******************************************************************************** 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/K562/fasta/RankLinear0.6_40/UBTF.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr12:52115493-52115573 1.0000 80 chr2:11796892-11796972 1.0000 80 chr22:42783830-42783910 1.0000 80 chr15:70669293-70669373 1.0000 80 chr15:35087651-35087731 1.0000 80 chr6:168228507-168228587 1.0000 80 chr15:70920995-70921075 1.0000 80 chr6:161860221-161860301 1.0000 80 chr10:181806-181886 1.0000 80 chr22:41698287-41698367 1.0000 80 chr11:113906973-11390705 1.0000 80 chr2:206950536-206950616 1.0000 80 chr2:100814211-100814291 1.0000 80 chr2:160568486-160568566 1.0000 80 chr21:46719563-46719643 1.0000 80 chr1:224621944-224622024 1.0000 80 chr4:2435017-2435097 1.0000 80 chr12:26985058-26985138 1.0000 80 chr11:62314218-62314298 1.0000 80 chr17:76892815-76892895 1.0000 80 chr11:67896367-67896447 1.0000 80 chr17:66755658-66755738 1.0000 80 chr7:44270782-44270862 1.0000 80 chr7:23637393-23637473 1.0000 80 chr6:118972642-118972722 1.0000 80 chr19:4065651-4065731 1.0000 80 chr1:230204037-230204117 1.0000 80 chr1:24673788-24673868 1.0000 80 chr10:130832326-13083240 1.0000 80 chr6:42420941-42421021 1.0000 80 chr19:1307592-1307672 1.0000 80 chr5:158526197-158526277 1.0000 80 chr6:36332788-36332868 1.0000 80 chr8:38239429-38239509 1.0000 80 chr10:22614711-22614791 1.0000 80 chr16:49889553-49889633 1.0000 80 chr3:124606197-124606277 1.0000 80 chr8:21767207-21767287 1.0000 80 chr15:85177352-85177432 1.0000 80 chr11:63606797-63606877 1.0000 80 chr21:39461199-39461279 1.0000 80 chr11:75967624-75967704 1.0000 80 chr4:183782659-183782739 1.0000 80 chr3:168867315-168867395 1.0000 80 chr18:29598588-29598668 1.0000 80 chr3:38870977-38871057 1.0000 80 chr1:247553619-247553699 1.0000 80 chr19:1333900-1333980 1.0000 80 chr9:133407179-133407259 1.0000 80 chr16:88868755-88868835 1.0000 80 chr2:85199179-85199259 1.0000 80 chr11:125324110-12532419 1.0000 80 chr16:58034390-58034470 1.0000 80 chr1:117210293-117210373 1.0000 80 chr10:21816074-21816154 1.0000 80 chr1:225997763-225997843 1.0000 80 chr19:16738431-16738511 1.0000 80 chr1:9352970-9353050 1.0000 80 chr1:180895873-180895953 1.0000 80 chr10:103454046-10345412 1.0000 80 chr6:106534240-106534320 1.0000 80 chr19:12751009-12751089 1.0000 80 chr18:18691955-18692035 1.0000 80 chr4:119810000-119810080 1.0000 80 chr2:241976075-241976155 1.0000 80 chr1:178063626-178063706 1.0000 80 chr1:65775107-65775187 1.0000 80 chr6:70577324-70577404 1.0000 80 chr5:138848199-138848279 1.0000 80 chr3:150126720-150126800 1.0000 80 chr16:3199748-3199828 1.0000 80 chr2:231822249-231822329 1.0000 80 chr16:68482320-68482400 1.0000 80 chr3:129315699-129315779 1.0000 80 chr1:27425693-27425773 1.0000 80 chr17:14205980-14206060 1.0000 80 chr10:121298227-12129830 1.0000 80 chr7:128001646-128001726 1.0000 80 chr3:155588017-155588097 1.0000 80 chr12:50067518-50067598 1.0000 80 chr17:37353826-37353906 1.0000 80 chr9:4985259-4985339 1.0000 80 chr3:182698054-182698134 1.0000 80 chr5:36877518-36877598 1.0000 80 chr18:46067710-46067790 1.0000 80 chr7:129251825-129251905 1.0000 80 chr1:92351501-92351581 1.0000 80 chr17:27507353-27507433 1.0000 80 chr8:67624917-67624997 1.0000 80 chr14:69618548-69618628 1.0000 80 chr20:656309-656389 1.0000 80 chr1:2460818-2460898 1.0000 80 chr8:145689496-145689576 1.0000 80 chr3:41747533-41747613 1.0000 80 chr15:85176815-85176895 1.0000 80 chr8:28268269-28268349 1.0000 80 chr2:119532172-119532252 1.0000 80 chr1:205290454-205290534 1.0000 80 chr2:102759140-102759220 1.0000 80 chr19:30251157-30251237 1.0000 80 chr3:179041492-179041572 1.0000 80 chr17:80834693-80834773 1.0000 80 chr22:18632833-18632913 1.0000 80 chr15:63569346-63569426 1.0000 80 chr20:30310621-30310701 1.0000 80 chr4:78739889-78739969 1.0000 80 chr9:139540949-139541029 1.0000 80 chr6:42749620-42749700 1.0000 80 chr12:121022475-12102255 1.0000 80 chr22:31198898-31198978 1.0000 80 chr5:141255585-141255665 1.0000 80 chr4:55525013-55525093 1.0000 80 chr1:23504286-23504366 1.0000 80 chr11:65292743-65292823 1.0000 80 chr19:49244549-49244629 1.0000 80 chr22:35653675-35653755 1.0000 80 chr16:89988241-89988321 1.0000 80 chr16:50300377-50300457 1.0000 80 chr7:158621894-158621974 1.0000 80 chr19:18705153-18705233 1.0000 80 chr13:42535259-42535339 1.0000 80 chr9:100955406-100955486 1.0000 80 chr1:40502422-40502502 1.0000 80 chr5:137688625-137688705 1.0000 80 chr19:52034927-52035007 1.0000 80 chr9:139112294-139112374 1.0000 80 chrX:110924872-110924952 1.0000 80 chr5:150158214-150158294 1.0000 80 chr1:23494218-23494298 1.0000 80 chr19:49623367-49623447 1.0000 80 chr1:35311233-35311313 1.0000 80 chr15:41044164-41044244 1.0000 80 chr16:57520306-57520386 1.0000 80 chr10:93668667-93668747 1.0000 80 chr1:156085073-156085153 1.0000 80 chr15:41788231-41788311 1.0000 80 chr15:66947402-66947482 1.0000 80 chr6:100676990-100677070 1.0000 80 chr1:46767811-46767891 1.0000 80 chr10:30791327-30791407 1.0000 80 chr3:25705953-25706033 1.0000 80 chr3:182973281-182973361 1.0000 80 chr1:65613256-65613336 1.0000 80 chr8:129026818-129026898 1.0000 80 chr17:27945058-27945138 1.0000 80 chr5:10602270-10602350 1.0000 80 chr1:203258767-203258847 1.0000 80 chr19:5293179-5293259 1.0000 80 chr2:38603664-38603744 1.0000 80 chr2:241395308-241395388 1.0000 80 chr8:64080716-64080796 1.0000 80 chr12:132315066-13231514 1.0000 80 chr19:48893991-48894071 1.0000 80 chr20:52355217-52355297 1.0000 80 chr19:2543753-2543833 1.0000 80 chr11:128418542-12841862 