******************************************************************************** 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/ETV6.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr20:52402766-52402786 1.0000 20 chr17:59628662-59628682 1.0000 20 chr20:52523043-52523063 1.0000 20 chr20:52416492-52416512 1.0000 20 chr20:52364891-52364911 1.0000 20 chr17:59856471-59856491 1.0000 20 chr20:52203990-52204010 1.0000 20 chr17:57199424-57199444 1.0000 20 chr20:52397603-52397623 1.0000 20 chr20:52867796-52867816 1.0000 20 chr17:59800806-59800826 1.0000 20 chr17:59882982-59883002 1.0000 20 chr17:57037663-57037683 1.0000 20 chr20:46011593-46011613 1.0000 20 chr20:49394069-49394089 1.0000 20 chr20:52993504-52993524 1.0000 20 chr20:45833198-45833218 1.0000 20 chr20:53073202-53073222 1.0000 20 chr20:52188495-52188515 1.0000 20 chr20:52213052-52213072 1.0000 20 chr20:46105364-46105384 1.0000 20 chr17:59804540-59804560 1.0000 20 chr17:58018162-58018182 1.0000 20 chr20:52755121-52755141 1.0000 20 chr3:64516370-64516390 1.0000 20 chr20:55820209-55820229 1.0000 20 chr17:59845955-59845975 1.0000 20 chr20:46135297-46135317 1.0000 20 chr17:59816510-59816530 1.0000 20 chr20:52724872-52724892 1.0000 20 chr20:45974201-45974221 1.0000 20 chr20:52996727-52996747 1.0000 20 chr20:55827693-55827713 1.0000 20 chr20:46334133-46334153 1.0000 20 chr20:52765784-52765804 1.0000 20 chr17:60095542-60095562 1.0000 20 chr20:55842284-55842304 1.0000 20 chr20:45989590-45989610 1.0000 20 chr20:49330339-49330359 1.0000 20 chr20:46115515-46115535 1.0000 20 chr17:59537523-59537543 1.0000 20 chr20:46641508-46641528 1.0000 20 chr17:59761016-59761036 1.0000 20 chr20:46225105-46225125 1.0000 20 chr17:59614106-59614126 1.0000 20 chr17:58136632-58136652 1.0000 20 chr17:59330843-59330863 1.0000 20 chr20:52246160-52246180 1.0000 20 chr17:59530454-59530474 1.0000 20 chr17:59519955-59519975 1.0000 20 chr17:59962468-59962488 1.0000 20 chr3:64165078-64165098 1.0000 20 chr17:59688873-59688893 1.0000 20 chr20:46284568-46284588 1.0000 20 chr3:64385053-64385073 1.0000 20 chr20:53096301-53096321 1.0000 20 chr20:55812251-55812271 1.0000 20 chr20:52410455-52410475 1.0000 20 chr3:64066693-64066713 1.0000 20 chr3:64061145-64061165 1.0000 20 chr20:52423411-52423431 1.0000 20 chr17:58380201-58380221 1.0000 20 chr20:55783759-55783779 1.0000 20 chr20:52235743-52235763 1.0000 20 chr3:63804365-63804385 1.0000 20 chr20:45918029-45918049 1.0000 20 chr17:56818521-56818541 1.0000 20 chr20:52577724-52577744 1.0000 20 chr20:46169767-46169787 1.0000 20 chr20:52618784-52618804 1.0000 20 chr20:55715811-55715831 1.0000 20 chr20:53550026-53550046 1.0000 20 chr20:45950284-45950304 1.0000 20 chr20:52816638-52816658 1.0000 20 chr17:56979862-56979882 1.0000 20 chr3:64681640-64681660 1.0000 20 chr20:55752805-55752825 1.0000 20 chr20:55711979-55711999 1.0000 20 chr20:52372473-52372493 1.0000 20 chr17:58716175-58716195 1.0000 20 chr20:52617642-52617662 1.0000 20 chr17:57134435-57134455 1.0000 20 chr20:52224874-52224894 1.0000 20 chr17:59357525-59357545 1.0000 20 chr17:57922264-57922284 1.0000 20 chr17:59945624-59945644 1.0000 20 chr20:52526080-52526100 1.0000 20 chr20:49358484-49358504 1.0000 20 chr17:58143504-58143524 1.0000 20 chr17:58063964-58063984 1.0000 20 chr17:58020812-58020832 1.0000 20 chr20:53371581-53371601 1.0000 20 chr3:62544555-62544575 1.0000 20 chr20:55756240-55756260 1.0000 20 chr20:49295250-49295270 1.0000 20 chr20:55797527-55797547 1.0000 20 chr3:64224875-64224895 1.0000 20 chr20:45962847-45962867 1.0000 20 chr20:46424329-46424349 1.0000 20 