******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/K562/fasta/RankLinear0.6_40/PHF8.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr9:123605099-123605179 1.0000 80 chr8:48173258-48173338 1.0000 80 chr2:103353171-103353251 1.0000 80 chr15:62682504-62682584 1.0000 80 chr7:23145474-23145554 1.0000 80 chr1:173991326-173991406 1.0000 80 chr1:46663937-46664017 1.0000 80 chr6:99968995-99969075 1.0000 80 chr7:134896127-134896207 1.0000 80 chr2:19547629-19547709 1.0000 80 chr3:184429630-184429710 1.0000 80 chr6:8435902-8435982 1.0000 80 chr18:11908513-11908593 1.0000 80 chr8:145515360-145515440 1.0000 80 chr5:443080-443160 1.0000 80 chr8:22298672-22298752 1.0000 80 chr14:36295761-36295841 1.0000 80 chr11:13484637-13484717 1.0000 80 chr5:79950583-79950663 1.0000 80 chr11:66247594-66247674 1.0000 80 chr10:16479083-16479163 1.0000 80 chr20:43104583-43104663 1.0000 80 chr15:81282024-81282104 1.0000 80 chr2:24346428-24346508 1.0000 80 chr12:50677505-50677585 1.0000 80 chr6:90062352-90062432 1.0000 80 chr20:58515565-58515645 1.0000 80 chr11:112097183-11209726 1.0000 80 chr12:69864230-69864310 1.0000 80 chr3:150321293-150321373 1.0000 80 chr6:71276691-71276771 1.0000 80 chr5:56205986-56206066 1.0000 80 chrX:130037051-130037131 1.0000 80 chrX:54070563-54070643 1.0000 80 chr5:159826902-159826982 1.0000 80 chr1:11322448-11322528 1.0000 80 chr21:33765545-33765625 1.0000 80 chr15:42264621-42264701 1.0000 80 chr1:92764401-92764481 1.0000 80 chr15:102264486-10226456 1.0000 80 chr16:25078333-25078413 1.0000 80 chr19:40503040-40503120 1.0000 80 chr15:80215933-80216013 1.0000 80 chr12:74931697-74931777 1.0000 80 chr5:89705408-89705488 1.0000 80 chr6:90348325-90348405 1.0000 80 chr20:56884860-56884940 1.0000 80 chr19:50979843-50979923 1.0000 80 chr7:143599095-143599175 1.0000 80 chr15:90645558-90645638 1.0000 80 chr12:105629751-10562983 1.0000 80 chr2:61921672-61921752 1.0000 80 chr6:8435616-8435696 1.0000 80 chr5:138533832-138533912 1.0000 80 chr15:75199019-75199099 1.0000 80 chr14:73525299-73525379 1.0000 80 chr15:40226428-40226508 1.0000 80 chr2:27651635-27651715 1.0000 80 chr10:7830206-7830286 1.0000 80 chr9:115512686-115512766 1.0000 80 chr11:126173776-12617385 1.0000 80 chr20:1306157-1306237 1.0000 80 chr22:21996223-21996303 1.0000 80 chr6:76311763-76311843 1.0000 80 chr3:58419409-58419489 1.0000 80 chr7:134001499-134001579 1.0000 80 chr20:30795757-30795837 1.0000 80 chr17:42766981-42767061 1.0000 80 chr2:99952641-99952721 1.0000 80 chr1:202858092-202858172 1.0000 80 chr19:33667625-33667705 1.0000 80 chr5:81267923-81268003 1.0000 80 chr3:49977656-49977736 1.0000 80 chr7:98741893-98741973 1.0000 80 chr19:18942838-18942918 1.0000 80 chr11:67806246-67806326 1.0000 80 chr17:58041942-58042022 1.0000 80 chr1:46664277-46664357 1.0000 80 chr6:52442126-52442206 1.0000 80 chr11:34938253-34938333 1.0000 80 chr5:114961583-114961663 1.0000 80 chr14:51707046-51707126 1.0000 80 chr1:227127534-227127614 1.0000 80 chr9:123605409-123605489 1.0000 80 chr1:9294917-9294997 1.0000 80 chr19:9649161-9649241 1.0000 80 chr7:23339029-23339109 1.0000 80 chr1:47069772-47069852 1.0000 80 chr18:12884046-12884126 1.0000 80 chr3:169490995-169491075 1.0000 80 chr22:39928607-39928687 1.0000 80 chr14:23398413-23398493 1.0000 80 chr11:67798228-67798308 1.0000 80 chr18:33767539-33767619 1.0000 80 chr15:68521866-68521946 1.0000 80 chr4:99182135-99182215 1.0000 80 chr20:37377193-37377273 1.0000 80 chr2:128051605-128051685 1.0000 80 