1.0000 80 chr18:20140130-20140210 1.0000 80 chr1:229693944-229694024 1.0000 80 chr9:137218857-137218937 1.0000 80 chr21:34776455-34776535 1.0000 80 chr16:90015110-90015190 1.0000 80 chr4:8200920-8201000 1.0000 80 chr6:14109112-14109192 1.0000 80 chr16:89894996-89895076 1.0000 80 chr10:82219006-82219086 1.0000 80 chr17:48227358-48227438 1.0000 80 chr18:30050947-30051027 1.0000 80 chr16:89767991-89768071 1.0000 80 chr1:206730560-206730640 1.0000 80 chr10:69644995-69645075 1.0000 80 chr9:35801729-35801809 1.0000 80 chr5:141488612-141488692 1.0000 80 chr1:150947258-150947338 1.0000 80 chr17:48194739-48194819 1.0000 80 chr2:179060064-179060144 1.0000 80 chr12:70083059-70083139 1.0000 80 chr17:65373369-65373449 1.0000 80 chr2:24713694-24713774 1.0000 80 chr12:53184030-53184110 1.0000 80 chr9:132647473-132647553 1.0000 80 chr8:38508623-38508703 1.0000 80 chr19:925515-925595 1.0000 80 chr10:6131200-6131280 1.0000 80 chr2:58273781-58273861 1.0000 80 chr4:120134238-120134318 1.0000 80 chr11:64110041-64110121 1.0000 80 chr19:49661031-49661111 1.0000 80 chr4:187645816-187645896 1.0000 80 chr8:66557411-66557491 1.0000 80 chr12:46120719-46120799 1.0000 80 chr4:154387552-154387632 1.0000 80 chr6:158244240-158244320 1.0000 80 chr5:134561982-134562062 1.0000 80 chr15:67142484-67142564 1.0000 80 chr18:21166322-21166402 1.0000 80 chr3:45266822-45266902 1.0000 80 chr2:128459769-128459849 1.0000 80 chr6:56407592-56407672 1.0000 80 chr12:133338791-13333887 1.0000 80 chr1:116694854-116694934 1.0000 80 chr1:208416689-208416769 1.0000 80 chr11:34073055-34073135 1.0000 80 chr12:54694759-54694839 1.0000 80 chr5:180514479-180514559 1.0000 80 chr10:124899118-12489919 1.0000 80 chr13:95619981-95620061 1.0000 80 chr6:107435548-107435628 1.0000 80 chr13:53226984-53227064 1.0000 80 chr19:18794202-18794282 1.0000 80 chr3:135914252-135914332 1.0000 80 chr5:36876027-36876107 1.0000 80 chr6:150038744-150038824 1.0000 80 chr17:76140537-76140617 1.0000 80 chr19:18854171-18854251 1.0000 80 chr16:75121687-75121767 1.0000 80 chr7:25019139-25019219 1.0000 80 chr8:86157890-86157970 1.0000 80 chr4:3043041-3043121 1.0000 80 chr19:14474545-14474625 1.0000 80 chr1:14076173-14076253 1.0000 80 chr16:15135639-15135719 1.0000 80 chr12:77718635-77718715 1.0000 80 chr7:56032627-56032707 1.0000 80 chr11:27494052-27494132 1.0000 80 chr10:80685739-80685819 1.0000 80 chr7:95401939-95402019 1.0000 80 chr16:87965206-87965286 1.0000 80 chr2:71680729-71680809 1.0000 80 chr5:171605403-171605483 1.0000 80 chr1:245319858-245319938 1.0000 80 chr14:31889172-31889252 1.0000 80 chr5:158635171-158635251 1.0000 80 chr12:53268216-53268296 1.0000 80 chr2:7148133-7148213 1.0000 80 chr5:79704279-79704359 1.0000 80 chr5:72112272-72112352 1.0000 80 chr1:154193715-154193795 1.0000 80 chr9:132648143-132648223 1.0000 80 chr19:6736592-6736672 1.0000 80 chr10:80908776-80908856 1.0000 80 chr3:47204858-47204938 1.0000 80 chr1:247635043-247635123 1.0000 80 chr17:42441125-42441205 1.0000 80 chr18:48366530-48366610 1.0000 80 chr16:86962842-86962922 1.0000 80 chr7:148787451-148787531 1.0000 80 chr14:60632091-60632171 1.0000 80 chr1:114472661-114472741 1.0000 80 chr20:33464438-33464518 1.0000 80 chr12:30907744-30907824 1.0000 80 ******************************************************************************** ******************************************************************************** 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/K562/inference_raw/MEME/RankLinear0.6_40_UBTF/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/UBTF.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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.146 C 0.361 G 0.353 T 0.14 Background letter frequencies (from file dataset with add-one prior applied): A 0.146 C 0.361 G 0.353 T 0.14 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF STGASTCA MEME-1 width = 8 sites = 23 llr = 205 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :2:9:::a pos.-specific C 4:1:5:a: probability G 4:9:3::: matrix T 28:11a:: bits 2.8 * * 2.6 * * 2.3 * * * * 2.0 * * * * Relative 1.7 * * * * Entropy 1.4 * * *** (12.9 bits) 1.1 *** *** 0.9 *** *** 0.6 *** *** 0.3 *** *** 0.0 -------- Multilevel CTGACTCA consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:53268216-53268296 20 1.64e-05 CCGGGAGAGC CTGACTCA GCAGGGGGAG chr3:182973281-182973361 23 1.64e-05 GAGGAGGAGG CTGACTCA GGCTGACCCT chr6:36332788-36332868 33 1.64e-05 CTTCTCTGCA GTGACTCA AGGCCAGTGC chr4:2435017-2435097 63 1.64e-05 AGCGGCCACG CTGACTCA CTGCTCTCGG chr15:35087651-35087731 47 1.64e-05 GGGCCGGGCG CTGACTCA CCGTCGGCGG chr12:70083059-70083139 22 3.25e-05 AGGAAGTTCA GTGAGTCA GCGCTGCCGG chr19:2543753-2543833 61 3.25e-05 GCGTGCCGGG GTGAGTCA GCCCCGGGGG chr9:139112294-139112374 45 3.25e-05 gcccggcGTG GTGAGTCA CCAAGAGCCG chr1:40502422-40502502 32 3.25e-05 AGGCAGTCCT CTGAGTCA GGCTGGGAAA chr16:89988241-89988321 70 3.25e-05 AGACCGGACG GTGAGTCA GCC chr8:21767207-21767287 22 3.25e-05 GGCGGCGGCA GTGAGTCA TGCGGCCGAG chr2:160568486-160568566 70 3.35e-05 AAGGCAGTGC TTGATTCA ATT chr19:1333900-1333980 56 3.88e-05 GCAGCGATCG GTGATTCA TGGCTCGATC chr6:161860221-161860301 27 4.16e-05 CAGAAGAACA ATGACTCA TTAGTCCCGG chr21:34776455-34776535 56 4.44e-05 GGCTGGAAGC TAGACTCA GTCCCTTTGT chr13:42535259-42535339 45 4.44e-05 GCCGGCTCAG TAGACTCA GCCCGGCCCT chr11:125324110-12532419 9 5.98e-05 GGGGGAGA GAGACTCA AGAAGGGCAA chr1:14076173-14076253 48 6.54e-05 GGCCCCGCTG CTGAATCA CGGCCGCCGC chr6:14109112-14109192 61 8.49e-05 CGCTGGGGAG CAGAGTCA GAAGGGGCTG chr9:35801729-35801809 