chr20:52803348-52803368 1.0000 20 chr20:52202318-52202338 1.0000 20 chr17:59429626-59429646 1.0000 20 chr3:64729709-64729729 1.0000 20 chr20:52430432-52430452 1.0000 20 chr20:52288100-52288120 1.0000 20 chr17:59858907-59858927 1.0000 20 chr17:58655005-58655025 1.0000 20 chr20:52404660-52404680 1.0000 20 chr1:115213798-115213818 1.0000 20 chr17:59471097-59471117 1.0000 20 chr20:52549300-52549320 1.0000 20 chr17:59422590-59422610 1.0000 20 chr20:46151806-46151826 1.0000 20 chr20:53467589-53467609 1.0000 20 chr20:53192328-53192348 1.0000 20 chr20:52592469-52592489 1.0000 20 chr17:58433530-58433550 1.0000 20 chr17:57968371-57968391 1.0000 20 chr20:55767841-55767861 1.0000 20 chr17:57094646-57094666 1.0000 20 chr17:57106272-57106292 1.0000 20 chr20:52500110-52500130 1.0000 20 chr20:52275513-52275533 1.0000 20 chr20:52590220-52590240 1.0000 20 chr20:52286299-52286319 1.0000 20 chr20:52693037-52693057 1.0000 20 chr20:52616990-52617010 1.0000 20 chr3:64044639-64044659 1.0000 20 chr20:52584119-52584139 1.0000 20 chr17:59715629-59715649 1.0000 20 chr17:57105041-57105061 1.0000 20 chr17:57118719-57118739 1.0000 20 chr17:59757165-59757185 1.0000 20 chr3:64152449-64152469 1.0000 20 chr17:58279831-58279851 1.0000 20 chr17:58544504-58544524 1.0000 20 chr17:60208799-60208819 1.0000 20 chr20:45967025-45967045 1.0000 20 chr17:56788485-56788505 1.0000 20 chr17:59744965-59744985 1.0000 20 chr20:52601448-52601468 1.0000 20 chr17:59710343-59710363 1.0000 20 chr20:46420968-46420988 1.0000 20 chr20:52555281-52555301 1.0000 20 chr17:58171292-58171312 1.0000 20 chr20:46210490-46210510 1.0000 20 chr20:45925870-45925890 1.0000 20 chr3:64090507-64090527 1.0000 20 chr20:52248686-52248706 1.0000 20 chr20:52349070-52349090 1.0000 20 chr20:40818955-40818975 1.0000 20 chr3:63912569-63912589 1.0000 20 chr20:53331561-53331581 1.0000 20 chr3:64269558-64269578 1.0000 20 chr3:64230221-64230241 1.0000 20 chr20:55782453-55782473 1.0000 20 chr17:59952934-59952954 1.0000 20 chr17:59860107-59860127 1.0000 20 chr17:57104362-57104382 1.0000 20 chr17:57195817-57195837 1.0000 20 chr17:59865986-59866006 1.0000 20 chr20:52605718-52605738 1.0000 20 chr17:59343478-59343498 1.0000 20 chr20:52884099-52884119 1.0000 20 chr17:56763783-56763803 1.0000 20 chr20:55748780-55748800 1.0000 20 chr1:206881601-206881621 1.0000 20 chr20:47291887-47291907 1.0000 20 chr20:52295337-52295357 1.0000 20 chr20:52317575-52317595 1.0000 20 chr17:58029651-58029671 1.0000 20 chr17:58434124-58434144 1.0000 20 chr17:58563504-58563524 1.0000 20 chr17:59845240-59845260 1.0000 20 chr17:59666479-59666499 1.0000 20 chr17:59751733-59751753 1.0000 20 chr20:46190775-46190795 1.0000 20 chr17:59743170-59743190 1.0000 20 chr20:52197279-52197299 1.0000 20 chr20:52560528-52560548 1.0000 20 chr20:52427388-52427408 1.0000 20 chr17:58331363-58331383 1.0000 20 chr20:52713418-52713438 1.0000 20 chr17:58703415-58703435 1.0000 20 chr17:58823124-58823144 1.0000 20 chr20:46089012-46089032 1.0000 20 chr20:55679493-55679513 1.0000 20 chr20:52565097-52565117 1.0000 20 chr17:58799645-58799665 1.0000 20 chr17:58671706-58671726 1.0000 20 chr20:53489183-53489203 1.0000 20 chr15:81293426-81293446 1.0000 20 chr17:58724365-58724385 1.0000 20 chr20:55689891-55689911 1.0000 20 chr3:63926229-63926249 1.0000 20 chr17:59639580-59639600 1.0000 20 chr20:55691786-55691806 1.0000 20 chr20:52473125-52473145 1.0000 20 chr20:55818375-55818395 1.0000 20 chr17:59421826-59421846 1.0000 20 chr3:64143102-64143122 1.0000 20 chr20:52215712-52215732 1.0000 20 chr17:59716374-59716394 1.0000 20 chr17:57994413-57994433 1.0000 