******************************************************************************** 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/RXRA.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr19:49613288-49613308 1.0000 20 chr17:73110332-73110352 1.0000 20 chr6:37137606-37137626 1.0000 20 chr19:46898964-46898984 1.0000 20 chr19:56135898-56135918 1.0000 20 chr1:23871342-23871362 1.0000 20 chr2:113403899-113403919 1.0000 20 chr1:236135201-236135221 1.0000 20 chr6:153304771-153304791 1.0000 20 chr20:48227817-48227837 1.0000 20 chr19:10330600-10330620 1.0000 20 chr19:47734597-47734617 1.0000 20 chr19:10982098-10982118 1.0000 20 chr6:32806614-32806634 1.0000 20 chrX:12996109-12996129 1.0000 20 chr1:225662842-225662862 1.0000 20 chr11:123355319-12335533 1.0000 20 chr9:132646887-132646907 1.0000 20 chr1:26799456-26799476 1.0000 20 chr2:148747544-148747564 1.0000 20 chr6:90539506-90539526 1.0000 20 chr8:52921204-52921224 1.0000 20 chr12:49524625-49524645 1.0000 20 chr5:153784942-153784962 1.0000 20 chr3:113557591-113557611 1.0000 20 chr19:49617660-49617680 1.0000 20 chr19:1445358-1445378 1.0000 20 chr19:11908406-11908426 1.0000 20 chr4:48965262-48965282 1.0000 20 chr3:52568016-52568036 1.0000 20 chr6:30509373-30509393 1.0000 20 chr11:64614744-64614764 1.0000 20 chr19:49977391-49977411 1.0000 20 chr22:42322192-42322212 1.0000 20 chr1:21985783-21985803 1.0000 20 chr20:4701487-4701507 1.0000 20 chr17:73030601-73030621 1.0000 20 chr5:149779435-149779455 1.0000 20 chr5:137688248-137688268 1.0000 20 chr8:86133017-86133037 1.0000 20 chr15:101458326-10145834 1.0000 20 chr17:29852546-29852566 1.0000 20 chr19:1088121-1088141 1.0000 20 chr17:42287946-42287966 1.0000 20 chr16:30064358-30064378 1.0000 20 chr22:24191893-24191913 1.0000 20 chr1:150952115-150952135 1.0000 20 chr3:48193153-48193173 1.0000 20 chr19:6577611-6577631 1.0000 20 chr1:59012538-59012558 1.0000 20 chr7:148659926-148659946 1.0000 20 chr13:100039834-10003985 1.0000 20 chr22:37252563-37252583 1.0000 20 chr16:85644236-85644256 1.0000 20 chr10:97134569-97134589 1.0000 20 chr3:124754260-124754280 1.0000 20 chr2:48648026-48648046 1.0000 20 chr12:75784962-75784982 1.0000 20 chr17:74178434-74178454 1.0000 20 chr3:15309616-15309636 1.0000 20 chr11:58912249-58912269 1.0000 20 chr19:41860023-41860043 1.0000 20 chr11:74303591-74303611 1.0000 20 chr11:65183936-65183956 1.0000 20 chr1:160163059-160163079 1.0000 20 chr14:105553295-10555331 1.0000 20 chr19:18390449-18390469 1.0000 20 chr3:127794557-127794577 1.0000 20 chr14:23019411-23019431 1.0000 20 chr13:92001319-92001339 1.0000 20 chr15:41523426-41523446 1.0000 20 chr9:100174199-100174219 1.0000 20 chr3:71924688-71924708 1.0000 20 chr6:119215152-119215172 1.0000 20 chr18:74534085-74534105 1.0000 20 chr9:37411524-37411544 1.0000 20 chr11:9770201-9770221 1.0000 20 chr17:1388291-1388311 1.0000 20 chr3:129033884-129033904 1.0000 20 chr10:92759398-92759418 1.0000 20 chrX:78526112-78526132 1.0000 20 chr12:111834913-11183493 1.0000 20 chr5:149780919-149780939 1.0000 20 chr17:74117699-74117719 1.0000 20 chr6:16771365-16771385 1.0000 20 chr2:30387976-30387996 1.0000 20 chr6:27655366-27655386 1.0000 20 chr21:44596884-44596904 1.0000 20 chr14:105512218-10551223 1.0000 20 chr16:4380513-4380533 1.0000 20 chr20:5100023-5100043 1.0000 20 chr19:4400677-4400697 1.0000 20 chr11:73036263-73036283 1.0000 20 chr12:54608650-54608670 1.0000 20 chr11:96076509-96076529 1.0000 20 chr11:46368904-46368924 1.0000 20 chr16:87905385-87905405 1.0000 20 chr7:75831121-75831141 1.0000 20 chr19:6048994-6049014 1.0000 20 chr17:40474925-40474945 1.0000 20 chr17:39819088-39819108 1.0000 20 chr1:235267656-235267676 1.0000 20 