******************************************************************************** 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/BRCA1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr10:135186921-13518694 1.0000 20 chr9:123605268-123605288 1.0000 20 chr5:139493618-139493638 1.0000 20 chr16:90089016-90089036 1.0000 20 chr1:231473972-231473992 1.0000 20 chr16:30412021-30412041 1.0000 20 chr12:49351323-49351343 1.0000 20 chr1:207226310-207226330 1.0000 20 chr16:87985079-87985099 1.0000 20 chr11:13484842-13484862 1.0000 20 chr17:40118668-40118688 1.0000 20 chr10:51565137-51565157 1.0000 20 chr1:232941093-232941113 1.0000 20 chr15:75287791-75287811 1.0000 20 chr10:75118564-75118584 1.0000 20 chr17:7760908-7760928 1.0000 20 chr14:100705153-10070517 1.0000 20 chr6:151711719-151711739 1.0000 20 chrX:46433662-46433682 1.0000 20 chr3:160117030-160117050 1.0000 20 chr17:55162362-55162382 1.0000 20 chr16:84150456-84150476 1.0000 20 chrX:70474087-70474107 1.0000 20 chr15:48470538-48470558 1.0000 20 chr20:25604763-25604783 1.0000 20 chr6:47445481-47445501 1.0000 20 chr6:108279387-108279407 1.0000 20 chr17:34900669-34900689 1.0000 20 chr17:4167277-4167297 1.0000 20 chr8:104311082-104311102 1.0000 20 chr8:42249123-42249143 1.0000 20 chr12:27091362-27091382 1.0000 20 chr2:225450248-225450268 1.0000 20 chr20:3767432-3767452 1.0000 20 chr17:53046070-53046090 1.0000 20 chr19:4124169-4124189 1.0000 20 chr4:144434620-144434640 1.0000 20 chr2:176032894-176032914 1.0000 20 chr17:27717295-27717315 1.0000 20 chr5:39074499-39074519 1.0000 20 chr4:15683249-15683269 1.0000 20 chr2:170683910-170683930 1.0000 20 chr1:207224380-207224400 1.0000 20 chr5:176449648-176449668 1.0000 20 chr11:66035219-66035239 1.0000 20 chr19:5828280-5828300 1.0000 20 chr4:26322600-26322620 1.0000 20 chr3:49131529-49131549 1.0000 20 chr9:98637863-98637883 1.0000 20 chr2:136743189-136743209 1.0000 20 chr4:140374870-140374890 1.0000 20 chrX:40944858-40944878 1.0000 20 chr19:13057097-13057117 1.0000 20 chr5:169010723-169010743 1.0000 20 chr6:44355252-44355272 1.0000 20 chr5:132387643-132387663 1.0000 20 chrX:118740411-118740431 1.0000 20 chr6:28863448-28863468 1.0000 20 chr3:194304670-194304690 1.0000 20 chr2:219773785-219773805 1.0000 20 chr15:66649020-66649040 1.0000 20 chr6:35436647-35436667 1.0000 20 chr2:85843336-85843356 1.0000 20 chr7:134671233-134671253 1.0000 20 chr8:67940834-67940854 1.0000 20 chr7:158497512-158497532 1.0000 20 chr12:12849193-12849213 1.0000 20 chr9:32550933-32550953 1.0000 20 chr5:56469857-56469877 1.0000 20 chr6:13574625-13574645 1.0000 20 chr15:69452884-69452904 1.0000 20 chr15:85197548-85197568 1.0000 20 chr16:87526655-87526675 1.0000 20 chr2:201754464-201754484 1.0000 20 chr3:169482934-169482954 1.0000 20 chr15:73925755-73925775 1.0000 20 chr5:138940742-138940762 1.0000 20 chr3:186501960-186501980 1.0000 20 chr16:14165150-14165170 1.0000 20 chr16:25269294-25269314 1.0000 20 chr4:57843885-57843905 1.0000 20 chr12:57940995-57941015 1.0000 20 chr17:4843558-4843578 1.0000 20 chr11:75294398-75294418 1.0000 20 chr9:88555920-88555940 1.0000 20 chr3:194815964-194815984 1.0000 20 chr6:43395554-43395574 1.0000 20 chr1:53308496-53308516 1.0000 20 chr2:120517280-120517300 1.0000 20 chr22:45809519-45809539 1.0000 20 chr13:21750741-21750761 1.0000 20 chr22:50689740-50689760 1.0000 20 chrX:153059824-153059844 1.0000 20 chr6:3849621-3849641 1.0000 20 chr6:71122940-71122960 1.0000 20 chr1:6296078-6296098 1.0000 20 chr4:103749206-103749226 1.0000 20 chr10:7830047-7830067 1.0000 20 chr6:146285606-146285626 1.0000 20 chr19:9434953-9434973 1.0000 20 chr10:102820535-10282055 1.0000 20 chr3:150421740-150421760 1.0000 20 chr19:56905015-56905035 1.0000 20 chr4:68411191-68411211 1.0000 20 chr4:26321228-26321248 1.0000 20 chrX:153607335-153607355 1.0000 20 chr2:160568952-160568972 1.0000 20 chr1:205718264-205718284 1.0000 20 chr2:74406026-74406046 1.0000 20 chr12:80328963-80328983 1.0000 20 chr8:144911539-144911559 1.0000 20 chr19:37341730-37341750 1.0000 20 chr1:104068547-104068567 1.0000 20 chr5:180673524-180673544 1.0000 20 chr10:15139064-15139084 1.0000 20 chr20:30539781-30539801 1.0000 20 chrX:63615393-63615413 1.0000 20 chr2:25194964-25194984 1.0000 20 chr6:97731159-97731179 1.0000 20 chr22:50051209-50051229 1.0000 20 chr22:38597778-38597798 1.0000 20 chr17:8079765-8079785 1.0000 20 chr12:11324244-11324264 1.0000 20 chr1:24306865-24306885 1.0000 20 chr17:37607588-37607608 1.0000 20 chr16:68119150-68119170 1.0000 20 chr10:112064716-11206473 1.0000 20 chr11:95976651-95976671 1.0000 20 chrX:117480061-117480081 1.0000 20 chr21:47673753-47673773 1.0000 20 chr11:11863454-11863474 1.0000 20 chr17:78428560-78428580 1.0000 20 chr6:149638642-149638662 1.0000 20 chr2:172017426-172017446 1.0000 20 chr12:29534187-29534207 1.0000 20 chr19:34663271-34663291 1.0000 20 chr17:79527826-79527846 1.0000 20 chr16:188671-188691 1.0000 20 chr10:75173848-75173868 1.0000 20 chr11:22851502-22851522 1.0000 20 chr15:22833405-22833425 1.0000 20 chr10:76871143-76871163 1.0000 20 chr1:1447151-1447171 1.0000 20 chr19:18530837-18530857 1.0000 20 chr4:17812537-17812557 1.0000 20 chr19:51228334-51228354 1.0000 20 chr1:78148368-78148388 1.0000 20 chr8:38089083-38089103 1.0000 20 chr1:10555511-10555531 1.0000 20 chr20:62601307-62601327 1.0000 20 chr19:18263825-18263845 1.0000 20 chr17:7343418-7343438 1.0000 20 chr17:2415237-2415257 1.0000 20 chr10:101380782-10138080 1.0000 20 chr1:167905782-167905802 1.0000 20 chrX:13752741-13752761 1.0000 20 chr17:28088558-28088578 1.0000 20 