20 chr17:58189154-58189174 1.0000 20 chr20:52614804-52614824 1.0000 20 chr20:52990740-52990760 1.0000 20 chr20:53045659-53045679 1.0000 20 chr20:52744018-52744038 1.0000 20 chr17:59923178-59923198 1.0000 20 chr3:64304778-64304798 1.0000 20 chr20:49422791-49422811 1.0000 20 chr20:55823185-55823205 1.0000 20 chr17:58834984-58835004 1.0000 20 chr3:63725360-63725380 1.0000 20 chr3:64787942-64787962 1.0000 20 chr17:59617267-59617287 1.0000 20 chr20:52905471-52905491 1.0000 20 chr17:58347673-58347693 1.0000 20 chr17:59585181-59585201 1.0000 20 chr17:59965294-59965314 1.0000 20 chr20:46618847-46618867 1.0000 20 chr20:53130124-53130144 1.0000 20 chr20:52701735-52701755 1.0000 20 chr20:46681448-46681468 1.0000 20 chr20:53519572-53519592 1.0000 20 chr20:46664864-46664884 1.0000 20 chr17:59428542-59428562 1.0000 20 chr20:53065922-53065942 1.0000 20 chr20:52441236-52441256 1.0000 20 chr20:52562744-52562764 1.0000 20 chr17:58352362-58352382 1.0000 20 chr20:46237753-46237773 1.0000 20 chr20:52722345-52722365 1.0000 20 chr20:49350084-49350104 1.0000 20 chr17:59364034-59364054 1.0000 20 chr17:58277985-58278005 1.0000 20 chr17:58464548-58464568 1.0000 20 chr3:64803699-64803719 1.0000 20 chr20:52472045-52472065 1.0000 20 chr17:59385084-59385104 1.0000 20 chr17:59598235-59598255 1.0000 20 chr20:52748102-52748122 1.0000 20 chr17:59332420-59332440 1.0000 20 chr20:46181002-46181022 1.0000 20 chr20:45805062-45805082 1.0000 20 chr17:59920420-59920440 1.0000 20 chr17:58450663-58450683 1.0000 20 chr17:58126676-58126696 1.0000 20 chr17:59641730-59641750 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_ETV6/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/ETV6.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 0.304 C 0.198 G 0.204 T 0.294 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.198 G 0.204 T 0.294 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CACCCCAC MEME-1 width = 8 sites = 2 llr = 24 E-value = 9.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a::::a: pos.-specific C a:aaaa:a probability G :::::::: matrix T :::::::: 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 CACCCCAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:55812251-55812271 5 5.57e-06 CCCA CACCCCAC TTTAATGA chr17:59537523-59537543 8 5.57e-06 GATGAGA CACCCCAC CCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:55812251-55812271 5.6e-06 4_[+1]_8 chr17:59537523-59537543 5.6e-06 7_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACCCCAC width=8 seqs=2 chr20:55812251-55812271 ( 5) CACCCCAC 1 chr17:59537523-59537543 ( 8) CACCCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 9.4e+002 -765 233 -765 -765 171 -765 -765 -765 -765 233 -765 -765 -765 233 -765 -765 -765 233 -765 -765 -765 233 -765 -765 171 -765 -765 -765 -765 233 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 9.4e+002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACCCCAC MEME-1 regular expression -------------------------------------------------------------------------------- CACCCCAC -------------------------------------------------------------------------------- Time 4.87 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCTTCCC MEME-2 width = 8 sites = 2 llr = 24 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a:a::aaa probability G :::::::: matrix T :a:aa::: bits 2.3 * * *** 2.1 * * *** 1.9 ******** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.0 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTCTTCCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:64803699-64803719 13 7.73e-06 gttactTTCT CTCTTCCC