******************************************************************************** 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/STAT1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:79086010-79086030 1.0000 20 chr12:113416322-11341634 1.0000 20 chr2:58136007-58136027 1.0000 20 chr17:26137423-26137443 1.0000 20 chr5:131826591-131826611 1.0000 20 chr3:46152803-46152823 1.0000 20 chr12:121476926-12147694 1.0000 20 chr1:840124-840144 1.0000 20 chr9:126760026-126760046 1.0000 20 chr14:93650956-93650976 1.0000 20 chr11:64456091-64456111 1.0000 20 chr19:54693298-54693318 1.0000 20 chr19:11201496-11201516 1.0000 20 chr22:36851140-36851160 1.0000 20 chr5:43008584-43008604 1.0000 20 chr9:102029031-102029051 1.0000 20 chr21:42798070-42798090 1.0000 20 chr2:7005977-7005997 1.0000 20 chr2:170655593-170655613 1.0000 20 chr1:159047054-159047074 1.0000 20 chr11:192115-192135 1.0000 20 chr7:140396806-140396826 1.0000 20 chr3:49208714-49208734 1.0000 20 chr9:132372959-132372979 1.0000 20 chr5:95194704-95194724 1.0000 20 chr20:17919841-17919861 1.0000 20 chr2:91815259-91815279 1.0000 20 chr2:25896161-25896181 1.0000 20 chr10:72575728-72575748 1.0000 20 chr6:33168224-33168244 1.0000 20 chr13:31774075-31774095 1.0000 20 chr1:202858084-202858104 1.0000 20 chr5:176560468-176560488 1.0000 20 chr14:107120051-10712007 1.0000 20 chr7:101922928-101922948 1.0000 20 chr22:50978091-50978111 1.0000 20 chr19:510775-510795 1.0000 20 chr16:2009504-2009524 1.0000 20 chr1:11538988-11539008 1.0000 20 chr1:161102493-161102513 1.0000 20 chr19:48018827-48018847 1.0000 20 chr9:139378193-139378213 1.0000 20 chr6:64308679-64308699 1.0000 20 chr6:90081908-90081928 1.0000 20 chr14:24605573-24605593 1.0000 20 chr22:24407592-24407612 1.0000 20 chr22:42093292-42093312 1.0000 20 chr6:144471503-144471523 1.0000 20 chr14:20774023-20774043 1.0000 20 chr9:126031159-126031179 1.0000 20 chr17:78965573-78965593 1.0000 20 chr17:73422643-73422663 1.0000 20 chr12:69202018-69202038 1.0000 20 chr19:19030021-19030041 1.0000 20 chr1:948716-948736 1.0000 20 chr15:68599014-68599034 1.0000 20 chr1:151584629-151584649 1.0000 20 chr4:174256084-174256104 1.0000 20 chr18:51751124-51751144 1.0000 20 chr1:226595809-226595829 1.0000 20 chr17:48278026-48278046 1.0000 20 chr15:22462265-22462285 1.0000 20 chrX:52950522-52950542 1.0000 20 chr12:52444667-52444687 1.0000 20 chr4:103681875-103681895 1.0000 20 chr17:66233904-66233924 1.0000 20 chr16:81030893-81030913 1.0000 20 chr14:23770783-23770803 1.0000 20 chr11:34073194-34073214 1.0000 20 chr1:46806435-46806455 1.0000 20 chr2:95787615-95787635 1.0000 20 chr3:169491003-169491023 1.0000 20 chr3:194980790-194980810 1.0000 20 chr6:31870144-31870164 1.0000 20 chr11:63952937-63952957 1.0000 20 chr7:21985674-21985694 1.0000 20 chr13:26828043-26828063 1.0000 20 chr15:41047471-41047491 1.0000 20 chr8:11324136-11324156 1.0000 20 chr17:30454734-30454754 1.0000 20 chr1:151254203-151254223 1.0000 20 chr2:86422361-86422381 1.0000 20 chr1:154580602-154580622 1.0000 20 chr1:16161216-16161236 1.0000 20 chr11:46958176-46958196 1.0000 20 chr1:156698798-156698818 1.0000 20 chr1:16940157-16940177 1.0000 20 chr3:122283208-122283228 1.0000 20 chr5:157286191-157286211 1.0000 20 chr3:25706129-25706149 1.0000 20 chr10:45470563-45470583 1.0000 20 chr17:20946075-20946095 1.0000 20 chr6:148675-148695 1.0000 20 chr16:90014990-90015010 1.0000 20 chr7:134966449-134966469 1.0000 20 chr15:66161418-66161438 1.0000 20 chr3:52178484-52178504 1.0000 20 chr2:219157327-219157347 1.0000 20 chr19:50321452-50321472 1.0000 20 chr4:184425443-184425463 