1.0000 20 chr5:178053701-178053721 1.0000 20 chr20:8000193-8000213 1.0000 20 chr2:223725982-223726002 1.0000 20 chr6:26158666-26158686 1.0000 20 chr16:28834838-28834858 1.0000 20 chr14:54907874-54907894 1.0000 20 chr13:30689144-30689164 1.0000 20 chr14:105957722-10595774 1.0000 20 chr3:101568526-101568546 1.0000 20 chr3:52931453-52931473 1.0000 20 chr9:74980003-74980023 1.0000 20 chr4:2757921-2757941 1.0000 20 chr11:47788523-47788543 1.0000 20 chr1:21113029-21113049 1.0000 20 chr16:21513395-21513415 1.0000 20 chr11:65268031-65268051 1.0000 20 chr17:8339459-8339479 1.0000 20 chr14:105487241-10548726 1.0000 20 chr7:33102010-33102030 1.0000 20 chr9:125667373-125667393 1.0000 20 chr2:239112014-239112034 1.0000 20 chr11:110167187-11016720 1.0000 20 chr11:14380520-14380540 1.0000 20 chr20:2083675-2083695 1.0000 20 chr1:26799184-26799204 1.0000 20 chr11:92931001-92931021 1.0000 20 chr9:139838904-139838924 1.0000 20 chr6:52442244-52442264 1.0000 20 chr14:72399221-72399241 1.0000 20 chr22:22221584-22221604 1.0000 20 chr8:101964063-101964083 1.0000 20 chr11:64809014-64809034 1.0000 20 chr1:249200486-249200506 1.0000 20 chr1:197871833-197871853 1.0000 20 chr17:62207253-62207273 1.0000 20 chr22:18484114-18484134 1.0000 20 chr7:44887462-44887482 1.0000 20 chr2:242641088-242641108 1.0000 20 chr9:117160552-117160572 1.0000 20 chr7:44836543-44836563 1.0000 20 chr12:133264357-13326437 1.0000 20 chr9:94124044-94124064 1.0000 20 chr2:24163419-24163439 1.0000 20 chr13:23949415-23949435 1.0000 20 chr12:96794040-96794060 1.0000 20 chr22:24129333-24129353 1.0000 20 chr15:74726109-74726129 1.0000 20 chr13:28194454-28194474 1.0000 20 chr6:64345867-64345887 1.0000 20 chr12:69202009-69202029 1.0000 20 chr4:139937200-139937220 1.0000 20 chr6:132833897-132833917 1.0000 20 chr10:105726971-10572699 1.0000 20 chr9:140500322-140500342 1.0000 20 chr11:694779-694799 1.0000 20 chr7:5568220-5568240 1.0000 20 chr10:93558367-93558387 1.0000 20 chr1:15573724-15573744 1.0000 20 chr8:132916472-132916492 1.0000 20 chr12:42538436-42538456 1.0000 20 chr5:176853887-176853907 1.0000 20 chr1:182992979-182992999 1.0000 20 chr4:53578876-53578896 1.0000 20 chr3:100053752-100053772 1.0000 20 chr1:17338378-17338398 1.0000 20 chr14:60794774-60794794 1.0000 20 chr1:236305979-236305999 1.0000 20 chr11:94277690-94277710 1.0000 20 chr19:14628960-14628980 1.0000 20 chr6:3068849-3068869 1.0000 20 chr19:11708508-11708528 1.0000 20 chr3:57678575-57678595 1.0000 20 chr6:71123502-71123522 1.0000 20 chr8:74659427-74659447 1.0000 20 chr6:43337040-43337060 1.0000 20 chr17:43394220-43394240 1.0000 20 chr14:90085523-90085543 1.0000 20 chr20:32078194-32078214 1.0000 20 chr1:226309302-226309322 1.0000 20 chr8:96146197-96146217 1.0000 20 chr18:56338894-56338914 1.0000 20 chr16:128346-128366 1.0000 20 chr7:30324678-30324698 1.0000 20 chr6:146135686-146135706 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_LARP7/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/LARP7.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 0.12 C 0.379 G 0.391 T 0.11 Background letter frequencies (from file dataset with add-one prior applied): A 0.121 C 0.379 G 0.391 T 0.11 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTWWTKKT MEME-1 width = 8 sites = 3 llr = 38 E-value = 7.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::73:::: pos.