chr3:64224875-64224895 8 7.73e-06 CACATTC CTCTTCCC TTAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:64803699-64803719 7.7e-06 12_[+2] chr3:64224875-64224895 7.7e-06 7_[+2]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCTTCCC width=8 seqs=2 chr3:64803699-64803719 ( 13) CTCTTCCC 1 chr3:64224875-64224895 ( 8) CTCTTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.4e+003 -765 233 -765 -765 -765 -765 -765 176 -765 233 -765 -765 -765 -765 -765 176 -765 -765 -765 176 -765 233 -765 -765 -765 233 -765 -765 -765 233 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.4e+003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTTCCC MEME-2 regular expression -------------------------------------------------------------------------------- CTCTTCCC -------------------------------------------------------------------------------- Time 8.12 secs. ******************************************************************************** ******************************************************************************** MOTIF CWGSCAGG MEME-3 width = 8 sites = 19 llr = 141 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :6::27:1 pos.-specific C 9:266::2 probability G 118421a8 matrix T :4:::2:: bits 2.3 * 2.1 * * 1.9 * * 1.6 * * * Relative 1.4 * ** ** Entropy 1.2 * ** ** (10.7 bits) 0.9 * *** ** 0.7 * ****** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CAGCCAGG consensus TCGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:58671706-58671726 7 1.24e-05 caatta caggcagg cgccac chr20:52423411-52423431 5 5.17e-05 CCAG CAGCAAGG CATCTGTC chr20:52744018-52744038 4 7.43e-05 ACC CAGGGAGG CATAGTATT chr20:52472045-52472065 6 9.57e-05 tctgt ctcccagg ttcaagc chr20:55748780-55748800 11 9.57e-05 GAACGCGGCA CAGGAAGG AG chr17:60208799-60208819 2 9.57e-05 c ctcccagg ttcaaatgat chr20:52549300-52549320 1 9.57e-05 . caggctgg agtgcagtgg chr20:52884099-52884119 13 1.12e-04 TGCTTTGAAC CAGGCAGC chr20:55689891-55689911 3 1.46e-04 AC CGGCCAGG AGGTGCCTCC chr20:46135297-46135317 6 1.46e-04 AGGTA CTGCCAGC CTAGGTC chr20:52202318-52202338 6 1.53e-04 TTTGC CTGGGAGG GTGAACA chr20:46284568-46284588 4 1.68e-04 TAA CTGGAAGG CAGCACTCC chr20:46105364-46105384 13 1.68e-04 ctctgttgcc ctggctgg chr17:59716374-59716394 5 2.19e-04 gaaa cagcgtgg tactgaca chr20:55679493-55679513 5 2.19e-04 cttt cacccggg attctgct chr20:55782453-55782473 13 2.19e-04 gtagaagaac cacccagc chr17:56818521-56818541 8 2.51e-04 gataacc gagccagg tatta chr17:59364034-59364054 9 3.22e-04 TCCCAGGG CAGCCAGA GGAG chr17:59471097-59471117 12 4.98e-04 GCCAGGGCAC CTGCAGGG C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:58671706-58671726 1.2e-05 6_[+3]_6 chr20:52423411-52423431 5.2e-05 4_[+3]_8 chr20:52744018-52744038 7.4e-05 3_[+3]_9 chr20:52472045-52472065 9.6e-05 5_[+3]_7 chr20:55748780-55748800 9.6e-05 10_[+3]_2 chr17:60208799-60208819 9.6e-05 1_[+3]_11 chr20:52549300-52549320 9.6e-05 [+3]_12 chr20:52884099-52884119 0.00011 12_[+3] chr20:55689891-55689911 0.00015 2_[+3]_10 chr20:46135297-46135317 0.00015 5_[+3]_7 chr20:52202318-52202338 0.00015 5_[+3]_7 chr20:46284568-46284588 0.00017 3_[+3]_9 chr20:46105364-46105384 0.00017 12_[+3] chr17:59716374-59716394 0.00022 4_[+3]_8 chr20:55679493-55679513 0.00022 4_[+3]_8 chr20:55782453-55782473 0.00022 12_[+3] chr17:56818521-56818541 0.00025 7_[+3]_5 chr17:59364034-59364054 0.00032 8_[+3]_4 chr17:59471097-59471117 0.0005 11_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CWGSCAGG width=8 seqs=19 chr17:58671706-58671726 ( 7) CAGGCAGG 1 chr20:52423411-52423431 ( 5) CAGCAAGG 1 chr20:52744018-52744038 ( 4) CAGGGAGG 