******************************************************************************** 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/MAZ.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr19:1315828-1315848 1.0000 20 chr10:51572254-51572274 1.0000 20 chr22:41488539-41488559 1.0000 20 chr22:46512532-46512552 1.0000 20 chr10:43601062-43601082 1.0000 20 chr10:104155346-10415536 1.0000 20 chr20:335299-335319 1.0000 20 chr1:167189986-167190006 1.0000 20 chrX:129116455-129116475 1.0000 20 chr11:96075016-96075036 1.0000 20 chr20:307964-307984 1.0000 20 chr20:4804286-4804306 1.0000 20 chr6:131384519-131384539 1.0000 20 chr17:27916716-27916736 1.0000 20 chr14:75760952-75760972 1.0000 20 chr14:23775932-23775952 1.0000 20 chr19:42637399-42637419 1.0000 20 chr19:41222818-41222838 1.0000 20 chr11:118977960-11897798 1.0000 20 chr11:85566075-85566095 1.0000 20 chr1:33647703-33647723 1.0000 20 chr20:39946559-39946579 1.0000 20 chr4:114683025-114683045 1.0000 20 chr19:8461685-8461705 1.0000 20 chr11:67171346-67171366 1.0000 20 chr3:48595742-48595762 1.0000 20 chr11:75918807-75918827 1.0000 20 chr6:31865513-31865533 1.0000 20 chr19:45250884-45250904 1.0000 20 chr17:42402248-42402268 1.0000 20 chr17:55333941-55333961 1.0000 20 chr11:75237006-75237026 1.0000 20 chr12:8123339-8123359 1.0000 20 chr17:45973887-45973907 1.0000 20 chr6:97345864-97345884 1.0000 20 chr2:129079538-129079558 1.0000 20 chr11:47574716-47574736 1.0000 20 chr15:55582094-55582114 1.0000 20 chr19:49149942-49149962 1.0000 20 chr18:9102599-9102619 1.0000 20 chr19:18391177-18391197 1.0000 20 chr14:89883595-89883615 1.0000 20 chr1:41826857-41826877 1.0000 20 chr19:50922087-50922107 1.0000 20 chr10:28591999-28592019 1.0000 20 chr12:107349435-10734945 1.0000 20 chr5:176856367-176856387 1.0000 20 chr19:1885525-1885545 1.0000 20 chr2:99964835-99964855 1.0000 20 chr8:128746320-128746340 1.0000 20 chr12:2904059-2904079 1.0000 20 chr17:45899231-45899251 1.0000 20 chr9:135230516-135230536 1.0000 20 chr11:76510444-76510464 1.0000 20 chr1:205030866-205030886 1.0000 20 chr9:129567268-129567288 1.0000 20 chr11:66623790-66623810 1.0000 20 chr20:25176272-25176292 1.0000 20 chr11:65420173-65420193 1.0000 20 chr8:101962889-101962909 1.0000 20 chr7:150777970-150777990 1.0000 20 chr10:60094684-60094704 1.0000 20 chr8:144635778-144635798 1.0000 20 chr1:47082614-47082634 1.0000 20 chr11:76092202-76092222 1.0000 20 chr5:175964494-175964514 1.0000 20 chr22:39268402-39268422 1.0000 20 chr19:10514989-10515009 1.0000 20 chr19:18058749-18058769 1.0000 20 chr1:204733078-204733098 1.0000 20 chr19:40927190-40927210 1.0000 20 chr16:47071866-47071886 1.0000 20 chr19:13215455-13215475 1.0000 20 chr2:61698351-61698371 1.0000 20 chr11:73358591-73358611 1.0000 20 chr19:47734617-47734637 1.0000 20 chr14:96829725-96829745 1.0000 20 chr2:48133851-48133871 1.0000 20 chr19:49137840-49137860 1.0000 20 chr6:35888984-35889004 1.0000 20 chr7:140624130-140624150 1.0000 20 chr10:17272021-17272041 1.0000 20 chr11:34255708-34255728 1.0000 20 chr22:31608098-31608118 1.0000 20 chr9:96328878-96328898 1.0000 20 chr11:75273090-75273110 1.0000 20 chrX:106916328-106916348 1.0000 20 chr6:38607433-38607453 1.0000 20 chr16:87984987-87985007 1.0000 20 chr4:129730774-129730794 1.0000 20 chr14:100772847-10077286 1.0000 20 chr1:180992167-180992187 1.0000 20 chr17:3796605-3796625 1.0000 20 chr22:21356465-21356485 1.0000 20 chr10:45470536-45470556 1.0000 20 chr2:225450246-225450266 1.0000 20 chr20:32582285-32582305 1.0000 20 chr7:25019835-25019855 1.0000 20 chr20:62710974-62710994 1.0000 20 chr19:48112064-48112084 1.0000 20 chr3:141944468-141944488 1.0000 20 chr12:2905045-2905065 1.0000 20 chr18:51751128-51751148 1.0000 20 chr19:48828734-48828754 1.0000 20 chr6:99963392-99963412 1.0000 20 chr5:95144536-95144556 1.0000 20 chr10:103874808-10387482 1.0000 20 chr17:42296002-42296022 1.0000 20 chr15:101142649-10114266 1.0000 20 chr1:205718650-205718670 1.0000 20 chr12:69633306-69633326 1.0000 20 chr9:92113088-92113108 1.0000 20 chr3:20081455-20081475 1.0000 20 chr16:3109393-3109413 1.0000 20 chr4:10020564-10020584 1.0000 20 chr19:41304874-41304894 1.0000 20 chr13:21635804-21635824 1.0000 20 chr10:80827217-80827237 1.0000 20 chr14:36789873-36789893 1.0000 20 chr19:46367462-46367482 1.0000 20 chr8:144623616-144623636 1.0000 20 chr10:73533336-73533356 1.0000 20 chr7:150757154-150757174 1.0000 20 chr19:3061488-3061508 1.0000 20 chr12:110906166-11090618 1.0000 20 chr4:101014755-101014775 1.0000 20 chr19:10138528-10138548 1.0000 20 chr5:157002882-157002902 1.0000 20 chr17:8023057-8023077 1.0000 20 chr17:7239822-7239842 1.0000 20 chr1:156052289-156052309 1.0000 20 chr12:57030762-57030782 1.0000 20 chr19:18402477-18402497 1.0000 20 chr1:156023695-156023715 1.0000 20 chr4:71570371-71570391 1.0000 20 chr19:50922992-50923012 1.0000 20 chr11:111472932-11147295 1.0000 20 chr8:126442234-126442254 1.0000 20 chr17:80818164-80818184 1.0000 20 chr21:46293676-46293696 1.0000 20 chr21:40684481-40684501 1.0000 20 chr1:35657725-35657745 1.0000 20 chr19:39894611-39894631 1.0000 20 chr9:132222739-132222759 1.0000 20 chr5:179285924-179285944 1.0000 20 chr16:88767513-88767533 1.0000 20 chr19:4007696-4007716 1.0000 20 