-specific C 7::::::: probability G :::::33: matrix T 3a37a77a bits 3.2 * * * 2.9 * * * 2.6 * * * 2.2 **** * Relative 1.9 **** * Entropy 1.6 ******* (18.4 bits) 1.3 ******* 1.0 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTATTTTT consensus T TA GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:128902686-128902706 11 3.39e-07 GTAGAGGCTG TTTATTTT GA chr14:45366843-45366863 3 1.17e-06 GC CTATTTGT CCGCAGTTCT chr1:173991163-173991183 1 1.17e-06 . CTATTGTT CCCGACTGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:128902686-128902706 3.4e-07 10_[+1]_2 chr14:45366843-45366863 1.2e-06 2_[+1]_10 chr1:173991163-173991183 1.2e-06 [+1]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTWWTKKT width=8 seqs=3 chr3:128902686-128902706 ( 11) TTTATTTT 1 chr14:45366843-45366863 ( 3) CTATTTGT 1 chr1:173991163-173991183 ( 1) CTATTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.5277 E= 7.0e+000 -823 81 -823 160 -823 -823 -823 318 246 -823 -823 160 146 -823 -823 260 -823 -823 -823 318 -823 -823 -23 260 -823 -823 -23 260 -823 -823 -823 318 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 7.0e+000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTWWTKKT MEME-1 regular expression -------------------------------------------------------------------------------- [CT]T[AT][TA]T[TG][TG]T -------------------------------------------------------------------------------- Time 2.33 secs. ******************************************************************************** ******************************************************************************** MOTIF YTGCTCTT MEME-2 width = 8 sites = 4 llr = 42 E-value = 7.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::3 pos.-specific C 5:3a:a:: probability G ::8:::3: matrix T 5a::a:88 bits 3.2 * * 2.9 * * 2.6 * * 2.2 * * * Relative 1.9 * * ** Entropy 1.6 * * ** (15.3 bits) 1.3 ** ***** 1.0 ** ***** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTGCTCTT consensus T C GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:28088259-28088279 5 1.78e-06 CGCC TTCCTCTT GCGGGCCA chr15:90645513-90645533 8 5.89e-06 GCCGCGG CTGCTCTT GCGAG chr2:232572654-232572674 9 1.31e-05 TGACCTCG TTGCTCGT CGTG chr2:128459534-128459554 7 1.65e-05 CCCGCG CTGCTCTA CATGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:28088259-28088279 1.8e-06 4_[+2]_8 chr15:90645513-90645533 5.9e-06 7_[+2]_5 chr2:232572654-232572674 1.3e-05 8_[+2]_4 chr2:128459534-128459554 1.7e-05 6_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YTGCTCTT width=8 seqs=4 chr17:28088259-28088279 ( 5) TTCCTCTT 1 chr15:90645513-90645533 ( 8) CTGCTCTT 1 chr2:232572654-232572674 ( 9) TTGCTCGT 1 chr2:128459534-128459554 ( 7) CTGCTCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.4021 E= 7.9e+002 -865 40 -865 219 -865 -865 -865 318 -865 -60 94 -865 -865 140 -865 -865 -865 -865 -865 318 -865 140 -865 -865 -865 -865 -64 277 105 -865 -865 277 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 7.9e+002 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTGCTCTT MEME-2 regular expression -------------------------------------------------------------------------------- [CT]T[GC]CTC[TG][TA] -------------------------------------------------------------------------------- Time 4.35 secs. ******************************************************************************** ******************************************************************************** MOTIF CGTCTYTW MEME-3 width = 8 sites = 2 llr = 24 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::5 pos.