chr4:37828377-37828457 1.0000 80 chr20:35234249-35234329 1.0000 80 chr8:42698228-42698308 1.0000 80 chr17:57970545-57970625 1.0000 80 chr13:26796254-26796334 1.0000 80 chr22:43411427-43411507 1.0000 80 chr16:3355563-3355643 1.0000 80 chr12:44200263-44200343 1.0000 80 chr8:91997325-91997405 1.0000 80 chr14:92506239-92506319 1.0000 80 chr19:57831943-57832023 1.0000 80 chr6:13328593-13328673 1.0000 80 chr11:107992374-10799245 1.0000 80 chr11:27528465-27528545 1.0000 80 chr2:114514063-114514143 1.0000 80 chr11:47587208-47587288 1.0000 80 chr19:14640481-14640561 1.0000 80 chr8:87520741-87520821 1.0000 80 chr14:75230124-75230204 1.0000 80 chr11:114271040-11427112 1.0000 80 chr7:130353424-130353504 1.0000 80 chr8:71581242-71581322 1.0000 80 chr3:33482631-33482711 1.0000 80 chr7:77325841-77325921 1.0000 80 chr16:66864687-66864767 1.0000 80 chr17:11900990-11901070 1.0000 80 chr1:43233012-43233092 1.0000 80 chr6:127588090-127588170 1.0000 80 chr4:108911083-108911163 1.0000 80 chr10:122610953-12261103 1.0000 80 chr8:82598383-82598463 1.0000 80 chr6:33217418-33217498 1.0000 80 chr3:140950356-140950436 1.0000 80 chr11:85375931-85376011 1.0000 80 chr5:89825249-89825329 1.0000 80 chr10:38146722-38146802 1.0000 80 chr3:180707356-180707436 1.0000 80 chr12:95397325-95397405 1.0000 80 chr22:41047972-41048052 1.0000 80 chr8:110346649-110346729 1.0000 80 chr6:28129623-28129703 1.0000 80 chr7:77166053-77166133 1.0000 80 chr16:74640843-74640923 1.0000 80 chr11:76155556-76155636 1.0000 80 chr2:61698576-61698656 1.0000 80 chr1:161359587-161359667 1.0000 80 chr2:27294374-27294454 1.0000 80 chrX:71496917-71496997 1.0000 80 chr3:196594850-196594930 1.0000 80 chr7:142960624-142960704 1.0000 80 chr7:23145178-23145258 1.0000 80 chr12:62860673-62860753 1.0000 80 chr7:73097581-73097661 1.0000 80 chr10:38265213-38265293 1.0000 80 chr15:76603575-76603655 1.0000 80 chr22:42486619-42486699 1.0000 80 chr2:183581063-183581143 1.0000 80 chr12:53846249-53846329 1.0000 80 chr3:186284941-186285021 1.0000 80 chr19:11485469-11485549 1.0000 80 chr19:46850413-46850493 1.0000 80 chr1:90460793-90460873 1.0000 80 chr13:22178140-22178220 1.0000 80 chr1:3816664-3816744 1.0000 80 chr11:107879858-10787993 1.0000 80 chr6:111280018-111280098 1.0000 80 chr11:17229698-17229778 1.0000 80 chr16:87351186-87351266 1.0000 80 chr6:117923540-117923620 1.0000 80 chr15:41624649-41624729 1.0000 80 chr1:183604740-183604820 1.0000 80 chr5:143550036-143550116 1.0000 80 chr4:113153026-113153106 1.0000 80 chr3:186857094-186857174 1.0000 80 chr1:161147156-161147236 1.0000 80 chr4:84376840-84376920 1.0000 80 chr1:21113974-21114054 1.0000 80 chr17:58603424-58603504 1.0000 80 chr8:145911475-145911555 1.0000 80 chr15:41099468-41099548 1.0000 80 chr19:2476197-2476277 1.0000 80 chr10:102295772-10229585 1.0000 80 chr18:33552296-33552376 1.0000 80 chr1:1209085-1209165 1.0000 80 chr5:141348836-141348916 1.0000 80 chr5:43313394-43313474 1.0000 80 chr14:55518477-55518557 1.0000 80 chr20:3451407-3451487 1.0000 80 chr12:123011370-12301145 1.0000 80 chr3:38180245-38180325 1.0000 80 chr6:88299551-88299631 1.0000 80 chr6:136611219-136611299 1.0000 80 chr16:50186881-50186961 1.0000 80 chr7:43966146-43966226 1.0000 80 chr3:141457229-141457309 1.0000 80 chr15:59225642-59225722 1.0000 80 chr7:103848335-103848415 1.0000 80 chr2:58468335-58468415 1.0000 80 chr9:132816237-132816317 1.0000 80 chr4:25378968-25379048 1.0000 80 chr5:16466083-16466163 1.0000 80 chr1:40204635-40204715 