1.0000 20 chr5:171433828-171433848 1.0000 20 chr19:18117960-18117980 1.0000 20 chr2:231280895-231280915 1.0000 20 chr15:93258175-93258195 1.0000 20 chr11:111742105-11174212 1.0000 20 chr12:106696456-10669647 1.0000 20 chr6:116422025-116422045 1.0000 20 chr2:219166210-219166230 1.0000 20 chr2:101179662-101179682 1.0000 20 chr16:81831914-81831934 1.0000 20 chr1:200638713-200638733 1.0000 20 chr17:18529040-18529060 1.0000 20 chr3:45698428-45698448 1.0000 20 chr15:34630159-34630179 1.0000 20 chr22:41252929-41252949 1.0000 20 chr1:36348759-36348779 1.0000 20 chr11:47788686-47788706 1.0000 20 chr12:1703935-1703955 1.0000 20 chr1:231664213-231664233 1.0000 20 chr1:32538556-32538576 1.0000 20 chr21:35288052-35288072 1.0000 20 chr16:71392547-71392567 1.0000 20 chr6:27806474-27806494 1.0000 20 chr14:75745384-75745404 1.0000 20 chr17:76250625-76250645 1.0000 20 chr19:41076502-41076522 1.0000 20 chr10:17243657-17243677 1.0000 20 chr20:62258625-62258645 1.0000 20 chr1:167905720-167905740 1.0000 20 chr11:62341138-62341158 1.0000 20 chr12:4386290-4386310 1.0000 20 chr2:47169229-47169249 1.0000 20 chr16:67850660-67850680 1.0000 20 chr6:35265597-35265617 1.0000 20 chr19:1940783-1940803 1.0000 20 chr19:48763347-48763367 1.0000 20 chr6:40995947-40995967 1.0000 20 chr17:46178680-46178700 1.0000 20 chr4:120375810-120375830 1.0000 20 chr1:208137003-208137023 1.0000 20 chr16:86597666-86597686 1.0000 20 chr3:197476733-197476753 1.0000 20 chrX:154255419-154255439 1.0000 20 chr2:20795589-20795609 1.0000 20 chr6:13712404-13712424 1.0000 20 chr8:95961692-95961712 1.0000 20 chr21:42733825-42733845 1.0000 20 chr17:41798038-41798058 1.0000 20 chr8:42249365-42249385 1.0000 20 chr20:33264972-33264992 1.0000 20 chr21:34863943-34863963 1.0000 20 chr1:31252587-31252607 1.0000 20 chr2:55921010-55921030 1.0000 20 chr17:20946975-20946995 1.0000 20 chr17:80452669-80452689 1.0000 20 chr20:37377201-37377221 1.0000 20 chr2:191746542-191746562 1.0000 20 chr14:23590244-23590264 1.0000 20 chr1:153756098-153756118 1.0000 20 chr7:5821328-5821348 1.0000 20 chr2:91816751-91816771 1.0000 20 chr18:56806933-56806953 1.0000 20 chr20:44065647-44065667 1.0000 20 chr17:66016121-66016141 1.0000 20 chr13:52158055-52158075 1.0000 20 chr2:233925928-233925948 1.0000 20 chr17:62340913-62340933 1.0000 20 chr2:179387905-179387925 1.0000 20 chr12:125412443-12541246 1.0000 20 chr16:1359315-1359335 1.0000 20 chr21:19191803-19191823 1.0000 20 chr3:48514471-48514491 1.0000 20 chr7:6746341-6746361 1.0000 20 chr12:2144233-2144253 1.0000 20 chr7:134680629-134680649 1.0000 20 chr19:42612837-42612857 1.0000 20 chr1:200860520-200860540 1.0000 20 chr1:155533006-155533026 1.0000 20 chr5:118324007-118324027 1.0000 20 chr9:132816102-132816122 1.0000 20 chr19:46087366-46087386 1.0000 20 chr1:63249516-63249536 1.0000 20 chr2:74405817-74405837 1.0000 20 chr1:150336248-150336268 1.0000 20 chr21:40685669-40685689 1.0000 20 chr16:81040672-81040692 1.0000 20 chr10:30723138-30723158 1.0000 20 chr19:56904804-56904824 1.0000 20 chr2:231789861-231789881 1.0000 20 chr1:182931873-182931893 1.0000 20 chr12:57082509-57082529 1.0000 20 chr15:77835815-77835835 1.0000 20 chr15:43622543-43622563 1.0000 20 chr22:23624131-23624151 1.0000 20 chr1:145290360-145290380 1.0000 20 chr6:26313365-26313385 1.0000 20 chr12:120907423-12090744 1.0000 20 chr18:72921741-72921761 1.0000 20 chr18:55253887-55253907 1.0000 20 chr3:52739834-52739854 1.0000 20 chr6:41336803-41336823 1.0000 20 chr6:149753237-149753257 1.0000 20 chr5:137368574-137368594 1.0000 20 chr3:47555161-47555181 1.0000 20 chr6:36391469-36391489 