chr18:10525923-10525943 1.0000 20 chr8:67976529-67976549 1.0000 20 chr1:153919223-153919243 1.0000 20 chr14:105487560-10548758 1.0000 20 chr17:37910632-37910652 1.0000 20 chr14:58666719-58666739 1.0000 20 chr12:57633039-57633059 1.0000 20 chr7:1105547-1105567 1.0000 20 chr12:12186442-12186462 1.0000 20 chr20:30556373-30556393 1.0000 20 chr1:114889295-114889315 1.0000 20 chr2:220110151-220110171 1.0000 20 chr16:3109402-3109422 1.0000 20 chr17:78400808-78400828 1.0000 20 chr7:155531554-155531574 1.0000 20 chr4:17812524-17812544 1.0000 20 chr20:47521744-47521764 1.0000 20 chr11:108369220-10836924 1.0000 20 chr17:78549327-78549347 1.0000 20 chr19:46386807-46386827 1.0000 20 chr11:61731015-61731035 1.0000 20 chr2:38304129-38304149 1.0000 20 chr7:5565787-5565807 1.0000 20 chr6:27841307-27841327 1.0000 20 chr14:106873666-10687368 1.0000 20 chr10:81107192-81107212 1.0000 20 chr10:43892141-43892161 1.0000 20 chr14:75372537-75372557 1.0000 20 chr1:155211073-155211093 1.0000 20 chr10:12349625-12349645 1.0000 20 chr12:125391471-12539149 1.0000 20 chr1:145457384-145457404 1.0000 20 chr11:67056539-67056559 1.0000 20 chr2:65100762-65100782 1.0000 20 chr18:60985446-60985466 1.0000 20 chr3:196347255-196347275 1.0000 20 chr4:83350151-83350171 1.0000 20 chr11:60897414-60897434 1.0000 20 chr5:131574139-131574159 1.0000 20 chr21:44344150-44344170 1.0000 20 chr9:125937336-125937356 1.0000 20 chr14:91710053-91710073 1.0000 20 chr6:36648384-36648404 1.0000 20 chr4:113445125-113445145 1.0000 20 chr20:49546076-49546096 1.0000 20 chr17:79075714-79075734 1.0000 20 chr17:80231465-80231485 1.0000 20 chr5:149789519-149789539 1.0000 20 chr12:122985629-12298564 1.0000 20 chr12:120933778-12093379 1.0000 20 chr9:112680752-112680772 1.0000 20 chr3:45970728-45970748 1.0000 20 chr8:144898040-144898060 1.0000 20 chr11:65652257-65652277 1.0000 20 chr3:169489998-169490018 1.0000 20 chr2:231577472-231577492 1.0000 20 chr12:7126257-7126277 1.0000 20 chr8:90996388-90996408 1.0000 20 chr17:42767166-42767186 1.0000 20 chr3:50264970-50264990 1.0000 20 chr6:32381421-32381441 1.0000 20 chr12:102333702-10233372 1.0000 20 chr3:58182375-58182395 1.0000 20 chr10:73808459-73808479 1.0000 20 chr11:66176054-66176074 1.0000 20 chr2:48338453-48338473 1.0000 20 chr6:15151591-15151611 1.0000 20 chr17:48238964-48238984 1.0000 20 chr1:154580688-154580708 1.0000 20 chr2:153032563-153032583 1.0000 20 chr7:141251125-141251145 1.0000 20 chr17:33416470-33416490 1.0000 20 chr16:2570411-2570431 1.0000 20 chr19:39888427-39888447 1.0000 20 chr17:45307291-45307311 1.0000 20 chr12:98897653-98897673 1.0000 20 chr4:106395189-106395209 1.0000 20 chr6:167200390-167200410 1.0000 20 chr6:30710570-30710590 1.0000 20 chr16:69599784-69599804 1.0000 20 chr17:7482834-7482854 1.0000 20 chr3:19584902-19584922 1.0000 20 chr2:38161814-38161834 1.0000 20 chr3:143393347-143393367 1.0000 20 chr5:149786395-149786415 1.0000 20 chr8:101572021-101572041 1.0000 20 chr9:112163840-112163860 1.0000 20 chr5:374038-374058 1.0000 20 chr12:122232266-12223228 1.0000 20 chr17:76684261-76684281 1.0000 20 chr22:42062830-42062850 1.0000 20 chr17:8124831-8124851 1.0000 20 chr15:75506022-75506042 1.0000 20 chr15:85131377-85131397 1.0000 20 chr5:154134619-154134639 1.0000 20 chr5:150880458-150880478 1.0000 20 chr11:4116002-4116022 1.0000 20 chr17:3749641-3749661 1.0000 20 chr17:7340458-7340478 1.0000 20 chr5:122335820-122335840 1.0000 20 chr10:72124416-72124436 1.0000 20 chr9:71199511-71199531 1.0000 20 chr6:5261112-5261132 1.0000 20 chr12:56132761-56132781 1.0000 20 chr7:43622461-43622481 1.0000 20 chr7:76961311-76961331 1.0000 20 chr2:232395210-232395230 1.0000 20 chr19:36036469-36036489 