chr1:36348703-36348723 1.0000 20 chr9:20622585-20622605 1.0000 20 chr17:4613730-4613750 1.0000 20 chr5:138534200-138534220 1.0000 20 chr3:69788488-69788508 1.0000 20 chr7:74072967-74072987 1.0000 20 chr1:11986535-11986555 1.0000 20 chr12:108956355-10895637 1.0000 20 chr10:30024911-30024931 1.0000 20 chr3:194980858-194980878 1.0000 20 chr2:65659906-65659926 1.0000 20 chr11:65641075-65641095 1.0000 20 chr10:105231252-10523127 1.0000 20 chr19:44031413-44031433 1.0000 20 chr11:129939750-12993977 1.0000 20 chr5:171534032-171534052 1.0000 20 chr14:31028314-31028334 1.0000 20 chr2:65662977-65662997 1.0000 20 chrX:119763928-119763948 1.0000 20 chr1:85725444-85725464 1.0000 20 chr1:54355571-54355591 1.0000 20 chr2:86116254-86116274 1.0000 20 chr1:29240930-29240950 1.0000 20 chr16:70473195-70473215 1.0000 20 chr16:1381858-1381878 1.0000 20 chr1:225615916-225615936 1.0000 20 chr17:47439613-47439633 1.0000 20 chr11:120894732-12089475 1.0000 20 chr6:43337386-43337406 1.0000 20 chr19:8274499-8274519 1.0000 20 chr6:30650488-30650508 1.0000 20 chr10:81963334-81963354 1.0000 20 chr1:28879574-28879594 1.0000 20 chr1:2478507-2478527 1.0000 20 chr17:16945580-16945600 1.0000 20 chr16:84633636-84633656 1.0000 20 chr14:77495201-77495221 1.0000 20 chr9:88357034-88357054 1.0000 20 chr16:68002616-68002636 1.0000 20 chr7:39663143-39663163 1.0000 20 chr16:2255806-2255826 1.0000 20 chr17:79484901-79484921 1.0000 20 chr5:141736570-141736590 1.0000 20 chr18:812366-812386 1.0000 20 chr13:108870775-10887079 1.0000 20 chr15:75230480-75230500 1.0000 20 chr12:794736-794756 1.0000 20 chr17:17727142-17727162 1.0000 20 chr8:102217966-102217986 1.0000 20 chr11:64655524-64655544 1.0000 20 chr1:166845657-166845677 1.0000 20 chr4:105416136-105416156 1.0000 20 chr17:27918822-27918842 1.0000 20 chr16:84651860-84651880 1.0000 20 chr11:58939516-58939536 1.0000 20 chr3:185304011-185304031 1.0000 20 chr2:128785063-128785083 1.0000 20 chrX:130838368-130838388 1.0000 20 chr12:58148703-58148723 1.0000 20 chr8:95274599-95274619 1.0000 20 chr6:31869931-31869951 1.0000 20 chr5:139017190-139017210 1.0000 20 chr5:110848285-110848305 1.0000 20 chr7:100797628-100797648 1.0000 20 chr2:157198207-157198227 1.0000 20 chr20:62708570-62708590 1.0000 20 chr17:77770923-77770943 1.0000 20 chr9:95857936-95857956 1.0000 20 chr14:74318532-74318552 1.0000 20 chr10:104421134-10442115 1.0000 20 chr19:44037506-44037526 1.0000 20 chr11:74109811-74109831 1.0000 20 chr8:117887089-117887109 1.0000 20 chr6:33285591-33285611 1.0000 20 chr22:17640173-17640193 1.0000 20 chr4:2538171-2538191 1.0000 20 chr22:50329909-50329929 1.0000 20 chrX:130887380-130887400 1.0000 20 chr1:23881390-23881410 1.0000 20 chr9:19127599-19127619 1.0000 20 chr17:74733715-74733735 1.0000 20 chr4:6785302-6785322 1.0000 20 chr15:40331468-40331488 1.0000 20 chr22:41940551-41940571 1.0000 20 chr6:109804465-109804485 1.0000 20 chr20:61075437-61075457 1.0000 20 chr12:89918620-89918640 1.0000 20 chr7:105925585-105925605 1.0000 20 chr11:71934298-71934318 1.0000 20 chr17:7388124-7388144 1.0000 20 chr8:12613183-12613203 1.0000 20 chr1:31252588-31252608 1.0000 20 chr10:120969140-12096916 1.0000 20 chr8:119124206-119124226 1.0000 20 chr17:7477062-7477082 1.0000 20 chr5:6713303-6713323 1.0000 20 chr6:31588432-31588452 1.0000 20 chr9:130965594-130965614 1.0000 20 chr7:23145344-23145364 1.0000 20 chr19:4969098-4969118 1.0000 20 chr12:104850662-10485068 1.0000 20 chr7:1980208-1980228 1.0000 20 chr7:100076966-100076986 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_MAZ/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/MAZ.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 0.121 C 0.38 G 0.364 T 0.135 Background letter frequencies (from file dataset with add-one prior applied): A 0.121 C 0.38 G 0.364 T 0.135 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGGMGGGG MEME-1 width = 8 sites = 44 llr = 293 E-value = 3.1e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3::5:122 pos.-specific C :::3:::: probability G 7aa:a988 matrix T :::2:::: bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 ** * (9.6 bits) 1.2 ** ** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGAGGGG consensus A C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr19:50922992-50923012 3 3.41e-05 GG AGGAGGGG GACATTTGCC chr2:48133851-48133871 8 3.41e-05 CCCGCCT AGGAGGGG GAAAG chr19:8461685-8461705 10 4.54e-05 tgtctgcag aggaggga ggg chr16:68002616-68002636 4 1.59e-04 AGC GGGAGGGG CTCGGCCGG chr1:156052289-156052309 5 1.59e-04 TGAC GGGAgggg ggcgcgcc chr15:101142649-10114266 6 1.59e-04 GGGTA AGGAGGAG AGAAGGA chr20:32582285-32582305 12 1.59e-04 GAGGGGCGGA GGGAGGGG A chr9:96328878-96328898 2 1.59e-04 A GGGAGGGG CTGGCGCTCG chr19:13215455-13215475 6 1.59e-04 AAGGT GGGAGGGG GAAGAGG chr5:176856367-176856387 13 1.59e-04 TGATGTGGCT GGGAGGGG chr6:31865513-31865533 11 1.59e-04 AGGGAGGGCG AGGAGGAG CC chr11:67171346-67171366 5 1.59e-04 CCTT GGGAGGGG CCCCCAGC chr19:48828734-48828754 3 1.97e-04 aa gggaggga ggaaggcggt chr14:89883595-89883615 9 1.97e-04 gaagcgcg gggaggga ggag chr11:74109811-74109831 12 2.31e-04 CGCCGGTTGG GGGAGGAG G chr6:43337386-43337406 7 2.31e-04 AAAGTG GGGAGGAG CACAGA chr1:11986535-11986555 6 2.31e-04 GCGGA