******************************************************************************** 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/SMARCA5.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr12:31000340-31000360 1.0000 20 chr22:39930942-39930962 1.0000 20 chr9:134615543-134615563 1.0000 20 chr19:2281754-2281774 1.0000 20 chr19:47750765-47750785 1.0000 20 chr10:102430950-10243097 1.0000 20 chr19:40164712-40164732 1.0000 20 chr2:131581770-131581790 1.0000 20 chr19:14307062-14307082 1.0000 20 chr19:16177604-16177624 1.0000 20 chr17:29046460-29046480 1.0000 20 chr6:26065003-26065023 1.0000 20 chr12:56583457-56583477 1.0000 20 chr20:56025208-56025228 1.0000 20 chr19:44173529-44173549 1.0000 20 chr21:43955753-43955773 1.0000 20 chr1:112290064-112290084 1.0000 20 chr19:3706193-3706213 1.0000 20 chr16:776832-776852 1.0000 20 chr17:48347586-48347606 1.0000 20 chr20:62687611-62687631 1.0000 20 chr1:1623865-1623885 1.0000 20 chr10:80741215-80741235 1.0000 20 chr1:90098564-90098584 1.0000 20 chr4:40624376-40624396 1.0000 20 chr11:36313958-36313978 1.0000 20 chr5:149969975-149969995 1.0000 20 chr16:30124269-30124289 1.0000 20 chr19:3344017-3344037 1.0000 20 chr3:128586495-128586515 1.0000 20 chr6:36750743-36750763 1.0000 20 chr19:3357526-3357546 1.0000 20 chr2:208905741-208905761 1.0000 20 chr10:116581472-11658149 1.0000 20 chr1:32713924-32713944 1.0000 20 chr16:89940126-89940146 1.0000 20 chr19:10982129-10982149 1.0000 20 chr17:17595795-17595815 1.0000 20 chr1:42152782-42152802 1.0000 20 chr11:119194355-11919437 1.0000 20 chr16:57336812-57336832 1.0000 20 chr1:896012-896032 1.0000 20 chr11:62380051-62380071 1.0000 20 chr12:57870151-57870171 1.0000 20 chr20:43017389-43017409 1.0000 20 chr7:5622217-5622237 1.0000 20 chr5:138728392-138728412 1.0000 20 chr12:121960891-12196091 1.0000 20 chr7:101933183-101933203 1.0000 20 chr9:126106659-126106679 1.0000 20 chr5:139015351-139015371 1.0000 20 chr8:134512838-134512858 1.0000 20 chr10:121069166-12106918 1.0000 20 chr10:73078797-73078817 1.0000 20 chr20:47405068-47405088 1.0000 20 chr17:77895405-77895425 1.0000 20 chr22:35806847-35806867 1.0000 20 chr18:46395776-46395796 1.0000 20 chr19:30277303-30277323 1.0000 20 chr19:13388059-13388079 1.0000 20 chr1:154915528-154915548 1.0000 20 chr7:69308788-69308808 1.0000 20 chr8:131027683-131027703 1.0000 20 chr19:5322055-5322075 1.0000 20 chr17:36762785-36762805 1.0000 20 chr2:132249972-132249992 1.0000 20 chr8:60964904-60964924 1.0000 20 chr9:117150535-117150555 1.0000 20 chr2:130939814-130939834 1.0000 20 chr3:47021303-47021323 1.0000 20 chr9:139686351-139686371 1.0000 20 chr19:40909319-40909339 1.0000 20 chr19:39035087-39035107 1.0000 20 chr17:1162534-1162554 1.0000 20 chr2:102035741-102035761 1.0000 20 chr2:43422521-43422541 1.0000 20 chr19:13323850-13323870 1.0000 20 chr1:202088281-202088301 1.0000 20 chr22:30822567-30822587 1.0000 20 chr19:11372765-11372785 1.0000 20 chr1:11025005-11025025 1.0000 20 chr3:195621848-195621868 1.0000 20 chr1:38397048-38397068 1.0000 20 chr9:139159419-139159439 1.0000 20 chr15:69959966-69959986 1.0000 20 chr16:56642365-56642385 1.0000 20 chr16:71641828-71641848 1.0000 20 chr9:100891848-100891868 1.0000 20 chr22:30193423-30193443 1.0000 20 chr19:4633369-4633389 1.0000 20 chr9:131486835-131486855 1.0000 20 chr6:158447410-158447430 1.0000 20 chr17:1962027-1962047 1.0000 20 chr19:6772265-6772285 1.0000 20 chr21:32534490-32534510 1.0000 20 chr11:64014194-64014214 1.0000 20 chr16:87350546-87350566 1.0000 20 chr9:77567287-77567307 