1.0000 20 chr19:35959786-35959806 1.0000 20 chr10:64370590-64370610 1.0000 20 chr10:104153848-10415386 1.0000 20 chr21:44772878-44772898 1.0000 20 chr5:133747620-133747640 1.0000 20 chr16:68544228-68544248 1.0000 20 chr17:72787771-72787791 1.0000 20 chr5:403123-403143 1.0000 20 chr8:135724914-135724934 1.0000 20 chr1:46806465-46806485 1.0000 20 chr10:46090329-46090349 1.0000 20 chr1:40781102-40781122 1.0000 20 chr3:121977831-121977851 1.0000 20 chr7:128731762-128731782 1.0000 20 chr19:10613532-10613552 1.0000 20 chr2:30556040-30556060 1.0000 20 chr15:67403004-67403024 1.0000 20 chr2:171785486-171785506 1.0000 20 chr5:157170656-157170676 1.0000 20 chr5:133375377-133375397 1.0000 20 chr11:73309212-73309232 1.0000 20 chr22:50946660-50946680 1.0000 20 chr19:42637425-42637445 1.0000 20 chr14:23039300-23039320 1.0000 20 chrX:39733934-39733954 1.0000 20 chr14:23292142-23292162 1.0000 20 chr14:24630409-24630429 1.0000 20 chr16:71533864-71533884 1.0000 20 chr13:42846088-42846108 1.0000 20 chr1:6673591-6673611 1.0000 20 chr1:9687210-9687230 1.0000 20 chr10:103815988-10381600 1.0000 20 chr12:56583413-56583433 1.0000 20 chr1:203242372-203242392 1.0000 20 chr17:7137945-7137965 1.0000 20 chr18:43753978-43753998 1.0000 20 chr6:14211565-14211585 1.0000 20 chr19:46320580-46320600 1.0000 20 chr7:24755393-24755413 1.0000 20 chr1:206291834-206291854 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_RXRA/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/RXRA.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 0.171 C 0.337 G 0.327 T 0.165 Background letter frequencies (from file dataset with add-one prior applied): A 0.171 C 0.337 G 0.327 T 0.165 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TRDGAAAA MEME-1 width = 8 sites = 6 llr = 65 E-value = 9.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :532aaaa pos.-specific C :::::::: probability G :538:::: matrix T a:3::::: bits 2.6 * **** 2.3 * **** 2.1 * **** 1.8 * **** Relative 1.6 * **** Entropy 1.3 * **** (15.6 bits) 1.0 ** ***** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TAAGAAAA consensus GG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:8124831-8124851 3 1.30e-06 GG TATGAAAA CCAGGAAAGA chr2:148747544-148747564 11 5.14e-06 GGCATTACTT TGTGAAAA GA chr10:12349625-12349645 7 1.03e-05 TCAAAA TGAGAAAA GGATGA chr5:149780919-149780939 6 1.03e-05 ggaca taggaaaa tgaaagc chrX:12996109-12996129 11 1.17e-05 TTTTAAGAGT TAAAAAAA GA chr14:24630409-24630429 5 1.66e-05 TTTC TGGGAAAA GGCCCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:8124831-8124851 1.3e-06 2_[+1]_10 chr2:148747544-148747564 5.1e-06 10_[+1]_2 chr10:12349625-12349645 1e-05 6_[+1]_6 chr5:149780919-149780939 1e-05 5_[+1]_7 chrX:12996109-12996129 1.2e-05 10_[+1]_2 chr14:24630409-24630429 1.7e-05 4_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TRDGAAAA width=8 seqs=6 chr17:8124831-8124851 ( 3) TATGAAAA 1 chr2:148747544-148747564 ( 11) TGTGAAAA 1 chr10:12349625-12349645 ( 7) TGAGAAAA 1 chr5:149780919-149780939 ( 6) TAGGAAAA 1 chrX:12996109-12996129 ( 11) TAAAAAAA 1 chr14:24630409-24630429 ( 5) TGGGAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.85264 E= 9.1e+000 -923 -923 -923 260 154 -923 61 -923 96 -923 3 101 -4 -923 135 -923 254 -923 -923 -923 254 -923 -923 -923 254 -923 -923 -923 254 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 9.1e+000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 0.333333 0.000000 0.333333 0.333333 0.166667 0.000000 0.833333 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 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TRDGAAAA MEME-1 regular expression -------------------------------------------------------------------------------- T[AG][AGT]GAAAA -------------------------------------------------------------------------------- Time 2.49 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCTGSTG MEME-2 width = 8 sites = 10 llr = 88 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::::2: pos.