40 8.85e-05 TGGTGAGCCC TTGTCTCA GCTGTTCCTC chr15:67142484-67142564 42 1.25e-04 AGGAGCTACA GTCACTCA GACCACTCCA chr17:27945058-27945138 32 1.25e-04 CGAGTTGCCG CTCACTCA TCCTGCTGAA chr4:3043041-3043121 42 1.43e-04 GAGGCCGGTA CTGTGTCA GGGATGAGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:53268216-53268296 1.6e-05 19_[+1]_53 chr3:182973281-182973361 1.6e-05 22_[+1]_50 chr6:36332788-36332868 1.6e-05 32_[+1]_40 chr4:2435017-2435097 1.6e-05 62_[+1]_10 chr15:35087651-35087731 1.6e-05 46_[+1]_26 chr12:70083059-70083139 3.2e-05 21_[+1]_51 chr19:2543753-2543833 3.2e-05 60_[+1]_12 chr9:139112294-139112374 3.2e-05 44_[+1]_28 chr1:40502422-40502502 3.2e-05 31_[+1]_41 chr16:89988241-89988321 3.2e-05 69_[+1]_3 chr8:21767207-21767287 3.2e-05 21_[+1]_51 chr2:160568486-160568566 3.4e-05 69_[+1]_3 chr19:1333900-1333980 3.9e-05 55_[+1]_17 chr6:161860221-161860301 4.2e-05 26_[+1]_46 chr21:34776455-34776535 4.4e-05 55_[+1]_17 chr13:42535259-42535339 4.4e-05 44_[+1]_28 chr11:125324110-12532419 6e-05 8_[+1]_64 chr1:14076173-14076253 6.5e-05 47_[+1]_25 chr6:14109112-14109192 8.5e-05 60_[+1]_12 chr9:35801729-35801809 8.9e-05 39_[+1]_33 chr15:67142484-67142564 0.00013 41_[+1]_31 chr17:27945058-27945138 0.00013 31_[+1]_41 chr4:3043041-3043121 0.00014 41_[+1]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STGASTCA width=8 seqs=23 chr12:53268216-53268296 ( 20) CTGACTCA 1 chr3:182973281-182973361 ( 23) CTGACTCA 1 chr6:36332788-36332868 ( 33) GTGACTCA 1 chr4:2435017-2435097 ( 63) CTGACTCA 1 chr15:35087651-35087731 ( 47) CTGACTCA 1 chr12:70083059-70083139 ( 22) GTGAGTCA 1 chr19:2543753-2543833 ( 61) GTGAGTCA 1 chr9:139112294-139112374 ( 45) GTGAGTCA 1 chr1:40502422-40502502 ( 32) CTGAGTCA 1 chr16:89988241-89988321 ( 70) GTGAGTCA 1 chr8:21767207-21767287 ( 22) GTGAGTCA 1 chr2:160568486-160568566 ( 70) TTGATTCA 1 chr19:1333900-1333980 ( 56) GTGATTCA 1 chr6:161860221-161860301 ( 27) ATGACTCA 1 chr21:34776455-34776535 ( 56) TAGACTCA 1 chr13:42535259-42535339 ( 45) TAGACTCA 1 chr11:125324110-12532419 ( 9) GAGACTCA 1 chr1:14076173-14076253 ( 48) CTGAATCA 1 chr6:14109112-14109192 ( 61) CAGAGTCA 1 chr9:35801729-35801809 ( 40) TTGTCTCA 1 chr15:67142484-67142564 ( 42) GTCACTCA 1 chr17:27945058-27945138 ( 32) CTCACTCA 1 chr4:3043041-3043121 ( 42) CTGTGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.0332 E= 1.5e+000 -175 12 15 31 25 -1117 -1117 256 -1117 -205 137 -1117 264 -1117 -1117 -69 -175 53 -2 -69 -1117 -1117 -1117 284 -1117 147 -1117 -1117 278 -1117 -1117 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 1.5e+000 0.043478 0.391304 0.391304 0.173913 0.173913 0.000000 0.000000 0.826087 0.000000 0.086957 0.913043 0.000000 0.913043 0.000000 0.000000 0.086957 0.043478 0.521739 0.347826 0.086957 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGASTCA MEME-1 regular expression -------------------------------------------------------------------------------- [CG]TGA[CG]TCA -------------------------------------------------------------------------------- Time 5.14 secs. ******************************************************************************** ******************************************************************************** MOTIF RGGAGGAR MEME-2 width = 8 sites = 54 llr = 409 E-value = 2.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 521a::94 pos.-specific C ::1::11: probability G 387:a9:6 matrix T 2::::::: bits 2.8 * 2.6 * 2.3 * * 2.0 * * Relative 1.7 * * Entropy 1.4 ** * (10.9 bits) 1.1 * ***** 0.9 ** ***** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel AGGAGGAG consensus GA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:33464438-33464518 60 7.06e-06 AGCCGGGGCC AGGAGGAA GCTGGAGCCG chr16:86962842-86962922 10 7.06e-06 CCGGGGAAG AGGAGGAA ACGGCCTGCC chr8:67624917-67624997 53 7.06e-06 TGACGCGTCA AGGAGGAA ACGCCGGCGC chr3:182698054-182698134 50 7.06e-06 GAAGGGGCGA AGGAGGAA GGGAGAGGCA chr11:64110041-64110121 47 2.70e-05 CCCCGCCTGC AGGAGGAG CTGAGGCGCT chr3:182973281-182973361 14 2.70e-05 GAGCACTCTG AGGAGGAG GCTGACTCAG chr5:150158214-150158294 36 2.70e-05 GGGACGCTGG AGGAGGAG CTGAGCTGGA chr19:52034927-52035007 64 2.70e-05 CTGTTCACAG AAGAGGAA CTGCGAAGC chr4:183782659-183782739 20 2.70e-05 tcacagcccc aggaggag ccaaccctgc chr9:4985259-4985339 4 3.41e-05 AGG AAGAGGAG CAGAAGGGGG chr10:21816074-21816154 72 4.38e-05 gccgggcagc tggaggaa g chr19:18854171-18854251 14 5.20e-05 agcaattctc agaaggag gcccggcggc chr15:67142484-67142564 29 5.20e-05 TTCTCAGCAA AGAAGGAG CTACAGTCAC chr12:26985058-26985138 22 5.20e-05 CGGCAAGGCC AAAAGGAA ACTGCTCCAG chr2:7148133-7148213 69 8.82e-05 GTTGGCGAGG GGGAGGAA AAGC chr9:132647473-132647553 40 8.82e-05 AGGTGCCGCA GGGAGGAA GGGAGCCTTC chr16:89894996-89895076 33 8.82e-05 GAGCTGTCCC TGGAGGAG GTGCTGAAGG chr4:8200920-8201000 19 8.82e-05 CTCAGGCGCA GGGAGGAA GTAGGGCAGG chr12:121022475-12102255 73 8.82e-05 CGCGGAGGCA TGGAGGAG chr1:180895873-180895953 66 8.82e-05 TCAGCCGCCT TGGAGGAG CTGTCTG chr21:46719563-46719643 64 8.82e-05 TGTCTGCACT GGGAGGAA GCCCGTTGG chr15:70669293-70669373 66 8.82e-05 CTGCCCGGCA TGGAGGAG ATAAAAC chr14:60632091-60632171 73 1.53e-04 GGAGCAGGCC GGGAGGAG chr8:66557411-66557491 73 1.53e-04 GCCGGCCTCC GGGAGGAG chr4:120134238-120134318 51 1.53e-04 CTCGCGAGGC GGGAGGAG GTGCTGTACT chr12:70083059-70083139 9 1.53e-04 GGGAAAGC AGCAGGAA GTTCAGTGAG chr9:100955406-100955486 19 1.53e-04 CCCGTCCGCA GGGAGGAG AGGAGCCGGG chr16:50300377-50300457 54 1.53e-04 ccgctgccgG AGCAGGAA GTGGTGGGTC chr18:46067710-46067790 69 1.53e-04 AGCCAGGGCC GAGAGGAA GGAG chr1:9352970-9353050 19 1.53e-04 GCGCGCTCGC