1.0000 80 chr19:19843750-19843830 1.0000 80 chr1:214454621-214454701 1.0000 80 chr2:187454810-187454890 1.0000 80 chr6:146135747-146135827 1.0000 80 chr15:77223727-77223807 1.0000 80 chr12:121648023-12164810 1.0000 80 chr2:27851988-27852068 1.0000 80 chr20:44044835-44044915 1.0000 80 chr19:42900947-42901027 1.0000 80 chr12:32908674-32908754 1.0000 80 chr11:27528188-27528268 1.0000 80 chr16:71495990-71496070 1.0000 80 chr10:60145247-60145327 1.0000 80 chr12:95867987-95868067 1.0000 80 chr1:236030496-236030576 1.0000 80 chr2:74056187-74056267 1.0000 80 chr7:155437396-155437476 1.0000 80 chr18:21166578-21166658 1.0000 80 chr22:22336992-22337072 1.0000 80 chr1:28696342-28696422 1.0000 80 chr16:3767692-3767772 1.0000 80 chr6:36515055-36515135 1.0000 80 chr5:167913553-167913633 1.0000 80 chr6:13328910-13328990 1.0000 80 chr12:2921933-2922013 1.0000 80 chr11:62494776-62494856 1.0000 80 chr19:9251171-9251251 1.0000 80 chr2:74007075-74007155 1.0000 80 chr5:108084232-108084312 1.0000 80 chr11:108338029-10833810 1.0000 80 chr12:100536480-10053656 1.0000 80 chr11:17229381-17229461 1.0000 80 chr1:33430281-33430361 1.0000 80 chr6:41039898-41039978 1.0000 80 chr10:32345191-32345271 1.0000 80 chr8:9912362-9912442 1.0000 80 chr22:21356236-21356316 1.0000 80 chr5:178977665-178977745 1.0000 80 chr6:88182792-88182872 1.0000 80 chr12:122150432-12215051 1.0000 80 chr11:118868555-11886863 1.0000 80 chr1:172502347-172502427 1.0000 80 chr6:13574926-13575006 1.0000 80 chr3:113464911-113464991 1.0000 80 chr5:150080418-150080498 1.0000 80 chr3:47204910-47204990 1.0000 80 chr17:60005107-60005187 1.0000 80 chr7:132937920-132938000 1.0000 80 chr7:99517017-99517097 1.0000 80 chr8:124085032-124085112 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/K562/inference_raw/MEME/RankLinear0.6_40_PHF8/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/PHF8.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 250 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.164 C 0.339 G 0.33 T 0.167 Background letter frequencies (from file dataset with add-one prior applied): A 0.164 C 0.339 G 0.33 T 0.167 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF ASAAAAAT MEME-1 width = 8 sites = 2 llr = 26 E-value = 7.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 Description -------------------------------------------------------------------------------- Simplified A a:aaaaa: pos.-specific C :5:::::: probability G :5:::::: matrix T :::::::a bits 2.6 * ****** 2.3 * ****** 2.1 * ****** 1.8 * ****** Relative 1.6 * ****** Entropy 1.3 * ****** (18.8 bits) 1.0 * ****** 0.8 * ****** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel ACAAAAAT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:22336992-22337072 69 2.17e-06 GAAACAAGCC AGAAAAAT GCGT chr20:1306157-1306237 2 2.17e-06 C ACAAAAAT AGATCAGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:22336992-22337072 2.2e-06 68_[+1]_4 chr20:1306157-1306237 2.2e-06 1_[+1]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ASAAAAAT width=8 seqs=2 chr22:22336992-22337072 ( 69) AGAAAAAT 1 chr20:1306157-1306237 ( 2) ACAAAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 7.3e+003 260 -765 -765 -765 -765 56 60 -765 260 -765 -765 -765 260 -765 -765 -765 260 -765 -765 -765 260 -765 -765 -765 260 -765 -765 -765 -765 -765 -765 258 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.3e+003 1.000000 0.000000 0.000000 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 