chr13:31736576-31736596 1.0000 20 chr3:137893772-137893792 1.0000 20 chr10:97803263-97803283 1.0000 20 chr15:65185810-65185830 1.0000 20 chr14:34931702-34931722 1.0000 20 chr2:19548149-19548169 1.0000 20 chr19:3434928-3434948 1.0000 20 chr9:6413143-6413163 1.0000 20 chr1:53019111-53019131 1.0000 20 chr12:132569516-13256953 1.0000 20 chr10:118608980-11860900 1.0000 20 chr15:78730455-78730475 1.0000 20 chr3:125803189-125803209 1.0000 20 chr11:107880047-10788006 1.0000 20 chr6:52284989-52285009 1.0000 20 chr17:73401756-73401776 1.0000 20 chr12:125473666-12547368 1.0000 20 chrX:48555111-48555131 1.0000 20 chr4:25378834-25378854 1.0000 20 chr1:41157274-41157294 1.0000 20 chrX:48660174-48660194 1.0000 20 chr15:65476873-65476893 1.0000 20 chr7:4814693-4814713 1.0000 20 chr1:70820404-70820424 1.0000 20 chr3:53231248-53231268 1.0000 20 chr14:71787008-71787028 1.0000 20 chr7:2443154-2443174 1.0000 20 chr1:26146645-26146665 1.0000 20 chrX:30907540-30907560 1.0000 20 chr16:83841570-83841590 1.0000 20 chr6:116601119-116601139 1.0000 20 chr3:139108514-139108534 1.0000 20 chr6:33168626-33168646 1.0000 20 chr20:3748597-3748617 1.0000 20 chr9:72873902-72873922 1.0000 20 chr10:102802882-10280290 1.0000 20 chr19:36980462-36980482 1.0000 20 chr12:129308559-12930857 1.0000 20 chr17:37009705-37009725 1.0000 20 chr11:70161131-70161151 1.0000 20 chr3:169684551-169684571 1.0000 20 chr1:78444864-78444884 1.0000 20 chr5:159846232-159846252 1.0000 20 chr15:76603812-76603832 1.0000 20 chr10:124768328-12476834 1.0000 20 chr16:31192023-31192043 1.0000 20 chrX:118987022-118987042 1.0000 20 chr6:35995442-35995462 1.0000 20 chr3:17784323-17784343 1.0000 20 chr7:100303613-100303633 1.0000 20 chr5:175788802-175788822 1.0000 20 chr10:101989355-10198937 1.0000 20 chr11:85376213-85376233 1.0000 20 chr9:82187519-82187539 1.0000 20 chr13:79177744-79177764 1.0000 20 chr2:207630319-207630339 1.0000 20 chr2:27632594-27632614 1.0000 20 chr7:35840576-35840596 1.0000 20 chr1:111991961-111991981 1.0000 20 chr3:127771027-127771047 1.0000 20 chrX:151999534-151999554 1.0000 20 chr5:65439986-65440006 1.0000 20 chr13:52769660-52769680 1.0000 20 chr1:59165743-59165763 1.0000 20 chr5:138629335-138629355 1.0000 20 chr12:72057659-72057679 1.0000 20 chr10:69609220-69609240 1.0000 20 chrX:53711355-53711375 1.0000 20 chr12:118407207-11840722 1.0000 20 chr10:75385790-75385810 1.0000 20 chr6:2765341-2765361 1.0000 20 chr14:64970470-64970490 1.0000 20 chr14:105767075-10576709 1.0000 20 chr9:6681687-6681707 1.0000 20 chr5:127418805-127418825 1.0000 20 chr1:11159901-11159921 1.0000 20 chr16:67867857-67867877 1.0000 20 chr8:52811810-52811830 1.0000 20 chr6:7313598-7313618 1.0000 20 chr9:100818762-100818782 1.0000 20 chr19:36103607-36103627 1.0000 20 chr14:74318596-74318616 1.0000 20 chr16:4524671-4524691 1.0000 20 chr12:7261155-7261175 1.0000 20 chr1:19923436-19923456 1.0000 20 chr20:30467934-30467954 1.0000 20 chr18:74535814-74535834 1.0000 20 chr2:20101456-20101476 1.0000 20 chr11:8704246-8704266 1.0000 20 chr20:44539711-44539731 1.0000 20 chr5:125691882-125691902 1.0000 20 chr19:12273858-12273878 1.0000 20 chr21:38445442-38445462 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_BRCA1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/BRCA1.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 0.172 C 0.333 G 0.318 T 0.178 Background letter frequencies (from file dataset with add-one prior applied): A 0.172 C 0.333 G 0.318 T 0.178 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCGCGMGA MEME-1 width = 8 sites = 79 llr = 557 E-value = 2.4e-067 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :11::5:9 pos.-specific C 191a:3:1 probability G 1:6:a29: matrix T 8:2:::1: bits 2.5 2.3 2.0 1.8 * * Relative 1.5 * ** * Entropy 1.3 ** ** ** (10.2 bits) 1.0 ** ** ** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TCGCGAGA consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:11159901-11159921 11 1.88e-05 ACGGCTCGTC TCGCGAGA GC chr9:6681687-6681707 6 1.88e-05 GGCTC TCGCGAGA CCCGGCG chr15:76603812-76603832 1 1.88e-05 . TCGCGAGA CGCGCGAACG chr1:70820404-70820424 5 1.88e-05 CCTC TCGCGAGA GCTCCCCC chr1:41157274-41157294 11 1.88e-05 TTCCCAATTC TCGCGAGA CC chr11:107880047-10788006 4 1.88e-05 GTC TCGCGAGA GTCCAAGTT chr9:6413143-6413163 6 1.88e-05 GGATC TCGCGAGA TCCGGCT chr11:11863454-11863474 5 1.88e-05 ATTC TCGCGAGA GCGGCCGC chr10:112064716-11206473 4 1.88e-05 GTC TCGCGAGA AATACAAAC chr6:3849621-3849641 6 1.88e-05 GGCTG TCGCGAGA GCCCGGG chrX:153059824-153059844 5 1.88e-05 GCTC TCGCGAGA GTTCGACG chr13:21750741-21750761 1 1.88e-05 . TCGCGAGA GCCGAAGTCT chr22:45809519-45809539 3 1.88e-05 TG TCGCGAGA AGAGAGCGAG chr2:120517280-120517300 1 1.88e-05 . TCGCGAGA TCGCCTCCTG chr5:56469857-56469877 8 1.88e-05 CACGATC TCGCGAGA CTTGG chr7:158497512-158497532 7 1.88e-05 CCGCTC TCGCGAGA GCTGGG chr2:136743189-136743209 7 1.88e-05 GAAAGA TCGCGAGA GCTGCG chr2:170683910-170683930 8 1.88e-05 CCGGGTA TCGCGAGA GTTGG chr17:53046070-53046090 7 1.88e-05 TCCGTC TCGCGAGA TCTGGG chr10:51565137-51565157 12 1.88e-05 AGCGGAGATC TCGCGAGA C chr5:139493618-139493638 11 1.88e-05 CCCGCAGATC TCGCGAGA GT chr11:70161131-70161151 9 7.58e-05 actcacta tcacgaga acgg chr3:53231248-53231268 6 7.58e-05 agttc tcacgaga ttggatg chr20:30539781-30539801 11 7.58e-05 CTTGCGGCTC TCGCGCGA CC chr8:67940834-67940854 6 7.58e-05 GCCGC TCACGAGA AATCTCG chr14:105767075-10576709 2 9.61e-05 c tctcgcga ggccccgctc chr7:2443154-2443174 13 9.61e-05 ggccgcgACG TCTCGCGA chr10:75173848-75173868 2 9.61e-05 G TCTCGCGA GCCCGTTAGG chr17:78428560-78428580 