-specific C 92a::6:: probability G ::::a4:a matrix T 18:a::8: bits 2.6 * 2.3 * 2.1 * 1.8 * * Relative 1.6 **** ** Entropy 1.3 ***** ** (12.8 bits) 1.0 ***** ** 0.8 ***** ** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CTCTGCTG consensus C GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:145457384-145457404 8 1.84e-05 CATGTCA CTCTGCTG CCCTC chr6:16771365-16771385 12 1.84e-05 CCTCAGCTCC CTCTGCTG G chr8:52921204-52921224 11 1.84e-05 CTGCCCTGCC CTCTGCTG GA chr5:150880458-150880478 8 3.62e-05 GAGAGCC CTCTGGTG GCTAA chr20:47521744-47521764 9 3.62e-05 TTGGTGCT CTCTGGTG GCCA chr3:19584902-19584922 4 5.53e-05 ttc ctctgcag tgtctctcc chr20:49546076-49546096 5 5.53e-05 CCCC CTCTGCAG CCTTACCC chr4:48965262-48965282 2 9.15e-05 G TTCTGGTG GCCATACTGG chr17:29852546-29852566 1 1.29e-04 . CCCTGCTG TCAGGTTCTC chr3:45970728-45970748 1 1.65e-04 . CCCTGGTG TCACTGTGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:145457384-145457404 1.8e-05 7_[+2]_5 chr6:16771365-16771385 1.8e-05 11_[+2]_1 chr8:52921204-52921224 1.8e-05 10_[+2]_2 chr5:150880458-150880478 3.6e-05 7_[+2]_5 chr20:47521744-47521764 3.6e-05 8_[+2]_4 chr3:19584902-19584922 5.5e-05 3_[+2]_9 chr20:49546076-49546096 5.5e-05 4_[+2]_8 chr4:48965262-48965282 9.1e-05 1_[+2]_11 chr17:29852546-29852566 0.00013 [+2]_12 chr3:45970728-45970748 0.00017 [+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCTGSTG width=8 seqs=10 chr1:145457384-145457404 ( 8) CTCTGCTG 1 chr6:16771365-16771385 ( 12) CTCTGCTG 1 chr8:52921204-52921224 ( 11) CTCTGCTG 1 chr5:150880458-150880478 ( 8) CTCTGGTG 1 chr20:47521744-47521764 ( 9) CTCTGGTG 1 chr3:19584902-19584922 ( 4) CTCTGCAG 1 chr20:49546076-49546096 ( 5) CTCTGCAG 1 chr4:48965262-48965282 ( 2) TTCTGGTG 1 chr17:29852546-29852566 ( 1) CCCTGCTG 1 chr3:45970728-45970748 ( 1) CCCTGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.5921 E= 2.3e+002 -997 142 -997 -72 -997 -75 -997 227 -997 157 -997 -997 -997 -997 -997 260 -997 -997 161 -997 -997 83 29 -997 22 -997 -997 227 -997 -997 161 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 2.3e+002 0.000000 0.900000 0.000000 0.100000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTGSTG MEME-2 regular expression -------------------------------------------------------------------------------- C[TC]CTG[CG][TA]G -------------------------------------------------------------------------------- Time 3.29 secs. ******************************************************************************** ******************************************************************************** MOTIF AYAAAYYT MEME-3 width = 8 sites = 6 llr = 61 E-value = 3.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:a88::: pos.-specific C :5::253: probability G :::2:::: matrix T :5:::57a bits 2.6 * * * 2.3 * * * 2.1 * * * 1.8 * *** * Relative 1.6 * *** * Entropy 1.3 * *** ** (14.7 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel ACAAACTT consensus T TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr16:71533864-71533884 12 6.34e-07 TGTCAGCGGG ATAAATTT C chr2:171785486-171785506 8 4.52e-06 CGTCTGC ATAAATCT AGTCC chr17:45307291-45307311 6 7.16e-06 AGATG ACAAACTT GCAACAG chr3:48193153-48193173 6 2.03e-05 AGGAG ACAAACCT GGGGCAC chr2:30556040-30556060 7 2.53e-05 CCACCC ACAGATTT CATAGC chr5:149786395-149786415 10 3.04e-05 CCAGGCGGG ATAACCTT GCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr16:71533864-71533884 