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 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ASAAAAAT MEME-1 regular expression -------------------------------------------------------------------------------- A[CG]AAAAAT -------------------------------------------------------------------------------- Time 5.08 secs. ******************************************************************************** ******************************************************************************** MOTIF ACTCACCA MEME-2 width = 8 sites = 14 llr = 135 E-value = 9.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9:::a::7 pos.-specific C :a:a:97: probability G :::::::3 matrix T 1:a::13: bits 2.6 * * 2.3 * * 2.1 * * * 1.8 * * * Relative 1.6 ***** * Entropy 1.3 ***** * (13.9 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel ACTCACCA consensus TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr19:19843750-19843830 9 9.73e-06 CCCCGCAC ACTCACCA TTTCCCAGCG chr5:43313394-43313474 58 9.73e-06 AGCGCGGGAC ACTCACCA AGCGTGACCG chr5:143550036-143550116 57 9.73e-06 GGCCTGGGTC ACTCACCA AACTCTGAGG chr3:180707356-180707436 26 9.73e-06 GGAAGGCCGC ACTCACCA TGGCTCCGGC chr18:12884046-12884126 20 9.73e-06 TGGGTCCGCG ACTCACCA AGTACAGCGG chr17:11900990-11901070 1 1.45e-05 . ACTCACTA ATCACTGTTC chr16:87351186-87351266 14 1.93e-05 CACTGGAGCC ACTCATCA TTTCCGACGG chr5:89705408-89705488 65 2.17e-05 TCAGAGCTAA ACTCATTA TCTCTTCG chr5:150080418-150080498 70 4.13e-05 CGGCAGGCAC ACTCACCG CAT chr22:21996223-21996303 71 4.13e-05 GTGTCCAGGG ACTCACCG GC chr1:11322448-11322528 48 4.13e-05 CAGGCCCTAG ACTCACCG CGCGGCTTCG chr5:108084232-108084312 4 6.08e-05 CCA TCTCACCA CGGCAGCCCA chr7:143599095-143599175 19 6.08e-05 GCTGAACCCC ACTCACTG TTTGCCCCGC chr2:99952641-99952721 40 6.57e-05 GTCGGATTCT TCTCACTA CCCTCTGCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:19843750-19843830 9.7e-06 8_[+2]_64 chr5:43313394-43313474 9.7e-06 57_[+2]_15 chr5:143550036-143550116 9.7e-06 56_[+2]_16 chr3:180707356-180707436 9.7e-06 25_[+2]_47 chr18:12884046-12884126 9.7e-06 19_[+2]_53 chr17:11900990-11901070 1.5e-05 [+2]_72 chr16:87351186-87351266 1.9e-05 13_[+2]_59 chr5:89705408-89705488 2.2e-05 64_[+2]_8 chr5:150080418-150080498 4.1e-05 69_[+2]_3 chr22:21996223-21996303 4.1e-05 70_[+2]_2 chr1:11322448-11322528 4.1e-05 47_[+2]_25 chr5:108084232-108084312 6.1e-05 3_[+2]_69 chr7:143599095-143599175 6.1e-05 18_[+2]_54 chr2:99952641-99952721 6.6e-05 39_[+2]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACTCACCA width=8 seqs=14 chr19:19843750-19843830 ( 9) ACTCACCA 1 chr5:43313394-43313474 ( 58) ACTCACCA 1 chr5:143550036-143550116 ( 57) ACTCACCA 1 chr3:180707356-180707436 ( 26) ACTCACCA 1 chr18:12884046-12884126 ( 20) ACTCACCA 1 chr17:11900990-11901070 ( 1) ACTCACTA 1 chr16:87351186-87351266 ( 14) ACTCATCA 1 chr5:89705408-89705488 ( 65) ACTCATTA 1 chr5:150080418-150080498 ( 70) ACTCACCG 1 chr22:21996223-21996303 ( 71) ACTCACCG 1 chr1:11322448-11322528 ( 48) ACTCACCG 1 chr5:108084232-108084312 ( 4) TCTCACCA 1 chr7:143599095-143599175 ( 19) ACTCACTG 1 chr2:99952641-99952721 ( 40) TCTCACTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.9532 E= 9.4e+003 238 -1045 -1045 -22 -1045 156 -1045 -1045 -1045 -1045 -1045 258 -1045 156 -1045 -1045 261 -1045 -1045 -1045 -1045 134 -1045 -22 -1045 107 -1045 78 212 -1045 -21 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 9.4e+003 0.857143 0.000000 0.000000 0.142857 0.000000 1.000000 0.000000 