1.0000 20 chr12:68752851-68752871 1.0000 20 chr8:81152983-81153003 1.0000 20 chr11:33278848-33278868 1.0000 20 chr16:11297361-11297381 1.0000 20 chr19:49973692-49973712 1.0000 20 chr9:139581758-139581778 1.0000 20 chr14:76964243-76964263 1.0000 20 chr9:69381717-69381737 1.0000 20 chr15:90602626-90602646 1.0000 20 chr16:30968352-30968372 1.0000 20 chr16:88478793-88478813 1.0000 20 chr16:730189-730209 1.0000 20 chr7:2442757-2442777 1.0000 20 chr17:72413654-72413674 1.0000 20 chr19:925371-925391 1.0000 20 chr12:6876074-6876094 1.0000 20 chr3:72148768-72148788 1.0000 20 chr1:32757932-32757952 1.0000 20 chr17:6918499-6918519 1.0000 20 chr15:78396145-78396165 1.0000 20 chr11:93276593-93276613 1.0000 20 chr3:140950584-140950604 1.0000 20 chr17:79269603-79269623 1.0000 20 chr7:5603364-5603384 1.0000 20 chr12:113416756-11341677 1.0000 20 chr16:47177442-47177462 1.0000 20 chr7:72971867-72971887 1.0000 20 chr19:47987133-47987153 1.0000 20 chr19:14152352-14152372 1.0000 20 chr22:32150252-32150272 1.0000 20 chr1:12138815-12138835 1.0000 20 chr1:25349838-25349858 1.0000 20 chr19:8259815-8259835 1.0000 20 chr10:112431991-11243201 1.0000 20 chr2:233951238-233951258 1.0000 20 chr9:100745588-100745608 1.0000 20 chr6:30785475-30785495 1.0000 20 chr7:635508-635528 1.0000 20 chr1:36852044-36852064 1.0000 20 chr11:44630735-44630755 1.0000 20 chr7:149194866-149194886 1.0000 20 chr11:44633851-44633871 1.0000 20 chr3:183735293-183735313 1.0000 20 chr10:88471025-88471045 1.0000 20 chr17:17584579-17584599 1.0000 20 chr7:89783716-89783736 1.0000 20 chr9:139736897-139736917 1.0000 20 chr14:95982370-95982390 1.0000 20 chr7:99942387-99942407 1.0000 20 chr22:29563192-29563212 1.0000 20 chr8:115310524-115310544 1.0000 20 chr6:56820100-56820120 1.0000 20 chr3:56952154-56952174 1.0000 20 chr15:101688555-10168857 1.0000 20 chr1:31238580-31238600 1.0000 20 chr7:104585289-104585309 1.0000 20 chr19:47217210-47217230 1.0000 20 chr9:117160506-117160526 1.0000 20 chr19:16251934-16251954 1.0000 20 chr22:39545235-39545255 1.0000 20 chr5:172462813-172462833 1.0000 20 chr7:148763034-148763054 1.0000 20 chr22:44578155-44578175 1.0000 20 chr15:66219573-66219593 1.0000 20 chr3:53290339-53290359 1.0000 20 chr22:35779447-35779467 1.0000 20 chr5:132578008-132578028 1.0000 20 chr8:8774807-8774827 1.0000 20 chr7:150705889-150705909 1.0000 20 chr19:18208295-18208315 1.0000 20 chr14:95965828-95965848 1.0000 20 chr2:232634401-232634421 1.0000 20 chr19:16560617-16560637 1.0000 20 chr7:44835850-44835870 1.0000 20 chr16:27418176-27418196 1.0000 20 chr12:108966061-10896608 1.0000 20 chr16:28935828-28935848 1.0000 20 chr10:88160595-88160615 1.0000 20 chr10:126411654-12641167 1.0000 20 chr16:58768257-58768277 1.0000 20 chr2:8716872-8716892 1.0000 20 chr7:98978332-98978352 1.0000 20 chr11:67806842-67806862 1.0000 20 chr2:86080816-86080836 1.0000 20 chr3:19989011-19989031 1.0000 20 chr1:42217538-42217558 1.0000 20 chr2:71222051-71222071 1.0000 20 chr17:78884825-78884845 1.0000 20 chr9:136688084-136688104 1.0000 20 chr10:70092570-70092590 1.0000 20 chr9:127019985-127020005 1.0000 20 chr1:111573359-111573379 1.0000 20 chr1:43424814-43424834 1.0000 20 chr20:47440971-47440991 1.0000 20 chr16:8985095-8985115 1.0000 20 chr5:131832264-131832284 1.0000 20 chr15:77926860-77926880 1.0000 20 chr1:221916386-221916406 1.0000 20 chr18:4640222-4640242 1.0000 20 chr19:14184348-14184368 1.0000 20 chr22:43112706-43112726 1.0000 20 chr12:15109209-15109229 1.0000 20 chr12:11714055-11714075 1.0000 20 chr7:55377280-55377300 