13 9.61e-05 GAAGCCTAAC TCTCGCGA chr6:97731159-97731179 13 9.61e-05 CCCCACGAAT TCTCGCGA chr2:25194964-25194984 5 9.61e-05 GGAG TCTCGCGA TGCTAGCG chr10:15139064-15139084 7 9.61e-05 GCATGG TCTCGCGA TACATA chr4:26321228-26321248 5 9.61e-05 ACGT TCTCGCGA GGTTTAGG chr6:146285606-146285626 5 9.61e-05 GGAG TCTCGCGA TAGCTCTG chr4:57843885-57843905 2 9.61e-05 T TCTCGCGA TTTAAGCTCT chr7:134671233-134671253 8 9.61e-05 TCCGAAG TCTCGCGA GGGCG chr15:66649020-66649040 13 9.61e-05 TAAGCGCGCT TCTCGCGA chr4:26322600-26322620 12 9.61e-05 TCGGGGGGAA TCTCGCGA G chr14:100705153-10070517 3 9.61e-05 AG TCTCGCGA GGCCGGGCCC chr19:12273858-12273878 7 1.41e-04 ACCTTC TCGCGGGA TTTTCA chr1:78148368-78148388 1 1.41e-04 . TCGCGATA CAAACCCACT chr6:71122940-71122960 3 1.41e-04 TC TCGCGGGA ACTTGGGAAC chr3:194304670-194304690 1 1.41e-04 . TCGCGGGA GGCGGTGGCT chr10:75118564-75118584 7 1.41e-04 CAAGAC TCGCGATA ACCCTC chr1:59165743-59165763 6 2.21e-04 CGTCC TCCCGAGA GATCCCG chr5:159846232-159846252 13 2.66e-04 CTGCTGCGTA TCGCGCTA chr10:69609220-69609240 6 3.71e-04 AGGCA TCGCGAGC ATCGCGA chr5:65439986-65440006 5 3.71e-04 AGCC GCGCGAGA ACCGCCGG chr3:17784323-17784343 3 3.71e-04 AG GCGCGAGA AGCGAGTAGG chr19:18530837-18530857 13 3.71e-04 TTGAGGGGGC GCGCGAGA chr3:150421740-150421760 1 3.71e-04 . TCGCGAGC GCGAGCCTCT chr6:43395554-43395574 2 3.71e-04 A CCGCGAGA ATGGGCGGGG chr6:151711719-151711739 1 3.71e-04 . GCGCGAGA GCCGGAGACA chr10:135186921-13518694 1 3.71e-04 . CCGCGAGA CCAGGCGGCC chr2:27632594-27632614 7 4.05e-04 CGAGAC TAGCGCGA CCACGC chr10:7830047-7830067 9 4.05e-04 CCTCGCCG TAGCGCGA AGAA chr5:169010723-169010743 1 4.05e-04 . TCGTGAGA CGTGGGACTT chr22:50689740-50689760 13 4.91e-04 TCCCGGTCGC TATCGCGA chr20:30467934-30467954 8 5.68e-04 GCGCAAG TCCCGCGA GCCCG chr4:15683249-15683269 13 5.68e-04 GAGGCGGAAA TCCCGCGA chr5:125691882-125691902 9 8.85e-04 attcactg ccacgaga atgg chrX:48555111-48555131 4 8.85e-04 CGC CCGCGCGA GCGCTCTTC chr12:27091362-27091382 10 9.20e-04 GCCCCACAG TAACGCGA GGA chrX:63615393-63615413 2 9.52e-04 A TCGCGACA CTTTGACCGT chr2:20101456-20101476 12 1.00e-03 GATAGTTACC TCCCGGGA C chr10:101989355-10198937 1 1.20e-03 . TCGCGCGT CTTTGTTCTC chr6:116601119-116601139 11 1.20e-03 ACTGGAGATC TCACGGTA TC chr5:175788802-175788822 7 1.46e-03 CGGAGA CCGCGGGA TCTCGC chr10:101380782-10138080 12 1.46e-03 CGGGATCTCG TCGCGGGC G chr15:22833405-22833425 1 1.46e-03 . GCGCGGGA GCGCGAACTC chr19:37341730-37341750 1 1.46e-03 . CCGCGATA ACTAGATTGT chr9:88555920-88555940 1 1.46e-03 . TCGCGATC GTCTCTAATC chr19:13057097-13057117 9 1.46e-03 CTCGCGGG GCGCGGGA GTCA chr19:4124169-4124189 1 1.50e-03 . TAACGGGA TCGGGAGCCG chr3:127771027-127771047 9 1.69e-03 CCGCGCGC TCTCGCGT TACC chr2:172017426-172017446 1 1.69e-03 . TCACGCGC CGCCTGTGCA chr1:111991961-111991981 7 1.85e-03 TCGCCC TCATGCGA TAGGCT chr10:76871143-76871163 10 1.85e-03 CGGTTCTCC TCTCGGGC CCA chr3:169482934-169482954 9 1.85e-03 AGTCACTC TCTCGGGC GGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:11159901-11159921 1.9e-05 10_[+1]_2 chr9:6681687-6681707 1.9e-05 5_[+1]_7 chr15:76603812-76603832 1.9e-05 [+1]_12 chr1:70820404-70820424 1.9e-05 4_[+1]_8 chr1:41157274-41157294 1.9e-05 10_[+1]_2 chr11:107880047-10788006 1.9e-05 3_[+1]_9 chr9:6413143-6413163 1.9e-05 5_[+1]_7 chr11:11863454-11863474 1.9e-05 4_[+1]_8 chr10:112064716-11206473 1.9e-05 3_[+1]_9 chr6:3849621-3849641 1.9e-05 5_[+1]_7 chrX:153059824-153059844 1.9e-05 4_[+1]_8 chr13:21750741-21750761 1.9e-05 [+1]_12 chr22:45809519-45809539 1.9e-05 2_[+1]_10 chr2:120517280-120517300 1.9e-05 [+1]_12 chr5:56469857-56469877 1.9e-05 7_[+1]_5 chr7:158497512-158497532 1.9e-05 6_[+1]_6 chr2:136743189-136743209 1.9e-05 6_[+1]_6 chr2:170683910-170683930 1.9e-05 7_[+1]_5 chr17:53046070-53046090 1.9e-05 6_[+1]_6 chr10:51565137-51565157 1.9e-05 11_[+1]_1 chr5:139493618-139493638 1.9e-05 10_[+1]_2 chr11:70161131-70161151 7.6e-05 8_[+1]_4 chr3:53231248-53231268 7.6e-05 5_[+1]_7 chr20:30539781-30539801 7.6e-05 10_[+1]_2 chr8:67940834-67940854 7.6e-05 5_[+1]_7 chr14:105767075-10576709 9.6e-05 1_[+1]_11 chr7:2443154-2443174 9.6e-05 12_[+1] chr10:75173848-75173868 9.6e-05 1_[+1]_11 chr17:78428560-78428580 9.6e-05 12_[+1] chr6:97731159-97731179 9.6e-05 12_[+1] chr2:25194964-25194984 9.6e-05 4_[+1]_8 chr10:15139064-15139084 9.6e-05 6_[+1]_6 chr4:26321228-26321248 9.6e-05 4_[+1]_8 chr6:146285606-146285626 9.6e-05 4_[+1]_8 chr4:57843885-57843905 9.6e-05 1_[+1]_11 chr7:134671233-134671253 9.6e-05 7_[+1]_5 chr15:66649020-66649040 9.6e-05 12_[+1] chr4:26322600-26322620 9.6e-05 11_[+1]_1 chr14:100705153-10070517 9.6e-05 2_[+1]_10 chr19:12273858-12273878 0.00014 6_[+1]_6 chr1:78148368-78148388 0.00014 [+1]_12 chr6:71122940-71122960 0.00014 2_[+1]_10 chr3:194304670-194304690 0.00014 [+1]_12 chr10:75118564-75118584 0.00014 6_[+1]_6 chr1:59165743-59165763 0.00022 5_[+1]_7 chr5:159846232-159846252 0.00027 12_[+1] chr10:69609220-69609240 0.00037 5_[+1]_7 chr5:65439986-65440006 0.00037 4_[+1]_8 chr3:17784323-17784343 0.00037 2_[+1]_10 chr19:18530837-18530857 0.00037 12_[+1] chr3:150421740-150421760 0.00037 [+1]_12 chr6:43395554-43395574 0.00037 1_[+1]_11 chr6:151711719-151711739 0.00037 [+1]_12 chr10:135186921-13518694 0.00037 [+1]_12 chr2:27632594-27632614 0.00041 6_[+1]_6 chr10:7830047-7830067 0.00041 8_[+1]_4 chr5:169010723-169010743 0.00041 [+1]_12 chr22:50689740-50689760 0.00049 12_[+1] chr20:30467934-30467954 0.00057 7_[+1]_5 chr4:15683249-15683269 0.00057 12_[+1] chr5:125691882-125691902 0.00088 8_[+1]_4 chrX:48555111-48555131 0.00088 3_[+1]_9 chr12:27091362-27091382 0.00092 9_[+1]_3 