1.0000 20 chr12:31226877-31226897 1.0000 20 chr11:77850615-77850635 1.0000 20 chr4:104119699-104119719 1.0000 20 chr1:1440497-1440517 1.0000 20 chr10:76970458-76970478 1.0000 20 chr8:29940443-29940463 1.0000 20 chr1:10490454-10490474 1.0000 20 chr19:3435238-3435258 1.0000 20 chr20:18268875-18268895 1.0000 20 chr19:488952-488972 1.0000 20 chr6:26199374-26199394 1.0000 20 chr20:44992823-44992843 1.0000 20 chr16:31153929-31153949 1.0000 20 chr14:23058538-23058558 1.0000 20 chr14:24630413-24630433 1.0000 20 chr16:577650-577670 1.0000 20 chr17:46662857-46662877 1.0000 20 chr12:108154990-10815501 1.0000 20 chr13:77601156-77601176 1.0000 20 chr7:2598650-2598670 1.0000 20 chr19:16477959-16477979 1.0000 20 chr9:71394985-71395005 1.0000 20 chr1:45273386-45273406 1.0000 20 chr3:50358971-50358991 1.0000 20 chr3:185277079-185277099 1.0000 20 chr1:114889290-114889310 1.0000 20 chr8:141467818-141467838 1.0000 20 chr16:66785666-66785686 1.0000 20 chr19:38864991-38865011 1.0000 20 chr11:314290-314310 1.0000 20 chr22:43583793-43583813 1.0000 20 chr9:106856439-106856459 1.0000 20 chr5:74532786-74532806 1.0000 20 chr16:3200761-3200781 1.0000 20 chr3:88108019-88108039 1.0000 20 chr6:18155743-18155763 1.0000 20 chr9:131873576-131873596 1.0000 20 chr1:212208761-212208781 1.0000 20 chr6:27763772-27763792 1.0000 20 chr6:112318441-112318461 1.0000 20 chr14:104029155-10402917 1.0000 20 chr16:27214895-27214915 1.0000 20 chr8:27169204-27169224 1.0000 20 chr7:151047450-151047470 1.0000 20 chr12:4714128-4714148 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_STAT1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/STAT1.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 0.16 C 0.339 G 0.332 T 0.169 Background letter frequencies (from file dataset with add-one prior applied): A 0.16 C 0.339 G 0.332 T 0.169 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTBWGTT MEME-1 width = 8 sites = 11 llr = 100 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:::5::1 pos.-specific C :::3:1:: probability G 11:327:: matrix T 89a532a9 bits 2.6 * * 2.4 * * 2.1 ** ** 1.8 ** ** Relative 1.6 *** ** Entropy 1.3 *** ** (13.1 bits) 1.1 *** * ** 0.8 *** **** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTTTAGTT consensus CT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr15:68599014-68599034 12 3.17e-06 CTGTGATTGG TTTTTGTT G chr1:79086010-79086030 12 5.61e-06 TTTTTGCTGC TTTGAGTT T chr3:194980790-194980810 2 8.09e-06 C TTTCAGTT CAGTGCTTTC chr12:113416322-11341634 4 8.09e-06 CAG TTTCAGTT TCCTGGCTC chr1:231664213-231664233 11 2.26e-05 CGCATCGTCT TTTTAGTA AC chr1:948716-948736 12 2.39e-05 GGTCATTCGG TTTTGTTT C chr19:48018827-48018847 3 3.09e-05 GC TTTTTCTT GCTCCCTCTG chr16:90014990-90015010 3 4.02e-05 GG TTTGGGTT TCAGCCACAG chr1:1440497-1440517 12 6.92e-05 caggctgcgc tgttattt a chr1:212208761-212208781 2 8.86e-05 A GTTGAGTT TGACGCCATG chr14:23058538-23058558 8 1.19e-04 GACCCTA ATTCTGTT AAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:68599014-68599034 3.2e-06 11_[+1]_1 chr1:79086010-79086030 5.6e-06 11_[+1]_1 chr3:194980790-194980810 8.1e-06 1_[+1]_11 chr12:113416322-11341634 8.1e-06 3_[+1]_9 chr1:231664213-231664233 2.3e-05 10_[+1]_2 chr1:948716-948736 2.4e-05 11_[+1]_1 chr19:48018827-48018847 3.1e-05 2_[+1]_10 chr16:90014990-90015010 4e-05 2_[+1]_10 chr1:1440497-1440517 6.9e-05 11_[+1]_1 chr1:212208761-212208781 8.9e-05 1_[+1]_11 chr14:23058538-23058558 0.00012 7_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTBWGTT width=8 seqs=11 chr15:68599014-68599034 ( 12) TTTTTGTT 1 chr1:79086010-79086030 ( 