-specific C a::a:5:: probability G :a:::::: matrix T ::a:a5a5 bits 3.2 * * * 2.9 * * * 2.6 * * * 2.2 * * ** Relative 1.9 * * ** Entropy 1.6 * * ** (17.1 bits) 1.3 ******** 1.0 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CGTCTCTA consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:43337040-43337060 12 1.90e-06 cccccgccgT CGTCTTTA G chr16:30346590-30346610 1 5.02e-06 . CGTCTCTT CCAGGGCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:43337040-43337060 1.9e-06 11_[+3]_1 chr16:30346590-30346610 5e-06 [+3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGTCTYTW width=8 seqs=2 chr6:43337040-43337060 ( 12) CGTCTTTA 1 chr16:30346590-30346610 ( 1) CGTCTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.7e+003 -765 140 -765 -765 -765 -765 135 -765 -765 -765 -765 318 -765 140 -765 -765 -765 -765 -765 318 -765 40 -765 218 -765 -765 -765 318 205 -765 -765 218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.7e+003 0.000000 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCTYTW MEME-3 regular expression -------------------------------------------------------------------------------- CGTCT[CT]T[AT] -------------------------------------------------------------------------------- Time 7.31 secs. ******************************************************************************** ******************************************************************************** MOTIF GGTTTMCA MEME-4 width = 8 sites = 2 llr = 25 E-value = 1.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::5:a pos.-specific C :::::5a: probability G aa:::::: matrix T ::aaa::: bits 3.2 *** * 2.9 *** * 2.6 *** * 2.2 *** * Relative 1.9 *** * Entropy 1.6 *** * (18.0 bits) 1.3 ******** 1.0 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGTTTACA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:211752517-211752537 7 1.13e-06 GCAGAC GGTTTACA AAAAAA chr9:117160552-117160572 8 4.67e-06 CGCGTGG GGTTTCCA CGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:211752517-211752537 1.1e-06 6_[+4]_6 chr9:117160552-117160572 4.7e-06 7_[+4]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGTTTMCA width=8 seqs=2 chr1:211752517-211752537 ( 7) GGTTTACA 1 chr9:117160552-117160572 ( 8) GGTTTCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.9e+003 -765 -765 135 -765 -765 -765 135 -765 -765 -765 -765 318 -765 -765 -765 318 -765 -765 -765 318 205 40 -765 -765 -765 140 -765 -765 305 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.9e+003 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTTMCA MEME-4 regular expression -------------------------------------------------------------------------------- GGTTT[AC]CA -------------------------------------------------------------------------------- Time 10.33 secs. ******************************************************************************** ******************************************************************************** MOTIF CTGAGGTW MEME-5 width = 8 sites = 2 llr = 24 E-value = 3.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a:::5 pos.