chrX:63615393-63615413 0.00095 1_[+1]_11 chr2:20101456-20101476 0.001 11_[+1]_1 chr10:101989355-10198937 0.0012 [+1]_12 chr6:116601119-116601139 0.0012 10_[+1]_2 chr5:175788802-175788822 0.0015 6_[+1]_6 chr10:101380782-10138080 0.0015 11_[+1]_1 chr15:22833405-22833425 0.0015 [+1]_12 chr19:37341730-37341750 0.0015 [+1]_12 chr9:88555920-88555940 0.0015 [+1]_12 chr19:13057097-13057117 0.0015 8_[+1]_4 chr19:4124169-4124189 0.0015 [+1]_12 chr3:127771027-127771047 0.0017 8_[+1]_4 chr2:172017426-172017446 0.0017 [+1]_12 chr1:111991961-111991981 0.0018 6_[+1]_6 chr10:76871143-76871163 0.0018 9_[+1]_3 chr3:169482934-169482954 0.0018 8_[+1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCGCGMGA width=8 seqs=79 chr1:11159901-11159921 ( 11) TCGCGAGA 1 chr9:6681687-6681707 ( 6) TCGCGAGA 1 chr15:76603812-76603832 ( 1) TCGCGAGA 1 chr1:70820404-70820424 ( 5) TCGCGAGA 1 chr1:41157274-41157294 ( 11) TCGCGAGA 1 chr11:107880047-10788006 ( 4) TCGCGAGA 1 chr9:6413143-6413163 ( 6) TCGCGAGA 1 chr11:11863454-11863474 ( 5) TCGCGAGA 1 chr10:112064716-11206473 ( 4) TCGCGAGA 1 chr6:3849621-3849641 ( 6) TCGCGAGA 1 chrX:153059824-153059844 ( 5) TCGCGAGA 1 chr13:21750741-21750761 ( 1) TCGCGAGA 1 chr22:45809519-45809539 ( 3) TCGCGAGA 1 chr2:120517280-120517300 ( 1) TCGCGAGA 1 chr5:56469857-56469877 ( 8) TCGCGAGA 1 chr7:158497512-158497532 ( 7) TCGCGAGA 1 chr2:136743189-136743209 ( 7) TCGCGAGA 1 chr2:170683910-170683930 ( 8) TCGCGAGA 1 chr17:53046070-53046090 ( 7) TCGCGAGA 1 chr10:51565137-51565157 ( 12) TCGCGAGA 1 chr5:139493618-139493638 ( 11) TCGCGAGA 1 chr11:70161131-70161151 ( 9) TCACGAGA 1 chr3:53231248-53231268 ( 6) TCACGAGA 1 chr20:30539781-30539801 ( 11) TCGCGCGA 1 chr8:67940834-67940854 ( 6) TCACGAGA 1 chr14:105767075-10576709 ( 2) TCTCGCGA 1 chr7:2443154-2443174 ( 13) TCTCGCGA 1 chr10:75173848-75173868 ( 2) TCTCGCGA 1 chr17:78428560-78428580 ( 13) TCTCGCGA 1 chr6:97731159-97731179 ( 13) TCTCGCGA 1 chr2:25194964-25194984 ( 5) TCTCGCGA 1 chr10:15139064-15139084 ( 7) TCTCGCGA 1 chr4:26321228-26321248 ( 5) TCTCGCGA 1 chr6:146285606-146285626 ( 5) TCTCGCGA 1 chr4:57843885-57843905 ( 2) TCTCGCGA 1 chr7:134671233-134671253 ( 8) TCTCGCGA 1 chr15:66649020-66649040 ( 13) TCTCGCGA 1 chr4:26322600-26322620 ( 12) TCTCGCGA 1 chr14:100705153-10070517 ( 3) TCTCGCGA 1 chr19:12273858-12273878 ( 7) TCGCGGGA 1 chr1:78148368-78148388 ( 1) TCGCGATA 1 chr6:71122940-71122960 ( 3) TCGCGGGA 1 chr3:194304670-194304690 ( 1) TCGCGGGA 1 chr10:75118564-75118584 ( 7) TCGCGATA 1 chr1:59165743-59165763 ( 6) TCCCGAGA 1 chr5:159846232-159846252 ( 13) TCGCGCTA 1 chr10:69609220-69609240 ( 6) TCGCGAGC 1 chr5:65439986-65440006 ( 5) GCGCGAGA 1 chr3:17784323-17784343 ( 3) GCGCGAGA 1 chr19:18530837-18530857 ( 13) GCGCGAGA 1 chr3:150421740-150421760 ( 1) TCGCGAGC 1 chr6:43395554-43395574 ( 2) CCGCGAGA 1 chr6:151711719-151711739 ( 1) GCGCGAGA 1 chr10:135186921-13518694 ( 1) CCGCGAGA 1 chr2:27632594-27632614 ( 7) TAGCGCGA 1 chr10:7830047-7830067 ( 9) TAGCGCGA 1 chr5:169010723-169010743 ( 1) TCGTGAGA 1 chr22:50689740-50689760 ( 13) TATCGCGA 1 chr20:30467934-30467954 ( 8) TCCCGCGA 1 chr4:15683249-15683269 ( 13) TCCCGCGA 1 chr5:125691882-125691902 ( 9) CCACGAGA 1 chrX:48555111-48555131 ( 4) CCGCGCGA 1 chr12:27091362-27091382 ( 10) TAACGCGA 1 chrX:63615393-63615413 ( 2) TCGCGACA 1 chr2:20101456-20101476 ( 12) TCCCGGGA 1 chr10:101989355-10198937 ( 1) TCGCGCGT 1 chr6:116601119-116601139 ( 11) TCACGGTA 1 chr5:175788802-175788822 ( 7) CCGCGGGA 1 chr10:101380782-10138080 ( 12) TCGCGGGC 1 chr15:22833405-22833425 ( 1) GCGCGGGA 1 chr19:37341730-37341750 ( 1) CCGCGATA 1 chr9:88555920-88555940 ( 1) TCGCGATC 1 chr19:13057097-13057117 ( 9) GCGCGGGA 1 chr19:4124169-4124189 ( 1) TAACGGGA 1 chr3:127771027-127771047 ( 9) TCTCGCGT 1 chr2:172017426-172017446 ( 1) TCACGCGC 1 chr1:111991961-111991981 ( 7) TCATGCGA 1 chr10:76871143-76871163 ( 10) TCTCGGGC 1 chr3:169482934-169482954 ( 9) TCTCGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.18385 E= 2.4e-067 -1295 -213 -206 225 -144 149 -1295 -1295 -59 -272 94 36 -1295 155 -1295 -281 -1295 -1295 165 -1295 156 4 -106 -1295 -1295 -471 152 -123 237 -191 -1295 -281 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 79 E= 2.4e-067 0.000000 0.075949 0.075949 0.848101 0.063291 0.936709 0.000000 0.000000 0.113924 0.050633 0.607595 0.227848 0.000000 0.974684 0.000000 0.025316 0.000000 0.000000 1.000000 0.000000 0.506329 0.341772 0.151899 0.000000 0.000000 0.012658 0.911392 0.075949 0.886076 0.088608 0.000000 0.025316 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGCGMGA MEME-1 regular expression -------------------------------------------------------------------------------- TC[GT]CG[AC]GA -------------------------------------------------------------------------------- Time 2.08 secs. ******************************************************************************** ******************************************************************************** MOTIF GRGVTCTC MEME-2 width = 8 sites = 45 llr = 292 E-value = 1.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1534:::: pos.