******************************************************************************** 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/ELK1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr5:169730306-169730326 1.0000 20 chr14:22940721-22940741 1.0000 20 chr10:73291491-73291511 1.0000 20 chr12:833781-833801 1.0000 20 chr16:57033651-57033671 1.0000 20 chr12:50616494-50616514 1.0000 20 chr5:137827840-137827860 1.0000 20 chr20:626315-626335 1.0000 20 chr8:42270508-42270528 1.0000 20 chr14:75760989-75761009 1.0000 20 chr6:28129529-28129549 1.0000 20 chr3:112233640-112233660 1.0000 20 chr8:22552941-22552961 1.0000 20 chr17:17654296-17654316 1.0000 20 chr13:21347400-21347420 1.0000 20 chr1:39492450-39492470 1.0000 20 chr10:16478997-16479017 1.0000 20 chr21:34753072-34753092 1.0000 20 chr2:73520791-73520811 1.0000 20 chr19:50819541-50819561 1.0000 20 chr14:89897023-89897043 1.0000 20 chr11:76758811-76758831 1.0000 20 chrX:13505602-13505622 1.0000 20 chr3:169482173-169482193 1.0000 20 chr11:126350775-12635079 1.0000 20 chr19:40926909-40926929 1.0000 20 chr17:2475550-2475570 1.0000 20 chr5:133450223-133450243 1.0000 20 chr15:91191989-91192009 1.0000 20 chr2:54807211-54807231 1.0000 20 chr1:11967934-11967954 1.0000 20 chr22:37374245-37374265 1.0000 20 chr10:6186835-6186855 1.0000 20 chr19:50169120-50169140 1.0000 20 chr9:33165927-33165947 1.0000 20 chr3:178787752-178787772 1.0000 20 chr6:126240319-126240339 1.0000 20 chr8:146228292-146228312 1.0000 20 chr19:6532831-6532851 1.0000 20 chr1:169278736-169278756 1.0000 20 chr19:19256993-19257013 1.0000 20 chr11:57282346-57282366 1.0000 20 chr4:140216982-140217002 1.0000 20 chr12:6882200-6882220 1.0000 20 chrX:51546176-51546196 1.0000 20 chr10:30814661-30814681 1.0000 20 chr5:137800801-137800821 1.0000 20 chr10:67940677-67940697 1.0000 20 chr19:42829585-42829605 1.0000 20 chr12:7054021-7054041 1.0000 20 chr7:5569406-5569426 1.0000 20 chr9:5851644-5851664 1.0000 20 chr3:149376434-149376454 1.0000 20 chr5:143550315-143550335 1.0000 20 chr5:65440008-65440028 1.0000 20 chr11:67030347-67030367 1.0000 20 chr1:43222786-43222806 1.0000 20 chr11:95976534-95976554 1.0000 20 chr1:159047163-159047183 1.0000 20 chr22:50415053-50415073 1.0000 20 chr3:124620316-124620336 1.0000 20 chr3:107352641-107352661 1.0000 20 chr8:29413883-29413903 1.0000 20 chr8:144373516-144373536 1.0000 20 chr1:40505653-40505673 1.0000 20 chr16:70333065-70333085 1.0000 20 chr2:241075740-241075760 1.0000 20 chr1:203259810-203259830 1.0000 20 chr15:90931276-90931296 1.0000 20 chr2:86669935-86669955 1.0000 20 chr19:13262696-13262716 1.0000 20 chr14:23340279-23340299 1.0000 20 chr5:34839218-34839238 1.0000 20 chr7:104584889-104584909 1.0000 20 chr10:64576489-64576509 1.0000 20 chr14:52314161-52314181 1.0000 20 chr15:101675984-10167600 1.0000 20 chr10:16859463-16859483 1.0000 20 chr20:33872595-33872615 1.0000 20 chr1:151431960-151431980 1.0000 20 chr1:8157578-8157598 1.0000 20 chr2:55361197-55361217 1.0000 20 chr14:74227040-74227060 1.0000 20 chr13:108978808-10897882 1.0000 20 chr12:15101893-15101913 1.0000 20 chr5:132732577-132732597 1.0000 20 chr12:52445138-52445158 1.0000 20 chr10:112257586-11225760 1.0000 20 chr9:88969356-88969376 1.0000 20 chr22:27068948-27068968 1.0000 20 chr19:53426469-53426489 1.0000 20 chr6:159516045-159516065 1.0000 20 chr13:25875678-25875698 1.0000 20 chr4:10118497-10118517 1.0000 20 chr9:129933147-129933167 1.0000 20 chr1:42128082-42128102 1.0000 20 chr1:109825886-109825906 1.0000 20 chr10:72124407-72124427 1.0000 20 chr15:91669523-91669543 1.0000 20 chr19:13278628-13278648 1.0000 20 chrX:133503719-133503739 1.0000 20 chr19:39322552-39322572 1.0000 20 chr12:9917433-9917453 1.0000 20 chr2:183989091-183989111 1.0000 20 chr9:127631377-127631397 1.0000 20 chr1:3663931-3663951 1.0000 20 chr22:36851298-36851318 1.0000 20 chr19:1174275-1174295 1.0000 20 chr13:36527764-36527784 1.0000 20 chr1:47082668-47082688 1.0000 20 chr17:16189481-16189501 1.0000 20 chr17:77784044-77784064 1.0000 20 chr5:158690253-158690273 1.0000 20 chr6:159420895-159420915 1.0000 20 chr12:104998559-10499857 1.0000 20 chr1:46251444-46251464 1.0000 20 chr2:152144896-152144916 1.0000 20 chr8:145980989-145981009 1.0000 20 chr19:57792707-57792727 1.0000 20 chr11:22802681-22802701 1.0000 20 chr9:77567885-77567905 1.0000 20 chr10:93683495-93683515 1.0000 20 chr6:51928501-51928521 1.0000 20 chr6:3069202-3069222 1.0000 20 chr17:80606328-80606348 1.0000 20 chr12:11912214-11912234 1.0000 20 chr1:154976636-154976656 1.0000 20 chr19:37825529-37825549 1.0000 20 chr10:131934669-13193468 1.0000 20 chr19:14800823-14800843 1.0000 20 chr10:106098368-10609838 1.0000 20 chr7:98978764-98978784 1.0000 20 chr5:79703680-79703700 1.0000 20 chr16:48278184-48278204 1.0000 20 chr1:205601151-205601171 1.0000 20 chr1:85742500-85742520 1.0000 20 chr1:22351993-22352013 1.0000 20 chr7:128802807-128802827 1.0000 20 chr11:65668111-65668131 1.0000 20 chrX:18693121-18693141 1.0000 20 chr2:219262857-219262877 1.0000 20 chr17:71228422-71228442 1.0000 20 chr5:78810465-78810485 1.0000 20 chr3:100428108-100428128 1.0000 20 chr1:174933729-174933749 1.0000 20 chr2:137181209-137181229 1.0000 20 chrX:15873164-15873184 1.0000 20 chr1:160681618-160681638 1.0000 20 chr4:2936621-2936641 1.0000 20 chr5:176882506-176882526 1.0000 20 chr12:56320886-56320906 1.0000 20 chr13:103109881-10310990 1.0000 20 chr4:148538551-148538571 1.0000 20 