-specific C a::::::: probability G ::a:aa:: matrix T :a::::a5 bits 3.2 * * * 2.9 * * * 2.6 * * * 2.2 * * ** Relative 1.9 * * ** Entropy 1.6 * * ** (17.0 bits) 1.3 ******** 1.0 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTGAGGTA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr10:64564652-64564672 13 3.65e-06 CGCGTGGCTG CTGAGGTT chr16:47177548-47177568 7 7.66e-06 GAAGGG CTGAGGTA GCGGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:64564652-64564672 3.6e-06 12_[+5] chr16:47177548-47177568 7.7e-06 6_[+5]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGAGGTW width=8 seqs=2 chr10:64564652-64564672 ( 13) CTGAGGTT 1 chr16:47177548-47177568 ( 7) CTGAGGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 3.6e+003 -765 140 -765 -765 -765 -765 -765 318 -765 -765 135 -765 305 -765 -765 -765 -765 -765 135 -765 -765 -765 135 -765 -765 -765 -765 318 205 -765 -765 218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.6e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGAGGTW MEME-5 regular expression -------------------------------------------------------------------------------- CTGAGGT[AT] -------------------------------------------------------------------------------- Time 13.65 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:859191-859211 9.82e-01 20 chr16:56659564-56659584 9.59e-01 20 chr1:856649-856669 6.57e-01 20 chr16:56716255-56716275 3.53e-01 20 chr16:56691750-56691770 7.26e-01 20 chr12:129308119-12930813 9.44e-01 20 chr9:132805119-132805139 8.54e-01 20 chr15:59041624-59041644 7.88e-01 20 chr1:16825424-16825444 6.53e-01 20 chr6:2245679-2245699 1.00e+00 20 chr16:56642351-56642371 9.91e-01 20 chr10:112258062-11225808 1.21e-01 20 chr16:47177548-47177568 5.20e-03 6_[+5(7.66e-06)]_6 chr1:51984655-51984675 5.47e-01 20 chr10:112679509-11267952 9.92e-01 20 chr18:46478007-46478027 1.80e-02 20 chr12:12714820-12714840 2.99e-02 20 chr10:69644724-69644744 9.80e-01 20 chr9:123963689-123963709 1.00e+00 20 chr10:81107467-81107487 8.70e-01 20 chr11:119077088-11907710 9.76e-01 20 chr2:128459534-128459554 3.35e-06 6_[+2(1.65e-05)]_6 chr11:74460209-74460229 1.00e+00 20 chr7:43622990-43623010 4.15e-01 20 chr5:179160072-179160092 1.00e+00 20 chr7:151216500-151216520 8.42e-01 20 chr4:185746877-185746897 7.76e-01 20 chr10:99400664-99400684 2.13e-02 20 chr17:76777643-76777663 6.41e-01 20 chr4:146101207-146101227 5.58e-01 20 chr4:15656835-15656855 8.10e-01 20 chr1:15736500-15736520 1.84e-01 20 chr2:65283817-65283837 9.87e-01 20 chr5:139028065-139028085 6.33e-01 20 chr22:36783765-36783785 9.83e-01 20 chr1:172502396-172502416 2.22e-01 20 chr2:11886562-11886582 8.42e-01 20 chr9:131644651-131644671 8.73e-01 20 chr19:10829018-10829038 3.33e-02 20 chr3:150264100-150264120 1.00e+00 20 chr2:174830480-174830500 2.25e-01 20 chr1:32403795-32403815 3.85e-01 20 chr10:181876-181896 2.18e-01 20 chr7:99516869-99516889 8.80e-01 20 chr1:173991163-173991183 5.31e-05 [+1(1.17e-06)]_12 chr14:50360085-50360105 1.60e-01 20 chr16:4675070-4675090 3.87e-01 20 chr19:16187441-16187461 9.96e-01 20 chr3:47205067-47205087 9.74e-01 20 chr8:76319585-76319605 6.75e-01 20 chr1:9189012-9189032 9.69e-01 20 chr15:79049401-79049421 9.21e-02 20 chr10:22292362-22292382 4.73e-01 20 chr1:224371145-224371165 7.17e-01 20 chr17:37910342-37910362 6.69e-01 20 chr5:130599821-130599841 9.26e-01 20 chr4:6718093-6718113 9.86e-01 20 chr3:25706072-25706092 5.65e-02 20 chr6:157802315-157802335 1.00e+00 20 chr4:83294839-83294859 4.63e-01 20 chr2:178129303-178129323 1.53e-01 20 chr16:68119544-68119564 3.37e-01 20 chr17:46985967-46985987 1.89e-01 20 chr17:42296759-42296779 9.62e-01 20 chr17:4046058-4046078 9.83e-01 20 chr9:128003343-128003363 3.60e-01 20 chr4:1341209-1341229 9.66e-01 20 