6.3e-07 11_[+3]_1 chr2:171785486-171785506 4.5e-06 7_[+3]_5 chr17:45307291-45307311 7.2e-06 5_[+3]_7 chr3:48193153-48193173 2e-05 5_[+3]_7 chr2:30556040-30556060 2.5e-05 6_[+3]_6 chr5:149786395-149786415 3e-05 9_[+3]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AYAAAYYT width=8 seqs=6 chr16:71533864-71533884 ( 12) ATAAATTT 1 chr2:171785486-171785506 ( 8) ATAAATCT 1 chr17:45307291-45307311 ( 6) ACAAACTT 1 chr3:48193153-48193173 ( 6) ACAAACCT 1 chr2:30556040-30556060 ( 7) ACAGATTT 1 chr5:149786395-149786415 ( 10) ATAACCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.1796 E= 3.4e+002 254 -923 -923 -923 -923 57 -923 160 254 -923 -923 -923 228 -923 -97 -923 228 -101 -923 -923 -923 57 -923 160 -923 -1 -923 201 -923 -923 -923 260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 3.4e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYAAAYYT MEME-3 regular expression -------------------------------------------------------------------------------- A[CT]AAA[CT][TC]T -------------------------------------------------------------------------------- Time 4.08 secs. ******************************************************************************** ******************************************************************************** MOTIF AAGTGGAT MEME-4 width = 8 sites = 2 llr = 24 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 Description -------------------------------------------------------------------------------- Simplified A aa::::a: pos.-specific C :::::::: probability G ::a:aa:: matrix T :::a:::a bits 2.6 ** * ** 2.3 ** * ** 2.1 ** * ** 1.8 ** * ** Relative 1.6 ******** Entropy 1.3 ******** (17.7 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAGTGGAT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:121977831-121977851 3 4.76e-06 CC AAGTGGAT GGAACAAGCA chr7:148659926-148659946 8 4.76e-06 CGTGGGA AAGTGGAT GGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:121977831-121977851 4.8e-06 2_[+4]_10 chr7:148659926-148659946 4.8e-06 7_[+4]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAGTGGAT width=8 seqs=2 chr3:121977831-121977851 ( 3) AAGTGGAT 1 chr7:148659926-148659946 ( 8) AAGTGGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.81663 E= 1.7e+003 254 -765 -765 -765 254 -765 -765 -765 -765 -765 161 -765 -765 -765 -765 259 -765 -765 161 -765 -765 -765 161 -765 254 -765 -765 -765 -765 -765 -765 259 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.7e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTGGAT MEME-4 regular expression -------------------------------------------------------------------------------- AAGTGGAT -------------------------------------------------------------------------------- Time 4.87 secs. ******************************************************************************** ******************************************************************************** MOTIF GTTTTYAM MEME-5 width = 8 sites = 6 llr = 57 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 Description -------------------------------------------------------------------------------- Simplified A 2:2:::a5 pos.