chr3:186524283-186524303 1.0000 20 chr22:51001411-51001431 1.0000 20 chr14:75745258-75745278 1.0000 20 chr8:145137523-145137543 1.0000 20 chr3:27526120-27526140 1.0000 20 chr16:25118450-25118470 1.0000 20 chr12:56401195-56401215 1.0000 20 chr2:55746729-55746749 1.0000 20 chr21:37692428-37692448 1.0000 20 chr1:114326304-114326324 1.0000 20 chr12:120875851-12087587 1.0000 20 chr7:44084179-44084199 1.0000 20 chr22:41260204-41260224 1.0000 20 chr1:29208720-29208740 1.0000 20 chr4:84133930-84133950 1.0000 20 chr19:9695193-9695213 1.0000 20 chr5:138677510-138677530 1.0000 20 chr1:36181279-36181299 1.0000 20 chr17:29421968-29421988 1.0000 20 chr12:107368522-10736854 1.0000 20 chr4:88480860-88480880 1.0000 20 chr15:80251173-80251193 1.0000 20 chr6:43138942-43138962 1.0000 20 chr20:30311750-30311770 1.0000 20 chr20:45181793-45181813 1.0000 20 chr3:187334231-187334251 1.0000 20 chr3:119528667-119528687 1.0000 20 chr12:65563321-65563341 1.0000 20 chr12:6862286-6862306 1.0000 20 chr17:43394656-43394676 1.0000 20 chr15:78423864-78423884 1.0000 20 chr9:126691813-126691833 1.0000 20 chr8:59323868-59323888 1.0000 20 chr9:273017-273037 1.0000 20 chr9:127703383-127703403 1.0000 20 chr3:49158278-49158298 1.0000 20 chr2:54343038-54343058 1.0000 20 chr5:36876810-36876830 1.0000 20 chr22:46431910-46431930 1.0000 20 chr19:44507100-44507120 1.0000 20 chr10:45496336-45496356 1.0000 20 chr2:170550923-170550943 1.0000 20 chr1:20834616-20834636 1.0000 20 chr8:53627080-53627100 1.0000 20 chr13:108867897-10886791 1.0000 20 chr15:40615732-40615752 1.0000 20 chr1:40506380-40506400 1.0000 20 chr3:9834490-9834510 1.0000 20 chr16:12639051-12639071 1.0000 20 chr10:15902498-15902518 1.0000 20 chr1:53662454-53662474 1.0000 20 chr17:6544044-6544064 1.0000 20 chr20:43104499-43104519 1.0000 20 chr2:62326903-62326923 1.0000 20 chr5:82373351-82373371 1.0000 20 chr12:122125072-12212509 1.0000 20 chr19:12904431-12904451 1.0000 20 chr1:161008793-161008813 1.0000 20 chr17:65362709-65362729 1.0000 20 chrX:13752828-13752848 1.0000 20 chr17:28050777-28050797 1.0000 20 chr10:101989386-10198940 1.0000 20 chr19:16296040-16296060 1.0000 20 chr19:44669128-44669148 1.0000 20 chr1:174998975-174998995 1.0000 20 chr7:6746633-6746653 1.0000 20 chr14:64912391-64912411 1.0000 20 chr8:90914234-90914254 1.0000 20 chr6:166756076-166756096 1.0000 20 chr19:45943246-45943266 1.0000 20 chr19:9785784-9785804 1.0000 20 chr17:40086836-40086856 1.0000 20 chr1:9971183-9971203 1.0000 20 chr17:7835236-7835256 1.0000 20 chr21:46293596-46293616 1.0000 20 chrX:153626442-153626462 1.0000 20 chr16:1823162-1823182 1.0000 20 chr11:9386077-9386097 1.0000 20 chr13:45915372-45915392 1.0000 20 chr3:50275608-50275628 1.0000 20 chr7:6617035-6617055 1.0000 20 chr17:41132166-41132186 1.0000 20 chr6:90348467-90348487 1.0000 20 chr15:66161768-66161788 1.0000 20 chr11:506863-506883 1.0000 20 chr1:55230361-55230381 1.0000 20 chr3:185000643-185000663 1.0000 20 chr20:2082792-2082812 1.0000 20 chr15:83736010-83736030 1.0000 20 chr6:139350797-139350817 1.0000 20 chr19:45542310-45542330 1.0000 20 chr2:45838411-45838431 1.0000 20 chr2:17699745-17699765 1.0000 20 chr13:77566211-77566231 1.0000 20 chr11:69490111-69490131 1.0000 20 chr11:57103406-57103426 1.0000 20 chr12:64798062-64798082 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_ELK1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/ELK1.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 0.196 C 0.3 G 0.305 T 0.2 Background letter frequencies (from file dataset with add-one prior applied): A 0.196 C 0.3 G 0.305 T 0.2 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RCTTCCGG MEME-1 width = 8 sites = 51 llr = 402 E-value = 2.2e-046 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5::::::: pos.-specific C 29::aa:2 probability G 3::1::88 matrix T :1a9::2: bits 2.4 2.1 * 1.9 ** 1.6 **** Relative 1.4 ***** Entropy 1.2 ****** (11.4 bits) 0.9 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel ACTTCCGG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:69490111-69490131 5 1.97e-05 ACCC ACTTCCGG AAGCGGCG chr1:174998975-174998995 7 1.97e-05 CTTAGC ACTTCCGG AAGCAG chr10:101989386-10198940 5 1.97e-05 CGTC ACTTCCGG TAACCGCT chr2:55746729-55746749 5 1.97e-05 CTTC ACTTCCGG GCCGCGGT chr1:22351993-22352013 5 1.97e-05 CATG ACTTCCGG TTCCCGCG chr1:205601151-205601171 3 1.97e-05 TC ACTTCCGG GGGAGGGGCT chr10:93683495-93683515 11 1.97e-05 AGCTTACGTC ACTTCCGG CG chr6:159420895-159420915 10 1.97e-05 GCACAAGGG ACTTCCGG CTC chr5:158690253-158690273 8 1.97e-05 ACCACCC ACTTCCGG TTTTT chr19:1174275-1174295 6 1.97e-05 CGCGC ACTTCCGG TCATGCC chr19:53426469-53426489 3 1.97e-05 TG ACTTCCGG ACTCCTAGGG chr9:88969356-88969376 10 1.97e-05 TTCGGCCCC ACTTCCGG CGC chr7:104584889-104584909 5 1.97e-05 GCTC ACTTCCGG TGTGAAAG chr19:6532831-6532851 13 1.97e-05 ATCCTCCGCC ACTTCCGG chr11:76758811-76758831 2 1.97e-05 a acttccgg tcgttgccat chr1:39492450-39492470 7 1.97e-05 gccagc acttccgg ctgtaa chr14:74227040-74227060 10 3.26e-05 GCGCCGCCC ACTTCCTG CGA chr14:23340279-23340299 11 3.26e-05 gatatggagc acttcctg ta chr11:95976534-95976554 5 3.26e-05 AGGC ACTTCCTG CTAGAGGA chr10:73291491-73291511 1 3.26e-05 . ACTTCCTG TGCAGGCAGG chr19:45542310-45542330 4 6.32e-05 TCC GCTTCCGG TGCGGGCCG chr19:45943246-45943266 11 6.32e-05 ACGACTCAGC GCTTCCGG GG chr9:127631377-127631397 9 6.32e-05 CTGACGGC GCTTCCGG ATCC chr2:241075740-241075760 5 6.32e-05 AGCC GCTTCCGG