******************************************************************************** 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/ARID3A.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr19:55127687-55127707 1.0000 20 chr18:9118625-9118645 1.0000 20 chr9:100686063-100686083 1.0000 20 chr1:229850994-229851014 1.0000 20 chr4:57657626-57657646 1.0000 20 chr8:67527611-67527631 1.0000 20 chr9:140652208-140652228 1.0000 20 chr10:67658025-67658045 1.0000 20 chr3:23366423-23366443 1.0000 20 chr12:90343908-90343928 1.0000 20 chr15:75301627-75301647 1.0000 20 chr6:2881887-2881907 1.0000 20 chr7:22925122-22925142 1.0000 20 chr17:73286211-73286231 1.0000 20 chr7:43878679-43878699 1.0000 20 chr8:67521729-67521749 1.0000 20 chr1:46798268-46798288 1.0000 20 chr2:200843084-200843104 1.0000 20 chr2:171806985-171807005 1.0000 20 chr22:41821813-41821833 1.0000 20 chr6:11461031-11461051 1.0000 20 chr3:10262434-10262454 1.0000 20 chr2:68441711-68441731 1.0000 20 chr8:59555018-59555038 1.0000 20 chr1:16290778-16290798 1.0000 20 chr7:44927155-44927175 1.0000 20 chr6:138121237-138121257 1.0000 20 chr15:101112821-10111284 1.0000 20 chr21:34696493-34696513 1.0000 20 chr4:144280403-144280423 1.0000 20 chrX:1365871-1365891 1.0000 20 chr1:199121345-199121365 1.0000 20 chr1:186834584-186834604 1.0000 20 chr3:128839416-128839436 1.0000 20 chr6:127624063-127624083 1.0000 20 chr4:159972962-159972982 1.0000 20 chr10:16821645-16821665 1.0000 20 chr2:64341417-64341437 1.0000 20 chrX:1324957-1324977 1.0000 20 chr6:113951812-113951832 1.0000 20 chr7:69289492-69289512 1.0000 20 chr2:228348038-228348058 1.0000 20 chr9:132654371-132654391 1.0000 20 chr1:9136571-9136591 1.0000 20 chr11:75619980-75620000 1.0000 20 chr18:56355497-56355517 1.0000 20 chr8:95453045-95453065 1.0000 20 chr2:136970659-136970679 1.0000 20 chr12:50016309-50016329 1.0000 20 chr8:105635966-105635986 1.0000 20 chr16:27274309-27274329 1.0000 20 chr6:26312015-26312035 1.0000 20 chr12:23713681-23713701 1.0000 20 chr8:38243746-38243766 1.0000 20 chr7:45035493-45035513 1.0000 20 chr2:37319177-37319197 1.0000 20 chr13:46739878-46739898 1.0000 20 chr4:22485322-22485342 1.0000 20 chr10:63664474-63664494 1.0000 20 chr17:34906518-34906538 1.0000 20 chr6:138777278-138777298 1.0000 20 chr17:58730064-58730084 1.0000 20 chr18:13597215-13597235 1.0000 20 chr6:135335677-135335697 1.0000 20 chr14:23259773-23259793 1.0000 20 chr21:16198089-16198109 1.0000 20 chr18:51788582-51788602 1.0000 20 chr12:52430801-52430821 1.0000 20 chr7:49811342-49811362 1.0000 20 chr2:26492888-26492908 1.0000 20 chr1:153814696-153814716 1.0000 20 chr16:27378969-27378989 1.0000 20 chr10:63661076-63661096 1.0000 20 chr1:234534812-234534832 1.0000 20 chr20:15967460-15967480 1.0000 20 chr11:102345615-10234563 1.0000 20 chr16:20915979-20915999 1.0000 20 chr2:54191953-54191973 1.0000 20 chr12:90257544-90257564 1.0000 20 chr1:113728521-113728541 1.0000 20 chr11:9767240-9767260 1.0000 20 chr2:223298752-223298772 1.0000 20 chr12:92963948-92963968 1.0000 20 chr12:80685092-80685112 1.0000 20 chr1:51733853-51733873 1.0000 20 chr5:126097008-126097028 1.0000 20 chr4:84197598-84197618 1.0000 20 chr2:38162420-38162440 1.0000 20 chr12:40561947-40561967 1.0000 20 chr8:99479735-99479755 1.0000 20 chr17:31156962-31156982 1.0000 20 chr15:85925298-85925318 1.0000 20 chr22:46171700-46171720 1.0000 20 chr19:7186481-7186501 1.0000 20 chr1:25358968-25358988 1.0000 20 chr12:129283282-12928330 1.0000 20 chr17:73779477-73779497 1.0000 20 chr5:43245069-43245089 1.0000 20 chr14:73092615-73092635 1.0000 20 chr2:9748140-9748160 1.0000 20 