1.0000 20 chr20:3776565-3776585 1.0000 20 chr17:61775415-61775435 1.0000 20 chr19:38469420-38469440 1.0000 20 chr19:18451243-18451263 1.0000 20 chr22:24129322-24129342 1.0000 20 chr15:22462201-22462221 1.0000 20 chr1:154946446-154946466 1.0000 20 chr19:2475599-2475619 1.0000 20 chr11:62554139-62554159 1.0000 20 chr16:50307903-50307923 1.0000 20 chr15:90581293-90581313 1.0000 20 chr11:65547586-65547606 1.0000 20 chr1:249200546-249200566 1.0000 20 chr6:52926686-52926706 1.0000 20 chr3:119278518-119278538 1.0000 20 chr19:17505866-17505886 1.0000 20 chr11:76384968-76384988 1.0000 20 chr14:95969751-95969771 1.0000 20 chr15:74677328-74677348 1.0000 20 chr12:93454613-93454633 1.0000 20 chr4:140216982-140217002 1.0000 20 chr10:112626116-11262613 1.0000 20 chr5:137225378-137225398 1.0000 20 chr19:597688-597708 1.0000 20 chr12:94543043-94543063 1.0000 20 chr19:55166494-55166514 1.0000 20 chr11:507093-507113 1.0000 20 chr8:23021110-23021130 1.0000 20 chr9:133807116-133807136 1.0000 20 chr11:65585850-65585870 1.0000 20 chr7:134680700-134680720 1.0000 20 chr4:3357305-3357325 1.0000 20 chr10:112148562-11214858 1.0000 20 chr5:176790770-176790790 1.0000 20 chr12:102271502-10227152 1.0000 20 chr19:40861975-40861995 1.0000 20 chr1:208042546-208042566 1.0000 20 chr16:15149509-15149529 1.0000 20 chr16:17352938-17352958 1.0000 20 chr19:14691550-14691570 1.0000 20 chr5:399784-399804 1.0000 20 chr17:7259471-7259491 1.0000 20 chr10:90751823-90751843 1.0000 20 chr17:1958328-1958348 1.0000 20 chr19:47033143-47033163 1.0000 20 chr20:49411466-49411486 1.0000 20 chr6:29721008-29721028 1.0000 20 chr19:18699573-18699593 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_SMARCA5/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/SMARCA5.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 0.2 C 0.305 G 0.298 T 0.197 Background letter frequencies (from file dataset with add-one prior applied): A 0.2 C 0.305 G 0.298 T 0.197 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CACACAGC MEME-1 width = 8 sites = 6 llr = 65 E-value = 5.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a:a:a:: pos.-specific C a:a:a::a probability G ::::::a: matrix T :::::::: bits 2.3 * * * 2.1 * * * 1.9 * * * 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (15.6 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CACACAGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:176790770-176790790 7 2.06e-05 caaagt cacacagc ACAAAT chr7:98978332-98978352 13 2.06e-05 TGTGGCTGGG CACACAGC chr7:2442757-2442777 11 2.06e-05 tgcccaaggt cacacagc ga chr9:126106659-126106679 11 2.06e-05 tgcctaaggt cacacagc tg chr5:149969975-149969995 5 2.06e-05 aggc cacacagc aacttggt chr17:48347586-48347606 8 2.06e-05 ctaaggt cacacagc acaac -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:176790770-176790790 2.1e-05 6_[+1]_6 chr7:98978332-98978352 2.1e-05 12_[+1] chr7:2442757-2442777 2.1e-05 10_[+1]_2 chr9:126106659-126106679 2.1e-05 10_[+1]_2 chr5:149969975-149969995 2.1e-05 4_[+1]_8 chr17:48347586-48347606 2.1e-05 7_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACACAGC width=8 seqs=6 chr5:176790770-176790790 ( 7) CACACAGC 1 chr7:98978332-98978352 ( 13) CACACAGC 1 chr7:2442757-2442777 ( 11) CACACAGC 1 chr9:126106659-126106679 ( 11) CACACAGC 1 chr5:149969975-149969995 ( 5) CACACAGC 1 chr17:48347586-48347606 ( 8) CACACAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.73685 E= 5.0e+000 -923 171 -923 -923 232 -923 -923 -923 -923 171 -923 -923 232 -923 -923 -923 -923 171 -923 -923 232 -923 -923 -923 -923 -923 175 -923 -923 171 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 5.0e+000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACACAGC MEME-1 regular expression -------------------------------------------------------------------------------- CACACAGC -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAGAGGT MEME-2 width = 8 sites = 5 llr = 54 E-value = 3.