1 chr20:52472045-52472065 ( 6) CTCCCAGG 1 chr20:55748780-55748800 ( 11) CAGGAAGG 1 chr17:60208799-60208819 ( 2) CTCCCAGG 1 chr20:52549300-52549320 ( 1) CAGGCTGG 1 chr20:52884099-52884119 ( 13) CAGGCAGC 1 chr20:55689891-55689911 ( 3) CGGCCAGG 1 chr20:46135297-46135317 ( 6) CTGCCAGC 1 chr20:52202318-52202338 ( 6) CTGGGAGG 1 chr20:46284568-46284588 ( 4) CTGGAAGG 1 chr20:46105364-46105384 ( 13) CTGGCTGG 1 chr17:59716374-59716394 ( 5) CAGCGTGG 1 chr20:55679493-55679513 ( 5) CACCCGGG 1 chr20:55782453-55782473 ( 13) CACCCAGC 1 chr17:56818521-56818541 ( 8) GAGCCAGG 1 chr17:59364034-59364054 ( 9) CAGCCAGA 1 chr17:59471097-59471117 ( 12) CTGCAGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.23087 E= 1.3e+002 -1089 226 -195 -1089 93 -1089 -195 32 -1089 9 195 -1089 -1089 155 105 -1089 -53 168 -37 -1089 128 -1089 -95 -90 -1089 -1089 229 -1089 -253 -32 195 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 1.3e+002 0.000000 0.947368 0.052632 0.000000 0.578947 0.000000 0.052632 0.368421 0.000000 0.210526 0.789474 0.000000 0.000000 0.578947 0.421053 0.000000 0.210526 0.631579 0.157895 0.000000 0.736842 0.000000 0.105263 0.157895 0.000000 0.000000 1.000000 0.000000 0.052632 0.157895 0.789474 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSCAGG MEME-3 regular expression -------------------------------------------------------------------------------- C[AT][GC][CG][CA]AGG -------------------------------------------------------------------------------- Time 10.80 secs. ******************************************************************************** ******************************************************************************** MOTIF TGWGTCAC MEME-4 width = 8 sites = 4 llr = 42 E-value = 2.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::5:::a: pos.-specific C :::::a:a probability G :a:a:::: matrix T a:5:a::: bits 2.3 * * * * 2.1 * * * * 1.9 ** *** * 1.6 ** ***** Relative 1.4 ** ***** Entropy 1.2 ** ***** (15.3 bits) 0.9 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGAGTCAC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:53130124-53130144 6 1.26e-05 agaag tgtgtcac taaagga chr1:115213798-115213818 6 1.26e-05 ctctt tgtgtcac tcacact chr20:46618847-46618867 6 2.56e-05 GAACC TGAGTCAC TAAGATT chr17:57106272-57106292 12 2.56e-05 AGTTAGAATC TGAGTCAC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:53130124-53130144 1.3e-05 5_[+4]_7 chr1:115213798-115213818 1.3e-05 5_[+4]_7 chr20:46618847-46618867 2.6e-05 5_[+4]_7 chr17:57106272-57106292 2.6e-05 11_[+4]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGWGTCAC width=8 seqs=4 chr20:53130124-53130144 ( 6) TGTGTCAC 1 chr1:115213798-115213818 ( 6) TGTGTCAC 1 chr20:46618847-46618867 ( 6) TGAGTCAC 1 chr17:57106272-57106292 ( 12) TGAGTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.81503 E= 2.7e+003 -865 -865 -865 176 -865 -865 229 -865 72 -865 -865 76 -865 -865 229 -865 -865 -865 -865 176 -865 234 -865 -865 171 -865 -865 -865 -865 234 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 2.7e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGWGTCAC MEME-4 regular expression -------------------------------------------------------------------------------- TG[AT]GTCAC -------------------------------------------------------------------------------- Time 11.60 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCAGCTA MEME-5 width = 8 sites = 2 llr = 23 E-value = 4.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a:::a pos.-specific C aaa::a:: probability G ::::a::: matrix T ::::::a: bits 2.3 *** ** 2.1 *** ** 1.9 *** *** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (16.