GGGAGGAG AGAGAGC chr12:794736-794756 11 2.80e-04 TGCGGTGGGG AGGTGGGG GC chr1:2478507-2478527 1 2.80e-04 . AGGTGGGG CTCTGGGGAA chr6:31588432-31588452 11 2.93e-04 GGGAGGTGGG AGGTGGGA GG chr7:1980208-1980228 5 5.38e-04 CAGA GGGTGGGG CCGCCTCC chr8:12613183-12613203 7 5.38e-04 CCCTCC GGGTGGGG GACGCA chrX:119763928-119763948 10 5.38e-04 GCGCCGCGA AGGCGGGG GTA chr14:100772847-10077286 6 5.38e-04 GGCCC GGGTGGGG GCGCCGA chr11:34255708-34255728 4 5.38e-04 TTG GGGTGGGG GCAAGGGTA chr7:140624130-140624150 11 5.38e-04 CCCACATCTG GGGTGGGG GC chr11:75918807-75918827 13 5.38e-04 CGGGCCGCGG AGGAGAGG chr10:30024911-30024931 2 6.20e-04 C AGGCGGGA GCACCCTCGG chr20:61075437-61075457 9 1.05e-03 GTGCGGGA GGGCGGGG GGAG chr22:41940551-41940571 3 1.05e-03 CG GGGCGGGG CTGCCTGTGT chr14:31028314-31028334 5 1.05e-03 TCGA GGGCGGGG CCGACCGC chr7:74072967-74072987 13 1.05e-03 TAACTGCGGC GGGCGGGG chr11:111472932-11147295 9 1.05e-03 CAGCGGTG AGGCGGAG GGGC chr22:21356465-21356485 9 1.05e-03 cgccaccg gggcgggg cggg chr16:87984987-87985007 8 1.05e-03 GCGCGGA GGGCGGGG GCCGA chr10:17272021-17272041 11 1.05e-03 GGGGGCTGGA GGGAGAGG GG chr11:66623790-66623810 2 1.05e-03 G AGGCGGAG GCCGGTTGGC chr19:1885525-1885545 11 1.05e-03 GGAGCGCGCG GGGCGGGG GT chr15:75230480-75230500 12 1.20e-03 TCTGGCGCGT GGGCGGGA G chr7:25019835-25019855 3 1.20e-03 AA GGGCGGGA GCGCAGGGGA chr8:101962889-101962909 5 1.20e-03 GGGG GGGAGAGA TGGGGAGC chr9:129567268-129567288 8 1.20e-03 TTTCGGG GGGCGGGA CCGGG chr19:44031413-44031433 6 1.32e-03 GGCGG GGGCGGAG CACGCCT chr3:185304011-185304031 2 1.38e-03 C AGGAGTGG TGGCGGGCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:50922992-50923012 3.4e-05 2_[+1]_10 chr2:48133851-48133871 3.4e-05 7_[+1]_5 chr19:8461685-8461705 4.5e-05 9_[+1]_3 chr16:68002616-68002636 0.00016 3_[+1]_9 chr1:156052289-156052309 0.00016 4_[+1]_8 chr15:101142649-10114266 0.00016 5_[+1]_7 chr20:32582285-32582305 0.00016 11_[+1]_1 chr9:96328878-96328898 0.00016 1_[+1]_11 chr19:13215455-13215475 0.00016 5_[+1]_7 chr5:176856367-176856387 0.00016 12_[+1] chr6:31865513-31865533 0.00016 10_[+1]_2 chr11:67171346-67171366 0.00016 4_[+1]_8 chr19:48828734-48828754 0.0002 2_[+1]_10 chr14:89883595-89883615 0.0002 8_[+1]_4 chr11:74109811-74109831 0.00023 11_[+1]_1 chr6:43337386-43337406 0.00023 6_[+1]_6 chr1:11986535-11986555 0.00023 5_[+1]_7 chr12:794736-794756 0.00028 10_[+1]_2 chr1:2478507-2478527 0.00028 [+1]_12 chr6:31588432-31588452 0.00029 10_[+1]_2 chr7:1980208-1980228 0.00054 4_[+1]_8 chr8:12613183-12613203 0.00054 6_[+1]_6 chrX:119763928-119763948 0.00054 9_[+1]_3 chr14:100772847-10077286 0.00054 5_[+1]_7 chr11:34255708-34255728 0.00054 3_[+1]_9 chr7:140624130-140624150 0.00054 10_[+1]_2 chr11:75918807-75918827 0.00054 12_[+1] chr10:30024911-30024931 0.00062 1_[+1]_11 chr20:61075437-61075457 0.0011 8_[+1]_4 chr22:41940551-41940571 0.0011 2_[+1]_10 chr14:31028314-31028334 0.0011 4_[+1]_8 chr7:74072967-74072987 0.0011 12_[+1] chr11:111472932-11147295 0.0011 8_[+1]_4 chr22:21356465-21356485 0.0011 8_[+1]_4 chr16:87984987-87985007 0.0011 7_[+1]_5 chr10:17272021-17272041 0.0011 10_[+1]_2 chr11:66623790-66623810 0.0011 1_[+1]_11 chr19:1885525-1885545 0.0011 10_[+1]_2 chr15:75230480-75230500 0.0012 11_[+1]_1 chr7:25019835-25019855 0.0012 2_[+1]_10 chr8:101962889-101962909 0.0012 4_[+1]_8 chr9:129567268-129567288 0.0012 7_[+1]_5 chr19:44031413-44031433 0.0013 5_[+1]_7 chr3:185304011-185304031 0.0014 1_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGMGGGG width=8 seqs=44 chr19:50922992-50923012 ( 3) AGGAGGGG 1 chr2:48133851-48133871 ( 8) AGGAGGGG 1 chr19:8461685-8461705 ( 10) AGGAGGGA 1 chr16:68002616-68002636 ( 4) GGGAGGGG 1 chr1:156052289-156052309 ( 5) GGGAGGGG 1 chr15:101142649-10114266 ( 6) AGGAGGAG 1 chr20:32582285-32582305 ( 12) GGGAGGGG 1 chr9:96328878-96328898 ( 2) GGGAGGGG 1 chr19:13215455-13215475 ( 6) GGGAGGGG 1 chr5:176856367-176856387 ( 13) GGGAGGGG 1 chr6:31865513-31865533 ( 11) AGGAGGAG 1 chr11:67171346-67171366 ( 5) GGGAGGGG 1 chr19:48828734-48828754 ( 3) GGGAGGGA 1 chr14:89883595-89883615 ( 9) GGGAGGGA 1 chr11:74109811-74109831 ( 12) GGGAGGAG 1 chr6:43337386-43337406 ( 7) GGGAGGAG 1 chr1:11986535-11986555 ( 6) GGGAGGAG 1 chr12:794736-794756 ( 11) AGGTGGGG 1 chr1:2478507-2478527 ( 1) AGGTGGGG 1 chr6:31588432-31588452 ( 11) AGGTGGGA 1 chr7:1980208-1980228 ( 5) GGGTGGGG 1 chr8:12613183-12613203 ( 7) GGGTGGGG 1 chrX:119763928-119763948 ( 10) AGGCGGGG 1 chr14:100772847-10077286 ( 6) GGGTGGGG 1 chr11:34255708-34255728 ( 4) GGGTGGGG 1 chr7:140624130-140624150 ( 11) GGGTGGGG 1 chr11:75918807-75918827 ( 13) AGGAGAGG 1 chr10:30024911-30024931 ( 2) AGGCGGGA 1 chr20:61075437-61075457 ( 9) GGGCGGGG 1 chr22:41940551-41940571 ( 3) GGGCGGGG 1 chr14:31028314-31028334 ( 5) GGGCGGGG 1 chr7:74072967-74072987 ( 13) GGGCGGGG 1 chr11:111472932-11147295 ( 9) AGGCGGAG 1 chr22:21356465-21356485 ( 9) GGGCGGGG 1 chr16:87984987-87985007 ( 8) GGGCGGGG 1 chr10:17272021-17272041 ( 11) GGGAGAGG 1 chr11:66623790-66623810 ( 2) AGGCGGAG 1 chr19:1885525-1885545 ( 11) GGGCGGGG 1 chr15:75230480-75230500 ( 12) GGGCGGGA 1 chr7:25019835-25019855 ( 3) GGGCGGGA 1 chr8:101962889-101962909 ( 5) GGGAGAGA 1 chr9:129567268-129567288 ( 8) GGGCGGGA 1 chr19:44031413-44031433 ( 6) GGGCGGAG 1 chr3:185304011-185304031 ( 2) AGGAGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.07592 E= 3.1e-010 139 -1210 90 -1210 -1210 -1210 146 -1210 -1210 -1210 146 -1210 198 -16 -1210 43 -1210 -1210 146 -1210 -83 -1210 132 -257 59 -1210 117 -1210 76 -1210 113 -1210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 3.1e-010 0.318182 0.000000 0.681818 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.477273 0.340909 0.000000 0.181818 0.000000 0.000000 1.000000 0.000000 0.068182 0.000000 0.909091 0.022727 0.181818 0.000000 0.818182 0.000000 0.204545 0.000000 0.795455 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGGGG MEME-1 regular expression -------------------------------------------------------------------------------- [GA]GG[AC]GGG[GA] -------------------------------------------------------------------------------- Time 2.87 secs. ******************************************************************************** ******************************************************************************** MOTIF CYCCKCCC MEME-2 width = 8 sites = 58 llr = 339 E-value = 1.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :1::1::: pos.-specific C a599:997 probability G ::::3::: matrix T :4116:13 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 (8.4 bits) 1.2 * *** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCCCTCCC consensus T G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:89918620-89918640 11 1.95e-05 TTCCCACTCA CTCCTCCT GG chr5:175964494-175964514 10 1.95e-05 TTTTTTAAC CTCCTCCT CGC chr12:104850662-10485068 12 7.44e-05 GGGTCCCTCC CTCCTCCC G chr6:38607433-38607453 13 7.44e-05 CCCGTCCCAG CTCCTCCC chr19:49137840-49137860 2 7.44e-05 C CTCCTCCC TTCCTCCCAG chr12:2904059-2904079 13 7.44e-05 TGCGCTCCCG CTCCTCCC chr14:77495201-77495221 9 1.29e-04 CCAGCCGG CCCCTCCT CCGC chr1:205718650-205718670 13 1.29e-04 GGTGCCTCCG CCCCTCCT chr19:48112064-48112084 3 1.29e-04 AG CCCCTCCT CCGGCGAGGG chr5:6713303-6713323 11 2.84e-04 CTCCCTCCAG CCCCTCCC AG chr10:104421134-10442115 11 2.84e-04 CCGCTCCTGC CCCCTCCC TC chr17:77770923-77770943 9 2.84e-04 ccgcggcc cccctccc gcgc chr11:120894732-12089475 9 2.84e-04 TCCGGCGC CCCCTCCC ATTC chr16:1381858-1381878 12 2.84e-04 GCAGCGGCTG CCCCTCCC A chr5:138534200-138534220 9 2.84e-04 CCCCCGTG CCCCTCCC CTTG chr7:150757154-150757174 9 2.84e-04 CCAGACCA CCCCTCCC CTCC chr11:73358591-73358611 7 2.84e-04 TCACTC CCCCTCCC TGGGGT chr6:97345864-97345884 4 2.84e-04 GAG CCCCTCCC TTCGGGGCG chrX:130887380-130887400 12 3.10e-04 TCAAAGTCCT CTTCTCCC G chr20:25176272-25176292 6 3.37e-04 CCCAC CTCCTCTC CCGCCTG chr1:166845657-166845677 12 3.43e-04 AAACTCTGCT CTCTTCCT C chr18:51751128-51751148 5 4.33e-04 TTGT CTCCGCCT TCTCGGGG chr11:65641075-65641095 6 6.30e-04 TCCGC CTCCGCCC GAAGTGG chr13:21635804-21635824 3 6.30e-04 CG CTCCGCCC AGCCCCGCCC chr19:40927190-40927210 4 6.30e-04 AGG CTCCGCCC TGTCCCTGC chr1:33647703-33647723 12 6.30e-04 ACCCAAGCAA CTCCGCCC C chr9:92113088-92113108 11 7.05e-04 ccttcccctt cctctccc cc chr10:120969140-12096916 3 7.41e-04 CG CCCCTCTT TCAGCCTTTG chr14:23775932-23775952 6 8.46e-04 CCCCG CCCCTCTC TCTGGAC chr8:102217966-102217986 2 8.72e-04 C CTCCTTCT GGCCCCCACC chr9:88357034-88357054 6 1.09e-03 CTGCG CCCCGCCT CTCTGCG chr1:41826857-41826877 12 1.09e-03 CCCCTAGCCC CCCCGCCT C chr20:307964-307984 3 1.09e-03 CT CCCTTCCC TGGGGGGAGG chr15:40331468-40331488 3 1.51e-03 CT CCCCGCCC GCCTAGCGCC chr12:58148703-58148723 9 1.51e-03 ACACTTGC CCCCGCCC CTGG chr1:28879574-28879594 1 1.51e-03 . CCCCGCCC GCAGAGCCCC chr17:7239822-7239842 7 1.51e-03 CCCAGG CCCCGCCC CTGCCC chr7:150777970-150777990 12 1.51e-03 GAGCCGCGAG CCCCGCCC G chr18:9102599-9102619 5 1.51e-03 CAGC CCCCGCCC CTCGGCGA chr15:55582094-55582114 13 1.51e-03 CGGGAgcggc ccccgccc chr6:131384519-131384539 5 1.51e-03 cagg ccccgccc ctgcgcgg chr4:105416136-105416156 1 1.52e-03 . cttctctc tctGTTTGTG chr11:118977960-11897798 6 1.54e-03 CCGCC CTCCTCCA GCGAGGG chr17:74733715-74733735 7 1.62e-03 CTGGGC CCCCACCT TTTTTT chr1:47082614-47082634 8 1.62e-03 CACTCGC CCCCACCT TCCCG chr22:46512532-46512552 7 1.62e-03 CCCCCC CCCCACCT CCGAGG chr7:23145344-23145364 3 1.84e-03 CT CTCCTCAT AGTGCCCCCG chrX:106916328-106916348 1 1.84e-03 . CATCTCCC TTTCCCCCCT chr11:76092202-76092222 12 2.10e-03 TCCCTCAGCC TTCCTCCC C chr7:105925585-105925605 5 2.27e-03 CCGC CTTCACCC CGTCACCC chr20:62710974-62710994 13 2.27e-03 TTTGAGCAAT CACTTCCC chr17:7477062-7477082 7 2.52e-03 GGCCGC CACCGCCC GCGGCC chr8:126442234-126442254 6 2.52e-03 GCCGC CTCCTGCC CAGCCCC chr9:135230516-135230536 10 2.52e-03 GCCGCGGTG CACCGCCC ACG chr20:4804286-4804306 10 2.52e-03 tccccttgt ctcctgcc ccc chr3:20081455-20081475 1 2.80e-03 . CCTCGCCC CCTGGCGGGC chr10:43601062-43601082 5 2.96e-03 cccg cccTTCTC CGGCTCGC chr19:41222818-41222838 12 3.33e-03 TCGGACAAGG CTCCGTCT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:89918620-89918640 1.9e-05 10_[+2]_2 chr5:175964494-175964514 1.9e-05 9_[+2]_3 chr12:104850662-10485068 7.4e-05 11_[+2]_1 chr6:38607433-38607453 7.4e-05 12_[+2] chr19:49137840-49137860 7.4e-05 1_[+2]_11 chr12:2904059-2904079 7.4e-05 12_[+2] chr14:77495201-77495221 0.00013 8_[+2]_4 chr1:205718650-205718670 0.00013 12_[+2] chr19:48112064-48112084 