-specific C ::::23:3 probability G 8::::2:2 matrix T :a8a85:: bits 2.6 * * * 2.3 * * * 2.1 * * * 1.8 **** * Relative 1.6 **** * Entropy 1.3 **** * (13.8 bits) 1.0 ***** * 0.8 ***** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GTTTTTAA consensus C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:5565787-5565807 5 7.69e-06 GAGA GTATTTAA CTCAGGGC chr12:75784962-75784982 1 1.22e-05 . GTTTTGAA GCTGCGGCTC chr16:87905385-87905405 4 1.34e-05 TTG ATTTTTAC AGAGGCAGG chr7:155531554-155531574 11 1.94e-05 TGCTTCATGG GTTTTCAC TG chr12:122985629-12298564 5 2.18e-05 TGTG GTTTCTAA GCGACTGG chr4:113445125-113445145 5 3.88e-05 GAGC GTTTTCAG GACGCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:5565787-5565807 7.7e-06 4_[+5]_8 chr12:75784962-75784982 1.2e-05 [+5]_12 chr16:87905385-87905405 1.3e-05 3_[+5]_9 chr7:155531554-155531574 1.9e-05 10_[+5]_2 chr12:122985629-12298564 2.2e-05 4_[+5]_8 chr4:113445125-113445145 3.9e-05 4_[+5]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTTTTYAM width=8 seqs=6 chr7:5565787-5565807 ( 5) GTATTTAA 1 chr12:75784962-75784982 ( 1) GTTTTGAA 1 chr16:87905385-87905405 ( 4) ATTTTTAC 1 chr7:155531554-155531574 ( 11) GTTTTCAC 1 chr12:122985629-12298564 ( 5) GTTTCTAA 1 chr4:113445125-113445145 ( 5) GTTTTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.52677 E= 1.4e+003 -4 -923 135 -923 -923 -923 -923 260 -4 -923 -923 233 -923 -923 -923 260 -923 -101 -923 233 -923 -1 -97 160 254 -923 -923 -923 154 -1 -97 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 1.4e+003 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.333333 0.166667 0.500000 1.000000 0.000000 0.000000 0.000000 0.500000 0.333333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTTTYAM MEME-5 regular expression -------------------------------------------------------------------------------- GTTTT[TC]A[AC] -------------------------------------------------------------------------------- Time 5.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:49613288-49613308 4.12e-01 20 chr17:73110332-73110352 1.90e-01 20 chr6:37137606-37137626 9.54e-01 20 chr19:46898964-46898984 3.50e-01 20 chr19:56135898-56135918 8.42e-01 20 chr1:23871342-23871362 1.64e-02 20 chr2:113403899-113403919 1.85e-01 20 chr1:236135201-236135221 1.84e-01 20 chr6:153304771-153304791 8.95e-01 20 chr20:48227817-48227837 9.50e-01 20 chr19:10330600-10330620 1.95e-01 20 chr19:47734597-47734617 1.00e+00 20 chr19:10982098-10982118 9.21e-01 20 chr6:32806614-32806634 9.85e-01 20 chrX:12996109-12996129 4.06e-03 10_[+1(1.17e-05)]_2 chr1:225662842-225662862 9.93e-01 20 chr11:123355319-12335533 7.56e-02 20 chr9:132646887-132646907 4.45e-01 20 chr1:26799456-26799476 9.84e-01 20 chr2:148747544-148747564 8.72e-05 10_[+1(5.14e-06)]_2 chr6:90539506-90539526 3.29e-01 20 chr8:52921204-52921224 3.77e-02 10_[+2(1.84e-05)]_2 chr12:49524625-49524645 9.99e-01 20 chr5:153784942-153784962 2.66e-01 20 chr3:113557591-113557611 9.98e-01 20 chr19:49617660-49617680 2.00e-01 20 chr19:1445358-1445378 9.78e-01 20 chr19:11908406-11908426 9.33e-01 20 chr4:48965262-48965282 3.05e-02 1_[+2(9.15e-05)]_11 chr3:52568016-52568036 8.02e-01 20 chr6:30509373-30509393 4.13e-01 20 chr11:64614744-64614764 9.17e-01 20 chr19:49977391-49977411 9.45e-01 20 chr22:42322192-42322212 9.57e-01 20 chr1:21985783-21985803 9.98e-01 20 chr20:4701487-4701507 7.34e-01 20 chr17:73030601-73030621 1.93e-01 20 chr5:149779435-149779455 3.25e-02 20 chr5:137688248-137688268 8.81e-01 20 chr8:86133017-86133037 3.49e-01 20 chr15:101458326-10145834 9.45e-01 20 chr17:29852546-29852566 4.19e-02 20 chr19:1088121-1088141 2.39e-01 20 chr17:42287946-42287966 2.54e-01 20 chr16:30064358-30064378 9.99e-01 20 chr22:24191893-24191913 9.88e-01 20 chr1:150952115-150952135 6.46e-01 20 chr3:48193153-48193173 2.98e-03 5_[+3(2.03e-05)]_7 chr19:6577611-6577631 9.37e-01 20 chr1:59012538-59012558 7.67e-01 20 chr7:148659926-148659946 2.47e-04 7_[+4(4.76e-06)]_5 chr13:100039834-10003985 9.05e-01 20 chr22:37252563-37252583 7.89e-01 20 chr16:85644236-85644256 8.29e-01 20 chr10:97134569-97134589 6.13e-01 20 chr3:124754260-124754280 5.07e-02 20 chr2:48648026-48648046 1.26e-02 20 chr12:75784962-75784982 1.66e-03 [+5(1.22e-05)]_12 