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A a2a:a::: pos.-specific C :::::::: probability G :8:a:aa: matrix T :::::::a bits 2.3 * * * * 2.1 * * * * 1.9 * * * * 1.6 * ****** Relative 1.4 * ****** Entropy 1.2 ******** (15.7 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AGAGAGGT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr15:77926860-77926880 7 1.24e-05 aggccc agagaggt tccagg chr14:95982370-95982390 11 1.24e-05 aatgaggctc agagaggt tg chr22:30822567-30822587 10 1.24e-05 gggaggctc agagaggt caa chr19:5322055-5322075 1 1.24e-05 . agagaggt ttcaacagtt chr19:16177604-16177624 1 2.08e-05 . AAAGAGGT GGGAGAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:77926860-77926880 1.2e-05 6_[+2]_6 chr14:95982370-95982390 1.2e-05 10_[+2]_2 chr22:30822567-30822587 1.2e-05 9_[+2]_3 chr19:5322055-5322075 1.2e-05 [+2]_12 chr19:16177604-16177624 2.1e-05 [+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGAGAGGT width=8 seqs=5 chr15:77926860-77926880 ( 7) AGAGAGGT 1 chr14:95982370-95982390 ( 11) AGAGAGGT 1 chr22:30822567-30822587 ( 10) AGAGAGGT 1 chr19:5322055-5322075 ( 1) AGAGAGGT 1 chr19:16177604-16177624 ( 1) AAAGAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.59397 E= 3.1e+001 232 -897 -897 -897 0 -897 142 -897 232 -897 -897 -897 -897 -897 174 -897 232 -897 -897 -897 -897 -897 174 -897 -897 -897 174 -897 -897 -897 -897 234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 3.1e+001 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAGAGGT MEME-2 regular expression -------------------------------------------------------------------------------- A[GA]AGAGGT -------------------------------------------------------------------------------- Time 4.13 secs. ******************************************************************************** ******************************************************************************** MOTIF TCCCAWTT MEME-3 width = 8 sites = 9 llr = 81 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::93:: pos.-specific C 299a:::1 probability G :::::::: matrix T 811:17a9 bits 2.3 * 2.1 * 1.9 * ** 1.6 ** ** Relative 1.4 * ***** Entropy 1.2 ******** (13.1 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCCCATTT consensus C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr19:18451243-18451263 11 8.55e-06 CATAAGAtgt tcccattt tg chr3:53290339-53290359 8 8.55e-06 CGGCGAA Tcccattt tagag chr1:11025005-11025025 9 8.55e-06 cataaaat tcccattt taca chr16:28935828-28935848 5 2.83e-05 TGGT TTCCATTT CTGCCAGG chr15:78396145-78396165 1 4.15e-05 . ccccattt cccagataag chr11:76384968-76384988 13 6.11e-05 AGACCTTTAT TCTCAATT chr12:121960891-12196091 5 7.46e-05 tcaa ccccaatt cacagatg chr9:117160506-117160526 9 8.78e-05 GGGCTCCC TCCCATTC CCGG chr1:31238580-31238600 13 9.63e-05 TTTCAATGGC TCCCTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:18451243-18451263 8.5e-06 10_[+3]_2 chr3:53290339-53290359 8.5e-06 7_[+3]_5 chr1:11025005-11025025 8.5e-06 8_[+3]_4 chr16:28935828-28935848 2.8e-05 4_[+3]_8 chr15:78396145-78396165 4.1e-05 [+3]_12 chr11:76384968-76384988 6.1e-05 12_[+3] chr12:121960891-12196091 7.5e-05 4_[+3]_8 chr9:117160506-117160526 