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 0.857143 0.000000 0.142857 0.000000 0.714286 0.000000 0.285714 0.714286 0.000000 0.285714 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCACCA MEME-2 regular expression -------------------------------------------------------------------------------- ACTCAC[CT][AG] -------------------------------------------------------------------------------- Time 8.92 secs. ******************************************************************************** ******************************************************************************** MOTIF GRGAGAAG MEME-3 width = 8 sites = 7 llr = 75 E-value = 3.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :6:a:aa: pos.-specific C :::::::: probability G a4a:a::a matrix T :::::::: bits 2.6 * ** 2.3 * ** 2.1 * ** 1.8 * ** Relative 1.6 * ****** Entropy 1.3 ******** (15.4 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GAGAGAAG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:143550036-143550116 22 8.58e-06 CACGGGTGTG GAGAGAAG CTGAACACTG chr13:26796254-26796334 36 8.58e-06 GGCCACTGAG GAGAGAAG CCGGAAGCCC chr2:128051605-128051685 69 8.58e-06 TACAGCAGCA GAGAGAAG ATGA chr1:202858092-202858172 17 8.58e-06 ACCTGTCGGC GAGAGAAG AGAGCGGTCC chr5:178977665-178977745 1 2.58e-05 . GGGAGAAG AGTTTGAGAT chr6:41039898-41039978 30 2.58e-05 GGGGGTGCGT GGGAGAAG GAAAGAGTCT chr11:107879858-10787993 25 2.58e-05 GACCATGTAG GGGAGAAG AGTGAGGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:143550036-143550116 8.6e-06 21_[+3]_51 chr13:26796254-26796334 8.6e-06 35_[+3]_37 chr2:128051605-128051685 8.6e-06 68_[+3]_4 chr1:202858092-202858172 8.6e-06 16_[+3]_56 chr5:178977665-178977745 2.6e-05 [+3]_72 chr6:41039898-41039978 2.6e-05 29_[+3]_43 chr11:107879858-10787993 2.6e-05 24_[+3]_48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GRGAGAAG width=8 seqs=7 chr5:143550036-143550116 ( 22) GAGAGAAG 1 chr13:26796254-26796334 ( 36) GAGAGAAG 1 chr2:128051605-128051685 ( 69) GAGAGAAG 1 chr1:202858092-202858172 ( 17) GAGAGAAG 1 chr5:178977665-178977745 ( 1) GGGAGAAG 1 chr6:41039898-41039978 ( 30) GGGAGAAG 1 chr11:107879858-10787993 ( 25) GGGAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.9536 E= 3.6e+004 -945 -945 160 -945 180 -945 38 -945 -945 -945 160 -945 261 -945 -945 -945 -945 -945 160 -945 261 -945 -945 -945 261 -945 -945 -945 -945 -945 160 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 3.6e+004 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGAGAAG MEME-3 regular expression -------------------------------------------------------------------------------- G[AG]GAGAAG -------------------------------------------------------------------------------- Time 12.74 secs. ******************************************************************************** ******************************************************************************** MOTIF AAWSAAAC MEME-4 width = 8 sites = 2 llr = 23 E-value = 1.1e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A aa5:aaa: pos.