chr5:139031798-139031818 1.0000 20 chr6:16421058-16421078 1.0000 20 chr8:98724058-98724078 1.0000 20 chr12:11802461-11802481 1.0000 20 chr1:200831386-200831406 1.0000 20 chr12:92439713-92439733 1.0000 20 chr16:10991224-10991244 1.0000 20 chr22:40221779-40221799 1.0000 20 chr19:9906912-9906932 1.0000 20 chr2:201319719-201319739 1.0000 20 chr1:218503576-218503596 1.0000 20 chr18:60452061-60452081 1.0000 20 chr20:10427789-10427809 1.0000 20 chr14:95678199-95678219 1.0000 20 chr7:20351213-20351233 1.0000 20 chr1:44229275-44229295 1.0000 20 chr5:124338603-124338623 1.0000 20 chr2:20357360-20357380 1.0000 20 chr7:128648895-128648915 1.0000 20 chr18:810458-810478 1.0000 20 chr6:106634867-106634887 1.0000 20 chr9:114672842-114672862 1.0000 20 chr10:90595517-90595537 1.0000 20 chr7:92263616-92263636 1.0000 20 chr11:22702975-22702995 1.0000 20 chr7:43556715-43556735 1.0000 20 chr3:178250382-178250402 1.0000 20 chr5:40487111-40487131 1.0000 20 chr5:114914475-114914495 1.0000 20 chrX:11551491-11551511 1.0000 20 chr7:142508902-142508922 1.0000 20 chr2:139025304-139025324 1.0000 20 chr12:94062892-94062912 1.0000 20 chr7:150073206-150073226 1.0000 20 chr5:138905487-138905507 1.0000 20 chr5:179967506-179967526 1.0000 20 chr17:8129494-8129514 1.0000 20 chr12:52444912-52444932 1.0000 20 chr2:208602273-208602293 1.0000 20 chr12:68151976-68151996 1.0000 20 chr2:182451641-182451661 1.0000 20 chr4:1213208-1213228 1.0000 20 chr8:119909548-119909568 1.0000 20 chr13:101195247-10119526 1.0000 20 chr2:37798441-37798461 1.0000 20 chr8:137083462-137083482 1.0000 20 chr19:6630905-6630925 1.0000 20 chr14:31449420-31449440 1.0000 20 chr10:93901982-93902002 1.0000 20 chr6:181474-181494 1.0000 20 chr5:65306413-65306433 1.0000 20 chr8:71065058-71065078 1.0000 20 chr12:121548151-12154817 1.0000 20 chr1:153714929-153714949 1.0000 20 chr2:55529555-55529575 1.0000 20 chr7:28191723-28191743 1.0000 20 chr18:39809719-39809739 1.0000 20 chr4:159998985-159999005 1.0000 20 chr5:131856647-131856667 1.0000 20 chr8:139175179-139175199 1.0000 20 chr8:56901895-56901915 1.0000 20 chr1:32378669-32378689 1.0000 20 chr6:4880139-4880159 1.0000 20 chr3:189391485-189391505 1.0000 20 chr8:9630937-9630957 1.0000 20 chr3:101510865-101510885 1.0000 20 chr3:88191377-88191397 1.0000 20 chr11:111700044-11170006 1.0000 20 chr10:22895266-22895286 1.0000 20 chr12:853273-853293 1.0000 20 chr16:68816814-68816834 1.0000 20 chr15:67196171-67196191 1.0000 20 chr11:115745819-11574583 1.0000 20 chr20:54949104-54949124 1.0000 20 chr6:106615407-106615427 1.0000 20 chr3:156382828-156382848 1.0000 20 chr12:46793446-46793466 1.0000 20 chr2:190817628-190817648 1.0000 20 chr12:12798961-12798981 1.0000 20 chr6:149376851-149376871 1.0000 20 chr19:48948864-48948884 1.0000 20 chr20:14810625-14810645 1.0000 20 chr7:110559341-110559361 1.0000 20 chr15:69396668-69396688 1.0000 20 chr2:44843964-44843984 1.0000 20 chr1:93050111-93050131 1.0000 20 chr2:159047708-159047728 1.0000 20 chr9:90115570-90115590 1.0000 20 chr10:135219599-13521961 1.0000 20 chr20:47405355-47405375 1.0000 20 chr3:142801185-142801205 1.0000 20 chr7:122269588-122269608 1.0000 20 chr2:65833766-65833786 1.0000 20 chr11:94335892-94335912 1.0000 20 chr15:67831988-67832008 1.0000 20 chr17:44223612-44223632 1.0000 20 chr6:4777587-4777607 1.0000 20 chr10:3668649-3668669 1.0000 20 chr11:22809276-22809296 1.0000 20 chr7:7860694-7860714 1.0000 20 chr11:64633340-64633360 1.0000 20 chr14:63938134-63938154 1.0000 20 chr20:35994943-35994963 1.0000 20 chrX:13275461-13275481 1.0000 20 chr6:97059478-97059498 1.0000 20 chr13:43619621-43619641 