chr16:30346590-30346610 5.24e-05 [+3(5.02e-06)]_12 chr2:88926720-88926740 1.00e+00 20 chr5:156693431-156693451 6.85e-01 20 chr16:1832332-1832352 7.55e-01 20 chr1:198126269-198126289 8.10e-01 20 chr11:13299559-13299579 9.56e-01 20 chr15:90645513-90645533 1.28e-05 7_[+2(5.89e-06)]_5 chr4:113153093-113153113 5.21e-01 20 chr3:196594997-196595017 5.14e-01 20 chr3:178866398-178866418 9.18e-01 20 chr17:76164723-76164743 1.31e-01 20 chr16:88878823-88878843 5.64e-01 20 chr5:55290653-55290673 7.38e-01 20 chr7:6414345-6414365 9.83e-01 20 chr16:11836465-11836485 2.82e-01 20 chr16:88877805-88877825 9.03e-01 20 chr15:40226425-40226445 9.76e-01 20 chr10:86088637-86088657 9.99e-01 20 chr17:28088259-28088279 4.85e-05 4_[+2(1.78e-06)]_8 chr12:39836824-39836844 5.64e-01 20 chr11:65838036-65838056 6.58e-01 20 chr14:64971726-64971746 8.70e-01 20 chr19:39340430-39340450 8.54e-01 20 chr11:63606805-63606825 8.48e-01 20 chr10:3827149-3827169 3.45e-02 20 chr6:3119134-3119154 9.30e-01 20 chr9:74525816-74525836 1.57e-01 20 chr17:20946150-20946170 1.00e+00 20 chr7:33148886-33148906 2.69e-02 20 chr14:45366843-45366863 7.73e-05 2_[+1(1.17e-06)]_10 chr5:132072961-132072981 5.90e-01 20 chr3:39194878-39194898 2.24e-01 20 chr16:88729279-88729299 9.05e-04 20 chr10:112257283-11225730 1.15e-01 20 chr4:110481537-110481557 9.35e-01 20 chr5:114961456-114961476 7.93e-01 20 chr4:184425418-184425438 9.49e-01 20 chr1:1285087-1285107 2.64e-01 20 chr6:149638368-149638388 9.71e-01 20 chr9:36400534-36400554 7.75e-01 20 chr15:60884060-60884080 9.61e-01 20 chr5:95067030-95067050 9.64e-01 20 chr4:156874905-156874925 7.47e-01 20 chr20:62886909-62886929 9.90e-01 20 chr1:167522828-167522848 9.45e-01 20 chr6:160148851-160148871 4.26e-02 20 chr17:54910870-54910890 9.99e-01 20 chr16:31154059-31154079 9.27e-01 20 chr16:30670799-30670819 4.68e-01 20 chr16:87417257-87417277 3.68e-01 20 chr5:142783122-142783142 4.92e-01 20 chr17:73892751-73892771 9.98e-01 20 chr6:139013696-139013716 9.89e-01 20 chr15:63414311-63414331 9.96e-01 20 chr1:117909560-117909580 1.10e-01 20 chr21:45662498-45662518 7.35e-01 20 chr19:54693195-54693215 9.94e-01 20 chr20:3870223-3870243 9.01e-01 20 chr19:1491266-1491286 1.05e-01 20 chr10:88854403-88854423 9.60e-01 20 chr19:45579630-45579650 9.84e-01 20 chr5:77071859-77071879 8.78e-01 20 chr15:78441940-78441960 1.30e-01 20 chr9:140095022-140095042 5.02e-02 20 chr5:179719394-179719414 8.46e-01 20 chr4:79860472-79860492 2.85e-01 20 chr9:71320189-71320209 9.98e-01 20 chr10:64564652-64564672 1.75e-04 12_[+5(3.65e-06)] chr5:178287220-178287240 6.12e-01 20 chr13:31774185-31774205 4.67e-01 20 chr3:128902686-128902706 4.16e-06 10_[+1(3.39e-07)]_2 chr3:182511632-182511652 9.96e-01 20 chr4:71705308-71705328 9.86e-01 20 chr12:862395-862415 2.58e-02 20 chr19:10679412-10679432 9.59e-01 20 chr2:232573521-232573541 3.02e-01 20 chr12:104850842-10485086 8.99e-01 20 chr6:70577319-70577339 9.56e-01 20 chr15:65116325-65116345 9.96e-01 20 chr7:138145371-138145391 9.98e-01 20 chr22:38240094-38240114 1.00e+00 20 chr17:29298193-29298213 1.08e-01 20 chr1:43232435-43232455 4.89e-01 20 chr3:118959590-118959610 7.24e-01 20 chr2:114341545-114341565 9.80e-02 20 chr10:104402360-10440238 9.99e-01 20 chr6:116422015-116422035 7.47e-01 20 chr6:37138067-37138087 6.30e-01 20 chr1:25072054-25072074 2.92e-01 20 chr2:232572654-232572674 1.02e-03 8_[+2(1.31e-05)]_4 chr2:208634391-208634411 7.65e-01 20 chr14:105767144-10576716 