8.8e-05 8_[+3]_4 chr1:31238580-31238600 9.6e-05 12_[+3] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCCCAWTT width=8 seqs=9 chr19:18451243-18451263 ( 11) TCCCATTT 1 chr3:53290339-53290359 ( 8) TCCCATTT 1 chr1:11025005-11025025 ( 9) TCCCATTT 1 chr16:28935828-28935848 ( 5) TTCCATTT 1 chr15:78396145-78396165 ( 1) CCCCATTT 1 chr11:76384968-76384988 ( 13) TCTCAATT 1 chr12:121960891-12196091 ( 5) CCCCAATT 1 chr9:117160506-117160526 ( 9) TCCCATTC 1 chr1:31238580-31238600 ( 13) TCCCTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.34207 E= 1.7e+002 -982 -46 -982 198 -982 154 -982 -83 -982 154 -982 -83 -982 171 -982 -982 215 -982 -982 -83 74 -982 -982 176 -982 -982 -982 234 -982 -145 -982 217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 1.7e+002 0.000000 0.222222 0.000000 0.777778 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCAWTT MEME-3 regular expression -------------------------------------------------------------------------------- [TC]CCCA[TA]TT -------------------------------------------------------------------------------- Time 4.98 secs. ******************************************************************************** ******************************************************************************** MOTIF YACAGATG MEME-4 width = 8 sites = 6 llr = 60 E-value = 4.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :8:a:8:: pos.-specific C 3:a::::: probability G :2::a::a matrix T 7::::2a: bits 2.3 * * 2.1 * * 1.9 * * 1.6 ******* Relative 1.4 ******* Entropy 1.2 ******** (14.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TACAGATG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:95969751-95969771 11 8.41e-06 cctgcctatt tacagatg aa chr2:43422521-43422541 1 8.41e-06 . tacagatg gcgaaactga chr19:16251934-16251954 12 2.14e-05 atgcccattg cacagatg c chr12:121960891-12196091 13 2.14e-05 aaccccaatt cacagatg chr19:13388059-13388079 8 2.97e-05 tgctata tacagttg cgcag chr18:4640222-4640242 2 4.22e-05 A TGCAGATG TCTATCTGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:95969751-95969771 8.4e-06 10_[+4]_2 chr2:43422521-43422541 8.4e-06 [+4]_12 chr19:16251934-16251954 2.1e-05 11_[+4]_1 chr12:121960891-12196091 2.1e-05 12_[+4] chr19:13388059-13388079 3e-05 7_[+4]_5 chr18:4640222-4640242 4.2e-05 1_[+4]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YACAGATG width=8 seqs=6 chr14:95969751-95969771 ( 11) TACAGATG 1 chr2:43422521-43422541 ( 1) TACAGATG 1 chr19:16251934-16251954 ( 12) CACAGATG 1 chr12:121960891-12196091 ( 13) CACAGATG 1 chr19:13388059-13388079 ( 8) TACAGTTG 1 chr18:4640222-4640242 ( 2) TGCAGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.1796 E= 4.6e+002 -923 13 -923 176 206 -923 -84 -923 -923 171 -923 -923 232 -923 -923 -923 -923 -923 175 -923 206 -923 -923 -24 -923 -923 -923 234 -923 -923 175 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 4.6e+002 0.000000 0.333333 0.000000 0.666667 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YACAGATG MEME-4 regular expression -------------------------------------------------------------------------------- [TC]ACAGATG -------------------------------------------------------------------------------- Time 5.79 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCAGTTT MEME-5 width = 8 sites = 2 llr = 24 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a:::: pos.