1.0000 20 chr10:97553662-97553682 1.0000 20 chr10:76613873-76613893 1.0000 20 chr1:108477327-108477347 1.0000 20 chr2:80694507-80694527 1.0000 20 chr13:49552184-49552204 1.0000 20 chr4:38940892-38940912 1.0000 20 chr5:72456176-72456196 1.0000 20 chr2:225384917-225384937 1.0000 20 chr11:110199019-11019903 1.0000 20 chr11:59943544-59943564 1.0000 20 chr3:170966821-170966841 1.0000 20 chr10:63747892-63747912 1.0000 20 chr2:143792058-143792078 1.0000 20 chr8:128219371-128219391 1.0000 20 chr11:65199009-65199029 1.0000 20 chr2:171017232-171017252 1.0000 20 chr6:111660378-111660398 1.0000 20 chr21:43948072-43948092 1.0000 20 chr4:110571161-110571181 1.0000 20 chr7:139357536-139357556 1.0000 20 chr1:170514848-170514868 1.0000 20 chr7:99994361-99994381 1.0000 20 chr11:75535572-75535592 1.0000 20 chr2:61220244-61220264 1.0000 20 chr11:74459616-74459636 1.0000 20 chr11:22225032-22225052 1.0000 20 chr20:57482998-57483018 1.0000 20 chr18:77283846-77283866 1.0000 20 chr19:18949731-18949751 1.0000 20 chr19:16560248-16560268 1.0000 20 chr10:63869833-63869853 1.0000 20 chr5:157157153-157157173 1.0000 20 chr3:104240878-104240898 1.0000 20 chr7:91763155-91763175 1.0000 20 chr6:15246056-15246076 1.0000 20 chr1:184712410-184712430 1.0000 20 chr2:216471079-216471099 1.0000 20 chr19:12111427-12111447 1.0000 20 chr5:134149768-134149788 1.0000 20 chr1:165723413-165723433 1.0000 20 chr17:68295205-68295225 1.0000 20 chr5:172411562-172411582 1.0000 20 chr11:67355543-67355563 1.0000 20 chr15:91201196-91201216 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_ARID3A/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/ARID3A.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 0.317 C 0.182 G 0.184 T 0.317 Background letter frequencies (from file dataset with add-one prior applied): A 0.317 C 0.182 G 0.184 T 0.317 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF MCACAKMC MEME-1 width = 8 sites = 15 llr = 118 E-value = 3.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5:8:a:7: pos.-specific C 3a:a:239 probability G :::::3:1 matrix T 2:2::5:: bits 2.5 * * 2.2 * * 2.0 * * * 1.7 * ** * Relative 1.5 * ** * Entropy 1.2 * ** * (11.4 bits) 1.0 **** ** 0.7 **** ** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel ACACATAC consensus C T GC sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr18:77283846-77283866 11 1.74e-05 TAACAGCTCA CCACATCC TG chr11:65199009-65199029 12 1.74e-05 tccgaggttc ccacatcc t chr3:128839416-128839436 8 1.74e-05 GTGGCAA CCACATCC TGCTG chr5:157157153-157157173 11 4.69e-05 GAGGATATAC ACACATAC TG chr2:171806985-171807005 7 4.69e-05 GGAAAA ACACATAC TGTGCG chr18:9118625-9118645 13 4.69e-05 TGTATTCACC ACACATAC chr6:113951812-113951832 1 9.67e-05 . acacacac acacTTCAAT chr6:11461031-11461051 12 9.67e-05 CGTTATGAac acacacac a chr12:12798961-12798981 13 1.45e-04 TCAGATTGGT TCACAGAC chr8:139175179-139175199 4 1.45e-04 TCA TCACAGAC AGTTAAGAC chr4:144280403-144280423 3 1.68e-04 CC CCTCATCC AGATGAGATG chr2:201319719-201319739 11 2.72e-04 GCCTGTTTTG ACTCAGCC AA chr2:225384917-225384937 2 2.78e-04 a ccacagag ataaaccaca chr11:94335892-94335912 12 3.13e-04 TATTCTTTAA ACACATAG T chr2:68441711-68441731 7 4.54e-04 atactg tctcacac cagtca -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr18:77283846-77283866 1.7e-05 10_[+1]_2 chr11:65199009-65199029 1.7e-05 11_[+1]_1 chr3:128839416-128839436 1.7e-05 7_[+1]_5 chr5:157157153-157157173 4.7e-05 10_[+1]_2 chr2:171806985-171807005 4.7e-05 6_[+1]_6 chr18:9118625-9118645 4.7e-05 12_[+1] chr6:113951812-113951832 9.7e-05 [+1]_12 chr6:11461031-11461051 9.7e-05 11_[+1]_1 