-specific C 2::337:a probability G 7372:::: matrix T :2::73a: bits 2.5 * 2.3 * 2.0 * 1.8 * Relative 1.5 * ** Entropy 1.3 * ** (9.4 bits) 1.0 * **** 0.8 ** **** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GAGATCTC consensus GACCT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:44539711-44539731 10 1.61e-05 CGAGACCCT GAGATTTC TCG chr5:127418805-127418825 4 1.61e-05 CGC GAGATTTC GGGCTCAGC chr5:138629335-138629355 10 4.52e-05 GGTGGGGGC GAGCTCTC TCG chr13:79177744-79177764 10 4.52e-05 CGTCCCGGG GAGCTCTC GCG chr3:186501960-186501980 10 4.52e-05 CGGCGCTCC GAGCTCTC GCG chr10:101380782-10138080 3 8.12e-05 GC GGGATCTC GTCGCGGGCG chr15:69452884-69452904 13 8.12e-05 TGCCGTGGCT GGGATCTC chr20:3767432-3767452 13 8.12e-05 cgggcggagc gggATCTC chr11:75294398-75294418 12 1.12e-04 CCCGCGTCCC GAGGTCTC G chr4:17812537-17812557 4 1.31e-04 CGC GGGATTTC CCCCTCTCG chr9:98637863-98637883 8 1.31e-04 AGAAAGG AAGATTTC GTTCT chrX:53711355-53711375 5 1.63e-04 CCAC GAGGTTTC CGACCCAC chr3:169684551-169684571 1 1.63e-04 . GAGGTTTC CACCGCCCCC chr15:22833405-22833425 13 1.63e-04 GCGGGAGCGC GAACTCTC chr12:12849193-12849213 10 1.63e-04 CTCCTCAGG CAGATCTC GCG chr7:35840576-35840596 10 1.83e-04 GGGGAGGCG GTAATCTC GCG chr17:27717295-27717315 11 1.83e-04 TGTCAGGCGG AAAATCTC GC chr5:180673524-180673544 12 2.25e-04 CACCCAGACC GAGACCTC G chr13:21750741-21750761 12 2.25e-04 CGCGAGAGCC GAAGTCTC T chr1:24306865-24306885 1 2.57e-04 . GAGACTTC ACTCCCGCCT chr5:39074499-39074519 7 2.71e-04 ACACCG GAAACCTC GCCCAA chrX:118987022-118987042 12 3.41e-04 GGGTCCTGCC AAGCTCTC G chrX:13752741-13752761 12 3.41e-04 ACCCTGGGAT GTGCTCTC G chr22:38597778-38597798 10 3.41e-04 ACACCCACG GGGCTCTC GCG chr8:104311082-104311102 7 4.97e-04 ATCGCT CAGCTCTC GCTCCC chr6:108279387-108279407 11 4.97e-04 ccgccgtcgc cAGCTCTC GC chr2:74406026-74406046 7 6.02e-04 CGAGCT AAGGTTTC GCTGCG chr19:56905015-56905035 10 6.02e-04 CCTTGAAGC CGGATCTC GCG chr19:5828280-5828300 12 6.02e-04 CGCGGCCCCG GGACTCTC G chr15:65185810-65185830 1 8.21e-04 . gtgacctc aggccagtca chr1:10555511-10555531 5 8.21e-04 GTCA GTGACCTC TGACTTCT chr2:85843336-85843356 3 8.21e-04 CG GGAGTCTC GCGGTTCCAC chr12:7261155-7261175 13 9.04e-04 CTAGGACTCA GAGGCCTC chr10:102820535-10282055 13 9.04e-04 CGACAGTTGC GAGGCCTC chr9:88555920-88555940 13 9.77e-04 GCGATCGTCT CTAATCTC chr6:44355252-44355272 6 9.77e-04 GAGCC GTAGTTTC TTCCATT chr5:169010723-169010743 12 9.77e-04 CGTGAGACGT GGGACTTC T chr6:33168626-33168646 10 1.20e-03 AGGTGGAAC GGAACTTC CTG chr12:80328963-80328983 8 1.20e-03 ATCTAAC GTAACTTC GCGAG chr20:25604763-25604783 11 1.27e-03 CTCCCAGGGT ATGGTCTC TC chr15:85197548-85197568 12 1.33e-03 GGGGGCCGCG CGGCTCTC G chr17:55162362-55162382 11 1.33e-03 GGAGAGATGA CGGCTCTC TC chr10:75385790-75385810 13 1.37e-03 ACACGAGAAG AGACTCTC chr3:125803189-125803209 2 1.59e-03 C GGGCCCTC CTCGCAGCTG chr2:176032894-176032914 3 2.50e-03 CA CAGGCTTC CGTCCTCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:44539711-44539731 1.6e-05 9_[+2]_3 chr5:127418805-127418825 1.6e-05 3_[+2]_9 chr5:138629335-138629355 4.5e-05 9_[+2]_3 chr13:79177744-79177764 4.5e-05 9_[+2]_3 chr3:186501960-186501980 4.5e-05 9_[+2]_3 chr10:101380782-10138080 8.1e-05 2_[+2]_10 chr15:69452884-69452904 8.1e-05 12_[+2] chr20:3767432-3767452 8.1e-05 12_[+2] chr11:75294398-75294418 0.00011 11_[+2]_1 chr4:17812537-17812557 0.00013 3_[+2]_9 chr9:98637863-98637883 0.00013 7_[+2]_5 chrX:53711355-53711375 0.00016 4_[+2]_8 chr3:169684551-169684571 0.00016 [+2]_12 chr15:22833405-22833425 0.00016 12_[+2] chr12:12849193-12849213 0.00016 9_[+2]_3 chr7:35840576-35840596 0.00018 9_[+2]_3 chr17:27717295-27717315 0.00018 10_[+2]_2 chr5:180673524-180673544 0.00022 11_[+2]_1 chr13:21750741-21750761 0.00022 11_[+2]_1 chr1:24306865-24306885 0.00026 [+2]_12 chr5:39074499-39074519 0.00027 6_[+2]_6 chrX:118987022-118987042 0.00034 11_[+2]_1 chrX:13752741-13752761 0.00034 11_[+2]_1 chr22:38597778-38597798 0.00034 9_[+2]_3 chr8:104311082-104311102 0.0005 6_[+2]_6 chr6:108279387-108279407 0.0005 10_[+2]_2 chr2:74406026-74406046 0.0006 6_[+2]_6 chr19:56905015-56905035 0.0006 9_[+2]_3 chr19:5828280-5828300 0.0006 11_[+2]_1 chr15:65185810-65185830 0.00082 [+2]_12 chr1:10555511-10555531 0.00082 4_[+2]_8 chr2:85843336-85843356 0.00082 2_[+2]_10 chr12:7261155-7261175 0.0009 12_[+2] chr10:102820535-10282055 0.0009 12_[+2] chr9:88555920-88555940 0.00098 12_[+2] chr6:44355252-44355272 0.00098 5_[+2]_7 chr5:169010723-169010743 0.00098 11_[+2]_1 chr6:33168626-33168646 0.0012 9_[+2]_3 chr12:80328963-80328983 0.0012 7_[+2]_5 chr20:25604763-25604783 0.0013 10_[+2]_2 chr15:85197548-85197568 0.0013 11_[+2]_1 chr17:55162362-55162382 0.0013 10_[+2]_2 chr10:75385790-75385810 0.0014 12_[+2] chr3:125803189-125803209 0.0016 1_[+2]_11 chr2:176032894-176032914 0.0025 2_[+2]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GRGVTCTC width=8 seqs=45 chr20:44539711-44539731 ( 10) GAGATTTC 1 chr5:127418805-127418825 ( 4) GAGATTTC 1 chr5:138629335-138629355 ( 10) GAGCTCTC 1 chr13:79177744-79177764 ( 10) GAGCTCTC 1 chr3:186501960-186501980 ( 10) GAGCTCTC 1 chr10:101380782-10138080 ( 3) GGGATCTC 1 chr15:69452884-69452904 ( 13) GGGATCTC 1 chr20:3767432-3767452 ( 13) GGGATCTC 1 chr11:75294398-75294418 ( 12) GAGGTCTC 1 chr4:17812537-17812557 ( 4) GGGATTTC 1 chr9:98637863-98637883 ( 8) AAGATTTC 1 chrX:53711355-53711375 ( 5) GAGGTTTC 1 chr3:169684551-169684571 ( 1) GAGGTTTC 1 chr15:22833405-22833425 ( 13) GAACTCTC 1 chr12:12849193-12849213 ( 10) CAGATCTC 1 chr7:35840576-35840596 ( 10) GTAATCTC 1 chr17:27717295-27717315 ( 11) AAAATCTC 1 chr5:180673524-180673544 ( 12) GAGACCTC 1 chr13:21750741-21750761 ( 12) GAAGTCTC 1 chr1:24306865-24306885 ( 1) GAGACTTC 1 chr5:39074499-39074519 ( 7) GAAACCTC 1 chrX:118987022-118987042 ( 12) AAGCTCTC 1 chrX:13752741-13752761 ( 12) GTGCTCTC 1 chr22:38597778-38597798 ( 10) GGGCTCTC 1 chr8:104311082-104311102 ( 7) CAGCTCTC 1 chr6:108279387-108279407 ( 11) CAGCTCTC 1 chr2:74406026-74406046 ( 7) AAGGTTTC 1 chr19:56905015-56905035 ( 10) CGGATCTC 1 chr19:5828280-5828300 ( 