-specific C ::a::::: probability G ::::a::: matrix T aa:::aaa bits 2.3 ** * *** 2.1 ** * *** 1.9 ** * *** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTCAGTTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr15:101688555-10168857 8 5.39e-06 tctgtgc ttcagttt cctca chr19:3357526-3357546 8 5.39e-06 tctgaga ttcagttt cctca -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:101688555-10168857 5.4e-06 7_[+5]_5 chr19:3357526-3357546 5.4e-06 7_[+5]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCAGTTT width=8 seqs=2 chr15:101688555-10168857 ( 8) TTCAGTTT 1 chr19:3357526-3357546 ( 8) TTCAGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.1e+003 -765 -765 -765 234 -765 -765 -765 234 -765 171 -765 -765 232 -765 -765 -765 -765 -765 174 -765 -765 -765 -765 234 -765 -765 -765 234 -765 -765 -765 234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.1e+003 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 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCAGTTT MEME-5 regular expression -------------------------------------------------------------------------------- TTCAGTTT -------------------------------------------------------------------------------- Time 7.05 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:31000340-31000360 2.40e-01 20 chr22:39930942-39930962 4.79e-01 20 chr9:134615543-134615563 7.71e-01 20 chr19:2281754-2281774 2.68e-01 20 chr19:47750765-47750785 8.88e-01 20 chr10:102430950-10243097 8.53e-01 20 chr19:40164712-40164732 2.40e-01 20 chr2:131581770-131581790 6.77e-01 20 chr19:14307062-14307082 8.77e-01 20 chr19:16177604-16177624 1.83e-02 [+2(2.08e-05)]_12 chr17:29046460-29046480 5.32e-01 20 chr6:26065003-26065023 7.40e-01 20 chr12:56583457-56583477 9.95e-01 20 chr20:56025208-56025228 1.52e-02 20 chr19:44173529-44173549 8.87e-01 20 chr21:43955753-43955773 4.44e-01 20 chr1:112290064-112290084 6.85e-01 20 chr19:3706193-3706213 7.14e-01 20 chr16:776832-776852 9.67e-01 20 chr17:48347586-48347606 1.69e-02 7_[+1(2.06e-05)]_5 chr20:62687611-62687631 1.68e-01 20 chr1:1623865-1623885 4.46e-01 20 chr10:80741215-80741235 8.40e-01 20 chr1:90098564-90098584 9.98e-01 20 chr4:40624376-40624396 8.99e-01 20 chr11:36313958-36313978 5.29e-01 20 chr5:149969975-149969995 1.21e-02 4_[+1(2.06e-05)]_8 chr16:30124269-30124289 4.13e-01 20 chr19:3344017-3344037 5.74e-01 20 chr3:128586495-128586515 4.89e-01 20 chr6:36750743-36750763 7.64e-01 20 chr19:3357526-3357546 6.80e-04 7_[+5(5.39e-06)]_5 chr2:208905741-208905761 3.97e-01 20 chr10:116581472-11658149 1.00e+00 20 chr1:32713924-32713944 9.85e-01 20 chr16:89940126-89940146 1.00e+00 20 chr19:10982129-10982149 3.76e-01 20 chr17:17595795-17595815 5.14e-01 20 chr1:42152782-42152802 7.39e-01 20 chr11:119194355-11919437 6.67e-01 20 chr16:57336812-57336832 6.53e-02 20 chr1:896012-896032 9.08e-01 20 chr11:62380051-62380071 8.09e-01 20 chr12:57870151-57870171 7.60e-01 20 chr20:43017389-43017409 9.99e-01 20 chr7:5622217-5622237 2.32e-01 20 chr5:138728392-138728412 8.15e-01 20 chr12:121960891-12196091 4.02e-05 4_[+3(7.46e-05)]_[+4(2.14e-05)] chr7:101933183-101933203 7.27e-01 20 chr9:126106659-126106679 2.13e-04 10_[+1(2.06e-05)]_2 chr5:139015351-139015371 9.98e-01 20 chr8:134512838-134512858 6.62e-01 20 chr10:121069166-12106918 2.43e-03 20 chr10:73078797-73078817 6.98e-01 20 chr20:47405068-47405088 3.15e-01 20 chr17:77895405-77895425 8.47e-01 20 chr22:35806847-35806867 7.41e-01 20 chr18:46395776-46395796 9.81e-01 20 chr19:30277303-30277323 9.92e-01 20 chr19:13388059-13388079 1.84e-04 7_[+4(2.97e-05)]_5 chr1:154915528-154915548 4.18e-01 20 chr7:69308788-69308808 5.05e-01 20 chr8:131027683-131027703 9.03e-01 20 chr19:5322055-5322075 2.29e-04 [+2(1.24e-05)]_12 