0.00013 2_[+2]_10 chr5:6713303-6713323 0.00028 10_[+2]_2 chr10:104421134-10442115 0.00028 10_[+2]_2 chr17:77770923-77770943 0.00028 8_[+2]_4 chr11:120894732-12089475 0.00028 8_[+2]_4 chr16:1381858-1381878 0.00028 11_[+2]_1 chr5:138534200-138534220 0.00028 8_[+2]_4 chr7:150757154-150757174 0.00028 8_[+2]_4 chr11:73358591-73358611 0.00028 6_[+2]_6 chr6:97345864-97345884 0.00028 3_[+2]_9 chrX:130887380-130887400 0.00031 11_[+2]_1 chr20:25176272-25176292 0.00034 5_[+2]_7 chr1:166845657-166845677 0.00034 11_[+2]_1 chr18:51751128-51751148 0.00043 4_[+2]_8 chr11:65641075-65641095 0.00063 5_[+2]_7 chr13:21635804-21635824 0.00063 2_[+2]_10 chr19:40927190-40927210 0.00063 3_[+2]_9 chr1:33647703-33647723 0.00063 11_[+2]_1 chr9:92113088-92113108 0.0007 10_[+2]_2 chr10:120969140-12096916 0.00074 2_[+2]_10 chr14:23775932-23775952 0.00085 5_[+2]_7 chr8:102217966-102217986 0.00087 1_[+2]_11 chr9:88357034-88357054 0.0011 5_[+2]_7 chr1:41826857-41826877 0.0011 11_[+2]_1 chr20:307964-307984 0.0011 2_[+2]_10 chr15:40331468-40331488 0.0015 2_[+2]_10 chr12:58148703-58148723 0.0015 8_[+2]_4 chr1:28879574-28879594 0.0015 [+2]_12 chr17:7239822-7239842 0.0015 6_[+2]_6 chr7:150777970-150777990 0.0015 11_[+2]_1 chr18:9102599-9102619 0.0015 4_[+2]_8 chr15:55582094-55582114 0.0015 12_[+2] chr6:131384519-131384539 0.0015 4_[+2]_8 chr4:105416136-105416156 0.0015 [+2]_12 chr11:118977960-11897798 0.0015 5_[+2]_7 chr17:74733715-74733735 0.0016 6_[+2]_6 chr1:47082614-47082634 0.0016 7_[+2]_5 chr22:46512532-46512552 0.0016 6_[+2]_6 chr7:23145344-23145364 0.0018 2_[+2]_10 chrX:106916328-106916348 0.0018 [+2]_12 chr11:76092202-76092222 0.0021 11_[+2]_1 chr7:105925585-105925605 0.0023 4_[+2]_8 chr20:62710974-62710994 0.0023 12_[+2] chr17:7477062-7477082 0.0025 6_[+2]_6 chr8:126442234-126442254 0.0025 5_[+2]_7 chr9:135230516-135230536 0.0025 9_[+2]_3 chr20:4804286-4804306 0.0025 9_[+2]_3 chr3:20081455-20081475 0.0028 [+2]_12 chr10:43601062-43601082 0.003 4_[+2]_8 chr19:41222818-41222838 0.0033 11_[+2]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CYCCKCCC width=8 seqs=58 chr12:89918620-89918640 ( 11) CTCCTCCT 1 chr5:175964494-175964514 ( 10) CTCCTCCT 1 chr12:104850662-10485068 ( 12) CTCCTCCC 1 chr6:38607433-38607453 ( 13) CTCCTCCC 1 chr19:49137840-49137860 ( 2) CTCCTCCC 1 chr12:2904059-2904079 ( 13) CTCCTCCC 1 chr14:77495201-77495221 ( 9) CCCCTCCT 1 chr1:205718650-205718670 ( 13) CCCCTCCT 1 chr19:48112064-48112084 ( 3) CCCCTCCT 1 chr5:6713303-6713323 ( 11) CCCCTCCC 1 chr10:104421134-10442115 ( 11) CCCCTCCC 1 chr17:77770923-77770943 ( 9) CCCCTCCC 1 chr11:120894732-12089475 ( 9) CCCCTCCC 1 chr16:1381858-1381878 ( 12) CCCCTCCC 1 chr5:138534200-138534220 ( 9) CCCCTCCC 1 chr7:150757154-150757174 ( 9) CCCCTCCC 1 chr11:73358591-73358611 ( 7) CCCCTCCC 1 chr6:97345864-97345884 ( 4) CCCCTCCC 1 chrX:130887380-130887400 ( 12) CTTCTCCC 1 chr20:25176272-25176292 ( 6) CTCCTCTC 1 chr1:166845657-166845677 ( 12) CTCTTCCT 1 chr18:51751128-51751148 ( 5) CTCCGCCT 1 chr11:65641075-65641095 ( 6) CTCCGCCC 1 chr13:21635804-21635824 ( 3) CTCCGCCC 1 chr19:40927190-40927210 ( 4) CTCCGCCC 1 chr1:33647703-33647723 ( 12) CTCCGCCC 1 chr9:92113088-92113108 ( 11) CCTCTCCC 1 chr10:120969140-12096916 ( 3) CCCCTCTT 1 chr14:23775932-23775952 ( 6) CCCCTCTC 1 chr8:102217966-102217986 ( 2) CTCCTTCT 1 chr9:88357034-88357054 ( 6) CCCCGCCT 1 chr1:41826857-41826877 ( 12) CCCCGCCT 1 chr20:307964-307984 ( 3) CCCTTCCC 1 chr15:40331468-40331488 ( 3) CCCCGCCC 1 chr12:58148703-58148723 ( 9) CCCCGCCC 1 chr1:28879574-28879594 ( 1) CCCCGCCC 1 chr17:7239822-7239842 ( 7) CCCCGCCC 1 chr7:150777970-150777990 ( 12) CCCCGCCC 1 chr18:9102599-9102619 ( 5) CCCCGCCC 1 chr15:55582094-55582114 ( 13) CCCCGCCC 1 chr6:131384519-131384539 ( 5) CCCCGCCC 1 chr4:105416136-105416156 ( 1) CTTCTCTC 1 chr11:118977960-11897798 ( 6) CTCCTCCA 1 chr17:74733715-74733735 ( 7) CCCCACCT 1 chr1:47082614-47082634 ( 8) CCCCACCT 1 chr22:46512532-46512552 ( 7) CCCCACCT 1 chr7:23145344-23145364 ( 3) CTCCTCAT 1 chrX:106916328-106916348 ( 1) CATCTCCC 1 chr11:76092202-76092222 ( 12) TTCCTCCC 1 chr7:105925585-105925605 ( 5) CTTCACCC 1 chr20:62710974-62710994 ( 13) CACTTCCC 1 chr17:7477062-7477082 ( 7) CACCGCCC 1 chr8:126442234-126442254 ( 6) CTCCTGCC 1 chr9:135230516-135230536 ( 10) CACCGCCC 1 chr20:4804286-4804306 ( 10) CTCCTGCC 1 chr3:20081455-20081475 ( 1) CCTCGCCC 1 chr10:43601062-43601082 ( 5) CCCTTCTC 1 chr19:41222818-41222838 ( 12) CTCCGTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 6.43238 E= 1.2e-004 -1250 137 -1250 -296 -81 49 -1250 156 -1250 124 -1250 -38 -1250 129 -1250 -97 -81 -1250 -15 216 -1250 129 -340 -196 -281 124 -1250 -64 -281 90 -1250 103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 1.2e-004 0.000000 0.982759 0.000000 0.017241 0.068966 0.534483 0.000000 0.396552 0.000000 0.896552 0.000000 0.103448 0.000000 0.931034 0.000000 0.068966 0.068966 0.000000 0.327586 0.603448 0.000000 0.931034 0.034483 0.034483 0.017241 0.896552 0.000000 0.086207 0.017241 0.706897 0.000000 0.275862 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCKCCC MEME-2 regular expression -------------------------------------------------------------------------------- C[CT]CC[TG]CC[CT] -------------------------------------------------------------------------------- Time 3.62 secs. ******************************************************************************** ******************************************************************************** MOTIF KTTWWTRA MEME-3 width = 8 sites = 8 llr = 76 E-value = 8.