1.00e+00 20 chr17:79875801-79875821 2.89e-01 20 chr2:223289406-223289426 9.97e-01 20 chr1:211752517-211752537 7.74e-04 6_[+4(1.13e-06)]_6 chr15:43425987-43426007 9.38e-01 20 chr4:147097053-147097073 2.75e-01 20 chr13:78271963-78271983 7.77e-01 20 chr11:64948866-64948886 1.02e-01 20 chr5:178053701-178053721 8.63e-01 20 chr20:8000193-8000213 8.62e-01 20 chr2:223725982-223726002 1.34e-01 20 chr6:26158666-26158686 2.66e-01 20 chr16:28834838-28834858 9.99e-01 20 chr14:54907874-54907894 9.79e-01 20 chr13:30689144-30689164 9.55e-01 20 chr14:105957722-10595774 5.98e-01 20 chr3:101568526-101568546 9.14e-01 20 chr3:52931453-52931473 3.11e-01 20 chr9:74980003-74980023 1.56e-01 20 chr4:2757921-2757941 4.34e-01 20 chr11:47788523-47788543 5.72e-01 20 chr1:21113029-21113049 6.26e-01 20 chr16:21513395-21513415 9.99e-01 20 chr11:65268031-65268051 9.98e-01 20 chr17:8339459-8339479 5.82e-02 20 chr14:105487241-10548726 9.12e-01 20 chr7:33102010-33102030 6.43e-01 20 chr9:125667373-125667393 1.96e-01 20 chr2:239112014-239112034 9.99e-01 20 chr11:110167187-11016720 9.56e-01 20 chr11:14380520-14380540 2.50e-01 20 chr20:2083675-2083695 9.45e-01 20 chr1:26799184-26799204 9.82e-01 20 chr11:92931001-92931021 7.44e-03 20 chr9:139838904-139838924 6.54e-01 20 chr6:52442244-52442264 7.55e-01 20 chr14:72399221-72399241 9.95e-01 20 chr22:22221584-22221604 9.42e-01 20 chr8:101964063-101964083 8.26e-01 20 chr11:64809014-64809034 2.56e-01 20 chr1:249200486-249200506 7.63e-04 20 chr1:197871833-197871853 9.66e-01 20 chr17:62207253-62207273 8.82e-01 20 chr22:18484114-18484134 3.63e-01 20 chr7:44887462-44887482 9.88e-01 20 chr2:242641088-242641108 8.19e-01 20 chr9:117160552-117160572 4.72e-06 7_[+4(4.67e-06)]_5 chr7:44836543-44836563 4.93e-01 20 chr12:133264357-13326437 6.21e-01 20 chr9:94124044-94124064 8.81e-01 20 chr2:24163419-24163439 4.70e-03 20 chr13:23949415-23949435 6.19e-01 20 chr12:96794040-96794060 1.00e+00 20 chr22:24129333-24129353 2.03e-01 20 chr15:74726109-74726129 2.13e-03 20 chr13:28194454-28194474 8.05e-01 20 chr6:64345867-64345887 2.04e-01 20 chr12:69202009-69202029 6.18e-02 20 chr4:139937200-139937220 8.20e-01 20 chr6:132833897-132833917 1.00e+00 20 chr10:105726971-10572699 9.71e-01 20 chr9:140500322-140500342 7.82e-01 20 chr11:694779-694799 5.63e-01 20 chr7:5568220-5568240 3.83e-01 20 chr10:93558367-93558387 6.12e-02 20 chr1:15573724-15573744 5.34e-01 20 chr8:132916472-132916492 7.46e-01 20 chr12:42538436-42538456 9.39e-01 20 chr5:176853887-176853907 8.77e-01 20 chr1:182992979-182992999 9.99e-01 20 chr4:53578876-53578896 2.17e-01 20 chr3:100053752-100053772 2.13e-01 20 chr1:17338378-17338398 8.04e-01 20 chr14:60794774-60794794 5.88e-03 20 chr1:236305979-236305999 8.08e-01 20 chr11:94277690-94277710 9.01e-01 20 chr19:14628960-14628980 5.04e-01 20 chr6:3068849-3068869 6.87e-01 20 chr19:11708508-11708528 2.04e-01 20 chr3:57678575-57678595 8.86e-01 20 chr6:71123502-71123522 2.06e-03 20 chr8:74659427-74659447 4.37e-01 20 chr6:43337040-43337060 4.84e-05 11_[+3(1.90e-06)]_1 chr17:43394220-43394240 9.99e-01 20 chr14:90085523-90085543 8.95e-01 20 chr20:32078194-32078214 9.48e-01 20 chr1:226309302-226309322 8.24e-01 20 chr8:96146197-96146217 1.87e-01 20 chr18:56338894-56338914 9.28e-01 20 chr16:128346-128366 9.22e-01 20 chr7:30324678-30324698 1.63e-02 20 chr6:146135686-146135706 9.96e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************