chr17:36762785-36762805 7.25e-01 20 chr2:132249972-132249992 9.91e-01 20 chr8:60964904-60964924 9.13e-01 20 chr9:117150535-117150555 7.86e-01 20 chr2:130939814-130939834 9.98e-01 20 chr3:47021303-47021323 1.18e-01 20 chr9:139686351-139686371 9.87e-01 20 chr19:40909319-40909339 2.54e-01 20 chr19:39035087-39035107 1.01e-01 20 chr17:1162534-1162554 9.91e-01 20 chr2:102035741-102035761 5.08e-01 20 chr2:43422521-43422541 1.27e-03 [+4(8.41e-06)]_12 chr19:13323850-13323870 6.88e-02 20 chr1:202088281-202088301 5.53e-01 20 chr22:30822567-30822587 1.60e-03 9_[+2(1.24e-05)]_3 chr19:11372765-11372785 7.97e-01 20 chr1:11025005-11025025 1.48e-03 8_[+3(8.55e-06)]_4 chr3:195621848-195621868 8.60e-01 20 chr1:38397048-38397068 6.77e-01 20 chr9:139159419-139159439 2.13e-01 20 chr15:69959966-69959986 8.57e-01 20 chr16:56642365-56642385 9.79e-01 20 chr16:71641828-71641848 9.58e-01 20 chr9:100891848-100891868 2.26e-01 20 chr22:30193423-30193443 5.33e-01 20 chr19:4633369-4633389 1.12e-01 20 chr9:131486835-131486855 7.69e-01 20 chr6:158447410-158447430 3.88e-01 20 chr17:1962027-1962047 9.01e-01 20 chr19:6772265-6772285 1.76e-02 20 chr21:32534490-32534510 7.80e-01 20 chr11:64014194-64014214 1.00e+00 20 chr16:87350546-87350566 1.42e-01 20 chr9:77567287-77567307 9.55e-01 20 chr12:68752851-68752871 3.14e-01 20 chr8:81152983-81153003 5.44e-01 20 chr11:33278848-33278868 9.71e-01 20 chr16:11297361-11297381 7.02e-01 20 chr19:49973692-49973712 9.90e-01 20 chr9:139581758-139581778 9.16e-01 20 chr14:76964243-76964263 9.19e-01 20 chr9:69381717-69381737 8.38e-01 20 chr15:90602626-90602646 2.81e-01 20 chr16:30968352-30968372 4.02e-01 20 chr16:88478793-88478813 6.68e-01 20 chr16:730189-730209 6.26e-01 20 chr7:2442757-2442777 1.83e-02 10_[+1(2.06e-05)]_2 chr17:72413654-72413674 8.62e-01 20 chr19:925371-925391 9.48e-01 20 chr12:6876074-6876094 8.53e-01 20 chr3:72148768-72148788 6.72e-01 20 chr1:32757932-32757952 3.71e-01 20 chr17:6918499-6918519 4.49e-01 20 chr15:78396145-78396165 2.00e-03 [+3(4.15e-05)]_12 chr11:93276593-93276613 9.48e-01 20 chr3:140950584-140950604 8.35e-01 20 chr17:79269603-79269623 3.30e-01 20 chr7:5603364-5603384 5.82e-01 20 chr12:113416756-11341677 7.52e-01 20 chr16:47177442-47177462 7.72e-01 20 chr7:72971867-72971887 9.81e-01 20 chr19:47987133-47987153 7.96e-01 20 chr19:14152352-14152372 6.88e-01 20 chr22:32150252-32150272 2.44e-01 20 chr1:12138815-12138835 8.57e-01 20 chr1:25349838-25349858 1.72e-01 20 chr19:8259815-8259835 6.88e-01 20 chr10:112431991-11243201 7.54e-01 20 chr2:233951238-233951258 5.08e-01 20 chr9:100745588-100745608 8.28e-01 20 chr6:30785475-30785495 4.60e-01 20 chr7:635508-635528 7.47e-01 20 chr1:36852044-36852064 4.67e-01 20 chr11:44630735-44630755 4.34e-01 20 chr7:149194866-149194886 9.21e-01 20 chr11:44633851-44633871 8.48e-01 20 chr3:183735293-183735313 5.64e-01 20 chr10:88471025-88471045 9.84e-01 20 chr17:17584579-17584599 2.34e-01 20 chr7:89783716-89783736 9.43e-01 20 chr9:139736897-139736917 5.38e-01 20 chr14:95982370-95982390 1.37e-03 10_[+2(1.24e-05)]_2 chr7:99942387-99942407 8.75e-01 20 chr22:29563192-29563212 2.52e-01 20 chr8:115310524-115310544 5.38e-02 20 chr6:56820100-56820120 2.96e-01 20 chr3:56952154-56952174 9.64e-01 20 chr15:101688555-10168857 8.86e-04 7_[+5(5.39e-06)]_5 chr1:31238580-31238600 3.22e-02 12_[+3(9.63e-05)] chr7:104585289-104585309 8.29e-01 20 chr19:47217210-47217230 8.99e-01 20 chr9:117160506-117160526 1.13e-01 8_[+3(8.78e-05)]_4 chr19:16251934-16251954 5.84e-04 11_[+4(2.14e-05)]_1 chr22:39545235-39545255 9.92e-01 