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1::44369 pos.-specific C 1::::::: probability G 433:::41 matrix T 488668:: bits 3.0 2.7 2.4 * 2.1 *** * Relative 1.8 ***** * Entropy 1.5 ******* (13.7 bits) 1.2 ******* 0.9 ******* 0.6 ******* 0.3 ******** 0.0 -------- Multilevel GTTTTTAA consensus TGGAAAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:175964494-175964514 1 8.86e-08 . TTTTTTAA CCTCCTCCTC chr4:101014755-101014775 2 4.23e-06 T TTTAATGA ACAAGAGGCA chr19:50922087-50922107 11 6.29e-06 CCCTGAGGGG ATTTTTGA GG chr2:99964835-99964855 12 1.85e-05 TAAGATTTGT GGTTATAA G chr9:95857936-95857956 4 2.45e-05 GGC GTTATAGA CGCCGGCGG chr19:3061488-3061508 13 3.34e-05 AGTGGGGGTG CGTTTTAA chr11:129939750-12993977 4 3.90e-05 TTG GTGTAAAA CCCCCGGGG chr2:65659906-65659926 1 1.01e-04 . TTGATTAG GGCTCCGGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:175964494-175964514 8.9e-08 [+3]_12 chr4:101014755-101014775 4.2e-06 1_[+3]_11 chr19:50922087-50922107 6.3e-06 10_[+3]_2 chr2:99964835-99964855 1.8e-05 11_[+3]_1 chr9:95857936-95857956 2.5e-05 3_[+3]_9 chr19:3061488-3061508 3.3e-05 12_[+3] chr11:129939750-12993977 3.9e-05 3_[+3]_9 chr2:65659906-65659926 0.0001 [+3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KTTWWTRA width=8 seqs=8 chr5:175964494-175964514 ( 1) TTTTTTAA 1 chr4:101014755-101014775 ( 2) TTTAATGA 1 chr19:50922087-50922107 ( 11) ATTTTTGA 1 chr2:99964835-99964855 ( 12) GGTTATAA 1 chr9:95857936-95857956 ( 4) GTTATAGA 1 chr19:3061488-3061508 ( 13) CGTTTTAA 1 chr11:129939750-12993977 ( 4) GTGTAAAA 1 chr2:65659906-65659926 ( 1) TTGATTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.98673 E= 8.6e+000 5 -160 4 148 -965 -965 -54 248 -965 -965 -54 248 163 -965 -965 221 163 -965 -965 221 104 -965 -965 248 237 -965 4 -965 285 -965 -154 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 8.6e+000 0.125000 0.125000 0.375000 0.375000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.375000 0.000000 0.000000 0.625000 0.375000 0.000000 0.000000 0.625000 0.250000 0.000000 0.000000 0.750000 0.625000 0.000000 0.375000 0.000000 0.875000 0.000000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KTTWWTRA MEME-3 regular expression -------------------------------------------------------------------------------- [GT][TG][TG][TA][TA][TA][AG]A -------------------------------------------------------------------------------- Time 4.31 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAGGAAA MEME-4 width = 8 sites = 4 llr = 47 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 8:a3:8aa pos.-specific C :::::::: probability G 3a:5a::: matrix T :::3:3:: bits 3.0 * ** 2.7 * ** 2.4 * ** 2.1 * *** Relative 1.8 * * *** Entropy 1.5 *** **** (16.8 bits) 1.2 *** **** 0.9 *** **** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel AGAGGAAA consensus G A T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:79484901-79484921 6 8.80e-07 AACGG AGATGAAA CCGAGGA chr10:103874808-10387482 9 2.13e-06 CCTCCCTG AGAggaaa gagg chr10:81963334-81963354 10 4.51e-06 CTGCCACCA AGAGGTAA GTC chr9:132222739-132222759 7 5.76e-06 tccGGG GGAAGAAA GGTCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:79484901-79484921 8.8e-07 5_[+4]_7 chr10:103874808-10387482 2.1e-06 8_[+4]_4 chr10:81963334-81963354 4.5e-06 9_[+4]_3 chr9:132222739-132222759 5.8e-06 6_[+4]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGAGGAAA width=8 seqs=4 chr17:79484901-79484921 ( 6) AGATGAAA 1 chr10:103874808-10387482 ( 9) AGAGGAAA 1 chr10:81963334-81963354 ( 10) AGAGGTAA 1 chr9:132222739-132222759 ( 7) GGAAGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 6.93199 E= 1.7e+001 263 -865 -54 -865 -865 -865 146 -865 304 -865 -865 -865 104 -865 46 89 -865 -865 146 -865 263 -865 -865 89 304 -865 -865 -865 304 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.7e+001 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGGAAA MEME-4 regular expression -------------------------------------------------------------------------------- [AG]GA[GAT]G[AT]AA -------------------------------------------------------------------------------- Time 4.98 secs. ******************************************************************************** ******************************************************************************** MOTIF TCWGAWTK MEME-5 width = 8 sites = 3 llr = 35 E-value = 4.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 Description -------------------------------------------------------------------------------- Simplified A :37:a7:: pos.