AGCAGGAA CCAGGCTCCA chr21:39461199-39461279 27 1.53e-04 GGCTCTGGAA GAGAGGAA GCCAGGGTGC chr17:48194739-48194819 1 1.94e-04 . AGCAGGAG GTGCGGCGCT chr9:139540949-139541029 14 1.94e-04 GAAGGCGGCG GAGAGGAG CGTTTCCGCG chr19:30251157-30251237 41 1.94e-04 CAAGGAGGGC AGCAGGAG GCAGGCGGCG chr1:230204037-230204117 12 1.94e-04 GGTGAGCGCC GAGAGGAG CCGGGACAGC chr6:168228507-168228587 71 1.94e-04 CTGGCTCCCT GAGAGGAG GA chr2:58273781-58273861 10 2.46e-04 CAGGCCGCT GAAAGGAA CCGGCTGCGG chr16:88868755-88868835 65 2.46e-04 TGGCGTCTCT GGAAGGAG TGGCTGTG chr1:2460818-2460898 36 2.66e-04 TACAGGCGAG AGGAGCAG GCTCGCCCTC chr5:138848199-138848279 72 2.80e-04 CAGAGAGATG GAAAggag g chr11:75967624-75967704 13 2.80e-04 TGGCCAAGGG GAAAGGAG CGGAGAGCAG chr1:27425693-27425773 51 2.88e-04 TGGGGGAAGT AAGAGCAG GCCAGCAGGA chr6:106534240-106534320 24 2.88e-04 GCGGAGAGGC AAGAGCAG CGACCGCGGC chr6:158244240-158244320 20 3.28e-04 TTTCAGGAAC TGCAGGAG CGTGCGGCGC chr19:49661031-49661111 65 3.28e-04 GGCCCTGGGC TGCAGGAG GTTGCGGC chr12:30907744-30907824 3 4.17e-04 GA GGCAGGAG CGCTGCGGAG chr10:82219006-82219086 7 4.17e-04 TCTTTT AGGAGGCA GCAGGCCAGG chr10:30791327-30791407 64 4.17e-04 TACCACGGAT AGGAGGCA CCACCCAGA chr1:154193715-154193795 63 4.54e-04 GGGCGGGGCT TGGAGCAG CCGTAGGAAG chr12:133338791-13333887 72 4.54e-04 CGTCCCGTCC TGGAGCAG G chr17:27507353-27507433 51 4.54e-04 CGGTCAGGGA TGGAGCAG AGCGCAGCGC chr19:18794202-18794282 39 5.24e-04 CCAGCGGGCC AGGAGGCG GATCACTGCG chr11:34073055-34073135 38 5.24e-04 ACCTGCGTCC AGGAGGCG CCCCACAGCG chr8:38508623-38508703 53 5.24e-04 CGCCAGGCCC AGGAGGCG GAGCAGGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:33464438-33464518 7.1e-06 59_[+2]_13 chr16:86962842-86962922 7.1e-06 9_[+2]_63 chr8:67624917-67624997 7.1e-06 52_[+2]_20 chr3:182698054-182698134 7.1e-06 49_[+2]_23 chr11:64110041-64110121 2.7e-05 46_[+2]_26 chr3:182973281-182973361 2.7e-05 13_[+2]_59 chr5:150158214-150158294 2.7e-05 35_[+2]_37 chr19:52034927-52035007 2.7e-05 63_[+2]_9 chr4:183782659-183782739 2.7e-05 19_[+2]_53 chr9:4985259-4985339 3.4e-05 3_[+2]_69 chr10:21816074-21816154 4.4e-05 71_[+2]_1 chr19:18854171-18854251 5.2e-05 13_[+2]_59 chr15:67142484-67142564 5.2e-05 28_[+2]_44 chr12:26985058-26985138 5.2e-05 21_[+2]_51 chr2:7148133-7148213 8.8e-05 68_[+2]_4 chr9:132647473-132647553 8.8e-05 39_[+2]_33 chr16:89894996-89895076 8.8e-05 32_[+2]_40 chr4:8200920-8201000 8.8e-05 18_[+2]_54 chr12:121022475-12102255 8.8e-05 72_[+2] chr1:180895873-180895953 8.8e-05 65_[+2]_7 chr21:46719563-46719643 8.8e-05 63_[+2]_9 chr15:70669293-70669373 8.8e-05 65_[+2]_7 chr14:60632091-60632171 0.00015 72_[+2] chr8:66557411-66557491 0.00015 72_[+2] chr4:120134238-120134318 0.00015 50_[+2]_22 chr12:70083059-70083139 0.00015 8_[+2]_64 chr9:100955406-100955486 0.00015 18_[+2]_54 chr16:50300377-50300457 0.00015 53_[+2]_19 chr18:46067710-46067790 0.00015 68_[+2]_4 chr1:9352970-9353050 0.00015 18_[+2]_54 chr21:39461199-39461279 0.00015 26_[+2]_46 chr17:48194739-48194819 0.00019 [+2]_72 chr9:139540949-139541029 0.00019 13_[+2]_59 chr19:30251157-30251237 0.00019 40_[+2]_32 chr1:230204037-230204117 0.00019 11_[+2]_61 chr6:168228507-168228587 0.00019 70_[+2]_2 chr2:58273781-58273861 0.00025 9_[+2]_63 chr16:88868755-88868835 0.00025 64_[+2]_8 chr1:2460818-2460898 0.00027 35_[+2]_37 chr5:138848199-138848279 0.00028 71_[+2]_1 chr11:75967624-75967704 0.00028 12_[+2]_60 chr1:27425693-27425773 0.00029 50_[+2]_22 chr6:106534240-106534320 0.00029 23_[+2]_49 chr6:158244240-158244320 0.00033 19_[+2]_53 chr19:49661031-49661111 0.00033 64_[+2]_8 chr12:30907744-30907824 0.00042 2_[+2]_70 chr10:82219006-82219086 0.00042 6_[+2]_66 chr10:30791327-30791407 0.00042 63_[+2]_9 chr1:154193715-154193795 0.00045 62_[+2]_10 chr12:133338791-13333887 0.00045 71_[+2]_1 chr17:27507353-27507433 0.00045 50_[+2]_22 chr19:18794202-18794282 0.00052 38_[+2]_34 chr11:34073055-34073135 0.00052 37_[+2]_35 chr8:38508623-38508703 0.00052 52_[+2]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RGGAGGAR width=8 seqs=54 chr20:33464438-33464518 ( 60) AGGAGGAA 1 chr16:86962842-86962922 ( 10) AGGAGGAA 1 chr8:67624917-67624997 ( 53) AGGAGGAA 1 chr3:182698054-182698134 ( 50) AGGAGGAA 1 chr11:64110041-64110121 ( 47) AGGAGGAG 1 chr3:182973281-182973361 ( 14) AGGAGGAG 1 chr5:150158214-150158294 ( 36) AGGAGGAG 1 chr19:52034927-52035007 ( 64) AAGAGGAA 1 chr4:183782659-183782739 ( 20) AGGAGGAG 1 chr9:4985259-4985339 ( 4) AAGAGGAG 1 chr10:21816074-21816154 ( 72) TGGAGGAA 1 chr19:18854171-18854251 ( 14) AGAAGGAG 1 chr15:67142484-67142564 ( 29) AGAAGGAG 1 chr12:26985058-26985138 ( 22) AAAAGGAA 1 chr2:7148133-7148213 ( 69) GGGAGGAA 1 chr9:132647473-132647553 ( 40) GGGAGGAA 1 chr16:89894996-89895076 ( 33) TGGAGGAG 1 chr4:8200920-8201000 ( 19) GGGAGGAA 1 chr12:121022475-12102255 ( 73) TGGAGGAG 1 chr1:180895873-180895953 ( 66) TGGAGGAG 1 chr21:46719563-46719643 ( 64) GGGAGGAA 1 chr15:70669293-70669373 ( 66) TGGAGGAG 1 chr14:60632091-60632171 ( 73) GGGAGGAG 1 chr8:66557411-66557491 ( 73) GGGAGGAG 1 chr4:120134238-120134318 ( 51) GGGAGGAG 1 chr12:70083059-70083139 ( 9) AGCAGGAA 1 chr9:100955406-100955486 ( 19) GGGAGGAG 1 chr16:50300377-50300457 ( 54) AGCAGGAA 1 chr18:46067710-46067790 ( 69) GAGAGGAA 1 chr1:9352970-9353050 ( 19) AGCAGGAA 1 chr21:39461199-39461279 ( 27) GAGAGGAA 1 chr17:48194739-48194819 ( 1) AGCAGGAG 1 chr9:139540949-139541029 ( 14) GAGAGGAG 1 chr19:30251157-30251237 ( 41) AGCAGGAG 1 chr1:230204037-230204117 ( 12) GAGAGGAG 1 chr6:168228507-168228587 ( 71) GAGAGGAG 1 chr2:58273781-58273861 ( 10) GAAAGGAA 1 