CGCGCGCC chr16:70333065-70333085 13 6.32e-05 GTGGCGCGCC GCTTCCGG chr5:65440008-65440028 13 6.32e-05 CCGGGGCGAC GCTTCCGG chr11:126350775-12635079 7 6.32e-05 ATCCCA GCTTCCGG TTTCCT chr8:146228292-146228312 1 8.26e-05 . ACTTCCGC CCTGCCCTTC chr6:28129529-28129549 12 8.26e-05 ACTGAGAGGG ACTTCCGC C chr1:36181279-36181299 13 1.13e-04 CGAATAAGCT CCTTCCGG chr19:13278628-13278648 3 1.13e-04 GC CCTTCCGG AGTGAAACTT chr6:166756076-166756096 4 1.33e-04 CCC GCTTCCTG TGCGTCAGC chr17:43394656-43394676 6 1.46e-04 GCACT ATTTCCGG ACGATGT chr11:65668111-65668131 12 2.02e-04 ACATGGTGTA ACTTCCTC G chr19:14800823-14800843 8 2.02e-04 CACAGCC ACTTCCGT TCCCG chr20:33872595-33872615 3 2.02e-04 CC ACTTCCGT CCAGGGAGAC chr19:40926909-40926929 9 2.02e-04 TGGGCACA ACTTCCTC TGCT chr14:75760989-75761009 11 2.52e-04 ccggcccgcc gcTTCCGC TC chr9:273017-273037 5 2.81e-04 GTAA CCTTCCGC TCAGTTTC chr17:17654296-17654316 3 2.81e-04 TT CCTTCCGC CTTCCACAGA chr4:2936621-2936641 6 3.10e-04 CGTTC TCTTCCGG CCGGAGT chr1:8157578-8157598 12 3.88e-04 GGCAACAGGA ACTGCCTG A chr19:50169120-50169140 7 3.88e-04 TTTTGG GTTTCCGG CCAGAG chr5:137827840-137827860 11 4.75e-04 CCTACAAGGC GCTTCCTC CC chr15:66161768-66161788 11 6.22e-04 AAGGCTGGGG CCTGCCGG AA chr12:122125072-12212509 8 6.22e-04 GGACGCT CCTGCCGG AAGTG chr3:119528667-119528687 1 6.22e-04 . CCTGCCGG AATGGCCAGA chr10:16478997-16479017 6 6.22e-04 GTTGG CCTGCCGG AAGTTCC chr2:62326903-62326923 4 6.68e-04 tgc gtttcctg gacaagcct chr13:45915372-45915392 10 7.58e-04 GCCCGCTGC GCCTCCGG AAG chr19:9785784-9785804 12 7.58e-04 TCCGCTCCGA GCCTCCGG C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:69490111-69490131 2e-05 4_[+1]_8 chr1:174998975-174998995 2e-05 6_[+1]_6 chr10:101989386-10198940 2e-05 4_[+1]_8 chr2:55746729-55746749 2e-05 4_[+1]_8 chr1:22351993-22352013 2e-05 4_[+1]_8 chr1:205601151-205601171 2e-05 2_[+1]_10 chr10:93683495-93683515 2e-05 10_[+1]_2 chr6:159420895-159420915 2e-05 9_[+1]_3 chr5:158690253-158690273 2e-05 7_[+1]_5 chr19:1174275-1174295 2e-05 5_[+1]_7 chr19:53426469-53426489 2e-05 2_[+1]_10 chr9:88969356-88969376 2e-05 9_[+1]_3 chr7:104584889-104584909 2e-05 4_[+1]_8 chr19:6532831-6532851 2e-05 12_[+1] chr11:76758811-76758831 2e-05 1_[+1]_11 chr1:39492450-39492470 2e-05 6_[+1]_6 chr14:74227040-74227060 3.3e-05 9_[+1]_3 chr14:23340279-23340299 3.3e-05 10_[+1]_2 chr11:95976534-95976554 3.3e-05 4_[+1]_8 chr10:73291491-73291511 3.3e-05 [+1]_12 chr19:45542310-45542330 6.3e-05 3_[+1]_9 chr19:45943246-45943266 6.3e-05 10_[+1]_2 chr9:127631377-127631397 6.3e-05 8_[+1]_4 chr2:241075740-241075760 6.3e-05 4_[+1]_8 chr16:70333065-70333085 6.3e-05 12_[+1] chr5:65440008-65440028 6.3e-05 12_[+1] chr11:126350775-12635079 6.3e-05 6_[+1]_6 chr8:146228292-146228312 8.3e-05 [+1]_12 chr6:28129529-28129549 8.3e-05 11_[+1]_1 chr1:36181279-36181299 0.00011 12_[+1] chr19:13278628-13278648 0.00011 2_[+1]_10 chr6:166756076-166756096 0.00013 3_[+1]_9 chr17:43394656-43394676 0.00015 5_[+1]_7 chr11:65668111-65668131 0.0002 11_[+1]_1 chr19:14800823-14800843 0.0002 7_[+1]_5 chr20:33872595-33872615 0.0002 2_[+1]_10 chr19:40926909-40926929 0.0002 8_[+1]_4 chr14:75760989-75761009 0.00025 10_[+1]_2 chr9:273017-273037 0.00028 4_[+1]_8 chr17:17654296-17654316 0.00028 2_[+1]_10 chr4:2936621-2936641 0.00031 5_[+1]_7 chr1:8157578-8157598 0.00039 11_[+1]_1 chr19:50169120-50169140 0.00039 6_[+1]_6 chr5:137827840-137827860 0.00047 10_[+1]_2 chr15:66161768-66161788 0.00062 10_[+1]_2 chr12:122125072-12212509 0.00062 7_[+1]_5 chr3:119528667-119528687 0.00062 [+1]_12 chr10:16478997-16479017 0.00062 5_[+1]_7 chr2:62326903-62326923 0.00067 3_[+1]_9 chr13:45915372-45915392 0.00076 9_[+1]_3 chr19:9785784-9785804 0.00076 11_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCTTCCGG width=8 seqs=51 chr11:69490111-69490131 ( 5) ACTTCCGG 1 chr1:174998975-174998995 ( 7) ACTTCCGG 1 chr10:101989386-10198940 ( 5) ACTTCCGG 1 chr2:55746729-55746749 ( 5) ACTTCCGG 1 chr1:22351993-22352013 ( 5) ACTTCCGG 1 chr1:205601151-205601171 ( 3) ACTTCCGG 1 chr10:93683495-93683515 ( 11) ACTTCCGG 1 chr6:159420895-159420915 ( 10) ACTTCCGG 1 chr5:158690253-158690273 ( 8) ACTTCCGG 1 chr19:1174275-1174295 ( 6) ACTTCCGG 1 chr19:53426469-53426489 ( 3) ACTTCCGG 1 chr9:88969356-88969376 ( 10) ACTTCCGG 1 chr7:104584889-104584909 ( 5) ACTTCCGG 1 chr19:6532831-6532851 ( 13) ACTTCCGG 1 chr11:76758811-76758831 ( 2) ACTTCCGG 1 chr1:39492450-39492470 ( 7) ACTTCCGG 1 chr14:74227040-74227060 ( 10) ACTTCCTG 1 chr14:23340279-23340299 ( 11) ACTTCCTG 1 chr11:95976534-95976554 ( 5) ACTTCCTG 1 chr10:73291491-73291511 ( 1) ACTTCCTG 1 chr19:45542310-45542330 ( 4) GCTTCCGG 1 chr19:45943246-45943266 ( 11) GCTTCCGG 1 chr9:127631377-127631397 ( 9) GCTTCCGG 1 chr2:241075740-241075760 ( 5) GCTTCCGG 1 chr16:70333065-70333085 ( 13) GCTTCCGG 1 chr5:65440008-65440028 ( 13) GCTTCCGG 1 chr11:126350775-12635079 ( 7) GCTTCCGG 1 chr8:146228292-146228312 ( 1) ACTTCCGC 1 chr6:28129529-28129549 ( 12) ACTTCCGC 1 chr1:36181279-36181299 ( 13) CCTTCCGG 1 chr19:13278628-13278648 ( 3) CCTTCCGG 1 chr6:166756076-166756096 ( 4) GCTTCCTG 1 chr17:43394656-43394676 ( 6) ATTTCCGG 1 chr11:65668111-65668131 ( 12) ACTTCCTC 1 chr19:14800823-14800843 ( 8) ACTTCCGT 1 chr20:33872595-33872615 ( 3) ACTTCCGT 1 chr19:40926909-40926929 ( 9) ACTTCCTC 1 chr14:75760989-75761009 ( 11) GCTTCCGC 1 chr9:273017-273037 ( 5) CCTTCCGC 1 chr17:17654296-17654316 ( 3) CCTTCCGC 1 chr4:2936621-2936641 ( 6) TCTTCCGG 