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCAGCTA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:59965294-59965314 1 8.52e-06 . cccagcta ttcaggaggc chr20:46151806-46151826 6 8.52e-06 gtagt cccagcta ctccgga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:59965294-59965314 8.5e-06 [+5]_12 chr20:46151806-46151826 8.5e-06 5_[+5]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCAGCTA width=8 seqs=2 chr17:59965294-59965314 ( 1) CCCAGCTA 1 chr20:46151806-46151826 ( 6) CCCAGCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 4.2e+003 -765 233 -765 -765 -765 233 -765 -765 -765 233 -765 -765 171 -765 -765 -765 -765 -765 229 -765 -765 233 -765 -765 -765 -765 -765 176 171 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.2e+003 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 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 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCAGCTA MEME-5 regular expression -------------------------------------------------------------------------------- CCCAGCTA -------------------------------------------------------------------------------- Time 12.32 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:52402766-52402786 9.97e-01 20 chr17:59628662-59628682 9.89e-01 20 chr20:52523043-52523063 5.77e-01 20 chr20:52416492-52416512 9.86e-01 20 chr20:52364891-52364911 4.96e-01 20 chr17:59856471-59856491 9.91e-01 20 chr20:52203990-52204010 8.94e-01 20 chr17:57199424-57199444 3.82e-01 20 chr20:52397603-52397623 2.87e-01 20 chr20:52867796-52867816 4.90e-01 20 chr17:59800806-59800826 7.50e-01 20 chr17:59882982-59883002 7.78e-01 20 chr17:57037663-57037683 9.15e-01 20 chr20:46011593-46011613 8.58e-01 20 chr20:49394069-49394089 9.43e-01 20 chr20:52993504-52993524 8.49e-03 20 chr20:45833198-45833218 7.22e-01 20 chr20:53073202-53073222 9.14e-01 20 chr20:52188495-52188515 1.65e-01 20 chr20:52213052-52213072 9.59e-02 20 chr20:46105364-46105384 1.20e-03 20 chr17:59804540-59804560 9.40e-01 20 chr17:58018162-58018182 9.98e-01 20 chr20:52755121-52755141 9.28e-01 20 chr3:64516370-64516390 7.64e-01 20 chr20:55820209-55820229 9.65e-01 20 chr17:59845955-59845975 9.44e-01 20 chr20:46135297-46135317 9.94e-03 20 chr17:59816510-59816530 9.86e-01 20 chr20:52724872-52724892 1.00e+00 20 chr20:45974201-45974221 9.08e-01 20 chr20:52996727-52996747 4.45e-01 20 chr20:55827693-55827713 1.71e-01 20 chr20:46334133-46334153 1.00e+00 20 chr20:52765784-52765804 6.39e-01 20 chr17:60095542-60095562 9.33e-01 20 chr20:55842284-55842304 4.97e-01 20 chr20:45989590-45989610 9.92e-01 20 chr20:49330339-49330359 7.15e-01 20 chr20:46115515-46115535 2.76e-02 20 chr17:59537523-59537543 3.67e-06 7_[+1(5.57e-06)]_5 chr20:46641508-46641528 9.85e-01 20 chr17:59761016-59761036 7.63e-01 20 chr20:46225105-46225125 5.88e-01 20 chr17:59614106-59614126 6.15e-01 20 chr17:58136632-58136652 6.34e-01 20 chr17:59330843-59330863 9.95e-01 20 chr20:52246160-52246180 7.78e-02 20 chr17:59530454-59530474 8.80e-01 20 chr17:59519955-59519975 1.44e-01 20 chr17:59962468-59962488 5.50e-01 20 chr3:64165078-64165098 7.56e-02 20 chr17:59688873-59688893 8.20e-01 20 chr20:46284568-46284588 2.69e-02 20 chr3:64385053-64385073 2.68e-01 20 chr20:53096301-53096321 4.41e-02 20 chr20:55812251-55812271 3.72e-04 4_[+1(5.57e-06)]_8 chr20:52410455-52410475 8.30e-01 20 chr3:64066693-64066713 5.72e-02 20 chr3:64061145-64061165 3.10e-01 20 chr20:52423411-52423431 3.05e-02 4_[+3(5.17e-05)]_8 chr17:58380201-58380221 9.98e-01 20 chr20:55783759-55783779 9.59e-01 20 