chr16:88868755-88868835 ( 65) GGAAGGAG 1 chr1:2460818-2460898 ( 36) AGGAGCAG 1 chr5:138848199-138848279 ( 72) GAAAGGAG 1 chr11:75967624-75967704 ( 13) GAAAGGAG 1 chr1:27425693-27425773 ( 51) AAGAGCAG 1 chr6:106534240-106534320 ( 24) AAGAGCAG 1 chr6:158244240-158244320 ( 20) TGCAGGAG 1 chr19:49661031-49661111 ( 65) TGCAGGAG 1 chr12:30907744-30907824 ( 3) GGCAGGAG 1 chr10:82219006-82219086 ( 7) AGGAGGCA 1 chr10:30791327-30791407 ( 64) AGGAGGCA 1 chr1:154193715-154193795 ( 63) TGGAGCAG 1 chr12:133338791-13333887 ( 72) TGGAGCAG 1 chr17:27507353-27507433 ( 51) TGGAGCAG 1 chr19:18794202-18794282 ( 39) AGGAGGCG 1 chr11:34073055-34073135 ( 38) AGGAGGCG 1 chr8:38508623-38508703 ( 53) AGGAGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.59303 E= 2.1e-002 172 -1240 -8 40 72 -1240 110 -1240 -17 -128 103 -1240 278 -1240 -1240 -1240 -1240 -1240 150 -1240 -1240 -170 133 -1240 264 -196 -1240 -1240 127 -1240 87 -1240 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 2.1e-002 0.481481 0.000000 0.333333 0.185185 0.240741 0.000000 0.759259 0.000000 0.129630 0.148148 0.722222 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.907407 0.092593 0.000000 0.000000 0.351852 0.000000 0.648148 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGGAGGAR MEME-2 regular expression -------------------------------------------------------------------------------- [AG][GA]GAGGA[GA] -------------------------------------------------------------------------------- Time 8.95 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTYCTCY MEME-3 width = 8 sites = 41 llr = 324 E-value = 2.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::2::1 pos.-specific C 76:67:a3 probability G :1:::::: matrix T 33a4:a:5 bits 2.8 * * 2.6 * * 2.3 * * 2.0 * * Relative 1.7 * * Entropy 1.4 * ** (11.4 bits) 1.1 ** ** 0.9 * ****** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCTCCTCT consensus TT TA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr9:100955406-100955486 68 1.40e-05 GGACGCCCTT CCTTCTCT CGGGA chr10:80685739-80685819 6 1.76e-05 agtta ccttatct ttaacatgag chr3:41747533-41747613 41 1.76e-05 ATTCCAACCC CCTTATCT GCGCTCCCAT chr2:11796892-11796972 19 1.76e-05 TCCCGCGCCG TCTTATCT GCGTTTGGAC chr5:138848199-138848279 26 2.67e-05 TGCTCTTTGC CTTCCTCT GGCCAGCAAA chr1:117210293-117210373 26 2.67e-05 GGACGCGCCG CTTCCTCT TCTCCCGCAA chr15:70920995-70921075 19 2.67e-05 aagggcctct cttcctct cttgcttgcc chr13:95619981-95620061 28 5.37e-05 TGCAGCTTAG CCTCCTCT GCGGGCGCCC chr11:128418542-12841862 69 5.37e-05 TCCTCTCCTC CCTCCTCT CCTG chr1:247553619-247553699 13 5.37e-05 AATGAGGGAC TCTCCTCT CAGTTAAGCA chr3:124606197-124606277 70 5.37e-05 gctccacttt cctcctct cct chr6:42420941-42421021 68 5.37e-05 GTCTCCTCCT CCTCCTCT GCGGG chr17:76892815-76892895 72 5.37e-05 CTGGGCCCAT TCTCCTCT C chr5:171605403-171605483 47 6.32e-05 CCTGTACAAC TCTCATCT CAGGCAGCAC chr5:150158214-150158294 1 7.59e-05 . CTTTCTCC CCGAACGCAG chr10:80908776-80908856 17 8.68e-05 GGCTGACCCA CCTTCTCA CCACTCAGGA chr9:139112294-139112374 4 8.68e-05 cta tcttctca ctgctgtgtc chr2:231822249-231822329 5 1.14e-04 TCTT CCTTCTCC CGCGGCGCCG chr11:113906973-11390705 66 1.14e-04 GGACCGTCAG CCTTCTCC CCTTCTG chr10:121298227-12129830 27 1.18e-04 GCCTGACAGC TCTTATCA AGGGGCCACT chr6:36332788-36332868 11 1.18e-04 GTCCAAGAGT CCTTATCA AGGACTTCTC chr1:114472661-114472741 16 1.45e-04 CCGGGGGCGC CTTCCTCA AAGGGCCCCT chrX:110924872-110924952 17 1.45e-04 CTCGGCAGTT TTTCCTCA GGCCCCCCTG chr15:85176815-85176895 69 1.45e-04 GCACAGGCCG CGTTCTCT CAGC chr19:14474545-14474625 22 1.69e-04 CTCCCACACG TTTCCTCC TAGAAGCCCA chr12:54694759-54694839 67 1.69e-04 GTTCTCAGTC CTTCCTCC AACCCT chr20:30310621-30310701 25 1.69e-04 CCCTCGCTTG CTTCCTCC TCCATCGCCC chr19:16738431-16738511 19 1.69e-04 CCCCCGTCTG CTTCCTCC GCCCAGGCCG chr16:86962842-86962922 39 2.00e-04 GGTCTAGACG CGTTATCT GGCCCCGTTC chr15:67142484-67142564 6 2.00e-04 GCCAG CGTTATCT GCGGCTTCTC chr8:28268269-28268349 30 2.00e-04 GGCGATGATA TGTTATCT GCTCCCATAA chr12:30907744-30907824 61 2.70e-04 CCTCCTCCTG TCTCCTCC CTCTCCCCTC chr12:53184030-53184110 61 2.70e-04 tccgccgtaa cctcctcc atagccaccT chr1:205290454-205290534 4 2.70e-04 CGC CCTCCTCC GCTCCCTGCC chr12:50067518-50067598 9 2.70e-04 GCGGGAGT CCTCCTCC ACCCAGCCCG chr16:49889553-49889633 27 2.70e-04 ctcgccggtc cctcctcc ctcgctccct chr22:42783830-42783910 20 2.70e-04 ATAGCCCAAG CCTCCTCC CAGGAAGCCC chr12:52115493-52115573 4 2.70e-04 CCT CTTCATCC CCATCCGGGC chr21:46719563-46719643 7 3.27e-04 GGCGTC TGTCCTCT GCGGATGATA chr5:134561982-134562062 60 3.39e-04 gcgggccACC CTTTTTCT TTCCTGTTGC chr19:6736592-6736672 19 3.45e-04 ACCAGCAGGG ACTTCTCT TCTGCCTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:100955406-100955486 1.4e-05 67_[+3]_5 chr10:80685739-80685819 1.8e-05 5_[+3]_67 chr3:41747533-41747613 1.8e-05 40_[+3]_32 chr2:11796892-11796972 1.8e-05 18_[+3]_54 chr5:138848199-138848279 2.7e-05 25_[+3]_47 chr1:117210293-117210373 2.7e-05 25_[+3]_47 chr15:70920995-70921075 2.7e-05 18_[+3]_54 chr13:95619981-95620061 5.4e-05 27_[+3]_45 chr11:128418542-12841862 5.4e-05 68_[+3]_4 chr1:247553619-247553699 5.4e-05 12_[+3]_60 chr3:124606197-124606277 5.4e-05 69_[+3]_3 chr6:42420941-42421021 5.4e-05 67_[+3]_5 chr17:76892815-76892895 5.4e-05 71_[+3]_1 chr5:171605403-171605483 6.3e-05 46_[+3]_26 chr5:150158214-150158294 7.6e-05 [+3]_72 chr10:80908776-80908856 8.7e-05 16_[+3]_56 chr9:139112294-139112374 8.7e-05 3_[+3]_69 chr2:231822249-231822329 0.00011 4_[+3]_68 chr11:113906973-11390705 0.00011 65_[+3]_7 chr10:121298227-12129830 0.00012 26_[+3]_46 chr6:36332788-36332868 