12) GGACTCTC 1 chr15:65185810-65185830 ( 1) GTGACCTC 1 chr1:10555511-10555531 ( 5) GTGACCTC 1 chr2:85843336-85843356 ( 3) GGAGTCTC 1 chr12:7261155-7261175 ( 13) GAGGCCTC 1 chr10:102820535-10282055 ( 13) GAGGCCTC 1 chr9:88555920-88555940 ( 13) CTAATCTC 1 chr6:44355252-44355272 ( 6) GTAGTTTC 1 chr5:169010723-169010743 ( 12) GGGACTTC 1 chr6:33168626-33168646 ( 10) GGAACTTC 1 chr12:80328963-80328983 ( 8) GTAACTTC 1 chr20:25604763-25604783 ( 11) ATGGTCTC 1 chr15:85197548-85197568 ( 12) CGGCTCTC 1 chr17:55162362-55162382 ( 11) CGGCTCTC 1 chr10:75385790-75385810 ( 13) AGACTCTC 1 chr3:125803189-125803209 ( 2) GGGCCCTC 1 chr2:176032894-176032914 ( 3) CAGGCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.71451 E= 1.0e-008 -37 -90 112 -1214 157 -1214 -3 0 63 -1214 121 -1214 137 -10 -38 -1214 -1214 -32 -1214 205 -1214 110 -1214 70 -1214 -1214 -1214 249 -1214 159 -1214 -1214 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 1.0e-008 0.133333 0.177778 0.688889 0.000000 0.511111 0.000000 0.311111 0.177778 0.266667 0.000000 0.733333 0.000000 0.444444 0.311111 0.244444 0.000000 0.000000 0.266667 0.000000 0.733333 0.000000 0.711111 0.000000 0.288889 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGVTCTC MEME-2 regular expression -------------------------------------------------------------------------------- G[AG][GA][ACG][TC][CT]TC -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** MOTIF GATAGTHA MEME-3 width = 8 sites = 4 llr = 43 E-value = 4.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:a:33a pos.-specific C ::::::5: probability G a:::a::: matrix T ::a::83: bits 2.5 *** * 2.3 *** * 2.0 *** * 1.8 ****** * Relative 1.5 ****** * Entropy 1.3 ****** * (15.7 bits) 1.0 ****** * 0.8 ****** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GATAGTCA consensus AA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:139108514-139108534 2 5.43e-06 C GATAGTCA GAGGCCAGGG chr2:20101456-20101476 2 1.11e-05 C GATAGTTA CCTCCCGGGA chr15:65476873-65476893 9 1.11e-05 CGCACAGT GATAGTAA CATC chr17:4843558-4843578 2 1.64e-05 C GATAGACA CAGCAACTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:139108514-139108534 5.4e-06 1_[+3]_11 chr2:20101456-20101476 1.1e-05 1_[+3]_11 chr15:65476873-65476893 1.1e-05 8_[+3]_4 chr17:4843558-4843578 1.6e-05 1_[+3]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GATAGTHA width=8 seqs=4 chr3:139108514-139108534 ( 2) GATAGTCA 1 chr2:20101456-20101476 ( 2) GATAGTTA 1 chr15:65476873-65476893 ( 9) GATAGTAA 1 chr17:4843558-4843578 ( 2) GATAGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.66445 E= 4.7e+002 -865 -865 165 -865 254 -865 -865 -865 -865 -865 -865 249 254 -865 -865 -865 -865 -865 165 -865 54 -865 -865 208 54 59 -865 49 254 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 4.7e+002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 0.250000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAGTHA MEME-3 regular expression -------------------------------------------------------------------------------- GATAG[TA][CAT]A -------------------------------------------------------------------------------- Time 3.39 secs. ******************************************************************************** ******************************************************************************** MOTIF AAWRCAAA MEME-4 width = 8 sites = 2 llr = 23 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A aa55:aaa pos.-specific C ::::a::: probability G :::5:::: matrix T ::5::::: bits 2.5 ** *** 2.3 ** *** 2.0 ** *** 1.8 ** *** Relative 1.5 *** **** Entropy 1.3 *** **** (16.9 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAACAAA consensus TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr10:112064716-11206473 12 3.02e-06 TCTCGCGAGA AATACAAA C chr12:57940995-57941015 11 8.60e-06 GCAGAAGGGT AAAGCAAA AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:112064716-11206473 3e-06 11_[+4]_1 chr12:57940995-57941015 8.6e-06 10_[+4]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAWRCAAA width=8 seqs=2 chr10:112064716-11206473 ( 12) AATACAAA 1 chr12:57940995-57941015 ( 11) AAAGCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.3e+003 253 -765 -765 -765 253 -765 -765 -765 154 -765 -765 149 154 -765 65 -765 -765 158 -765 -765 253 -765 -765 -765 253 -765 -765 -765 253 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.3e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWRCAAA MEME-4 regular expression -------------------------------------------------------------------------------- AA[AT][AG]CAAA -------------------------------------------------------------------------------- Time 5.89 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAAGAVG MEME-5 width = 8 sites = 5 llr = 50 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 Description -------------------------------------------------------------------------------- Simplified A a:8a:a42 pos.