12) TTTGAGTT 1 chr3:194980790-194980810 ( 2) TTTCAGTT 1 chr12:113416322-11341634 ( 4) TTTCAGTT 1 chr1:231664213-231664233 ( 11) TTTTAGTA 1 chr1:948716-948736 ( 12) TTTTGTTT 1 chr19:48018827-48018847 ( 3) TTTTTCTT 1 chr16:90014990-90015010 ( 3) TTTGGGTT 1 chr1:1440497-1440517 ( 12) TGTTATTT 1 chr1:212208761-212208781 ( 2) GTTGAGTT 1 chr14:23058538-23058558 ( 8) ATTCTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.55806 E= 1.5e+000 -82 -1010 -186 227 -1010 -1010 -186 242 -1010 -1010 -1010 256 -1010 -31 -28 142 177 -1010 -87 69 -1010 -189 113 10 -1010 -1010 -1010 256 -82 -1010 -1010 242 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 1.5e+000 0.090909 0.000000 0.090909 0.818182 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.000000 1.000000 0.000000 0.272727 0.272727 0.454545 0.545455 0.000000 0.181818 0.272727 0.000000 0.090909 0.727273 0.181818 0.000000 0.000000 0.000000 1.000000 0.090909 0.000000 0.000000 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTBWGTT MEME-1 regular expression -------------------------------------------------------------------------------- TTT[TCG][AT]GTT -------------------------------------------------------------------------------- Time 1.93 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAGADGV MEME-2 width = 8 sites = 9 llr = 83 E-value = 8.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9a93a2:3 pos.-specific C :::::::2 probability G :::7:3a4 matrix T 1:1::4:: bits 2.6 * * 2.4 * * 2.1 *** * 1.8 *** * Relative 1.6 *** * * Entropy 1.3 *** * * (13.3 bits) 1.1 ***** * 0.8 ******* 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAGATGG consensus A G A sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:36391469-36391489 7 2.89e-06 TATCAT AAAGATGA AGGGGA chr12:69202018-69202038 5 8.90e-06 TCGG AAAGATGG AGCAAGAA chr17:73422643-73422663 9 8.90e-06 TTGGCTCC AAAAATGG ATTC chr3:88108019-88108039 12 1.73e-05 GAAAAGGAAG AAAGAGGA G chr2:219166210-219166230 5 4.09e-05 CTAG AAAAAGGG AGCCTTgg chr13:77601156-77601176 13 4.68e-05 GGCTGCCCAG AAAGAAGC chr3:52739834-52739854 6 5.88e-05 CAGGG AAAAAGGC CGTCGCC chr19:16477959-16477979 11 7.76e-05 AACATCTGGG AATGATGG CA chr16:81040672-81040692 13 8.34e-05 TGCACACTTC TAAGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:36391469-36391489 2.9e-06 6_[+2]_6 chr12:69202018-69202038 8.9e-06 4_[+2]_8 chr17:73422643-73422663 8.9e-06 8_[+2]_4 chr3:88108019-88108039 1.7e-05 11_[+2]_1 chr2:219166210-219166230 4.1e-05 4_[+2]_8 chr13:77601156-77601176 4.7e-05 12_[+2] chr3:52739834-52739854 5.9e-05 5_[+2]_7 chr19:16477959-16477979 7.8e-05 10_[+2]_2 chr16:81040672-81040692 8.3e-05 12_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAGADGV width=8 seqs=9 chr6:36391469-36391489 ( 7) AAAGATGA 1 chr12:69202018-69202038 ( 5) AAAGATGG 1 chr17:73422643-73422663 ( 9) AAAAATGG 1 chr3:88108019-88108039 ( 12) AAAGAGGA 1 chr2:219166210-219166230 ( 5) AAAAAGGG 1 chr13:77601156-77601176 ( 13) AAAGAAGC 1 chr3:52739834-52739854 ( 6) AAAAAGGC 1 chr19:16477959-16477979 ( 11) AATGATGG 1 chr16:81040672-81040692 ( 13) TAAGAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.62696 E= 8.7e+000 247 -982 -982 -61 264 -982 -982 -982 247 -982 -982 -61 106 -982 101 -982 264 -982 -982 -982 47 -982 1 139 -982 -982 159 -982 106 -61 42 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 8.7e+000 0.888889 0.000000 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.333333 0.444444 0.000000 0.000000 1.000000 0.000000 0.333333 0.222222 0.444444 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGADGV MEME-2 regular expression -------------------------------------------------------------------------------- AAA[GA]A[TGA]G[GAC] -------------------------------------------------------------------------------- Time 2.72 secs. ******************************************************************************** ******************************************************************************** MOTIF AAACGCAA MEME-3 width = 8 sites = 2 llr = 25 E-value = 7.