-specific C :7:::::: probability G :::a:::3 matrix T a:3::3a7 bits 3.0 * 2.7 * * * 2.4 * * * 2.1 * * *** Relative 1.8 * * *** Entropy 1.5 * ****** (17.0 bits) 1.2 * ****** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TCAGAATT consensus AT T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2:99964835-99964855 2 1.22e-06 T TAAGATTT GTGGTTATAA chr12:57030762-57030782 12 2.57e-06 CCCAGGGGCC TCTGAATT G chr1:205030866-205030886 3 5.70e-06 TC TCAGAATG CTCATGGCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:99964835-99964855 1.2e-06 1_[+5]_11 chr12:57030762-57030782 2.6e-06 11_[+5]_1 chr1:205030866-205030886 5.7e-06 2_[+5]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCWGAWTK width=8 seqs=3 chr2:99964835-99964855 ( 2) TAAGATTT 1 chr12:57030762-57030782 ( 12) TCTGAATT 1 chr1:205030866-205030886 ( 3) TCAGAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.73854 E= 4.9e+002 -823 -823 -823 289 146 81 -823 -823 246 -823 -823 130 -823 -823 145 -823 304 -823 -823 -823 246 -823 -823 130 -823 -823 -823 289 -823 -823 -13 230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 4.9e+002 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCWGAWTK MEME-5 regular expression -------------------------------------------------------------------------------- T[CA][AT]GA[AT]T[TG] -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- chr19:1315828-1315848 8.63e-01 20 chr10:51572254-51572274 9.93e-01 20 chr22:41488539-41488559 6.01e-01 20 chr22:46512532-46512552 6.22e-01 20 chr10:43601062-43601082 6.06e-01 20 chr10:104155346-10415536 8.12e-01 20 chr20:335299-335319 2.21e-01 20 chr1:167189986-167190006 9.97e-01 20 chrX:129116455-129116475 4.25e-01 20 chr11:96075016-96075036 9.16e-01 20 chr20:307964-307984 8.39e-02 20 chr20:4804286-4804306 4.20e-01 20 chr6:131384519-131384539 5.94e-01 20 chr17:27916716-27916736 1.00e+00 20 chr14:75760952-75760972 9.98e-01 20 chr14:23775932-23775952 2.04e-01 20 chr19:42637399-42637419 6.91e-01 20 chr19:41222818-41222838 1.52e-01 20 chr11:118977960-11897798 5.31e-01 20 chr11:85566075-85566095 6.30e-01 20 chr1:33647703-33647723 9.57e-02 20 chr20:39946559-39946579 3.39e-01 20 chr4:114683025-114683045 7.83e-01 20 chr19:8461685-8461705 2.22e-03 9_[+1(4.54e-05)]_3 chr11:67171346-67171366 7.67e-02 20 chr3:48595742-48595762 3.35e-01 20 chr11:75918807-75918827 4.04e-03 20 chr6:31865513-31865533 3.63e-02 20 chr19:45250884-45250904 9.89e-01 20 chr17:42402248-42402268 7.58e-01 20 chr17:55333941-55333961 9.75e-01 20 chr11:75237006-75237026 9.20e-01 20 chr12:8123339-8123359 7.68e-01 20 chr17:45973887-45973907 9.94e-01 20 chr6:97345864-97345884 2.59e-01 20 chr2:129079538-129079558 9.96e-01 20 chr11:47574716-47574736 1.43e-01 20 chr15:55582094-55582114 8.12e-02 20 chr19:49149942-49149962 1.08e-01 20 chr18:9102599-9102619 6.37e-01 20 chr19:18391177-18391197 9.90e-01 20 chr14:89883595-89883615 3.45e-02 20 chr1:41826857-41826877 5.73e-01 20 chr19:50922087-50922107 9.10e-04 10_[+3(6.29e-06)]_2 chr10:28591999-28592019 2.59e-01 20 chr12:107349435-10734945 9.44e-01 20 chr5:176856367-176856387 1.85e-02 20 chr19:1885525-1885545 5.41e-01 20 chr2:99964835-99964855 1.92e-06 1_[+5(1.22e-06)]_2_[+3(1.85e-05)]_1 chr8:128746320-128746340 4.93e-01 20 chr12:2904059-2904079 7.43e-02 12_[+2(7.44e-05)] chr17:45899231-45899251 9.96e-01 20 chr9:135230516-135230536 6.26e-01 20 chr11:76510444-76510464 9.26e-01 20 chr1:205030866-205030886 1.00e-02 2_[+5(5.70e-06)]_10 chr9:129567268-129567288 3.34e-01 20 chr11:66623790-66623810 1.93e-01 20 chr20:25176272-25176292 3.29e-01 20 chr11:65420173-65420193 8.49e-01 20 chr8:101962889-101962909 1.57e-02 20 chr7:150777970-150777990 4.23e-01 20 chr10:60094684-60094704 7.39e-01 20 chr8:144635778-144635798 6.42e-01 20 chr1:47082614-47082634 5.52e-01 20 chr11:76092202-76092222 9.83e-02 20 chr5:175964494-175964514 1.02e-06 [+3(8.86e-08)]_1_[+2(1.95e-05)]_3 chr22:39268402-39268422 9.85e-01 20 chr19:10514989-10515009 5.86e-01 20 chr19:18058749-18058769 9.24e-01 20 chr1:204733078-204733098 6.64e-01 20 chr19:40927190-40927210 3.68e-01 20 chr16:47071866-47071886 1.88e-01 20 chr19:13215455-13215475 4.06e-03 20 chr2:61698351-61698371 9.76e-01 20 chr11:73358591-73358611 2.79e-01 20 chr19:47734617-47734637 7.24e-01 20 chr14:96829725-96829745 2.57e-02 20 chr2:48133851-48133871 2.47e-04 7_[+1(3.41e-05)]_5 chr19:49137840-49137860 1.35e-01 1_[+2(7.44e-05)]_11 chr6:35888984-35889004 6.94e-01 20 chr7:140624130-140624150 7.19e-02 20 chr10:17272021-17272041 3.31e-02 20 chr11:34255708-34255728 2.57e-02 20 chr22:31608098-31608118 7.43e-01 20 chr9:96328878-96328898 1.28e-01 20 chr11:75273090-75273110 1.10e-01 20 chrX:106916328-106916348 3.08e-01 20 chr6:38607433-38607453 1.10e-01 12_[+2(7.44e-05)] chr16:87984987-87985007 3.65e-01 20 chr4:129730774-129730794 4.27e-03 20 chr14:100772847-10077286 3.20e-01 20 chr1:180992167-180992187 8.45e-01 20 chr17:3796605-3796625 5.63e-01 20 chr22:21356465-21356485 5.23e-01 20 chr10:45470536-45470556 8.98e-01 20 chr2:225450246-225450266 7.13e-02 20 chr20:32582285-32582305 3.41e-02 20 chr7:25019835-25019855 3.64e-01 20 chr20:62710974-62710994 2.78e-02 20 chr19:48112064-48112084 8.14e-02 20 chr3:141944468-141944488 1.00e+00 20 chr12:2905045-2905065 5.31e-01 20 chr18:51751128-51751148 8.85e-02 20 chr19:48828734-48828754 2.08e-03 20 chr6:99963392-99963412 1.00e+00 20 chr5:95144536-95144556 1.28e-01 20 chr10:103874808-10387482 1.69e-05 8_[+4(2.13e-06)]_4 chr17:42296002-42296022 7.15e-01 20 chr15:101142649-10114266 3.30e-05 20 chr1:205718650-205718670 2.08e-01 20 chr12:69633306-69633326 2.03e-01 20 chr9:92113088-92113108 3.86e-01 