chr17:74178434-74178454 8.84e-03 20 chr3:15309616-15309636 9.89e-01 20 chr11:58912249-58912269 7.26e-01 20 chr19:41860023-41860043 3.81e-01 20 chr11:74303591-74303611 3.68e-01 20 chr11:65183936-65183956 6.56e-01 20 chr1:160163059-160163079 1.46e-01 20 chr14:105553295-10555331 9.22e-01 20 chr19:18390449-18390469 2.95e-01 20 chr3:127794557-127794577 9.63e-01 20 chr14:23019411-23019431 3.92e-02 20 chr13:92001319-92001339 6.18e-01 20 chr15:41523426-41523446 8.72e-01 20 chr9:100174199-100174219 9.41e-01 20 chr3:71924688-71924708 8.41e-01 20 chr6:119215152-119215172 9.95e-01 20 chr18:74534085-74534105 8.36e-01 20 chr9:37411524-37411544 1.84e-01 20 chr11:9770201-9770221 3.19e-01 20 chr17:1388291-1388311 9.43e-01 20 chr3:129033884-129033904 9.73e-01 20 chr10:92759398-92759418 1.59e-01 20 chrX:78526112-78526132 9.65e-01 20 chr12:111834913-11183493 2.22e-01 20 chr5:149780919-149780939 2.70e-03 5_[+1(1.03e-05)]_7 chr17:74117699-74117719 7.79e-01 20 chr6:16771365-16771385 2.79e-02 11_[+2(1.84e-05)]_1 chr2:30387976-30387996 5.56e-02 20 chr6:27655366-27655386 1.00e+00 20 chr21:44596884-44596904 3.43e-01 20 chr14:105512218-10551223 2.46e-01 20 chr16:4380513-4380533 4.59e-01 20 chr20:5100023-5100043 2.95e-01 20 chr19:4400677-4400697 9.21e-01 20 chr11:73036263-73036283 9.76e-01 20 chr12:54608650-54608670 8.57e-01 20 chr11:96076509-96076529 9.63e-01 20 chr11:46368904-46368924 8.09e-01 20 chr16:87905385-87905405 4.06e-03 3_[+5(1.34e-05)]_9 chr7:75831121-75831141 2.57e-01 20 chr19:6048994-6049014 7.53e-01 20 chr17:40474925-40474945 9.30e-01 20 chr17:39819088-39819108 1.00e+00 20 chr1:235267656-235267676 7.91e-01 20 chr18:10525923-10525943 7.15e-01 20 chr8:67976529-67976549 6.67e-01 20 chr1:153919223-153919243 4.81e-01 20 chr14:105487560-10548758 6.70e-01 20 chr17:37910632-37910652 7.15e-01 20 chr14:58666719-58666739 2.75e-01 20 chr12:57633039-57633059 4.41e-01 20 chr7:1105547-1105567 6.92e-01 20 chr12:12186442-12186462 4.11e-01 20 chr20:30556373-30556393 9.65e-01 20 chr1:114889295-114889315 4.52e-01 20 chr2:220110151-220110171 1.96e-01 20 chr16:3109402-3109422 9.99e-01 20 chr17:78400808-78400828 9.98e-01 20 chr7:155531554-155531574 8.70e-03 10_[+5(1.94e-05)]_2 chr4:17812524-17812544 7.83e-01 20 chr20:47521744-47521764 5.81e-02 8_[+2(3.62e-05)]_4 chr11:108369220-10836924 7.44e-01 20 chr17:78549327-78549347 2.05e-02 20 chr19:46386807-46386827 6.14e-01 20 chr11:61731015-61731035 6.04e-01 20 chr2:38304129-38304149 7.28e-01 20 chr7:5565787-5565807 4.92e-04 4_[+5(7.69e-06)]_8 chr6:27841307-27841327 7.36e-01 20 chr14:106873666-10687368 5.72e-02 20 chr10:81107192-81107212 5.19e-01 20 chr10:43892141-43892161 7.96e-01 20 chr14:75372537-75372557 3.37e-01 20 chr1:155211073-155211093 7.98e-01 20 chr10:12349625-12349645 6.76e-04 6_[+1(1.03e-05)]_6 chr12:125391471-12539149 7.83e-02 20 chr1:145457384-145457404 6.44e-03 7_[+2(1.84e-05)]_5 chr11:67056539-67056559 8.19e-01 20 chr2:65100762-65100782 9.14e-01 20 chr18:60985446-60985466 1.30e-01 20 chr3:196347255-196347275 2.12e-01 20 chr4:83350151-83350171 7.90e-01 20 chr11:60897414-60897434 9.03e-01 20 chr5:131574139-131574159 3.56e-01 20 chr21:44344150-44344170 4.45e-01 20 chr9:125937336-125937356 8.05e-02 20 chr14:91710053-91710073 8.93e-01 20 chr6:36648384-36648404 9.84e-01 20 chr4:113445125-113445145 1.83e-02 4_[+5(3.88e-05)]_8 chr20:49546076-49546096 8.70e-03 4_[+2(5.53e-05)]_8 chr17:79075714-79075734 8.16e-01 20 chr17:80231465-80231485 9.42e-01 20 chr5:149789519-149789539 2.63e-01 20 chr12:122985629-12298564 5.80e-03 4_[+5(2.18e-05)]_8 chr12:120933778-12093379 3.89e-02 20 chr9:112680752-112680772 1.71e-01 20 chr3:45970728-45970748 2.05e-02 20 chr8:144898040-144898060 