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A aaa:::aa pos.-specific C :::a:a:: probability G ::::a::: matrix T :::::::: bits 2.6 *** ** 2.4 *** ** 2.1 *** ** 1.8 *** ** Relative 1.6 ******** Entropy 1.3 ******** (17.9 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAACGCAA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr16:27214895-27214915 4 4.00e-06 ACC AAACGCAA CGAGTCTTC chr5:95194704-95194724 6 4.00e-06 GTGGC AAACGCAA ACGATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr16:27214895-27214915 4e-06 3_[+3]_9 chr5:95194704-95194724 4e-06 5_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAACGCAA width=8 seqs=2 chr16:27214895-27214915 ( 4) AAACGCAA 1 chr5:95194704-95194724 ( 6) AAACGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 7.9e+002 264 -765 -765 -765 264 -765 -765 -765 264 -765 -765 -765 -765 156 -765 -765 -765 -765 159 -765 -765 156 -765 -765 264 -765 -765 -765 264 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.9e+002 1.000000 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACGCAA MEME-3 regular expression -------------------------------------------------------------------------------- AAACGCAA -------------------------------------------------------------------------------- Time 5.65 secs. ******************************************************************************** ******************************************************************************** MOTIF AGARTTWA MEME-4 width = 8 sites = 2 llr = 24 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 Description -------------------------------------------------------------------------------- Simplified A a:a5::5a pos.-specific C :::::::: probability G :a:5:::: matrix T ::::aa5: bits 2.6 * * ** * 2.4 * * ** * 2.1 * * ** * 1.8 * * ** * Relative 1.6 *** **** Entropy 1.3 *** **** (17.4 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGAATTAA consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:20774023-20774043 1 2.04e-06 . AGAATTTA ATCTACGGCC chr5:171433828-171433848 2 6.29e-06 A AGAGTTAA GAGCTTGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:20774023-20774043 2e-06 [+4]_12 chr5:171433828-171433848 6.3e-06 1_[+4]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGARTTWA width=8 seqs=2 chr14:20774023-20774043 ( 1) AGAATTTA 1 chr5:171433828-171433848 ( 2) AGAGTTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.4e+003 264 -765 -765 -765 -765 -765 159 -765 264 -765 -765 -765 164 -765 59 -765 -765 -765 -765 256 -765 -765 -765 256 164 -765 -765 156 264 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.4e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGARTTWA MEME-4 regular expression -------------------------------------------------------------------------------- AGA[AG]TT[AT]A -------------------------------------------------------------------------------- Time 8.50 secs. ******************************************************************************** ******************************************************************************** MOTIF AGSAAGAA MEME-5 width = 8 sites = 2 llr = 24 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::aa:aa pos.