1 chr1:8157578-8157598 ( 12) ACTGCCTG 1 chr19:50169120-50169140 ( 7) GTTTCCGG 1 chr5:137827840-137827860 ( 11) GCTTCCTC 1 chr15:66161768-66161788 ( 11) CCTGCCGG 1 chr12:122125072-12212509 ( 8) CCTGCCGG 1 chr3:119528667-119528687 ( 1) CCTGCCGG 1 chr10:16478997-16479017 ( 6) CCTGCCGG 1 chr2:62326903-62326923 ( 4) GTTTCCTG 1 chr13:45915372-45915392 ( 10) GCCTCCGG 1 chr19:9785784-9785804 ( 12) GCCTCCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 5.69854 E= 2.2e-046 149 -93 -15 -335 -1232 165 -1232 -176 -1232 -293 -1232 227 -1232 -1232 -164 218 -1232 174 -1232 -1232 -1232 174 -1232 -1232 -1232 -1232 140 -3 -1232 -93 140 -235 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 2.2e-046 0.549020 0.156863 0.274510 0.019608 0.000000 0.941176 0.000000 0.058824 0.000000 0.039216 0.000000 0.960784 0.000000 0.000000 0.098039 0.901961 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.803922 0.196078 0.000000 0.156863 0.803922 0.039216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCTTCCGG MEME-1 regular expression -------------------------------------------------------------------------------- [AG]CTTCCGG -------------------------------------------------------------------------------- Time 2.04 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGAAGTG MEME-2 width = 8 sites = 29 llr = 251 E-value = 3.3e-023 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::aa:11 pos.-specific C 9:::::22 probability G :aa::a:6 matrix T ::::::7: bits 2.4 ** 2.1 ** 1.9 ** 1.6 ***** Relative 1.4 ***** Entropy 1.2 ****** (12.5 bits) 0.9 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CGGAAGTG consensus CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:2082792-2082812 6 1.99e-05 CCGCC CGGAAGTG GAGGTGC chr6:90348467-90348487 7 1.99e-05 CAGGAG CGGAAGTG GGGTTC chr10:15902498-15902518 2 1.99e-05 C CGGAAGTG CTGGTGCCAC chr1:40506380-40506400 4 1.99e-05 GCC CGGAAGTG GGTCGCGCG chr5:138677510-138677530 4 1.99e-05 CGA CGGAAGTG AAGTCACTT chr21:37692428-37692448 1 1.99e-05 . CGGAAGTG GGTGGGAGGG chr8:145137523-145137543 1 1.99e-05 . CGGAAGTG CGGGCGAGCG chr1:154976636-154976656 11 1.99e-05 TTTGGGACAC CGGAAGTG GG chr9:77567885-77567905 10 1.99e-05 CCTCGCGAC CGGAAGTG CGC chr8:144373516-144373536 4 1.99e-05 CGC CGGAAGTG CCGAGGGGG chr1:43222786-43222806 10 1.99e-05 AAAAGAGAC CGGAAGTG CCA chr11:67030347-67030367 9 1.99e-05 tgccactc cggaagtg ggga chr13:77566211-77566231 1 5.24e-05 . CGGAAGTA CTGGGTGCAG chr7:6746633-6746653 9 5.24e-05 GAATGCAC CGGAAGTC CGCC chr8:53627080-53627100 1 5.24e-05 . CGGAAGTC GGCAGCCTGC chr5:78810465-78810485 2 5.24e-05 C CGGAAGTA CTGCTAAATT chr9:33165927-33165947 3 5.24e-05 AC CGGAAGTA CCAGAAATGG chr1:114326304-114326324 2 6.54e-05 a aggaagtg gcttgccctc chr19:12904431-12904451 11 9.53e-05 GCTGACGCAG CGGAAGCG CT chrX:15873164-15873184 8 9.53e-05 CGTGACC CGGAAGCG GCGTT chr16:48278184-48278204 6 9.53e-05 GTAGC CGGAAGCG GAGGCGT chr4:10118497-10118517 1 9.53e-05 . CGGAAGCG CGGTCCCGCG chr2:45838411-45838431 12 1.28e-04 CGGTTCCCGC CGGAAGTT T chr5:169730306-169730326 4 1.49e-04 AGG AGGAAGTA CTTATTTGG chr8:145980989-145981009 9 1.98e-04 CCGGGAAC CGGAAGCC AGCC chr3:169482173-169482193 10 2.30e-04 AACAAAAAG CGGAAGAC GGG chr8:42270508-42270528 12 2.30e-04 GCTGCTGAAC CGGAAGAC T chr15:91191989-91192009 10 2.62e-04 tggtcgaaa aggaagag gaa chr7:5569406-5569426 4 3.22e-04 CAA AGGAAGCC GGGCCGGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:2082792-2082812 2e-05 5_[+2]_7 chr6:90348467-90348487 2e-05 6_[+2]_6 chr10:15902498-15902518 2e-05 1_[+2]_11 chr1:40506380-40506400 2e-05 3_[+2]_9 chr5:138677510-138677530 2e-05 3_[+2]_9 chr21:37692428-37692448 2e-05 [+2]_12 chr8:145137523-145137543 2e-05 [+2]_12 chr1:154976636-154976656 2e-05 10_[+2]_2 chr9:77567885-77567905 2e-05 9_[+2]_3 chr8:144373516-144373536 2e-05 3_[+2]_9 chr1:43222786-43222806 2e-05 9_[+2]_3 chr11:67030347-67030367 2e-05 8_[+2]_4 chr13:77566211-77566231 5.2e-05 [+2]_12 chr7:6746633-6746653 5.2e-05 8_[+2]_4 chr8:53627080-53627100 5.2e-05 [+2]_12 chr5:78810465-78810485 5.2e-05 1_[+2]_11 chr9:33165927-33165947 5.2e-05 2_[+2]_10 chr1:114326304-114326324 6.5e-05 1_[+2]_11 chr19:12904431-12904451 9.5e-05 10_[+2]_2 chrX:15873164-15873184 9.5e-05 7_[+2]_5 chr16:48278184-48278204 9.5e-05 5_[+2]_7 chr4:10118497-10118517 9.5e-05 [+2]_12 chr2:45838411-45838431 0.00013 11_[+2]_1 chr5:169730306-169730326 0.00015 3_[+2]_9 chr8:145980989-145981009 0.0002 8_[+2]_4 chr3:169482173-169482193 0.00023 9_[+2]_3 chr8:42270508-42270528 0.00023 11_[+2]_1 chr15:91191989-91192009 0.00026 9_[+2]_3 chr7:5569406-5569426 0.00032 3_[+2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGGAAGTG width=8 seqs=29 chr20:2082792-2082812 ( 6) CGGAAGTG 1 chr6:90348467-90348487 ( 7) CGGAAGTG 1 chr10:15902498-15902518 ( 2) CGGAAGTG 1 chr1:40506380-40506400 ( 4) CGGAAGTG 1 chr5:138677510-138677530 ( 4) CGGAAGTG 1 chr21:37692428-37692448 ( 1) CGGAAGTG 1 chr8:145137523-145137543 ( 1) CGGAAGTG 1 chr1:154976636-154976656 ( 11) CGGAAGTG 1 chr9:77567885-77567905 ( 10) CGGAAGTG 1 chr8:144373516-144373536 ( 4) CGGAAGTG 1 chr1:43222786-43222806 ( 10) CGGAAGTG 1 chr11:67030347-67030367 ( 9) CGGAAGTG 1 chr13:77566211-77566231 ( 1) CGGAAGTA 1 chr7:6746633-6746653 ( 9) CGGAAGTC 1 chr8:53627080-53627100 ( 1) CGGAAGTC 1 chr5:78810465-78810485 ( 2) CGGAAGTA 1 chr9:33165927-33165947 ( 3) CGGAAGTA 1 chr1:114326304-114326324 ( 2) AGGAAGTG 1 chr19:12904431-12904451 ( 11) CGGAAGCG 