-specific C ::::::4: probability G :a::a:28 matrix T ::2::::: bits 2.5 * * * 2.3 * * * 2.0 * * * 1.8 ****** Relative 1.5 ****** Entropy 1.3 ****** (14.3 bits) 1.0 ****** * 0.8 ****** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGAAGAAG consensus T CA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:52811810-52811830 1 1.68e-05 . AGAAGACG ATGGCGGTAG chr17:2415237-2415257 10 1.68e-05 CTTGAAGAA AGAAGAAA CCC chr2:219773785-219773805 4 1.68e-05 GCG AGAAGACG CGCTATCGC chr2:225450248-225450268 1 2.58e-05 . AGAAGAGG GCGAGCGCGC chr19:9434953-9434973 6 3.59e-05 GCGAG AGTAGAAG GGTGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:52811810-52811830 1.7e-05 [+5]_12 chr17:2415237-2415257 1.7e-05 9_[+5]_3 chr2:219773785-219773805 1.7e-05 3_[+5]_9 chr2:225450248-225450268 2.6e-05 [+5]_12 chr19:9434953-9434973 3.6e-05 5_[+5]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGAAGAVG width=8 seqs=5 chr8:52811810-52811830 ( 1) AGAAGACG 1 chr17:2415237-2415257 ( 10) AGAAGAAA 1 chr2:219773785-219773805 ( 4) AGAAGACG 1 chr2:225450248-225450268 ( 1) AGAAGAGG 1 chr19:9434953-9434973 ( 6) AGTAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.2866 E= 1.8e+003 254 -897 -897 -897 -897 -897 165 -897 222 -897 -897 17 254 -897 -897 -897 -897 -897 165 -897 254 -897 -897 -897 122 27 -67 -897 22 -897 133 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.8e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGAVG MEME-5 regular expression -------------------------------------------------------------------------------- AG[AT]AGA[ACG][GA] -------------------------------------------------------------------------------- Time 8.50 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:135186921-13518694 3.34e-02 20 chr9:123605268-123605288 5.35e-01 20 chr5:139493618-139493638 3.92e-04 10_[+1(1.88e-05)]_2 chr16:90089016-90089036 3.91e-01 20 chr1:231473972-231473992 7.42e-01 20 chr16:30412021-30412041 4.00e-01 20 chr12:49351323-49351343 1.48e-01 20 chr1:207226310-207226330 1.15e-01 20 chr16:87985079-87985099 1.14e-01 20 chr11:13484842-13484862 4.39e-01 20 chr17:40118668-40118688 2.39e-01 20 chr10:51565137-51565157 1.26e-05 5_[+2(1.05e-05)]_7 chr1:232941093-232941113 1.25e-01 20 chr15:75287791-75287811 3.18e-01 20 chr10:75118564-75118584 1.26e-02 20 chr17:7760908-7760928 3.63e-01 20 chr14:100705153-10070517 1.08e-01 2_[+1(9.61e-05)]_10 chr6:151711719-151711739 2.58e-02 20 chrX:46433662-46433682 2.93e-02 20 chr3:160117030-160117050 1.14e-01 20 chr17:55162362-55162382 6.81e-03 20 chr16:84150456-84150476 8.07e-01 20 chrX:70474087-70474107 6.91e-01 20 chr15:48470538-48470558 1.12e-01 20 chr20:25604763-25604783 2.08e-01 20 chr6:47445481-47445501 8.26e-01 20 chr6:108279387-108279407 1.63e-01 20 chr17:34900669-34900689 9.26e-01 20 chr17:4167277-4167297 1.00e+00 20 chr8:104311082-104311102 5.93e-02 20 chr8:42249123-42249143 4.63e-02 20 chr12:27091362-27091382 1.65e-02 20 chr2:225450248-225450268 7.56e-03 [+5(2.58e-05)]_12 chr20:3767432-3767452 1.14e-02 12_[+2(8.12e-05)] chr17:53046070-53046090 3.85e-03 6_[+1(1.88e-05)]_6 chr19:4124169-4124189 5.46e-02 20 chr4:144434620-144434640 2.56e-01 20 chr2:176032894-176032914 6.13e-01 20 chr17:27717295-27717315 4.17e-02 20 chr5:39074499-39074519 1.24e-02 20 chr4:15683249-15683269 6.72e-03 20 chr2:170683910-170683930 1.86e-03 7_[+1(1.88e-05)]_5 chr1:207224380-207224400 3.15e-01 20 chr5:176449648-176449668 9.96e-01 20 chr11:66035219-66035239 8.89e-01 20 chr19:5828280-5828300 1.08e-01 20 chr4:26322600-26322620 2.81e-03 11_[+1(9.61e-05)]_1 chr3:49131529-49131549 8.43e-01 20 chr9:98637863-98637883 1.42e-04 20 chr2:136743189-136743209 9.45e-04 6_[+1(1.88e-05)]_6 chr4:140374870-140374890 7.31e-01 20 chrX:40944858-40944878 9.45e-01 20 chr19:13057097-13057117 1.07e-01 20 chr5:169010723-169010743 4.83e-03 20 chr6:44355252-44355272 1.27e-01 20 chr5:132387643-132387663 7.48e-01 20 chrX:118740411-118740431 3.00e-01 20 chr6:28863448-28863468 1.41e-01 20 chr3:194304670-194304690 7.90e-02 20 chr2:219773785-219773805 7.99e-03 3_[+5(1.68e-05)]_9 chr15:66649020-66649040 6.04e-02 12_[+1(9.61e-05)] chr6:35436647-35436667 7.09e-01 20 chr2:85843336-85843356 6.82e-02 20 chr7:134671233-134671253 1.77e-03 7_[+1(9.61e-05)]_5 chr8:67940834-67940854 3.18e-06 11_[+2(2.18e-05)]_1 chr7:158497512-158497532 4.88e-03 6_[+1(1.88e-05)]_6 chr12:12849193-12849213 2.49e-02 20 chr9:32550933-32550953 2.53e-01 20 chr5:56469857-56469877 2.84e-03 7_[+1(1.88e-05)]_5 chr6:13574625-13574645 8.31e-01 20 chr15:69452884-69452904 1.07e-01 12_[+2(8.12e-05)] chr15:85197548-85197568 3.69e-01 20 chr16:87526655-87526675 8.23e-01 20 chr2:201754464-201754484 4.22e-01 20 chr3:169482934-169482954 4.70e-01 20 chr15:73925755-73925775 4.43e-01 20 chr5:138940742-138940762 6.21e-01 20 chr3:186501960-186501980 9.45e-02 9_[+2(4.52e-05)]_3 chr16:14165150-14165170 7.90e-01 20 chr16:25269294-25269314 9.80e-01 20 chr4:57843885-57843905 1.03e-02 1_[+1(9.61e-05)]_11 chr12:57940995-57941015 9.38e-04 10_[+4(8.60e-06)]_2 chr17:4843558-4843578 1.63e-03 1_[+3(1.64e-05)]_11 chr11:75294398-75294418 4.15e-02 20 chr9:88555920-88555940 1.00e-02 20 chr3:194815964-194815984 3.44e-01 20 chr6:43395554-43395574 5.27e-02 20 chr1:53308496-53308516 9.83e-01 20 chr2:120517280-120517300 3.86e-03 [+1(1.88e-05)]_12 chr22:45809519-45809539 1.21e-05 2_[+1(1.88e-05)]_10 chr13:21750741-21750761 1.52e-05 [+1(1.88e-05)]_12 chr22:50689740-50689760 2.00e-01 20 chrX:153059824-153059844 4.50e-04 4_[+1(1.88e-05)]_8 chr6:3849621-3849641 9.48e-03 5_[+1(1.88e-05)]_7 chr6:71122940-71122960 5.50e-02 20 chr1:6296078-6296098 9.95e-01 20 chr4:103749206-103749226 6.22e-02 20 chr10:7830047-7830067 1.02e-01 20 chr6:146285606-146285626 9.64e-04 4_[+1(9.61e-05)]_8 chr19:9434953-9434973 2.82e-03 5_[+5(3.59e-05)]_7 chr10:102820535-10282055 4.13e-02 20 chr3:150421740-150421760 3.19e-02 20 chr19:56905015-56905035 6.33e-02 20 chr4:68411191-68411211 1.60e-01 20 chr4:26321228-26321248 1.16e-02 4_[+1(9.61e-05)]_8 chrX:153607335-153607355 9.61e-01 20 chr2:160568952-160568972 4.24e-01 20 chr1:205718264-205718284 6.78e-02 20 chr2:74406026-74406046 1.52e-01 20 chr12:80328963-80328983 3.74e-02 20 chr8:144911539-144911559 9.15e-01 20 chr19:37341730-37341750 7.16e-03 20 