-specific C ::5::::: probability G :a5::a:: matrix T :::::::: bits 2.6 * ** ** 2.4 * ** ** 2.1 * ** ** 1.8 * ** ** Relative 1.6 ** ***** Entropy 1.3 ** ***** (17.0 bits) 1.1 ** ***** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGCAAGAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:5821328-5821348 13 7.76e-06 GACTAAGGAC AGGAAGAA chr12:69202018-69202038 13 7.76e-06 GGAAAGATGG AGCAAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:5821328-5821348 7.8e-06 12_[+5] chr12:69202018-69202038 7.8e-06 12_[+5] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGSAAGAA width=8 seqs=2 chr7:5821328-5821348 ( 13) AGGAAGAA 1 chr12:69202018-69202038 ( 13) AGCAAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.1e+003 264 -765 -765 -765 -765 -765 159 -765 -765 56 59 -765 264 -765 -765 -765 264 -765 -765 -765 -765 -765 159 -765 264 -765 -765 -765 264 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.1e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGSAAGAA MEME-5 regular expression -------------------------------------------------------------------------------- AG[CG]AAGAA -------------------------------------------------------------------------------- Time 10.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:79086010-79086030 1.01e-02 11_[+1(5.61e-06)]_1 chr12:113416322-11341634 1.22e-02 3_[+1(8.09e-06)]_9 chr2:58136007-58136027 1.01e-01 20 chr17:26137423-26137443 9.81e-02 20 chr5:131826591-131826611 1.41e-01 20 chr3:46152803-46152823 8.34e-01 20 chr12:121476926-12147694 8.58e-01 20 chr1:840124-840144 9.99e-01 20 chr9:126760026-126760046 1.01e-01 20 chr14:93650956-93650976 9.10e-01 20 chr11:64456091-64456111 8.79e-01 20 chr19:54693298-54693318 1.00e+00 20 chr19:11201496-11201516 5.56e-01 20 chr22:36851140-36851160 1.00e+00 20 chr5:43008584-43008604 3.16e-01 20 chr9:102029031-102029051 8.96e-01 20 chr21:42798070-42798090 9.68e-01 20 chr2:7005977-7005997 9.49e-01 20 chr2:170655593-170655613 9.97e-01 20 chr1:159047054-159047074 6.38e-02 20 chr11:192115-192135 1.38e-01 20 chr7:140396806-140396826 6.03e-01 20 chr3:49208714-49208734 9.58e-01 20 chr9:132372959-132372979 3.01e-01 20 chr5:95194704-95194724 1.30e-04 5_[+3(4.00e-06)]_7 chr20:17919841-17919861 1.00e+00 20 chr2:91815259-91815279 9.33e-01 20 chr2:25896161-25896181 6.71e-01 20 chr10:72575728-72575748 9.97e-01 20 chr6:33168224-33168244 3.54e-01 20 chr13:31774075-31774095 5.01e-01 20 chr1:202858084-202858104 9.98e-01 20 chr5:176560468-176560488 1.00e+00 20 chr14:107120051-10712007 7.74e-01 20 chr7:101922928-101922948 2.33e-01 20 chr22:50978091-50978111 4.95e-01 20 chr19:510775-510795 9.03e-02 20 chr16:2009504-2009524 2.21e-01 20 chr1:11538988-11539008 3.92e-01 20 chr1:161102493-161102513 9.47e-01 20 chr19:48018827-48018847 9.66e-02 2_[+1(3.09e-05)]_10 chr9:139378193-139378213 1.00e+00 20 chr6:64308679-64308699 9.33e-02 20 chr6:90081908-90081928 6.64e-01 20 chr14:24605573-24605593 1.00e+00 20 chr22:24407592-24407612 8.24e-01 20 chr22:42093292-42093312 1.28e-01 20 chr6:144471503-144471523 6.57e-01 20 chr14:20774023-20774043 4.18e-04 [+4(2.04e-06)]_12 chr9:126031159-126031179 1.00e+00 20 chr17:78965573-78965593 1.00e+00 20 chr17:73422643-73422663 3.47e-05 8_[+2(8.90e-06)]_4 chr12:69202018-69202038 2.70e-06 4_[+2(8.90e-06)]_[+5(7.76e-06)] chr19:19030021-19030041 9.96e-01 20 chr1:948716-948736 5.97e-02 11_[+1(2.39e-05)]_1 chr15:68599014-68599034 8.72e-03 11_[+1(3.17e-06)]_1 chr1:151584629-151584649 8.43e-01 20 chr4:174256084-174256104 9.58e-01 20 chr18:51751124-51751144 9.84e-01 20 chr1:226595809-226595829 8.01e-01 20 chr17:48278026-48278046 