chr12:12798961-12798981 0.00014 12_[+1] chr8:139175179-139175199 0.00014 3_[+1]_9 chr4:144280403-144280423 0.00017 2_[+1]_10 chr2:201319719-201319739 0.00027 10_[+1]_2 chr2:225384917-225384937 0.00028 1_[+1]_11 chr11:94335892-94335912 0.00031 11_[+1]_1 chr2:68441711-68441731 0.00045 6_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MCACAKMC width=8 seqs=15 chr18:77283846-77283866 ( 11) CCACATCC 1 chr11:65199009-65199029 ( 12) CCACATCC 1 chr3:128839416-128839436 ( 8) CCACATCC 1 chr5:157157153-157157173 ( 11) ACACATAC 1 chr2:171806985-171807005 ( 7) ACACATAC 1 chr18:9118625-9118645 ( 13) ACACATAC 1 chr6:113951812-113951832 ( 1) ACACACAC 1 chr6:11461031-11461051 ( 12) ACACACAC 1 chr12:12798961-12798981 ( 13) TCACAGAC 1 chr8:139175179-139175199 ( 4) TCACAGAC 1 chr4:144280403-144280423 ( 3) CCTCATCC 1 chr2:201319719-201319739 ( 11) ACTCAGCC 1 chr2:225384917-225384937 ( 2) CCACAGAG 1 chr11:94335892-94335912 ( 12) ACACATAG 1 chr2:68441711-68441731 ( 7) TCTCACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.0312 E= 3.9e+002 56 87 -1055 -67 -1055 246 -1055 -1055 134 -1055 -1055 -67 -1055 246 -1055 -1055 166 -1055 -1055 -1055 -1055 14 54 75 107 87 -1055 -1055 -1055 225 -46 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 3.9e+002 0.466667 0.333333 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.266667 0.533333 0.666667 0.333333 0.000000 0.000000 0.000000 0.866667 0.133333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACAKMC MEME-1 regular expression -------------------------------------------------------------------------------- [ACT]C[AT]CA[TGC][AC]C -------------------------------------------------------------------------------- Time 2.01 secs. ******************************************************************************** ******************************************************************************** MOTIF TGGGVCTG MEME-2 width = 8 sites = 8 llr = 74 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::3::: pos.-specific C ::::49:: probability G :9a941:8 matrix T a1:1::a3 bits 2.5 * 2.2 * 2.0 * * 1.7 **** ** Relative 1.5 **** *** Entropy 1.2 **** *** (13.4 bits) 1.0 **** *** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGGGCCTG consensus G T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:75535572-75535592 10 7.67e-06 CTAATAAGT TGGGCCTG AAG chr12:52444912-52444932 1 7.67e-06 . TGGGCCTG GGAGCTGCTA chr12:92963948-92963968 6 7.67e-06 ACACG TGGGGCTG ATATCTT chr12:50016309-50016329 6 2.75e-05 AGAGC TGGGCCTT CATTTGA chr20:57482998-57483018 1 6.17e-05 . TGGTGCTG ATGATCTATT chr6:4880139-4880159 9 6.17e-05 cagcaaaa ttgggctg aaaa chr12:92439713-92439733 5 7.32e-05 CCAA TGGGACTT ACATGCTT chr20:47405355-47405375 11 7.99e-05 tggggtatca tgggagtg ga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:75535572-75535592 7.7e-06 9_[+2]_3 chr12:52444912-52444932 7.7e-06 [+2]_12 chr12:92963948-92963968 7.7e-06 5_[+2]_7 chr12:50016309-50016329 2.8e-05 5_[+2]_7 chr20:57482998-57483018 6.2e-05 [+2]_12 chr6:4880139-4880159 6.2e-05 8_[+2]_4 chr12:92439713-92439733 7.3e-05 4_[+2]_8 chr20:47405355-47405375 8e-05 10_[+2]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGGGVCTG width=8 seqs=8 chr11:75535572-75535592 ( 10) TGGGCCTG 1 chr12:52444912-52444932 ( 1) TGGGCCTG 1 chr12:92963948-92963968 ( 6) TGGGGCTG 1 chr12:50016309-50016329 ( 6) TGGGCCTT 1 chr20:57482998-57483018 ( 1) TGGTGCTG 1 chr6:4880139-4880159 ( 9) TTGGGCTG 1 chr12:92439713-92439733 ( 5) TGGGACTT 1 chr20:47405355-47405375 ( 11) TGGGAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.40106 E= 1.5e+003 -965 -965 -965 165 -965 -965 225 -134 -965 -965 244 -965 -965 -965 225 -134 -34 104 103 -965 -965 227 -56 -965 -965 -965 -965 165 -965 -965 203 -34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 1.5e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.250000 0.375000 0.375000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGVCTG MEME-2 regular expression -------------------------------------------------------------------------------- TGGG[CGA]CT[GT] -------------------------------------------------------------------------------- Time 3.00 secs. ******************************************************************************** ******************************************************************************** MOTIF TCCCACSC MEME-3 width = 8 sites = 2 llr = 24 E-value = 2.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C :aaa:a5a probability G ::::::5: matrix T a::::::: bits 2.5 *** * * 2.2 *** * * 2.0 *** * * 1.7 ****** * Relative 1.5 ******** Entropy 1.2 ******** (17.1 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCCCACCC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:149376851-149376871 4 7.34e-06 CAC TCCCACCC ATGTCTTAT chr10:22895266-22895286 11 7.34e-06 GAGTGTTGGC TCCCACGC AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:149376851-149376871 7.3e-06 3_[+3]_9 chr10:22895266-22895286 7.3e-06 10_[+3]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCCCACSC width=8 seqs=2 chr6:149376851-149376871 ( 4) TCCCACCC 1 chr10:22895266-22895286 ( 11) TCCCACGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.81663 E= 2.4e+003 -765 -765 -765 165 -765 245 -765 -765 -765 245 -765 -765 -765 245 -765 -765 165 -765 -765 -765 -765 245 -765 -765 -765 145 144 -765 -765 245 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.4e+003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCACSC MEME-3 regular expression -------------------------------------------------------------------------------- TCCCAC[CG]C -------------------------------------------------------------------------------- Time 4.54 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCCCCRC MEME-4 width = 8 sites = 2 llr = 25 E-value = 6.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::5: pos.-specific C ::aaaa:a probability G aa::::5: matrix T :::::::: bits 2.5 ****** * 2.2 ****** * 2.0 ****** * 1.7 ****** * Relative 1.5 ****** * Entropy 1.2 ****** * (18.2 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGCCCCAC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:11802461-11802481 2 1.24e-06 c ggccccgc tacccgggtt chr8:95453045-95453065 9 3.39e-06 aaccccat ggccccac ctga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:11802461-11802481 1.2e-06 1_[+4]_11 chr8:95453045-95453065 3.4e-06 8_[+4]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCCCCRC width=8 seqs=2 chr12:11802461-11802481 ( 2) GGCCCCGC 1 chr8:95453045-95453065 ( 9) GGCCCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 6.5e+002 -765 -765 244 -765 -765 -765 244 -765 -765 245 -765 -765 -765 245 -765 -765 -765 245 -765 -765 -765 245 -765 -765 66 -765 144 -765 -765 245 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.5e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCCCRC MEME-4 regular expression -------------------------------------------------------------------------------- GGCCCC[AG]C -------------------------------------------------------------------------------- Time 5.69 secs. ******************************************************************************** ******************************************************************************** MOTIF TCCTCGGG MEME-5 width = 8 sites = 2 llr = 25 E-value = 2.