1 chrX:15873164-15873184 ( 8) CGGAAGCG 1 chr16:48278184-48278204 ( 6) CGGAAGCG 1 chr4:10118497-10118517 ( 1) CGGAAGCG 1 chr2:45838411-45838431 ( 12) CGGAAGTT 1 chr5:169730306-169730326 ( 4) AGGAAGTA 1 chr8:145980989-145981009 ( 9) CGGAAGCC 1 chr3:169482173-169482193 ( 10) CGGAAGAC 1 chr8:42270508-42270528 ( 12) CGGAAGAC 1 chr15:91191989-91192009 ( 10) AGGAAGAG 1 chr7:5569406-5569426 ( 4) AGGAAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 6.67952 E= 3.3e-023 -51 152 -1150 -1150 -1150 -1150 171 -1150 -1150 -1150 171 -1150 235 -1150 -1150 -1150 235 -1150 -1150 -1150 -1150 -1150 171 -1150 -92 -53 -1150 179 -51 -53 103 -253 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.3e-023 0.137931 0.862069 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.103448 0.206897 0.000000 0.689655 0.137931 0.206897 0.620690 0.034483 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAGTG MEME-2 regular expression -------------------------------------------------------------------------------- CGGAAG[TC][GC] -------------------------------------------------------------------------------- Time 2.79 secs. ******************************************************************************** ******************************************************************************** MOTIF RCCWTATA MEME-3 width = 8 sites = 23 llr = 186 E-value = 2.5e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 5::63a:7 pos.-specific C 1a8:::1: probability G 3::::::: matrix T ::247:93 bits 2.4 2.1 * 1.9 ** 1.6 * ** Relative 1.4 * ***** Entropy 1.2 ******* (11.7 bits) 0.9 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel ACCATATA consensus G TA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:41260204-41260224 4 5.31e-06 cag accatata gggtaactt chr2:55361197-55361217 9 5.31e-06 cctttcag accatata tggt chr2:86669935-86669955 12 5.31e-06 GTGGGATATG ACCATATA T chr12:9917433-9917453 6 1.07e-05 GTGTG ACCTTATA TGTAGAA chr12:107368522-10736854 13 2.96e-05 CTTTCACGTG ACCATATT chr17:16189481-16189501 3 2.96e-05 AG ACCAAATA AGGGCGTGTG chr10:112257586-11225760 8 4.16e-05 ATATTTG GCCTTATA TGGGC chr12:50616494-50616514 11 4.16e-05 AAACAGGATG GCCTTATA AG chr12:833781-833801 11 4.16e-05 CTTTCTCCTT GCCTTATA TG chr5:137800801-137800821 2 5.25e-05 C ACCTTATT TGGAGTGGCC chr11:57282346-57282366 11 5.61e-05 GCGGCTGCTG ACTTTATA AG chr12:15101893-15101913 12 6.42e-05 GACAAAAAAG CCCATATA A chr3:187334231-187334251 13 8.07e-05 CATGGGGGTG GCCAAATA chr6:159516045-159516065 3 8.07e-05 GT GCCAAATA TGGCCCATGG chrX:18693121-18693141 5 1.48e-04 TGGG ACTTTATT CATAGACT chr1:46251444-46251464 13 1.72e-04 AGATTGCATG CCCATATT chr14:89897023-89897043 13 1.72e-04 TTTTAAAAGG CCCAAATA chrX:13752828-13752848 7 2.02e-04 GGGAAG GCTATATT TAGCAG chr1:11967934-11967954 8 2.07e-04 CGCATGA ACCATTTA AGGTA chr7:98978764-98978784 11 2.19e-04 CGGGGCCCTC ACCTTACA CA chr15:91669523-91669543 7 2.72e-04 cctcca tccaaata tgggtt chr1:53662454-53662474 11 3.79e-04 GGAGCCGATG GCCTTACA GG chr5:78810465-78810485 12 3.79e-04 CGGAAGTACT GCTAAATT A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:41260204-41260224 5.3e-06 3_[+3]_9 chr2:55361197-55361217 5.3e-06 8_[+3]_4 chr2:86669935-86669955 5.3e-06 11_[+3]_1 chr12:9917433-9917453 1.1e-05 5_[+3]_7 chr12:107368522-10736854 3e-05 12_[+3] chr17:16189481-16189501 3e-05 2_[+3]_10 chr10:112257586-11225760 4.2e-05 7_[+3]_5 chr12:50616494-50616514 4.2e-05 10_[+3]_2 chr12:833781-833801 4.2e-05 10_[+3]_2 chr5:137800801-137800821 5.2e-05 1_[+3]_11 chr11:57282346-57282366 5.6e-05 10_[+3]_2 chr12:15101893-15101913 6.4e-05 11_[+3]_1 chr3:187334231-187334251 8.1e-05 12_[+3] chr6:159516045-159516065 8.1e-05 2_[+3]_10 chrX:18693121-18693141 0.00015 4_[+3]_8 chr1:46251444-46251464 0.00017 12_[+3] chr14:89897023-89897043 0.00017 12_[+3] chrX:13752828-13752848 0.0002 6_[+3]_6 chr1:11967934-11967954 0.00021 7_[+3]_5 chr7:98978764-98978784 0.00022 10_[+3]_2 chr15:91669523-91669543 0.00027 6_[+3]_6 chr1:53662454-53662474 0.00038 10_[+3]_2 chr5:78810465-78810485 0.00038 11_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCCWTATA width=8 seqs=23 chr22:41260204-41260224 ( 4) ACCATATA 1 chr2:55361197-55361217 ( 9) ACCATATA 1 chr2:86669935-86669955 ( 12) ACCATATA 1 chr12:9917433-9917453 ( 6) ACCTTATA 1 chr12:107368522-10736854 ( 13) ACCATATT 1 chr17:16189481-16189501 ( 3) ACCAAATA 1 chr10:112257586-11225760 ( 8) GCCTTATA 1 chr12:50616494-50616514 ( 11) GCCTTATA 1 chr12:833781-833801 ( 11) GCCTTATA 1 chr5:137800801-137800821 ( 2) ACCTTATT 1 chr11:57282346-57282366 ( 11) ACTTTATA 1 chr12:15101893-15101913 ( 12) CCCATATA 1 chr3:187334231-187334251 ( 13) GCCAAATA 1 chr6:159516045-159516065 ( 3) GCCAAATA 1 chrX:18693121-18693141 ( 5) ACTTTATT 1 chr1:46251444-46251464 ( 13) CCCATATT 1 chr14:89897023-89897043 ( 13) CCCAAATA 1 chrX:13752828-13752848 ( 7) GCTATATT 1 chr1:11967934-11967954 ( 8) ACCATTTA 1 chr7:98978764-98978784 ( 11) ACCTTACA 1 chr15:91669523-91669543 ( 7) TCCAAATA 1 chr1:53662454-53662474 ( 11) GCCTTACA 1 chr5:78810465-78810485 ( 12) GCTAAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.0312 E= 2.5e-009 129 -120 19 -220 -1117 174 -1117 -1117 -1117 146 -1117 -20 164 -1117 -1117 97 41 -1117 -1117 189 229 -1117 -1117 -220 -1117 -178 -1117 219 192 -1117 -1117 39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.5e-009 0.478261 0.130435 0.347826 0.043478 0.000000 1.000000 0.000000 0.000000 0.000000 0.826087 0.000000 0.173913 0.608696 0.000000 0.000000 0.391304 0.260870 0.000000 0.000000 0.739130 0.956522 0.000000 0.000000 0.043478 0.000000 0.086957 0.000000 0.913043 0.739130 0.000000 0.000000 0.260870 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCWTATA MEME-3 regular expression -------------------------------------------------------------------------------- [AG]CC[AT][TA]AT[AT] -------------------------------------------------------------------------------- Time 3.54 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAHATGG MEME-4 width = 8 sites = 9 llr = 87 E-value = 1.