9.79e-01 20 chr15:22462265-22462285 7.54e-01 20 chrX:52950522-52950542 4.46e-01 20 chr12:52444667-52444687 3.59e-01 20 chr4:103681875-103681895 7.38e-01 20 chr17:66233904-66233924 9.52e-01 20 chr16:81030893-81030913 3.36e-01 20 chr14:23770783-23770803 9.87e-01 20 chr11:34073194-34073214 9.99e-01 20 chr1:46806435-46806455 1.08e-01 20 chr2:95787615-95787635 9.52e-01 20 chr3:169491003-169491023 5.58e-01 20 chr3:194980790-194980810 8.16e-03 1_[+1(8.09e-06)]_11 chr6:31870144-31870164 1.00e+00 20 chr11:63952937-63952957 9.61e-01 20 chr7:21985674-21985694 6.38e-01 20 chr13:26828043-26828063 9.88e-01 20 chr15:41047471-41047491 1.00e+00 20 chr8:11324136-11324156 9.80e-01 20 chr17:30454734-30454754 3.58e-01 20 chr1:151254203-151254223 6.74e-01 20 chr2:86422361-86422381 3.14e-01 20 chr1:154580602-154580622 8.44e-01 20 chr1:16161216-16161236 2.67e-02 20 chr11:46958176-46958196 8.43e-01 20 chr1:156698798-156698818 1.92e-02 [+4(9.06e-05)]_12 chr1:16940157-16940177 5.02e-01 20 chr3:122283208-122283228 8.47e-01 20 chr5:157286191-157286211 1.00e+00 20 chr3:25706129-25706149 8.66e-01 20 chr10:45470563-45470583 9.96e-01 20 chr17:20946075-20946095 9.99e-01 20 chr6:148675-148695 4.92e-01 20 chr16:90014990-90015010 1.13e-02 2_[+1(4.02e-05)]_10 chr7:134966449-134966469 1.71e-01 20 chr15:66161418-66161438 5.26e-01 20 chr3:52178484-52178504 7.75e-01 20 chr2:219157327-219157347 8.15e-01 20 chr19:50321452-50321472 9.93e-01 20 chr4:184425443-184425463 9.99e-01 20 chr5:171433828-171433848 1.27e-03 1_[+4(6.29e-06)]_11 chr19:18117960-18117980 9.71e-01 20 chr2:231280895-231280915 7.24e-01 20 chr15:93258175-93258195 9.50e-01 20 chr11:111742105-11174212 9.92e-01 20 chr12:106696456-10669647 5.66e-01 20 chr6:116422025-116422045 8.79e-01 20 chr2:219166210-219166230 3.31e-04 4_[+2(4.09e-05)]_8 chr2:101179662-101179682 9.98e-01 20 chr16:81831914-81831934 8.32e-01 20 chr1:200638713-200638733 4.18e-01 20 chr17:18529040-18529060 9.94e-01 20 chr3:45698428-45698448 3.42e-01 20 chr15:34630159-34630179 7.52e-02 20 chr22:41252929-41252949 7.68e-01 20 chr1:36348759-36348779 9.81e-01 20 chr11:47788686-47788706 1.00e+00 20 chr12:1703935-1703955 2.21e-01 20 chr1:231664213-231664233 3.56e-02 10_[+1(2.26e-05)]_2 chr1:32538556-32538576 6.20e-01 20 chr21:35288052-35288072 9.94e-01 20 chr16:71392547-71392567 1.00e+00 20 chr6:27806474-27806494 1.88e-03 20 chr14:75745384-75745404 5.93e-01 20 chr17:76250625-76250645 9.13e-01 20 chr19:41076502-41076522 1.00e+00 20 chr10:17243657-17243677 7.81e-01 20 chr20:62258625-62258645 9.98e-01 20 chr1:167905720-167905740 8.49e-02 20 chr11:62341138-62341158 8.41e-01 20 chr12:4386290-4386310 6.41e-02 20 chr2:47169229-47169249 8.14e-01 20 chr16:67850660-67850680 7.49e-02 20 chr6:35265597-35265617 9.42e-01 20 chr19:1940783-1940803 7.69e-02 20 chr19:48763347-48763367 6.29e-01 20 chr6:40995947-40995967 9.44e-01 20 chr17:46178680-46178700 9.89e-01 20 chr4:120375810-120375830 9.35e-01 20 chr1:208137003-208137023 8.52e-01 20 chr16:86597666-86597686 9.46e-01 20 chr3:197476733-197476753 1.00e+00 20 chrX:154255419-154255439 7.93e-01 20 chr2:20795589-20795609 9.67e-01 20 chr6:13712404-13712424 1.72e-01 20 chr8:95961692-95961712 1.00e+00 20 chr21:42733825-42733845 3.34e-02 20 chr17:41798038-41798058 9.95e-01 20 chr8:42249365-42249385 9.98e-01 20 chr20:33264972-33264992 1.00e+00 20 chr21:34863943-34863963 1.07e-01 20 chr1:31252587-31252607 7.63e-01 20 chr2:55921010-55921030 9.96e-01 20 chr17:20946975-20946995 9.92e-01 20 chr17:80452669-80452689 1.06e-01 20 chr20:37377201-37377221 8.13e-01 20 chr2:191746542-191746562 1.00e+00 20 