chr1:104068547-104068567 4.84e-02 20 chr5:180673524-180673544 6.63e-03 20 chr10:15139064-15139084 1.92e-05 6_[+1(9.61e-05)]_6 chr20:30539781-30539801 1.41e-02 10_[+1(7.58e-05)]_2 chrX:63615393-63615413 1.64e-01 20 chr2:25194964-25194984 1.67e-03 4_[+1(9.61e-05)]_8 chr6:97731159-97731179 1.23e-02 12_[+1(9.61e-05)] chr22:50051209-50051229 1.46e-01 20 chr22:38597778-38597798 1.95e-01 20 chr17:8079765-8079785 4.65e-01 20 chr12:11324244-11324264 6.24e-01 20 chr1:24306865-24306885 3.00e-02 20 chr17:37607588-37607608 7.86e-01 20 chr16:68119150-68119170 2.78e-01 20 chr10:112064716-11206473 4.77e-07 3_[+1(1.88e-05)]_[+4(3.02e-06)]_1 chr11:95976651-95976671 9.41e-01 20 chrX:117480061-117480081 8.27e-01 20 chr21:47673753-47673773 8.97e-01 20 chr11:11863454-11863474 2.37e-02 4_[+1(1.88e-05)]_8 chr17:78428560-78428580 1.54e-03 12_[+1(9.61e-05)] chr6:149638642-149638662 9.48e-01 20 chr2:172017426-172017446 1.18e-01 20 chr12:29534187-29534207 3.88e-01 20 chr19:34663271-34663291 4.74e-01 20 chr17:79527826-79527846 9.11e-01 20 chr16:188671-188691 9.72e-01 20 chr10:75173848-75173868 9.08e-02 1_[+1(9.61e-05)]_11 chr11:22851502-22851522 4.47e-01 20 chr15:22833405-22833425 3.85e-03 20 chr10:76871143-76871163 2.51e-01 20 chr1:1447151-1447171 9.99e-01 20 chr19:18530837-18530857 1.15e-01 20 chr4:17812537-17812557 1.52e-01 20 chr19:51228334-51228354 5.21e-01 20 chr1:78148368-78148388 2.06e-05 20 chr8:38089083-38089103 7.95e-01 20 chr1:10555511-10555531 1.09e-01 20 chr20:62601307-62601327 9.91e-01 20 chr19:18263825-18263845 3.81e-01 20 chr17:7343418-7343438 9.26e-01 20 chr17:2415237-2415257 5.02e-04 9_[+5(1.68e-05)]_3 chr10:101380782-10138080 1.06e-02 2_[+2(8.12e-05)]_10 chr1:167905782-167905802 1.78e-01 20 chrX:13752741-13752761 1.21e-01 20 chr17:28088558-28088578 6.31e-01 20 chr13:31736576-31736596 9.22e-01 20 chr3:137893772-137893792 7.24e-01 20 chr10:97803263-97803283 2.01e-02 20 chr15:65185810-65185830 5.75e-02 20 chr14:34931702-34931722 9.65e-01 20 chr2:19548149-19548169 1.03e-01 20 chr19:3434928-3434948 8.92e-01 20 chr9:6413143-6413163 1.82e-02 5_[+1(1.88e-05)]_7 chr1:53019111-53019131 2.42e-01 20 chr12:132569516-13256953 9.63e-01 20 chr10:118608980-11860900 8.60e-01 20 chr15:78730455-78730475 9.90e-01 20 chr3:125803189-125803209 5.38e-01 20 chr11:107880047-10788006 2.17e-04 3_[+1(1.88e-05)]_9 chr6:52284989-52285009 8.19e-01 20 chr17:73401756-73401776 9.99e-01 20 chr12:125473666-12547368 9.48e-01 20 chrX:48555111-48555131 1.35e-01 20 chr4:25378834-25378854 9.00e-01 20 chr1:41157274-41157294 4.51e-03 10_[+1(1.88e-05)]_2 chrX:48660174-48660194 6.84e-01 20 chr15:65476873-65476893 4.56e-04 8_[+3(1.11e-05)]_4 chr7:4814693-4814713 1.97e-03 20 chr1:70820404-70820424 3.53e-03 4_[+1(1.88e-05)]_8 chr3:53231248-53231268 1.89e-02 5_[+1(7.58e-05)]_7 chr14:71787008-71787028 9.64e-01 20 chr7:2443154-2443174 3.26e-02 12_[+1(9.61e-05)] chr1:26146645-26146665 6.46e-01 20 chrX:30907540-30907560 7.67e-01 20 chr16:83841570-83841590 1.63e-01 20 chr6:116601119-116601139 2.11e-04 4_[+2(1.05e-05)]_8 chr3:139108514-139108534 2.01e-03 1_[+3(5.43e-06)]_11 chr6:33168626-33168646 4.23e-02 20 chr20:3748597-3748617 1.49e-01 20 chr9:72873902-72873922 9.50e-01 20 chr10:102802882-10280290 3.89e-01 20 chr19:36980462-36980482 4.72e-01 20 chr12:129308559-12930857 3.44e-01 20 chr17:37009705-37009725 5.77e-01 20 chr11:70161131-70161151 2.58e-02 8_[+1(7.58e-05)]_4 chr3:169684551-169684571 1.37e-01 20 chr1:78444864-78444884 8.54e-01 20 chr5:159846232-159846252 1.78e-01 20 chr15:76603812-76603832 1.42e-02 [+1(1.88e-05)]_12 chr10:124768328-12476834 7.86e-01 20 chr16:31192023-31192043 4.85e-01 20 chrX:118987022-118987042 7.42e-02 20 chr6:35995442-35995462 9.06e-01 20 chr3:17784323-17784343 7.91e-03 20 chr7:100303613-100303633 7.96e-01 20 chr5:175788802-175788822 6.46e-03 10_[+2(8.12e-05)]_2 chr10:101989355-10198937 3.92e-01 20 chr11:85376213-85376233 6.89e-01 20 chr9:82187519-82187539 9.86e-01 20 chr13:79177744-79177764 6.88e-02 9_[+2(4.52e-05)]_3 chr2:207630319-207630339 3.09e-01 20 chr2:27632594-27632614 5.59e-02 20 chr7:35840576-35840596 6.88e-02 20 chr1:111991961-111991981 4.39e-02 20 chr3:127771027-127771047 1.74e-01 20 chrX:151999534-151999554 1.33e-01 20 chr5:65439986-65440006 6.96e-02 20 chr13:52769660-52769680 7.33e-01 20 chr1:59165743-59165763 5.72e-03 20 chr5:138629335-138629355 6.31e-02 9_[+2(4.52e-05)]_3 chr12:72057659-72057679 2.01e-01 20 chr10:69609220-69609240 1.16e-01 20 chrX:53711355-53711375 9.55e-02 20 chr12:118407207-11840722 8.66e-01 20 chr10:75385790-75385810 2.10e-04 7_[+5(4.07e-05)]_5 chr6:2765341-2765361 6.93e-01 20 chr14:64970470-64970490 8.12e-01 20 chr14:105767075-10576709 7.12e-02 1_[+1(9.61e-05)]_11 chr9:6681687-6681707 2.15e-02 5_[+1(1.88e-05)]_7 chr5:127418805-127418825 8.90e-03 3_[+2(1.61e-05)]_9 chr1:11159901-11159921 1.33e-02 10_[+1(1.88e-05)]_2 chr16:67867857-67867877 1.53e-01 20 chr8:52811810-52811830 4.93e-03 [+5(1.68e-05)]_12 chr6:7313598-7313618 8.87e-01 20 chr9:100818762-100818782 8.47e-01 20 chr19:36103607-36103627 8.74e-01 20 chr14:74318596-74318616 2.64e-01 20 chr16:4524671-4524691 7.92e-01 20 chr12:7261155-7261175 9.50e-02 20 chr1:19923436-19923456 5.03e-01 20 chr20:30467934-30467954 1.07e-01 20 chr18:74535814-74535834 8.48e-01 20 chr2:20101456-20101476 4.21e-04 1_[+3(1.11e-05)]_11 chr11:8704246-8704266 8.59e-01 20 chr20:44539711-44539731 4.77e-03 9_[+2(1.61e-05)]_3 chr5:125691882-125691902 8.80e-02 20 chr19:12273858-12273878 3.22e-03 20 chr21:38445442-38445462 9.00e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************