9.99e-01 20 chr11:65652257-65652277 2.12e-01 20 chr3:169489998-169490018 1.63e-02 20 chr2:231577472-231577492 9.94e-01 20 chr12:7126257-7126277 7.82e-01 20 chr8:90996388-90996408 9.46e-02 20 chr17:42767166-42767186 9.67e-01 20 chr3:50264970-50264990 8.39e-01 20 chr6:32381421-32381441 6.02e-01 20 chr12:102333702-10233372 9.90e-02 20 chr3:58182375-58182395 1.77e-01 20 chr10:73808459-73808479 4.51e-03 10_[+4(3.41e-05)]_2 chr11:66176054-66176074 8.67e-01 20 chr2:48338453-48338473 6.08e-01 20 chr6:15151591-15151611 7.43e-01 20 chr17:48238964-48238984 7.41e-01 20 chr1:154580688-154580708 3.78e-01 20 chr2:153032563-153032583 9.60e-01 20 chr7:141251125-141251145 9.02e-01 20 chr17:33416470-33416490 7.35e-01 20 chr16:2570411-2570431 9.97e-01 20 chr19:39888427-39888447 9.12e-01 20 chr17:45307291-45307311 2.41e-04 5_[+3(7.16e-06)]_7 chr12:98897653-98897673 2.58e-01 20 chr4:106395189-106395209 9.55e-01 20 chr6:167200390-167200410 6.36e-01 20 chr6:30710570-30710590 5.59e-01 20 chr16:69599784-69599804 9.44e-01 20 chr17:7482834-7482854 3.30e-01 20 chr3:19584902-19584922 8.45e-03 3_[+2(5.53e-05)]_9 chr2:38161814-38161834 2.04e-01 20 chr3:143393347-143393367 2.39e-01 20 chr5:149786395-149786415 1.19e-02 9_[+3(3.04e-05)]_3 chr8:101572021-101572041 5.32e-01 20 chr9:112163840-112163860 5.03e-01 20 chr5:374038-374058 5.07e-01 20 chr12:122232266-12223228 9.88e-01 20 chr17:76684261-76684281 8.87e-01 20 chr22:42062830-42062850 5.78e-01 20 chr17:8124831-8124851 8.80e-04 2_[+1(1.30e-06)]_10 chr15:75506022-75506042 7.52e-01 20 chr15:85131377-85131397 9.64e-01 20 chr5:154134619-154134639 1.00e+00 20 chr5:150880458-150880478 9.03e-04 7_[+2(3.62e-05)]_5 chr11:4116002-4116022 4.98e-01 20 chr17:3749641-3749661 9.81e-01 20 chr17:7340458-7340478 7.61e-01 20 chr5:122335820-122335840 2.76e-01 20 chr10:72124416-72124436 5.32e-01 20 chr9:71199511-71199531 2.11e-01 20 chr6:5261112-5261132 4.26e-02 20 chr12:56132761-56132781 3.82e-01 20 chr7:43622461-43622481 9.18e-01 20 chr7:76961311-76961331 4.56e-01 20 chr2:232395210-232395230 5.36e-01 20 chr19:36036469-36036489 1.00e+00 20 chr19:35959786-35959806 2.95e-01 20 chr10:64370590-64370610 5.54e-01 20 chr10:104153848-10415386 1.51e-02 20 chr21:44772878-44772898 6.14e-01 20 chr5:133747620-133747640 9.25e-01 20 chr16:68544228-68544248 9.80e-01 20 chr17:72787771-72787791 5.48e-01 20 chr5:403123-403143 1.11e-01 20 chr8:135724914-135724934 3.30e-01 20 chr1:46806465-46806485 3.83e-01 20 chr10:46090329-46090349 7.38e-01 20 chr1:40781102-40781122 1.88e-01 20 chr3:121977831-121977851 2.49e-04 2_[+4(4.76e-06)]_10 chr7:128731762-128731782 1.95e-01 20 chr19:10613532-10613552 7.12e-01 20 chr2:30556040-30556060 3.74e-03 6_[+3(2.53e-05)]_6 chr15:67403004-67403024 5.09e-01 20 chr2:171785486-171785506 2.50e-05 7_[+3(4.52e-06)]_5 chr5:157170656-157170676 4.63e-01 20 chr5:133375377-133375397 1.87e-01 20 chr11:73309212-73309232 8.17e-01 20 chr22:50946660-50946680 2.90e-01 20 chr19:42637425-42637445 9.84e-01 20 chr14:23039300-23039320 8.59e-01 20 chrX:39733934-39733954 7.17e-01 20 chr14:23292142-23292162 6.96e-02 20 chr14:24630409-24630429 4.40e-03 4_[+1(1.66e-05)]_8 chr16:71533864-71533884 1.43e-04 11_[+3(6.34e-07)]_1 chr13:42846088-42846108 7.12e-01 20 chr1:6673591-6673611 5.50e-01 20 chr1:9687210-9687230 5.45e-01 20 chr10:103815988-10381600 8.42e-01 20 chr12:56583413-56583433 8.69e-01 20 chr1:203242372-203242392 9.41e-01 20 chr17:7137945-7137965 9.48e-01 20 chr18:43753978-43753998 4.53e-01 20 chr6:14211565-14211585 1.00e+00 20 chr19:46320580-46320600 9.87e-01 20 chr7:24755393-24755413 1.30e-01 20 chr1:206291834-206291854 3.96e-02 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************