chr20:52235743-52235763 1.83e-01 20 chr3:63804365-63804385 6.11e-01 20 chr20:45918029-45918049 8.04e-01 20 chr17:56818521-56818541 7.25e-03 20 chr20:52577724-52577744 8.70e-01 20 chr20:46169767-46169787 3.05e-02 20 chr20:52618784-52618804 6.08e-01 20 chr20:55715811-55715831 7.57e-01 20 chr20:53550026-53550046 7.89e-01 20 chr20:45950284-45950304 3.50e-02 20 chr20:52816638-52816658 8.14e-01 20 chr17:56979862-56979882 6.73e-01 20 chr3:64681640-64681660 8.90e-01 20 chr20:55752805-55752825 8.63e-01 20 chr20:55711979-55711999 3.00e-01 20 chr20:52372473-52372493 4.72e-01 20 chr17:58716175-58716195 6.91e-01 20 chr20:52617642-52617662 9.88e-01 20 chr17:57134435-57134455 7.85e-01 20 chr20:52224874-52224894 9.96e-01 20 chr17:59357525-59357545 2.42e-02 20 chr17:57922264-57922284 9.98e-01 20 chr17:59945624-59945644 5.83e-01 20 chr20:52526080-52526100 5.49e-01 20 chr20:49358484-49358504 9.87e-01 20 chr17:58143504-58143524 9.95e-01 20 chr17:58063964-58063984 1.00e+00 20 chr17:58020812-58020832 7.85e-01 20 chr20:53371581-53371601 9.53e-01 20 chr3:62544555-62544575 9.60e-01 20 chr20:55756240-55756260 1.49e-02 [+5(6.80e-05)]_12 chr20:49295250-49295270 9.92e-01 20 chr20:55797527-55797547 7.86e-01 20 chr3:64224875-64224895 5.86e-03 7_[+2(7.73e-06)]_5 chr20:45962847-45962867 4.40e-01 20 chr20:46424329-46424349 2.26e-01 20 chr20:52803348-52803368 5.58e-01 20 chr20:52202318-52202338 1.23e-01 20 chr17:59429626-59429646 7.38e-01 20 chr3:64729709-64729729 7.52e-01 20 chr20:52430432-52430452 2.35e-01 20 chr20:52288100-52288120 6.05e-02 20 chr17:59858907-59858927 3.98e-01 20 chr17:58655005-58655025 9.72e-01 20 chr20:52404660-52404680 9.98e-01 20 chr1:115213798-115213818 1.33e-02 5_[+4(1.26e-05)]_7 chr17:59471097-59471117 3.77e-02 20 chr20:52549300-52549320 1.62e-01 [+3(9.57e-05)]_12 chr17:59422590-59422610 1.09e-01 20 chr20:46151806-46151826 1.20e-04 5_[+5(8.52e-06)]_7 chr20:53467589-53467609 4.00e-01 20 chr20:53192328-53192348 9.45e-01 20 chr20:52592469-52592489 1.68e-01 20 chr17:58433530-58433550 2.85e-01 20 chr17:57968371-57968391 2.35e-01 20 chr20:55767841-55767861 8.75e-01 20 chr17:57094646-57094666 8.74e-01 20 chr17:57106272-57106292 6.66e-02 11_[+4(2.56e-05)]_1 chr20:52500110-52500130 9.01e-01 20 chr20:52275513-52275533 9.99e-01 20 chr20:52590220-52590240 8.74e-01 20 chr20:52286299-52286319 3.77e-01 20 chr20:52693037-52693057 8.72e-01 20 chr20:52616990-52617010 9.68e-01 20 chr3:64044639-64044659 7.55e-01 20 chr20:52584119-52584139 9.81e-01 20 chr17:59715629-59715649 8.12e-01 20 chr17:57105041-57105061 9.89e-01 20 chr17:57118719-57118739 6.54e-01 20 chr17:59757165-59757185 9.06e-01 20 chr3:64152449-64152469 2.09e-01 20 chr17:58279831-58279851 2.22e-01 20 chr17:58544504-58544524 1.00e+00 20 chr17:60208799-60208819 2.71e-03 1_[+3(9.57e-05)]_11 chr20:45967025-45967045 8.29e-03 20 chr17:56788485-56788505 9.66e-01 20 chr17:59744965-59744985 9.75e-01 20 chr20:52601448-52601468 8.31e-02 20 chr17:59710343-59710363 8.20e-01 20 chr20:46420968-46420988 9.17e-01 20 chr20:52555281-52555301 3.51e-01 20 chr17:58171292-58171312 3.03e-01 20 chr20:46210490-46210510 9.27e-02 20 chr20:45925870-45925890 1.74e-01 20 chr3:64090507-64090527 1.04e-01 20 chr20:52248686-52248706 2.48e-02 20 chr20:52349070-52349090 9.81e-01 20 chr20:40818955-40818975 5.53e-01 20 chr3:63912569-63912589 7.35e-01 20 chr20:53331561-53331581 2.04e-01 20 chr3:64269558-64269578 9.26e-01 20 chr3:64230221-64230241 9.96e-01 20 chr20:55782453-55782473 8.18e-04 20 chr17:59952934-59952954 1.00e+00 20 chr17:59860107-59860127 7.67e-01 20 chr17:57104362-57104382 9.96e-01 20 