0.00012 10_[+3]_62 chr1:114472661-114472741 0.00015 15_[+3]_57 chrX:110924872-110924952 0.00015 16_[+3]_56 chr15:85176815-85176895 0.00015 68_[+3]_4 chr19:14474545-14474625 0.00017 21_[+3]_51 chr12:54694759-54694839 0.00017 66_[+3]_6 chr20:30310621-30310701 0.00017 24_[+3]_48 chr19:16738431-16738511 0.00017 18_[+3]_54 chr16:86962842-86962922 0.0002 38_[+3]_34 chr15:67142484-67142564 0.0002 5_[+3]_67 chr8:28268269-28268349 0.0002 29_[+3]_43 chr12:30907744-30907824 0.00027 60_[+3]_12 chr12:53184030-53184110 0.00027 60_[+3]_12 chr1:205290454-205290534 0.00027 3_[+3]_69 chr12:50067518-50067598 0.00027 8_[+3]_64 chr16:49889553-49889633 0.00027 26_[+3]_46 chr22:42783830-42783910 0.00027 19_[+3]_53 chr12:52115493-52115573 0.00027 3_[+3]_69 chr21:46719563-46719643 0.00033 6_[+3]_66 chr5:134561982-134562062 0.00034 59_[+3]_13 chr19:6736592-6736672 0.00035 18_[+3]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCTYCTCY width=8 seqs=41 chr9:100955406-100955486 ( 68) CCTTCTCT 1 chr10:80685739-80685819 ( 6) CCTTATCT 1 chr3:41747533-41747613 ( 41) CCTTATCT 1 chr2:11796892-11796972 ( 19) TCTTATCT 1 chr5:138848199-138848279 ( 26) CTTCCTCT 1 chr1:117210293-117210373 ( 26) CTTCCTCT 1 chr15:70920995-70921075 ( 19) CTTCCTCT 1 chr13:95619981-95620061 ( 28) CCTCCTCT 1 chr11:128418542-12841862 ( 69) CCTCCTCT 1 chr1:247553619-247553699 ( 13) TCTCCTCT 1 chr3:124606197-124606277 ( 70) CCTCCTCT 1 chr6:42420941-42421021 ( 68) CCTCCTCT 1 chr17:76892815-76892895 ( 72) TCTCCTCT 1 chr5:171605403-171605483 ( 47) TCTCATCT 1 chr5:150158214-150158294 ( 1) CTTTCTCC 1 chr10:80908776-80908856 ( 17) CCTTCTCA 1 chr9:139112294-139112374 ( 4) TCTTCTCA 1 chr2:231822249-231822329 ( 5) CCTTCTCC 1 chr11:113906973-11390705 ( 66) CCTTCTCC 1 chr10:121298227-12129830 ( 27) TCTTATCA 1 chr6:36332788-36332868 ( 11) CCTTATCA 1 chr1:114472661-114472741 ( 16) CTTCCTCA 1 chrX:110924872-110924952 ( 17) TTTCCTCA 1 chr15:85176815-85176895 ( 69) CGTTCTCT 1 chr19:14474545-14474625 ( 22) TTTCCTCC 1 chr12:54694759-54694839 ( 67) CTTCCTCC 1 chr20:30310621-30310701 ( 25) CTTCCTCC 1 chr19:16738431-16738511 ( 19) CTTCCTCC 1 chr16:86962842-86962922 ( 39) CGTTATCT 1 chr15:67142484-67142564 ( 6) CGTTATCT 1 chr8:28268269-28268349 ( 30) TGTTATCT 1 chr12:30907744-30907824 ( 61) TCTCCTCC 1 chr12:53184030-53184110 ( 61) CCTCCTCC 1 chr1:205290454-205290534 ( 4) CCTCCTCC 1 chr12:50067518-50067598 ( 9) CCTCCTCC 1 chr16:49889553-49889633 ( 27) CCTCCTCC 1 chr22:42783830-42783910 ( 20) CCTCCTCC 1 chr12:52115493-52115573 ( 4) CTTCATCC 1 chr21:46719563-46719643 ( 7) TGTCCTCT 1 chr5:134561982-134562062 ( 60) CTTTTTCT 1 chr19:6736592-6736672 ( 19) ACTTCTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.2866 E= 2.2e+001 -258 97 -1200 94 -1200 70 -153 107 -1200 -1200 -1200 284 -1200 70 -1200 157 74 102 -1200 -252 -1200 -1200 -1200 284 -1200 147 -1200 -1200 0 -8 -1200 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.2e+001 0.024390 0.707317 0.000000 0.268293 0.000000 0.585366 0.121951 0.292683 0.000000 0.000000 0.000000 1.000000 0.000000 0.585366 0.000000 0.414634 0.243902 0.731707 0.000000 0.024390 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.146341 0.341463 0.000000 0.512195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTYCTCY MEME-3 regular expression -------------------------------------------------------------------------------- [CT][CT]T[CT][CA]TC[TC] -------------------------------------------------------------------------------- Time 12.65 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTTTTGA MEME-4 width = 8 sites = 2 llr = 28 E-value = 2.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::a pos.-specific C :::::::: probability G :a::::a: matrix T a:aaaa:: bits 2.8 * **** * 2.6 * **** * 2.3 * **** * 2.0 * **** * Relative 1.7 * **** * Entropy 1.4 ******** (20.0 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TGTTTTGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:134561982-134562062 5 9.78e-07 TGGG TGTTTTGA TCTCCATGAC chr3:41747533-41747613 3 9.78e-07 AC TGTTTTGA GTTCCTCCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:134561982-134562062 9.8e-07 4_[+4]_68 chr3:41747533-41747613 9.8e-07 2_[+4]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTTTTGA width=8 seqs=2 chr5:134561982-134562062 ( 5) TGTTTTGA 1 chr3:41747533-41747613 ( 3) TGTTTTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 2.0e+003 -765 -765 -765 283 -765 -765 150 -765 -765 -765 -765 283 -765 -765 -765 283 -765 -765 -765 283 -765 -765 -765 283 -765 -765 150 -765 277 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.0e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTTTGA MEME-4 regular expression -------------------------------------------------------------------------------- TGTTTTGA -------------------------------------------------------------------------------- Time 16.27 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTCAWAA MEME-5 width = 8 sites = 2 llr = 28 E-value = 3.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::a5aa pos.