20 chr3:20081455-20081475 5.60e-01 20 chr16:3109393-3109413 7.96e-01 20 chr4:10020564-10020584 6.85e-01 20 chr19:41304874-41304894 2.99e-01 20 chr13:21635804-21635824 4.70e-01 20 chr10:80827217-80827237 1.50e-01 20 chr14:36789873-36789893 3.46e-02 20 chr19:46367462-46367482 9.50e-01 20 chr8:144623616-144623636 6.55e-01 20 chr10:73533336-73533356 9.94e-01 20 chr7:150757154-150757174 1.81e-01 20 chr19:3061488-3061508 3.50e-03 12_[+3(3.34e-05)] chr12:110906166-11090618 8.31e-03 20 chr4:101014755-101014775 3.41e-05 1_[+3(4.23e-06)]_11 chr19:10138528-10138548 9.56e-01 20 chr5:157002882-157002902 2.43e-01 20 chr17:8023057-8023077 1.01e-01 20 chr17:7239822-7239842 6.18e-01 20 chr1:156052289-156052309 1.23e-01 20 chr12:57030762-57030782 9.38e-04 11_[+5(2.57e-06)]_1 chr19:18402477-18402497 8.95e-01 20 chr1:156023695-156023715 8.94e-01 20 chr4:71570371-71570391 4.05e-01 20 chr19:50922992-50923012 7.00e-04 2_[+1(3.41e-05)]_10 chr11:111472932-11147295 4.20e-02 20 chr8:126442234-126442254 7.23e-01 20 chr17:80818164-80818184 3.91e-02 20 chr21:46293676-46293696 8.00e-01 20 chr21:40684481-40684501 5.36e-01 20 chr1:35657725-35657745 2.65e-02 20 chr19:39894611-39894631 1.87e-01 20 chr9:132222739-132222759 4.95e-05 6_[+4(5.76e-06)]_6 chr5:179285924-179285944 8.32e-01 20 chr16:88767513-88767533 6.74e-01 20 chr19:4007696-4007716 2.79e-01 20 chr1:36348703-36348723 1.00e+00 20 chr9:20622585-20622605 3.28e-01 20 chr17:4613730-4613750 3.60e-01 20 chr5:138534200-138534220 1.82e-01 20 chr3:69788488-69788508 8.23e-01 20 chr7:74072967-74072987 3.18e-01 20 chr1:11986535-11986555 1.96e-03 20 chr12:108956355-10895637 7.89e-01 20 chr10:30024911-30024931 2.62e-01 20 chr3:194980858-194980878 7.00e-02 20 chr2:65659906-65659926 2.60e-02 20 chr11:65641075-65641095 5.43e-02 20 chr10:105231252-10523127 2.85e-01 20 chr19:44031413-44031433 3.28e-01 20 chr11:129939750-12993977 2.65e-03 3_[+3(3.90e-05)]_9 chr5:171534032-171534052 8.01e-01 20 chr14:31028314-31028334 4.63e-01 20 chr2:65662977-65662997 6.64e-01 20 chrX:119763928-119763948 2.55e-01 20 chr1:85725444-85725464 8.97e-01 20 chr1:54355571-54355591 7.05e-01 20 chr2:86116254-86116274 1.45e-01 20 chr1:29240930-29240950 2.76e-01 20 chr16:70473195-70473215 9.90e-01 20 chr16:1381858-1381878 1.49e-01 20 chr1:225615916-225615936 9.83e-01 20 chr17:47439613-47439633 6.78e-01 20 chr11:120894732-12089475 9.98e-02 20 chr6:43337386-43337406 2.22e-02 20 chr19:8274499-8274519 6.73e-01 20 chr6:30650488-30650508 6.22e-01 20 chr10:81963334-81963354 4.39e-04 9_[+4(4.51e-06)]_3 chr1:28879574-28879594 4.26e-01 20 chr1:2478507-2478527 8.08e-03 20 chr17:16945580-16945600 8.83e-01 20 chr16:84633636-84633656 9.89e-02 20 chr14:77495201-77495221 2.05e-01 20 chr9:88357034-88357054 4.98e-01 20 chr16:68002616-68002636 6.53e-02 20 chr7:39663143-39663163 9.78e-01 20 chr16:2255806-2255826 6.05e-01 20 chr17:79484901-79484921 2.95e-04 5_[+4(8.80e-07)]_7 chr5:141736570-141736590 4.85e-01 20 chr18:812366-812386 9.45e-01 20 chr13:108870775-10887079 1.35e-02 20 chr15:75230480-75230500 2.99e-01 20 chr12:794736-794756 5.87e-02 20 chr17:17727142-17727162 6.91e-01 20 chr8:102217966-102217986 3.31e-01 20 chr11:64655524-64655544 8.28e-01 20 chr1:166845657-166845677 6.94e-02 20 chr4:105416136-105416156 6.09e-03 20 chr17:27918822-27918842 8.38e-01 20 chr16:84651860-84651880 1.64e-02 20 chr11:58939516-58939536 8.00e-01 20 chr3:185304011-185304031 6.54e-02 20 chr2:128785063-128785083 7.90e-01 20 chrX:130838368-130838388 3.13e-01 20 chr12:58148703-58148723 6.25e-01 20 chr8:95274599-95274619 4.51e-01 20 chr6:31869931-31869951 4.53e-02 20 chr5:139017190-139017210 5.42e-01 20 chr5:110848285-110848305 9.83e-01 20 chr7:100797628-100797648 1.00e+00 20 chr2:157198207-157198227 7.35e-03 20 chr20:62708570-62708590 7.66e-01 20 chr17:77770923-77770943 3.41e-01 20 chr9:95857936-95857956 2.27e-02 3_[+3(2.45e-05)]_9 chr14:74318532-74318552 9.31e-01 20 chr10:104421134-10442115 3.37e-01 20 chr19:44037506-44037526 7.59e-01 20 chr11:74109811-74109831 9.87e-03 20 chr8:117887089-117887109 9.94e-01 20 chr6:33285591-33285611 6.14e-01 20 chr22:17640173-17640193 9.85e-01 20 chr4:2538171-2538191 5.59e-01 20 chr22:50329909-50329929 9.32e-01 20 chrX:130887380-130887400 2.82e-02 20 chr1:23881390-23881410 3.10e-02 20 chr9:19127599-19127619 9.74e-01 20 chr17:74733715-74733735 1.28e-01 20 chr4:6785302-6785322 2.68e-01 20 chr15:40331468-40331488 6.23e-01 20 chr22:41940551-41940571 3.41e-01 20 chr6:109804465-109804485 9.74e-01 20 chr20:61075437-61075457 3.34e-01 20 chr12:89918620-89918640 4.62e-02 10_[+2(1.95e-05)]_2 chr7:105925585-105925605 6.12e-01 20 chr11:71934298-71934318 3.25e-01 20 chr17:7388124-7388144 1.81e-01 20 chr8:12613183-12613203 8.86e-02 20 chr1:31252588-31252608 2.32e-01 20 chr10:120969140-12096916 1.64e-02 20 chr8:119124206-119124226 9.39e-01 20 chr17:7477062-7477082 6.92e-01 20 chr5:6713303-6713323 3.39e-01 20 chr6:31588432-31588452 3.37e-02 20 chr9:130965594-130965614 6.08e-01 20 chr7:23145344-23145364 5.84e-02 20 chr19:4969098-4969118 9.78e-01 20 chr12:104850662-10485068 1.72e-01 11_[+2(7.44e-05)]_1 chr7:1980208-1980228 1.34e-01 20 chr7:100076966-100076986 9.80e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************