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :aa:a::: probability G :::::aaa matrix T a::a:::: bits 2.5 ** **** 2.2 ** **** 2.0 ** **** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (18.0 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCCTCGGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr19:48948864-48948884 12 3.77e-06 GCCTTATGGG TCCTCGGG G chr8:38243746-38243766 2 3.77e-06 T TCCTCGGG CGTTAGCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:48948864-48948884 3.8e-06 11_[+5]_1 chr8:38243746-38243766 3.8e-06 1_[+5]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCCTCGGG width=8 seqs=2 chr19:48948864-48948884 ( 12) TCCTCGGG 1 chr8:38243746-38243766 ( 2) TCCTCGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.1e+003 -765 -765 -765 165 -765 245 -765 -765 -765 245 -765 -765 -765 -765 -765 165 -765 245 -765 -765 -765 -765 244 -765 -765 -765 244 -765 -765 -765 244 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.1e+003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCGGG MEME-5 regular expression -------------------------------------------------------------------------------- TCCTCGGG -------------------------------------------------------------------------------- Time 6.80 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:55127687-55127707 7.57e-01 20 chr18:9118625-9118645 5.16e-03 12_[+1(4.69e-05)] chr9:100686063-100686083 9.80e-01 20 chr1:229850994-229851014 8.05e-01 20 chr4:57657626-57657646 9.33e-01 20 chr8:67527611-67527631 2.41e-01 20 chr9:140652208-140652228 9.86e-01 20 chr10:67658025-67658045 1.00e-01 20 chr3:23366423-23366443 9.91e-01 20 chr12:90343908-90343928 9.04e-01 20 chr15:75301627-75301647 1.41e-01 20 chr6:2881887-2881907 9.88e-01 20 chr7:22925122-22925142 1.04e-02 20 chr17:73286211-73286231 9.98e-01 20 chr7:43878679-43878699 1.12e-02 20 chr8:67521729-67521749 1.00e+00 20 chr1:46798268-46798288 4.71e-01 20 chr2:200843084-200843104 8.38e-01 20 chr2:171806985-171807005 3.68e-02 6_[+1(4.69e-05)]_6 chr22:41821813-41821833 8.43e-01 20 chr6:11461031-11461051 1.05e-02 9_[+1(9.67e-05)]_3 chr3:10262434-10262454 9.23e-01 20 chr2:68441711-68441731 7.09e-03 20 chr8:59555018-59555038 6.90e-01 20 chr1:16290778-16290798 4.25e-01 20 chr7:44927155-44927175 9.94e-01 20 chr6:138121237-138121257 9.52e-01 20 chr15:101112821-10111284 1.00e+00 20 chr21:34696493-34696513 5.55e-01 20 chr4:144280403-144280423 2.04e-02 20 chrX:1365871-1365891 2.87e-01 20 chr1:199121345-199121365 8.94e-01 20 chr1:186834584-186834604 9.24e-01 20 chr3:128839416-128839436 6.73e-04 7_[+1(1.74e-05)]_5 chr6:127624063-127624083 5.77e-01 20 chr4:159972962-159972982 4.96e-01 20 chr10:16821645-16821665 8.80e-02 20 chr2:64341417-64341437 5.27e-01 20 chrX:1324957-1324977 9.67e-01 20 chr6:113951812-113951832 2.60e-02 [+1(9.67e-05)]_12 chr7:69289492-69289512 4.99e-01 20 chr2:228348038-228348058 5.19e-01 20 chr9:132654371-132654391 8.76e-01 20 chr1:9136571-9136591 7.20e-01 20 chr11:75619980-75620000 9.95e-01 20 chr18:56355497-56355517 9.94e-01 20 chr8:95453045-95453065 8.84e-05 8_[+4(3.39e-06)]_4 chr2:136970659-136970679 9.42e-01 20 chr12:50016309-50016329 5.86e-03 5_[+2(2.75e-05)]_7 chr8:105635966-105635986 6.32e-01 20 chr16:27274309-27274329 8.23e-01 20 chr6:26312015-26312035 6.21e-01 20 chr12:23713681-23713701 7.47e-01 20 chr8:38243746-38243766 1.23e-04 1_[+5(3.77e-06)]_11 chr7:45035493-45035513 8.93e-01 20 chr2:37319177-37319197 9.94e-01 20 chr13:46739878-46739898 1.69e-01 20 chr4:22485322-22485342 6.99e-01 20 chr10:63664474-63664494 4.60e-01 20 chr17:34906518-34906538 