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A a8a2a::: pos.-specific C :::2:1:: probability G :2:1::aa matrix T :::4:9:: bits 2.4 * * * 2.1 * * * 1.9 * * * 1.6 * * **** Relative 1.4 *** **** Entropy 1.2 *** **** (14.0 bits) 0.9 *** **** 0.7 *** **** 0.5 *** **** 0.2 ******** 0.0 -------- Multilevel AAATATGG consensus G A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr4:84133930-84133950 2 5.49e-06 C AAATATGG TCCTGTTTGG chr17:2475550-2475570 3 5.49e-06 ct aaatatgg ccctaagggt chr16:57033651-57033671 1 5.49e-06 . AAATATGG TCAACTTGGT chr9:126691813-126691833 1 1.91e-05 . AAACATGG GGAGGTGCTT chr2:73520791-73520811 4 1.91e-05 CCC AAACATGG ACACAGGAT chr3:178787752-178787772 3 2.77e-05 AC AGATATGG TCATTTTAGA chr19:9695193-9695213 11 3.60e-05 CAGCGCCGGA AAAGATGG CG chr9:33165927-33165947 13 4.44e-05 CGGAAGTACC AGAAATGG chr1:160681618-160681638 4 7.35e-05 GCT AAAAACGG AACTTACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:84133930-84133950 5.5e-06 1_[+4]_11 chr17:2475550-2475570 5.5e-06 2_[+4]_10 chr16:57033651-57033671 5.5e-06 [+4]_12 chr9:126691813-126691833 1.9e-05 [+4]_12 chr2:73520791-73520811 1.9e-05 3_[+4]_9 chr3:178787752-178787772 2.8e-05 2_[+4]_10 chr19:9695193-9695213 3.6e-05 10_[+4]_2 chr9:33165927-33165947 4.4e-05 12_[+4] chr1:160681618-160681638 7.4e-05 3_[+4]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAHATGG width=8 seqs=9 chr4:84133930-84133950 ( 2) AAATATGG 1 chr17:2475550-2475570 ( 3) AAATATGG 1 chr16:57033651-57033671 ( 1) AAATATGG 1 chr9:126691813-126691833 ( 1) AAACATGG 1 chr2:73520791-73520811 ( 4) AAACATGG 1 chr3:178787752-178787772 ( 3) AGATATGG 1 chr19:9695193-9695213 ( 11) AAAGATGG 1 chr9:33165927-33165947 ( 13) AGAAATGG 1 chr1:160681618-160681638 ( 4) AAAAACGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.34207 E= 1.0e+000 235 -982 -982 -982 199 -982 -46 -982 235 -982 -982 -982 18 -43 -145 115 235 -982 -982 -982 -982 -143 -982 215 -982 -982 171 -982 -982 -982 171 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 1.0e+000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.222222 0.111111 0.444444 1.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAHATGG MEME-4 regular expression -------------------------------------------------------------------------------- A[AG]A[TAC]ATGG -------------------------------------------------------------------------------- Time 5.25 secs. ******************************************************************************** ******************************************************************************** MOTIF MAACAGGA MEME-5 width = 8 sites = 10 llr = 87 E-value = 9.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 Description -------------------------------------------------------------------------------- Simplified A 57a3a:18 pos.-specific C 53:7:::2 probability G :::::a9: matrix T :::::::: bits 2.4 * * 2.1 * * 1.9 * * 1.6 * ** Relative 1.4 * **** Entropy 1.2 ** **** (12.6 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AAACAGGA consensus CC A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:50616494-50616514 1 8.07e-06 . AAACAGGA TGGCCTTATA chr16:12639051-12639071 1 2.57e-05 . AAAAAGGA AGGGGTGGGG chr4:88480860-88480880 7 2.57e-05 AAGGGA CAACAGGA AACAAA chr1:8157578-8157598 4 2.57e-05 AGG CAACAGGA ACTGCCTGA chr2:73520791-73520811 12 4.61e-05 CCAAACATGG ACACAGGA T chr17:28050777-28050797 12 7.31e-05 GTCATACAAA CCACAGGA A chr1:47082668-47082688 1 7.31e-05 . ACAAAGGA CTAACTGAGC chr17:6544044-6544064 3 1.41e-04 AG CAACAGGC GCAGGGCGGC chr10:64576489-64576509 1 1.41e-04 . AAAAAGGC GAAGATCCGG chr4:140216982-140217002 4 1.41e-04 TGG CAACAGAA CCAGCGCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:50616494-50616514 8.1e-06 [+5]_12 chr16:12639051-12639071 2.6e-05 [+5]_12 chr4:88480860-88480880 2.6e-05 6_[+5]_6 chr1:8157578-8157598 2.6e-05 3_[+5]_9 chr2:73520791-73520811 4.6e-05 11_[+5]_1 chr17:28050777-28050797 7.3e-05 11_[+5]_1 chr1:47082668-47082688 7.3e-05 [+5]_12 chr17:6544044-6544064 0.00014 2_[+5]_10 chr10:64576489-64576509 0.00014 [+5]_12 chr4:140216982-140217002 0.00014 3_[+5]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MAACAGGA width=8 seqs=10 chr12:50616494-50616514 ( 1) AAACAGGA 1 chr16:12639051-12639071 ( 1) AAAAAGGA 1 chr4:88480860-88480880 ( 7) CAACAGGA 1 chr1:8157578-8157598 ( 4) CAACAGGA 1 chr2:73520791-73520811 ( 12) ACACAGGA 1 chr17:28050777-28050797 ( 12) CCACAGGA 1 chr1:47082668-47082688 ( 1) ACAAAGGA 1 chr17:6544044-6544064 ( 3) CAACAGGC 1 chr10:64576489-64576509 ( 1) AAAAAGGC 1 chr4:140216982-140217002 ( 4) CAACAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.77211 E= 9.4e+002 135 74 -997 -997 184 0 -997 -997 235 -997 -997 -997 61 122 -997 -997 235 -997 -997 -997 -997 -997 171 -997 -97 -997 156 -997 203 -58 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 9.4e+002 0.500000 0.500000 0.000000 0.000000 0.700000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.800000 0.200000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAACAGGA MEME-5 regular expression -------------------------------------------------------------------------------- [AC][AC]A[CA]AGG[AC] -------------------------------------------------------------------------------- Time 5.