-specific C :::a:::: probability G :::::::: matrix T aaa::5:: bits 2.8 *** * ** 2.6 *** * ** 2.3 *** * ** 2.0 *** * ** Relative 1.7 *** **** Entropy 1.4 ******** (20.1 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TTTCAAAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr10:80685739-80685819 40 8.82e-07 gcctagatga tttcaaaa tccttcccag chr18:20140130-20140210 12 8.82e-07 CGCGTGCACT TTTCATAA CTCTTCCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:80685739-80685819 8.8e-07 39_[+5]_33 chr18:20140130-20140210 8.8e-07 11_[+5]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTCAWAA width=8 seqs=2 chr10:80685739-80685819 ( 40) TTTCAAAA 1 chr18:20140130-20140210 ( 12) TTTCATAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 3.7e+003 -765 -765 -765 283 -765 -765 -765 283 -765 -765 -765 283 -765 147 -765 -765 277 -765 -765 -765 177 -765 -765 183 277 -765 -765 -765 277 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.7e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCAWAA MEME-5 regular expression -------------------------------------------------------------------------------- TTTCA[AT]AA -------------------------------------------------------------------------------- Time 19.88 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:52115493-52115573 6.34e-02 80 chr2:11796892-11796972 7.37e-03 18_[+3(1.76e-05)]_54 chr22:42783830-42783910 2.20e-02 80 chr15:70669293-70669373 7.30e-02 65_[+2(8.82e-05)]_7 chr15:35087651-35087731 7.84e-02 46_[+1(1.64e-05)]_26 chr6:168228507-168228587 3.24e-01 80 chr15:70920995-70921075 4.19e-02 18_[+3(2.67e-05)]_54 chr6:161860221-161860301 1.38e-03 26_[+1(4.16e-05)]_46 chr10:181806-181886 4.98e-01 80 chr22:41698287-41698367 8.37e-01 80 chr11:113906973-11390705 2.96e-01 80 chr2:206950536-206950616 9.99e-01 80 chr2:100814211-100814291 5.19e-01 80 chr2:160568486-160568566 3.12e-03 69_[+1(3.35e-05)]_3 chr21:46719563-46719643 2.50e-03 63_[+2(8.82e-05)]_9 chr1:224621944-224622024 2.47e-01 80 chr4:2435017-2435097 1.06e-03 62_[+1(1.64e-05)]_10 chr12:26985058-26985138 3.39e-02 21_[+2(5.20e-05)]_51 chr11:62314218-62314298 9.52e-01 80 chr17:76892815-76892895 1.88e-01 71_[+3(5.37e-05)]_1 chr11:67896367-67896447 2.10e-02 80 chr17:66755658-66755738 2.79e-02 80 chr7:44270782-44270862 6.10e-01 80 chr7:23637393-23637473 8.26e-02 80 chr6:118972642-118972722 5.26e-01 80 chr19:4065651-4065731 9.99e-01 80 chr1:230204037-230204117 5.57e-01 80 chr1:24673788-24673868 8.64e-01 80 chr10:130832326-13083240 5.73e-01 80 chr6:42420941-42421021 9.97e-02 67_[+3(5.37e-05)]_5 chr19:1307592-1307672 8.40e-01 80 chr5:158526197-158526277 2.77e-01 80 chr6:36332788-36332868 2.86e-05 32_[+1(1.64e-05)]_40 chr8:38239429-38239509 6.65e-01 80 chr10:22614711-22614791 9.92e-01 80 chr16:49889553-49889633 3.05e-01 80 chr3:124606197-124606277 8.44e-02 69_[+3(5.37e-05)]_3 chr8:21767207-21767287 4.14e-02 21_[+1(3.25e-05)]_51 chr15:85177352-85177432 7.90e-01 80 chr11:63606797-63606877 9.59e-01 80 chr21:39461199-39461279 1.99e-01 80 chr11:75967624-75967704 2.65e-01 80 chr4:183782659-183782739 8.23e-04 19_[+2(2.70e-05)]_53 chr3:168867315-168867395 8.82e-01 80 chr18:29598588-29598668 6.29e-01 80 chr3:38870977-38871057 7.53e-02 80 chr1:247553619-247553699 1.32e-02 12_[+3(5.37e-05)]_60 chr19:1333900-1333980 2.54e-02 55_[+1(3.88e-05)]_17 chr9:133407179-133407259 3.57e-02 80 chr16:88868755-88868835 3.72e-02 80 chr2:85199179-85199259 9.88e-01 80 chr11:125324110-12532419 2.24e-02 8_[+1(5.98e-05)]_64 chr16:58034390-58034470 1.00e+00 80 chr1:117210293-117210373 3.85e-02 25_[+3(2.67e-05)]_47 chr10:21816074-21816154 3.16e-01 71_[+2(4.38e-05)]_1 chr1:225997763-225997843 2.68e-01 80 chr19:16738431-16738511 3.40e-01 80 chr1:9352970-9353050 4.63e-01 80 chr1:180895873-180895953 1.06e-02 65_[+2(8.82e-05)]_7 chr10:103454046-10345412 9.81e-01 80 chr6:106534240-106534320 1.15e-01 80 chr19:12751009-12751089 1.03e-02 80 chr18:18691955-18692035 5.17e-01 80 chr4:119810000-119810080 7.36e-01 80 chr2:241976075-241976155 1.91e-01 80 chr1:178063626-178063706 2.72e-01 80 chr1:65775107-65775187 9.85e-01 80 chr6:70577324-70577404 3.31e-01 80 chr5:138848199-138848279 5.40e-03 25_[+3(2.67e-05)]_47 chr3:150126720-150126800 7.65e-01 80 chr16:3199748-3199828 8.57e-01 80 chr2:231822249-231822329 8.84e-02 80 chr16:68482320-68482400 9.99e-01 80 chr3:129315699-129315779 1.28e-01 80 chr1:27425693-27425773 3.67e-01 80 chr17:14205980-14206060 8.42e-01 80 chr10:121298227-12129830 2.63e-02 80 chr7:128001646-128001726 9.54e-01 80 chr3:155588017-155588097 1.58e-01 80 chr12:50067518-50067598 2.62e-01 80 chr17:37353826-37353906 7.50e-01 80 chr9:4985259-4985339 1.80e-01 3_[+2(3.41e-05)]_69 chr3:182698054-182698134 8.61e-03 49_[+2(7.06e-06)]_23 chr5:36877518-36877598 9.71e-01 80 chr18:46067710-46067790 1.30e-01 80 chr7:129251825-129251905 9.95e-01 80 chr1:92351501-92351581 9.54e-01 80 chr17:27507353-27507433 5.46e-01 80 chr8:67624917-67624997 6.41e-02 52_[+2(7.06e-06)]_20 chr14:69618548-69618628 2.85e-01 80 chr20:656309-656389 1.62e-02 80 chr1:2460818-2460898 2.12e-01 80 chr8:145689496-145689576 1.96e-02 80 chr3:41747533-41747613 7.84e-05 2_[+4(9.78e-07)]_30_[+3(1.76e-05)]_\ 32 chr15:85176815-85176895 2.42e-02 80 chr8:28268269-28268349 2.96e-03 80 chr2:119532172-119532252 9.35e-01 80 chr1:205290454-205290534 1.12e-01 80 chr2:102759140-102759220 3.81e-01 80 chr19:30251157-30251237 4.72e-01 80 chr3:179041492-179041572 8.72e-01 80 chr17:80834693-80834773 6.66e-02 80 chr22:18632833-18632913 3.06e-01 80 chr15:63569346-63569426 9.45e-01 80 chr20:30310621-30310701 3.31e-01 80 chr4:78739889-78739969 8.08e-01 80 chr9:139540949-139541029 6.49e-03 57_[+5(9.64e-05)]_15 chr6:42749620-42749700 9.39e-01 80 chr12:121022475-12102255 2.10e-03 72_[+2(8.82e-05)] chr22:31198898-31198978 6.47e-01 80 chr5:141255585-141255665 9.02e-01 80 chr4:55525013-55525093 6.02e-02 80 chr1:23504286-23504366 3.14e-01 80 chr11:65292743-65292823 9.09e-01 80 chr19:49244549-49244629 8.24e-02 80 chr22:35653675-35653755 9.64e-01 80 chr16:89988241-89988321 1.60e-02 69_[+1(3.25e-05)]_3 