9.98e-01 20 chr6:138777278-138777298 3.46e-01 20 chr17:58730064-58730084 6.68e-01 20 chr18:13597215-13597235 9.65e-01 20 chr6:135335677-135335697 5.02e-01 20 chr14:23259773-23259793 1.71e-01 20 chr21:16198089-16198109 5.17e-01 20 chr18:51788582-51788602 8.80e-01 20 chr12:52430801-52430821 2.39e-01 20 chr7:49811342-49811362 6.28e-01 20 chr2:26492888-26492908 1.00e+00 20 chr1:153814696-153814716 9.92e-01 20 chr16:27378969-27378989 3.56e-01 20 chr10:63661076-63661096 8.64e-01 20 chr1:234534812-234534832 9.92e-01 20 chr20:15967460-15967480 8.55e-01 20 chr11:102345615-10234563 8.28e-01 20 chr16:20915979-20915999 8.72e-01 20 chr2:54191953-54191973 9.87e-01 20 chr12:90257544-90257564 9.98e-01 20 chr1:113728521-113728541 9.98e-01 20 chr11:9767240-9767260 9.76e-01 20 chr2:223298752-223298772 7.22e-01 20 chr12:92963948-92963968 2.23e-03 5_[+2(7.67e-06)]_7 chr12:80685092-80685112 9.50e-01 20 chr1:51733853-51733873 1.00e+00 20 chr5:126097008-126097028 2.75e-01 20 chr4:84197598-84197618 7.84e-01 20 chr2:38162420-38162440 7.39e-01 20 chr12:40561947-40561967 4.29e-01 20 chr8:99479735-99479755 6.33e-01 20 chr17:31156962-31156982 7.06e-01 20 chr15:85925298-85925318 4.97e-01 20 chr22:46171700-46171720 3.44e-01 20 chr19:7186481-7186501 8.18e-01 20 chr1:25358968-25358988 8.79e-01 20 chr12:129283282-12928330 8.24e-01 20 chr17:73779477-73779497 2.89e-01 20 chr5:43245069-43245089 4.48e-01 20 chr14:73092615-73092635 9.37e-01 20 chr2:9748140-9748160 9.70e-01 20 chr5:139031798-139031818 3.78e-01 20 chr6:16421058-16421078 4.53e-01 20 chr8:98724058-98724078 7.16e-01 20 chr12:11802461-11802481 1.86e-05 1_[+4(1.24e-06)]_11 chr1:200831386-200831406 4.09e-01 20 chr12:92439713-92439733 3.48e-03 4_[+2(7.32e-05)]_8 chr16:10991224-10991244 7.76e-01 20 chr22:40221779-40221799 5.17e-01 20 chr19:9906912-9906932 6.54e-01 20 chr2:201319719-201319739 7.94e-03 20 chr1:218503576-218503596 6.86e-01 20 chr18:60452061-60452081 9.26e-01 20 chr20:10427789-10427809 9.97e-01 20 chr14:95678199-95678219 2.56e-01 20 chr7:20351213-20351233 6.23e-01 20 chr1:44229275-44229295 7.58e-02 20 chr5:124338603-124338623 1.60e-01 20 chr2:20357360-20357380 3.72e-01 20 chr7:128648895-128648915 9.91e-01 20 chr18:810458-810478 9.64e-01 20 chr6:106634867-106634887 9.43e-01 20 chr9:114672842-114672862 8.95e-01 20 chr10:90595517-90595537 4.69e-01 20 chr7:92263616-92263636 1.82e-01 20 chr11:22702975-22702995 9.33e-01 20 chr7:43556715-43556735 8.50e-01 20 chr3:178250382-178250402 6.04e-01 20 chr5:40487111-40487131 6.23e-01 20 chr5:114914475-114914495 1.00e+00 20 chrX:11551491-11551511 9.34e-01 20 chr7:142508902-142508922 4.59e-01 20 chr2:139025304-139025324 5.16e-01 20 chr12:94062892-94062912 9.95e-01 20 chr7:150073206-150073226 7.25e-01 20 chr5:138905487-138905507 5.05e-01 20 chr5:179967506-179967526 6.94e-01 20 chr17:8129494-8129514 1.00e+00 20 chr12:52444912-52444932 1.05e-03 [+2(7.67e-06)]_12 chr2:208602273-208602293 5.97e-01 20 chr12:68151976-68151996 1.75e-01 20 chr2:182451641-182451661 6.47e-01 20 chr4:1213208-1213228 8.77e-01 20 chr8:119909548-119909568 9.97e-01 20 chr13:101195247-10119526 1.17e-01 20 chr2:37798441-37798461 3.51e-01 20 chr8:137083462-137083482 9.98e-01 20 chr19:6630905-6630925 8.01e-01 20 chr14:31449420-31449440 3.47e-01 20 chr10:93901982-93902002 8.02e-01 20 chr6:181474-181494 9.13e-01 20 chr5:65306413-65306433 5.72e-01 20 chr8:71065058-71065078 5.03e-01 20 chr12:121548151-12154817 5.15e-01 20 chr1:153714929-153714949 5.61e-01 20 chr2:55529555-55529575 9.90e-01 20 chr7:28191723-28191743 9.91e-01 20 chr18:39809719-39809739 6.74e-01 20 chr4:159998985-159999005 