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:169730306-169730326 4.66e-03 20 chr14:22940721-22940741 7.61e-01 20 chr10:73291491-73291511 6.88e-03 [+1(3.26e-05)]_12 chr12:833781-833801 2.01e-02 10_[+3(4.16e-05)]_2 chr16:57033651-57033671 7.03e-03 [+4(5.49e-06)]_12 chr12:50616494-50616514 4.90e-06 [+5(8.07e-06)]_2_[+3(4.16e-05)]_2 chr5:137827840-137827860 1.08e-01 20 chr20:626315-626335 7.00e-01 20 chr8:42270508-42270528 2.13e-02 20 chr14:75760989-75761009 3.03e-01 20 chr6:28129529-28129549 3.02e-02 11_[+1(8.26e-05)]_1 chr3:112233640-112233660 9.89e-01 20 chr8:22552941-22552961 4.50e-01 20 chr17:17654296-17654316 1.01e-01 20 chr13:21347400-21347420 1.21e-02 20 chr1:39492450-39492470 1.93e-02 6_[+1(1.97e-05)]_6 chr10:16478997-16479017 8.33e-03 20 chr21:34753072-34753092 9.27e-01 20 chr2:73520791-73520811 1.00e-05 3_[+4(1.91e-05)]_[+5(4.61e-05)]_1 chr19:50819541-50819561 9.90e-01 20 chr14:89897023-89897043 1.14e-02 20 chr11:76758811-76758831 3.05e-02 1_[+1(1.97e-05)]_11 chrX:13505602-13505622 1.69e-01 20 chr3:169482173-169482193 1.58e-03 20 chr11:126350775-12635079 7.97e-02 6_[+1(6.32e-05)]_6 chr19:40926909-40926929 1.43e-01 20 chr17:2475550-2475570 4.65e-03 2_[+4(5.49e-06)]_10 chr5:133450223-133450243 8.23e-01 20 chr15:91191989-91192009 4.32e-03 20 chr2:54807211-54807231 8.28e-01 20 chr1:11967934-11967954 6.09e-02 20 chr22:37374245-37374265 6.45e-01 20 chr10:6186835-6186855 7.79e-01 20 chr19:50169120-50169140 3.27e-01 20 chr9:33165927-33165947 8.84e-05 2_[+2(5.24e-05)]_2_[+4(4.44e-05)] chr3:178787752-178787772 1.49e-02 2_[+4(2.77e-05)]_10 chr6:126240319-126240339 5.69e-02 20 chr8:146228292-146228312 6.76e-02 [+1(8.26e-05)]_12 chr19:6532831-6532851 3.29e-02 12_[+1(1.97e-05)] chr1:169278736-169278756 4.69e-01 20 chr19:19256993-19257013 8.17e-01 20 chr11:57282346-57282366 4.32e-02 10_[+3(5.61e-05)]_2 chr4:140216982-140217002 4.10e-02 20 chr12:6882200-6882220 3.03e-01 20 chrX:51546176-51546196 9.35e-01 20 chr10:30814661-30814681 1.07e-01 20 chr5:137800801-137800821 4.27e-02 1_[+3(5.25e-05)]_11 chr10:67940677-67940697 6.00e-01 20 chr19:42829585-42829605 6.77e-01 20 chr12:7054021-7054041 3.22e-02 20 chr7:5569406-5569426 2.25e-02 20 chr9:5851644-5851664 2.39e-01 20 chr3:149376434-149376454 1.39e-01 20 chr5:143550315-143550335 4.97e-01 20 chr5:65440008-65440028 1.26e-01 12_[+1(6.32e-05)] chr11:67030347-67030367 2.22e-03 8_[+2(1.99e-05)]_4 chr1:43222786-43222806 1.09e-03 9_[+2(1.99e-05)]_3 chr11:95976534-95976554 6.69e-03 4_[+1(3.26e-05)]_8 chr1:159047163-159047183 7.42e-01 20 chr22:50415053-50415073 3.61e-02 20 chr3:124620316-124620336 5.54e-02 20 chr3:107352641-107352661 8.31e-02 20 chr8:29413883-29413903 3.80e-01 20 chr8:144373516-144373536 3.54e-02 3_[+2(1.99e-05)]_9 chr1:40505653-40505673 3.40e-01 20 chr16:70333065-70333085 1.35e-01 12_[+1(6.32e-05)] chr2:241075740-241075760 1.21e-01 4_[+1(6.32e-05)]_8 chr1:203259810-203259830 1.96e-01 20 chr15:90931276-90931296 1.69e-01 20 chr2:86669935-86669955 4.44e-03 11_[+3(5.31e-06)]_1 chr19:13262696-13262716 7.44e-01 20 chr14:23340279-23340299 3.44e-02 10_[+1(3.26e-05)]_2 chr5:34839218-34839238 3.17e-01 20 chr7:104584889-104584909 2.91e-02 4_[+1(1.97e-05)]_8 chr10:64576489-64576509 9.18e-03 20 chr14:52314161-52314181 5.99e-01 20 chr15:101675984-10167600 3.67e-01 20 chr10:16859463-16859483 9.74e-01 20 chr20:33872595-33872615 4.36e-02 20 chr1:151431960-151431980 4.46e-01 20 chr1:8157578-8157598 4.19e-05 3_[+5(2.57e-05)]_9 chr2:55361197-55361217 2.68e-04 8_[+3(5.31e-06)]_4 chr14:74227040-74227060 5.95e-02 9_[+1(3.26e-05)]_3 chr13:108978808-10897882 3.36e-01 20 chr12:15101893-15101913 1.29e-03 11_[+3(6.42e-05)]_1 chr5:132732577-132732597 6.73e-01 20 chr12:52445138-52445158 6.83e-01 20 chr10:112257586-11225760 1.04e-02 7_[+3(4.16e-05)]_5 chr9:88969356-88969376 3.43e-02 9_[+1(1.97e-05)]_3 chr22:27068948-27068968 2.71e-02 20 chr19:53426469-53426489 1.78e-02 2_[+1(1.97e-05)]_10 chr6:159516045-159516065 1.02e-04 5_[+4(5.49e-06)]_7 chr13:25875678-25875698 7.44e-01 20 chr4:10118497-10118517 6.29e-02 [+2(9.53e-05)]_12 chr9:129933147-129933167 5.54e-01 20 chr1:42128082-42128102 8.88e-01 20 chr1:109825886-109825906 9.86e-01 20 chr10:72124407-72124427 9.69e-01 20 chr15:91669523-91669543 2.31e-04 9_[+4(5.49e-06)]_3 chr19:13278628-13278648 2.93e-02 20 chrX:133503719-133503739 2.13e-01 20 chr19:39322552-39322572 4.35e-01 20 chr12:9917433-9917453 1.22e-02 5_[+3(1.07e-05)]_7 chr2:183989091-183989111 2.88e-01 20 chr9:127631377-127631397 8.68e-02 8_[+1(6.32e-05)]_4 chr1:3663931-3663951 2.74e-01 20 chr22:36851298-36851318 8.47e-01 20 chr19:1174275-1174295 3.71e-02 5_[+1(1.97e-05)]_7 chr13:36527764-36527784 6.74e-01 20 chr1:47082668-47082688 1.15e-02 [+5(7.31e-05)]_12 chr17:16189481-16189501 8.53e-05 2_[+3(2.96e-05)]_10 chr17:77784044-77784064 9.52e-01 20 chr5:158690253-158690273 1.68e-02 7_[+1(1.97e-05)]_5 chr6:159420895-159420915 2.29e-03 9_[+1(1.97e-05)]_3 chr12:104998559-10499857 2.31e-01 20 chr1:46251444-46251464 3.88e-02 20 chr2:152144896-152144916 3.34e-02 20 chr8:145980989-145981009 