chr14:23590244-23590264 9.92e-01 20 chr1:153756098-153756118 1.00e+00 20 chr7:5821328-5821348 3.52e-04 12_[+5(7.76e-06)] chr2:91816751-91816771 2.01e-01 20 chr18:56806933-56806953 8.74e-01 20 chr20:44065647-44065667 8.47e-01 20 chr17:66016121-66016141 8.12e-01 20 chr13:52158055-52158075 1.00e+00 20 chr2:233925928-233925948 9.99e-01 20 chr17:62340913-62340933 9.55e-01 20 chr2:179387905-179387925 3.93e-01 20 chr12:125412443-12541246 2.72e-01 20 chr16:1359315-1359335 9.91e-01 20 chr21:19191803-19191823 1.00e+00 20 chr3:48514471-48514491 1.00e+00 20 chr7:6746341-6746361 9.98e-01 20 chr12:2144233-2144253 9.96e-01 20 chr7:134680629-134680649 7.62e-02 20 chr19:42612837-42612857 1.71e-01 20 chr1:200860520-200860540 8.92e-01 20 chr1:155533006-155533026 7.50e-01 20 chr5:118324007-118324027 1.00e+00 20 chr9:132816102-132816122 5.24e-01 20 chr19:46087366-46087386 2.80e-01 20 chr1:63249516-63249536 5.74e-03 12_[+4(9.06e-05)] chr2:74405817-74405837 9.70e-01 20 chr1:150336248-150336268 1.82e-02 20 chr21:40685669-40685689 9.68e-01 20 chr16:81040672-81040692 6.77e-03 12_[+2(8.34e-05)] chr10:30723138-30723158 9.61e-01 20 chr19:56904804-56904824 9.88e-01 20 chr2:231789861-231789881 2.07e-01 20 chr1:182931873-182931893 5.39e-02 20 chr12:57082509-57082529 6.95e-01 20 chr15:77835815-77835835 9.97e-01 20 chr15:43622543-43622563 9.98e-01 20 chr22:23624131-23624151 2.60e-02 20 chr1:145290360-145290380 1.24e-01 20 chr6:26313365-26313385 9.93e-01 20 chr12:120907423-12090744 1.00e+00 20 chr18:72921741-72921761 9.21e-01 20 chr18:55253887-55253907 1.00e+00 20 chr3:52739834-52739854 7.92e-04 5_[+2(5.88e-05)]_7 chr6:41336803-41336823 3.18e-01 20 chr6:149753237-149753257 5.05e-01 20 chr5:137368574-137368594 8.87e-01 20 chr3:47555161-47555181 9.41e-01 20 chr6:36391469-36391489 2.73e-05 6_[+2(2.89e-06)]_6 chr12:31226877-31226897 2.25e-01 20 chr11:77850615-77850635 5.40e-01 20 chr4:104119699-104119719 2.39e-01 20 chr1:1440497-1440517 3.00e-02 11_[+1(6.92e-05)]_1 chr10:76970458-76970478 7.69e-01 20 chr8:29940443-29940463 9.93e-01 20 chr1:10490454-10490474 9.10e-01 20 chr19:3435238-3435258 5.95e-01 20 chr20:18268875-18268895 5.50e-01 20 chr19:488952-488972 9.97e-01 20 chr6:26199374-26199394 9.79e-01 20 chr20:44992823-44992843 8.00e-01 20 chr16:31153929-31153949 9.90e-01 20 chr14:23058538-23058558 1.99e-02 20 chr14:24630413-24630433 9.18e-02 20 chr16:577650-577670 9.56e-01 20 chr17:46662857-46662877 5.45e-01 20 chr12:108154990-10815501 7.58e-01 20 chr13:77601156-77601176 1.95e-06 10_[+5(1.16e-05)]_2 chr7:2598650-2598670 9.20e-01 20 chr19:16477959-16477979 1.22e-02 10_[+2(7.76e-05)]_2 chr9:71394985-71395005 1.00e+00 20 chr1:45273386-45273406 7.32e-01 20 chr3:50358971-50358991 8.29e-01 20 chr3:185277079-185277099 9.26e-01 20 chr1:114889290-114889310 9.48e-01 20 chr8:141467818-141467838 8.58e-01 20 chr16:66785666-66785686 8.57e-01 20 chr19:38864991-38865011 7.41e-01 20 chr11:314290-314310 8.25e-01 20 chr22:43583793-43583813 9.46e-01 20 chr9:106856439-106856459 2.11e-01 20 chr5:74532786-74532806 1.00e+00 20 chr16:3200761-3200781 7.62e-01 20 chr3:88108019-88108039 6.43e-08 5_[+5(7.76e-06)]_7 chr6:18155743-18155763 8.23e-01 20 chr9:131873576-131873596 1.00e+00 20 chr1:212208761-212208781 2.38e-03 1_[+1(8.86e-05)]_11 chr6:27763772-27763792 7.06e-04 20 chr6:112318441-112318461 9.61e-02 20 chr14:104029155-10402917 8.66e-01 20 chr16:27214895-27214915 6.95e-04 3_[+3(4.00e-06)]_9 chr8:27169204-27169224 1.69e-01 20 chr7:151047450-151047470 4.53e-01 20 chr12:4714128-4714148 9.65e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************