20 chr5:172462813-172462833 3.95e-01 20 chr7:148763034-148763054 9.70e-01 20 chr22:44578155-44578175 8.69e-01 20 chr15:66219573-66219593 1.29e-01 20 chr3:53290339-53290359 7.89e-03 7_[+3(8.55e-06)]_5 chr22:35779447-35779467 9.46e-02 20 chr5:132578008-132578028 6.33e-02 20 chr8:8774807-8774827 1.09e-01 20 chr7:150705889-150705909 9.01e-01 20 chr19:18208295-18208315 7.53e-01 20 chr14:95965828-95965848 9.85e-02 20 chr2:232634401-232634421 3.49e-01 20 chr19:16560617-16560637 3.14e-01 20 chr7:44835850-44835870 9.91e-01 20 chr16:27418176-27418196 3.81e-01 20 chr12:108966061-10896608 1.12e-01 20 chr16:28935828-28935848 2.36e-03 4_[+3(2.83e-05)]_8 chr10:88160595-88160615 4.94e-01 20 chr10:126411654-12641167 9.35e-01 20 chr16:58768257-58768277 9.03e-01 20 chr2:8716872-8716892 8.87e-01 20 chr7:98978332-98978352 4.07e-02 12_[+1(2.06e-05)] chr11:67806842-67806862 1.27e-01 20 chr2:86080816-86080836 6.58e-01 20 chr3:19989011-19989031 9.75e-01 20 chr1:42217538-42217558 4.79e-02 20 chr2:71222051-71222071 9.93e-01 20 chr17:78884825-78884845 6.26e-01 20 chr9:136688084-136688104 1.00e+00 20 chr10:70092570-70092590 4.79e-02 20 chr9:127019985-127020005 9.99e-01 20 chr1:111573359-111573379 8.47e-01 20 chr1:43424814-43424834 9.96e-01 20 chr20:47440971-47440991 5.96e-02 20 chr16:8985095-8985115 6.98e-01 20 chr5:131832264-131832284 1.57e-01 20 chr15:77926860-77926880 1.34e-03 6_[+2(1.24e-05)]_6 chr1:221916386-221916406 9.81e-01 20 chr18:4640222-4640242 1.38e-03 1_[+4(4.22e-05)]_11 chr19:14184348-14184368 9.99e-01 20 chr22:43112706-43112726 6.83e-02 20 chr12:15109209-15109229 9.93e-01 20 chr12:11714055-11714075 9.59e-01 20 chr7:55377280-55377300 4.43e-01 20 chr20:3776565-3776585 2.97e-01 20 chr17:61775415-61775435 6.36e-01 20 chr19:38469420-38469440 5.62e-01 20 chr19:18451243-18451263 5.20e-04 10_[+3(8.55e-06)]_2 chr22:24129322-24129342 9.98e-01 20 chr15:22462201-22462221 6.77e-01 20 chr1:154946446-154946466 9.68e-01 20 chr19:2475599-2475619 8.65e-01 20 chr11:62554139-62554159 9.99e-01 20 chr16:50307903-50307923 1.57e-01 20 chr15:90581293-90581313 2.00e-01 20 chr11:65547586-65547606 6.90e-01 20 chr1:249200546-249200566 1.08e-01 20 chr6:52926686-52926706 9.93e-01 20 chr3:119278518-119278538 4.63e-01 20 chr19:17505866-17505886 8.21e-01 20 chr11:76384968-76384988 7.64e-04 12_[+3(6.11e-05)] chr14:95969751-95969771 1.06e-04 10_[+4(8.41e-06)]_2 chr15:74677328-74677348 3.19e-01 20 chr12:93454613-93454633 6.70e-01 20 chr4:140216982-140217002 5.08e-01 20 chr10:112626116-11262613 5.08e-01 20 chr5:137225378-137225398 4.44e-01 20 chr19:597688-597708 8.37e-01 20 chr12:94543043-94543063 8.31e-01 20 chr19:55166494-55166514 2.01e-01 20 chr11:507093-507113 5.61e-01 20 chr8:23021110-23021130 9.22e-01 20 chr9:133807116-133807136 7.22e-01 20 chr11:65585850-65585870 3.59e-01 20 chr7:134680700-134680720 2.71e-01 20 chr4:3357305-3357325 5.16e-01 20 chr10:112148562-11214858 6.53e-01 20 chr5:176790770-176790790 1.79e-02 6_[+1(2.06e-05)]_6 chr12:102271502-10227152 9.85e-01 20 chr19:40861975-40861995 2.42e-01 20 chr1:208042546-208042566 9.48e-01 20 chr16:15149509-15149529 9.88e-01 20 chr16:17352938-17352958 8.25e-01 20 chr19:14691550-14691570 3.11e-02 20 chr5:399784-399804 9.87e-01 20 chr17:7259471-7259491 8.90e-01 20 chr10:90751823-90751843 4.27e-01 20 chr17:1958328-1958348 7.31e-01 20 chr19:47033143-47033163 3.08e-02 20 chr20:49411466-49411486 1.00e+00 20 chr6:29721008-29721028 4.60e-01 20 chr19:18699573-18699593 9.98e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************