chr17:57195817-57195837 9.52e-01 20 chr17:59865986-59866006 4.40e-01 20 chr20:52605718-52605738 9.50e-01 20 chr17:59343478-59343498 8.98e-01 20 chr20:52884099-52884119 2.49e-02 20 chr17:56763783-56763803 7.47e-01 20 chr20:55748780-55748800 1.36e-03 10_[+3(9.57e-05)]_2 chr1:206881601-206881621 1.03e-01 20 chr20:47291887-47291907 9.03e-01 20 chr20:52295337-52295357 9.97e-01 20 chr20:52317575-52317595 8.36e-02 20 chr17:58029651-58029671 9.64e-01 20 chr17:58434124-58434144 9.93e-01 20 chr17:58563504-58563524 8.62e-01 20 chr17:59845240-59845260 2.08e-01 20 chr17:59666479-59666499 6.27e-01 20 chr17:59751733-59751753 3.93e-01 20 chr20:46190775-46190795 6.34e-01 20 chr17:59743170-59743190 2.12e-01 20 chr20:52197279-52197299 4.96e-01 20 chr20:52560528-52560548 1.48e-01 20 chr20:52427388-52427408 8.08e-01 20 chr17:58331363-58331383 7.38e-01 20 chr20:52713418-52713438 9.75e-01 20 chr17:58703415-58703435 9.72e-01 20 chr17:58823124-58823144 8.86e-03 20 chr20:46089012-46089032 1.00e+00 20 chr20:55679493-55679513 1.05e-02 20 chr20:52565097-52565117 1.45e-01 20 chr17:58799645-58799665 9.67e-01 20 chr17:58671706-58671726 1.63e-03 6_[+3(1.24e-05)]_6 chr20:53489183-53489203 9.31e-01 20 chr15:81293426-81293446 8.89e-03 20 chr17:58724365-58724385 6.84e-01 20 chr20:55689891-55689911 7.98e-03 20 chr3:63926229-63926249 9.96e-01 20 chr17:59639580-59639600 9.32e-01 20 chr20:55691786-55691806 1.00e+00 20 chr20:52473125-52473145 6.18e-01 20 chr20:55818375-55818395 8.91e-01 20 chr17:59421826-59421846 9.50e-01 20 chr3:64143102-64143122 6.75e-01 20 chr20:52215712-52215732 3.04e-01 20 chr17:59716374-59716394 7.98e-02 20 chr17:57994413-57994433 9.53e-01 20 chr17:58189154-58189174 8.16e-01 20 chr20:52614804-52614824 8.81e-01 20 chr20:52990740-52990760 4.70e-01 20 chr20:53045659-53045679 6.75e-01 20 chr20:52744018-52744038 5.60e-03 3_[+3(7.43e-05)]_9 chr17:59923178-59923198 9.86e-01 20 chr3:64304778-64304798 1.46e-01 20 chr20:49422791-49422811 2.89e-01 20 chr20:55823185-55823205 3.43e-01 20 chr17:58834984-58835004 9.93e-01 20 chr3:63725360-63725380 9.55e-01 20 chr3:64787942-64787962 9.87e-01 20 chr17:59617267-59617287 5.50e-01 20 chr20:52905471-52905491 3.83e-01 20 chr17:58347673-58347693 9.85e-01 20 chr17:59585181-59585201 9.99e-01 20 chr17:59965294-59965314 5.24e-04 [+5(8.52e-06)]_12 chr20:46618847-46618867 2.46e-02 5_[+4(2.56e-05)]_7 chr20:53130124-53130144 3.40e-02 5_[+4(1.26e-05)]_7 chr20:52701735-52701755 6.90e-01 20 chr20:46681448-46681468 9.89e-01 20 chr20:53519572-53519592 9.99e-01 20 chr20:46664864-46664884 8.21e-01 20 chr17:59428542-59428562 4.01e-01 20 chr20:53065922-53065942 1.31e-01 20 chr20:52441236-52441256 9.97e-01 20 chr20:52562744-52562764 2.60e-01 20 chr17:58352362-58352382 9.92e-01 20 chr20:46237753-46237773 1.00e+00 20 chr20:52722345-52722365 8.27e-01 20 chr20:49350084-49350104 6.89e-02 20 chr17:59364034-59364054 4.80e-02 20 chr17:58277985-58278005 9.91e-01 20 chr17:58464548-58464568 9.87e-01 20 chr3:64803699-64803719 5.41e-03 12_[+2(7.73e-06)] chr20:52472045-52472065 1.41e-04 5_[+3(9.57e-05)]_7 chr17:59385084-59385104 7.63e-01 20 chr17:59598235-59598255 1.00e+00 20 chr20:52748102-52748122 7.69e-01 20 chr17:59332420-59332440 6.26e-01 20 chr20:46181002-46181022 8.52e-01 20 chr20:45805062-45805082 9.64e-01 20 chr17:59920420-59920440 8.67e-01 20 chr17:58450663-58450683 3.12e-01 20 chr17:58126676-58126696 4.17e-01 20 chr17:59641730-59641750 1.00e+00 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n09.farnam.hpc.yale.internal ********************************************************************************