9.84e-01 20 chr5:131856647-131856667 8.57e-01 20 chr8:139175179-139175199 4.33e-02 20 chr8:56901895-56901915 6.26e-02 20 chr1:32378669-32378689 1.00e+00 20 chr6:4880139-4880159 7.67e-02 8_[+2(6.17e-05)]_4 chr3:189391485-189391505 5.82e-01 20 chr8:9630937-9630957 9.85e-01 20 chr3:101510865-101510885 9.93e-01 20 chr3:88191377-88191397 9.39e-01 20 chr11:111700044-11170006 6.33e-01 20 chr10:22895266-22895286 7.64e-05 10_[+3(7.34e-06)]_2 chr12:853273-853293 9.97e-01 20 chr16:68816814-68816834 2.80e-01 20 chr15:67196171-67196191 9.98e-01 20 chr11:115745819-11574583 5.58e-01 20 chr20:54949104-54949124 8.13e-01 20 chr6:106615407-106615427 1.15e-01 20 chr3:156382828-156382848 5.27e-01 20 chr12:46793446-46793466 8.66e-01 20 chr2:190817628-190817648 7.38e-01 20 chr12:12798961-12798981 2.29e-02 20 chr6:149376851-149376871 1.04e-03 3_[+3(7.34e-06)]_9 chr19:48948864-48948884 2.01e-04 11_[+5(3.77e-06)]_1 chr20:14810625-14810645 9.72e-01 20 chr7:110559341-110559361 9.27e-01 20 chr15:69396668-69396688 8.27e-01 20 chr2:44843964-44843984 9.05e-01 20 chr1:93050111-93050131 1.27e-01 20 chr2:159047708-159047728 1.00e+00 20 chr9:90115570-90115590 9.93e-01 20 chr10:135219599-13521961 2.76e-01 20 chr20:47405355-47405375 2.94e-02 10_[+2(7.99e-05)]_2 chr3:142801185-142801205 6.94e-01 20 chr7:122269588-122269608 4.60e-02 20 chr2:65833766-65833786 8.08e-01 20 chr11:94335892-94335912 1.66e-01 20 chr15:67831988-67832008 8.12e-01 20 chr17:44223612-44223632 7.60e-02 20 chr6:4777587-4777607 9.57e-01 20 chr10:3668649-3668669 9.29e-01 20 chr11:22809276-22809296 7.83e-04 8_[+3(5.17e-05)]_4 chr7:7860694-7860714 8.98e-01 20 chr11:64633340-64633360 9.06e-01 20 chr14:63938134-63938154 8.21e-01 20 chr20:35994943-35994963 3.28e-02 20 chrX:13275461-13275481 9.63e-01 20 chr6:97059478-97059498 9.81e-01 20 chr13:43619621-43619641 7.71e-01 20 chr10:97553662-97553682 7.68e-01 20 chr10:76613873-76613893 8.28e-01 20 chr1:108477327-108477347 4.85e-01 20 chr2:80694507-80694527 7.64e-01 20 chr13:49552184-49552204 7.39e-01 20 chr4:38940892-38940912 9.32e-01 20 chr5:72456176-72456196 3.51e-04 20 chr2:225384917-225384937 6.77e-02 20 chr11:110199019-11019903 9.82e-01 20 chr11:59943544-59943564 9.19e-01 20 chr3:170966821-170966841 7.06e-01 20 chr10:63747892-63747912 7.25e-01 20 chr2:143792058-143792078 1.19e-01 20 chr8:128219371-128219391 3.22e-01 20 chr11:65199009-65199029 2.04e-05 11_[+1(1.74e-05)]_1 chr2:171017232-171017252 7.63e-01 20 chr6:111660378-111660398 1.00e+00 20 chr21:43948072-43948092 8.13e-01 20 chr4:110571161-110571181 6.77e-01 20 chr7:139357536-139357556 8.90e-01 20 chr1:170514848-170514868 9.35e-01 20 chr7:99994361-99994381 9.83e-01 20 chr11:75535572-75535592 5.65e-03 9_[+2(7.67e-06)]_3 chr2:61220244-61220264 6.96e-01 20 chr11:74459616-74459636 9.98e-01 20 chr11:22225032-22225052 4.39e-01 20 chr20:57482998-57483018 7.48e-02 [+2(6.17e-05)]_12 chr18:77283846-77283866 3.51e-03 10_[+1(1.74e-05)]_2 chr19:18949731-18949751 8.90e-01 20 chr19:16560248-16560268 5.06e-01 20 chr10:63869833-63869853 2.65e-01 20 chr5:157157153-157157173 4.83e-02 10_[+1(4.69e-05)]_2 chr3:104240878-104240898 4.28e-01 20 chr7:91763155-91763175 2.19e-01 20 chr6:15246056-15246076 2.55e-02 20 chr1:184712410-184712430 2.35e-01 20 chr2:216471079-216471099 9.98e-01 20 chr19:12111427-12111447 9.80e-01 20 chr5:134149768-134149788 9.24e-01 20 chr1:165723413-165723433 9.98e-01 20 chr17:68295205-68295225 1.00e+00 20 chr5:172411562-172411582 5.80e-02 20 chr11:67355543-67355563 5.67e-01 20 chr15:91201196-91201216 8.97e-03 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************