3.53e-02 20 chr19:57792707-57792727 4.20e-02 20 chr11:22802681-22802701 5.77e-01 20 chr9:77567885-77567905 9.67e-03 9_[+2(1.99e-05)]_3 chr10:93683495-93683515 2.45e-02 10_[+1(1.97e-05)]_2 chr6:51928501-51928521 9.88e-01 20 chr6:3069202-3069222 9.66e-01 20 chr17:80606328-80606348 9.77e-01 20 chr12:11912214-11912234 3.27e-01 20 chr1:154976636-154976656 1.31e-03 10_[+2(1.99e-05)]_2 chr19:37825529-37825549 6.40e-01 20 chr10:131934669-13193468 1.33e-01 20 chr19:14800823-14800843 1.63e-01 20 chr10:106098368-10609838 3.94e-01 20 chr7:98978764-98978784 1.90e-01 20 chr5:79703680-79703700 2.83e-01 20 chr16:48278184-48278204 2.61e-02 5_[+2(9.53e-05)]_7 chr1:205601151-205601171 2.28e-02 2_[+1(1.97e-05)]_10 chr1:85742500-85742520 5.01e-02 20 chr1:22351993-22352013 5.44e-02 4_[+1(1.97e-05)]_8 chr7:128802807-128802827 5.03e-01 20 chr11:65668111-65668131 1.65e-01 20 chrX:18693121-18693141 5.82e-02 20 chr2:219262857-219262877 9.70e-01 20 chr17:71228422-71228442 9.93e-01 20 chr5:78810465-78810485 6.95e-04 1_[+2(5.24e-05)]_11 chr3:100428108-100428128 1.28e-02 20 chr1:174933729-174933749 4.76e-01 20 chr2:137181209-137181229 5.38e-01 20 chrX:15873164-15873184 5.13e-02 7_[+2(9.53e-05)]_5 chr1:160681618-160681638 1.08e-04 3_[+4(7.35e-05)]_9 chr4:2936621-2936641 2.06e-01 20 chr5:176882506-176882526 8.34e-01 20 chr12:56320886-56320906 9.13e-02 20 chr13:103109881-10310990 4.43e-01 20 chr4:148538551-148538571 6.99e-01 20 chr3:186524283-186524303 3.57e-01 20 chr22:51001411-51001431 4.94e-01 20 chr14:75745258-75745278 7.57e-01 20 chr8:145137523-145137543 1.82e-02 [+2(1.99e-05)]_12 chr3:27526120-27526140 5.00e-01 20 chr16:25118450-25118470 9.87e-01 20 chr12:56401195-56401215 5.41e-01 20 chr2:55746729-55746749 5.26e-02 4_[+1(1.97e-05)]_8 chr21:37692428-37692448 2.57e-02 [+2(1.99e-05)]_12 chr1:114326304-114326324 2.23e-02 1_[+2(6.54e-05)]_11 chr12:120875851-12087587 8.30e-01 20 chr7:44084179-44084199 7.14e-01 20 chr22:41260204-41260224 2.14e-03 3_[+3(5.31e-06)]_9 chr1:29208720-29208740 9.51e-01 20 chr4:84133930-84133950 5.43e-03 1_[+4(5.49e-06)]_11 chr19:9695193-9695213 1.12e-03 10_[+4(3.60e-05)]_2 chr5:138677510-138677530 2.48e-02 3_[+2(1.99e-05)]_9 chr1:36181279-36181299 2.33e-02 20 chr17:29421968-29421988 7.63e-01 20 chr12:107368522-10736854 5.09e-02 12_[+3(2.96e-05)] chr4:88480860-88480880 5.33e-03 6_[+5(2.57e-05)]_6 chr15:80251173-80251193 9.12e-01 20 chr6:43138942-43138962 1.74e-01 20 chr20:30311750-30311770 6.91e-01 20 chr20:45181793-45181813 8.47e-01 20 chr3:187334231-187334251 5.19e-02 12_[+3(8.07e-05)] chr3:119528667-119528687 1.66e-02 20 chr12:65563321-65563341 9.96e-01 20 chr12:6862286-6862306 9.08e-01 20 chr17:43394656-43394676 6.36e-03 20 chr15:78423864-78423884 7.88e-01 20 chr9:126691813-126691833 2.94e-03 [+4(1.91e-05)]_12 chr8:59323868-59323888 6.98e-01 20 chr9:273017-273037 2.20e-01 20 chr9:127703383-127703403 8.95e-01 20 chr3:49158278-49158298 9.67e-01 20 chr2:54343038-54343058 3.61e-01 20 chr5:36876810-36876830 9.08e-01 20 chr22:46431910-46431930 4.61e-01 20 chr19:44507100-44507120 9.97e-01 20 chr10:45496336-45496356 7.58e-01 20 chr2:170550923-170550943 3.17e-01 20 chr1:20834616-20834636 9.96e-02 20 chr8:53627080-53627100 1.82e-02 [+2(5.24e-05)]_12 chr13:108867897-10886791 3.75e-01 20 chr15:40615732-40615752 2.79e-01 20 chr1:40506380-40506400 2.25e-02 3_[+2(1.99e-05)]_9 chr3:9834490-9834510 5.45e-01 20 chr16:12639051-12639071 1.01e-03 [+5(2.57e-05)]_12 chr10:15902498-15902518 2.13e-02 1_[+2(1.99e-05)]_11 chr1:53662454-53662474 8.44e-02 20 chr17:6544044-6544064 5.24e-02 20 chr20:43104499-43104519 9.22e-01 20 chr2:62326903-62326923 2.27e-01 20 chr5:82373351-82373371 8.81e-01 20 chr12:122125072-12212509 2.25e-03 12_[+2(1.99e-05)] chr19:12904431-12904451 3.30e-02 10_[+2(9.53e-05)]_2 chr1:161008793-161008813 9.05e-01 20 chr17:65362709-65362729 5.01e-01 20 chrX:13752828-13752848 4.23e-02 20 chr17:28050777-28050797 8.81e-03 11_[+5(7.31e-05)]_1 chr10:101989386-10198940 3.00e-02 4_[+1(1.97e-05)]_8 chr19:16296040-16296060 9.04e-02 20 chr19:44669128-44669148 5.40e-01 20 chr1:174998975-174998995 6.68e-04 6_[+1(1.97e-05)]_6 chr7:6746633-6746653 2.20e-02 8_[+2(5.24e-05)]_4 chr14:64912391-64912411 8.39e-01 20 chr8:90914234-90914254 9.28e-01 20 chr6:166756076-166756096 1.94e-01 20 chr19:45943246-45943266 8.19e-02 10_[+1(6.32e-05)]_2 chr19:9785784-9785804 2.99e-01 20 chr17:40086836-40086856 3.95e-01 20 chr1:9971183-9971203 5.77e-02 20 chr17:7835236-7835256 2.49e-01 20 chr21:46293596-46293616 4.87e-02 20 chrX:153626442-153626462 9.01e-01 20 chr16:1823162-1823182 7.08e-01 20 chr11:9386077-9386097 1.64e-01 20 chr13:45915372-45915392 2.44e-01 20 chr3:50275608-50275628 7.21e-01 20 chr7:6617035-6617055 5.09e-01 20 chr17:41132166-41132186 5.84e-01 20 chr6:90348467-90348487 2.09e-02 6_[+2(1.99e-05)]_6 chr15:66161768-66161788 1.16e-01 20 chr11:506863-506883 9.12e-01 20 chr1:55230361-55230381 7.79e-01 20 chr3:185000643-185000663 9.63e-01 20 chr20:2082792-2082812 9.62e-03 5_[+2(1.99e-05)]_7 chr15:83736010-83736030 5.71e-01 20 chr6:139350797-139350817 3.41e-01 20 chr19:45542310-45542330 1.21e-01 3_[+1(6.32e-05)]_9 chr2:45838411-45838431 1.17e-02 20 chr2:17699745-17699765 9.90e-01 20 chr13:77566211-77566231 2.20e-02 [+2(5.24e-05)]_12 chr11:69490111-69490131 9.79e-05 4_[+1(1.97e-05)]_8 chr11:57103406-57103426 3.97e-01 20 chr12:64798062-64798082 5.81e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************