chr16:50300377-50300457 1.73e-01 80 chr7:158621894-158621974 7.41e-01 80 chr19:18705153-18705233 9.28e-01 80 chr13:42535259-42535339 1.33e-01 44_[+1(4.44e-05)]_28 chr9:100955406-100955486 3.86e-03 67_[+3(1.40e-05)]_5 chr1:40502422-40502502 9.75e-04 31_[+1(3.25e-05)]_41 chr5:137688625-137688705 9.97e-01 80 chr19:52034927-52035007 1.07e-02 14_[+2(8.82e-05)]_41_[+2(2.70e-05)]_\ 9 chr9:139112294-139112374 2.21e-04 3_[+3(8.68e-05)]_33_[+1(3.25e-05)]_\ 10_[+1(8.49e-05)]_10 chrX:110924872-110924952 2.95e-03 80 chr5:150158214-150158294 7.24e-03 [+3(7.59e-05)]_27_[+2(2.70e-05)]_37 chr1:23494218-23494298 5.19e-01 80 chr19:49623367-49623447 7.88e-01 80 chr1:35311233-35311313 4.31e-01 80 chr15:41044164-41044244 8.81e-02 80 chr16:57520306-57520386 8.68e-01 80 chr10:93668667-93668747 2.51e-01 80 chr1:156085073-156085153 9.37e-01 80 chr15:41788231-41788311 3.51e-01 80 chr15:66947402-66947482 7.07e-01 80 chr6:100676990-100677070 9.27e-01 80 chr1:46767811-46767891 6.42e-01 80 chr10:30791327-30791407 1.70e-02 2_[+5(9.64e-05)]_70 chr3:25705953-25706033 8.01e-01 80 chr3:182973281-182973361 1.24e-03 13_[+2(2.70e-05)]_1_[+1(1.64e-05)]_\ 50 chr1:65613256-65613336 9.80e-01 80 chr8:129026818-129026898 4.00e-01 80 chr17:27945058-27945138 1.84e-02 80 chr5:10602270-10602350 6.47e-01 80 chr1:203258767-203258847 4.25e-01 80 chr19:5293179-5293259 9.78e-01 80 chr2:38603664-38603744 8.32e-01 80 chr2:241395308-241395388 9.02e-01 80 chr8:64080716-64080796 2.59e-01 80 chr12:132315066-13231514 9.00e-01 80 chr19:48893991-48894071 3.92e-01 80 chr20:52355217-52355297 3.19e-02 80 chr19:2543753-2543833 9.57e-03 60_[+1(3.25e-05)]_12 chr11:128418542-12841862 2.31e-01 68_[+3(5.37e-05)]_4 chr18:20140130-20140210 3.25e-04 11_[+5(8.82e-07)]_61 chr1:229693944-229694024 4.41e-01 80 chr9:137218857-137218937 9.93e-01 80 chr21:34776455-34776535 7.55e-02 55_[+1(4.44e-05)]_17 chr16:90015110-90015190 7.97e-01 80 chr4:8200920-8201000 1.59e-01 18_[+2(8.82e-05)]_54 chr6:14109112-14109192 1.80e-03 60_[+1(8.49e-05)]_12 chr16:89894996-89895076 2.33e-01 32_[+2(8.82e-05)]_40 chr10:82219006-82219086 4.98e-03 80 chr17:48227358-48227438 6.85e-02 80 chr18:30050947-30051027 9.65e-01 80 chr16:89767991-89768071 7.08e-01 80 chr1:206730560-206730640 8.29e-01 80 chr10:69644995-69645075 7.77e-01 80 chr9:35801729-35801809 1.12e-02 39_[+1(8.85e-05)]_33 chr5:141488612-141488692 9.42e-01 80 chr1:150947258-150947338 9.78e-01 80 chr17:48194739-48194819 1.10e-01 80 chr2:179060064-179060144 1.35e-01 80 chr12:70083059-70083139 1.28e-02 21_[+1(3.25e-05)]_51 chr17:65373369-65373449 9.18e-01 80 chr2:24713694-24713774 5.61e-01 80 chr12:53184030-53184110 1.50e-01 80 chr9:132647473-132647553 7.58e-02 39_[+2(8.82e-05)]_33 chr8:38508623-38508703 6.83e-01 80 chr19:925515-925595 7.02e-01 80 chr10:6131200-6131280 3.49e-01 80 chr2:58273781-58273861 2.01e-01 80 chr4:120134238-120134318 1.83e-01 80 chr11:64110041-64110121 1.84e-01 46_[+2(2.70e-05)]_26 chr19:49661031-49661111 6.78e-02 80 chr4:187645816-187645896 9.98e-01 80 chr8:66557411-66557491 2.55e-01 80 chr12:46120719-46120799 6.64e-01 80 chr4:154387552-154387632 5.44e-01 80 chr6:158244240-158244320 4.78e-03 80 chr5:134561982-134562062 1.97e-04 4_[+4(9.78e-07)]_68 chr15:67142484-67142564 1.86e-04 28_[+2(5.20e-05)]_44 chr18:21166322-21166402 3.30e-03 80 chr3:45266822-45266902 8.62e-02 80 chr2:128459769-128459849 9.64e-01 80 chr6:56407592-56407672 8.13e-01 80 chr12:133338791-13333887 1.25e-01 80 chr1:116694854-116694934 1.89e-01 80 chr1:208416689-208416769 4.56e-01 80 chr11:34073055-34073135 5.73e-01 80 chr12:54694759-54694839 2.09e-02 80 chr5:180514479-180514559 5.51e-01 80 chr10:124899118-12489919 6.84e-01 80 chr13:95619981-95620061 9.45e-02 27_[+3(5.37e-05)]_45 chr6:107435548-107435628 9.36e-01 80 chr13:53226984-53227064 6.17e-01 80 chr19:18794202-18794282 5.34e-02 80 chr3:135914252-135914332 3.25e-01 80 chr5:36876027-36876107 7.24e-01 80 chr6:150038744-150038824 8.45e-01 80 chr17:76140537-76140617 9.73e-02 80 chr19:18854171-18854251 1.06e-03 13_[+2(5.20e-05)]_59 chr16:75121687-75121767 5.94e-02 80 chr7:25019139-25019219 7.43e-01 80 chr8:86157890-86157970 6.94e-01 80 chr4:3043041-3043121 1.29e-01 80 chr19:14474545-14474625 1.91e-01 80 chr1:14076173-14076253 2.07e-01 47_[+1(6.54e-05)]_25 chr16:15135639-15135719 9.79e-01 80 chr12:77718635-77718715 6.06e-01 80 chr7:56032627-56032707 9.00e-01 80 chr11:27494052-27494132 5.22e-01 80 chr10:80685739-80685819 1.81e-06 5_[+3(1.76e-05)]_26_[+5(8.82e-07)]_\ 33 chr7:95401939-95402019 4.53e-01 80 chr16:87965206-87965286 6.28e-01 80 chr2:71680729-71680809 1.85e-01 80 chr5:171605403-171605483 1.24e-02 46_[+3(6.32e-05)]_26 chr1:245319858-245319938 5.05e-01 80 chr14:31889172-31889252 9.10e-01 80 chr5:158635171-158635251 5.83e-01 80 chr12:53268216-53268296 7.13e-03 19_[+1(1.64e-05)]_53 chr2:7148133-7148213 8.15e-03 68_[+2(8.82e-05)]_4 chr5:79704279-79704359 9.72e-01 80 chr5:72112272-72112352 5.56e-01 80 chr1:154193715-154193795 3.27e-01 80 chr9:132648143-132648223 5.66e-01 80 chr19:6736592-6736672 3.08e-02 80 chr10:80908776-80908856 5.09e-04 16_[+3(8.68e-05)]_56 chr3:47204858-47204938 8.05e-01 80 chr1:247635043-247635123 1.87e-01 80 chr17:42441125-42441205 1.00e+00 80 chr18:48366530-48366610 1.18e-01 80 chr16:86962842-86962922 1.91e-04 9_[+2(7.06e-06)]_63 chr7:148787451-148787531 4.57e-01 80 chr14:60632091-60632171 4.75e-01 80 chr1:114472661-114472741 8.19e-02 80 chr20:33464438-33464518 1.04e-02 59_[+2(7.06e-06)]_13 chr12:30907744-30907824 4.01e-02 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************