-specific C :::5:::a probability G :::5:::: matrix T ::5::::: bits 2.6 ** *** 2.3 ** *** 2.1 ** *** 1.8 ** *** Relative 1.6 *** **** Entropy 1.3 *** **** (16.8 bits) 1.0 *** **** 0.8 *** **** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAACAAAC consensus TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:108338029-10833810 16 8.91e-06 GCTTTAGAGG AATGAAAC GTCCTTAAGA chr12:74931697-74931777 3 8.91e-06 CA AAACAAAC AGAAGGACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:108338029-10833810 8.9e-06 15_[+4]_57 chr12:74931697-74931777 8.9e-06 2_[+4]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAWSAAAC width=8 seqs=2 chr11:108338029-10833810 ( 16) AATGAAAC 1 chr12:74931697-74931777 ( 3) AAACAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 1.1e+005 260 -765 -765 -765 260 -765 -765 -765 160 -765 -765 158 -765 56 60 -765 260 -765 -765 -765 260 -765 -765 -765 260 -765 -765 -765 -765 156 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.1e+005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.500000 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 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWSAAAC MEME-4 regular expression -------------------------------------------------------------------------------- AA[AT][CG]AAAC -------------------------------------------------------------------------------- Time 16.53 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAAATCT MEME-5 width = 8 sites = 2 llr = 26 E-value = 2.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A a:aaa::: pos.-specific C ::::::a: probability G :a:::::: matrix T :::::a:a bits 2.6 * **** * 2.3 * **** * 2.1 * **** * 1.8 * **** * Relative 1.6 ******** Entropy 1.3 ******** (18.8 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGAAATCT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:33482631-33482711 73 2.26e-06 GCCAAAAGAC AGAAATCT chr14:73525299-73525379 35 2.26e-06 AGCGACGGGC AGAAATCT CGAACCAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:33482631-33482711 2.3e-06 72_[+5] chr14:73525299-73525379 2.3e-06 34_[+5]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGAAATCT width=8 seqs=2 chr3:33482631-33482711 ( 73) AGAAATCT 1 chr14:73525299-73525379 ( 35) AGAAATCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 2.1e+004 260 -765 -765 -765 -765 -765 159 -765 260 -765 -765 -765 260 -765 -765 -765 260 -765 -765 -765 -765 -765 -765 258 -765 156 -765 -765 -765 -765 -765 258 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.1e+004 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 1.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAATCT MEME-5 regular expression -------------------------------------------------------------------------------- AGAAATCT -------------------------------------------------------------------------------- Time 20.24 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:123605099-123605179 7.52e-02 80 chr8:48173258-48173338 3.53e-01 80 chr2:103353171-103353251 9.32e-01 80 chr15:62682504-62682584 9.42e-01 80 chr7:23145474-23145554 9.97e-01 80 chr1:173991326-173991406 1.00e+00 80 chr1:46663937-46664017 5.32e-01 80 chr6:99968995-99969075 9.28e-01 80 chr7:134896127-134896207 9.07e-01 80 chr2:19547629-19547709 8.16e-01 80 chr3:184429630-184429710 9.96e-01 80 chr6:8435902-8435982 4.57e-02 80 chr18:11908513-11908593 8.17e-01 80 chr8:145515360-145515440 1.00e+00 80 chr5:443080-443160 2.26e-01 80 chr8:22298672-22298752 8.46e-01 80 chr14:36295761-36295841 1.95e-01 80 chr11:13484637-13484717 3.25e-01 80 chr5:79950583-79950663 2.21e-01 80 chr11:66247594-66247674 9.72e-01 80 chr10:16479083-16479163 9.72e-01 80 chr20:43104583-43104663 1.00e+00 80 chr15:81282024-81282104 7.50e-01 80 chr2:24346428-24346508 1.00e+00 80 chr12:50677505-50677585 3.67e-01 80 chr6:90062352-90062432 6.62e-01 80 chr20:58515565-58515645 2.90e-01 80 chr11:112097183-11209726 4.27e-01 80 chr12:69864230-69864310 7.04e-01 80 chr3:150321293-150321373 1.00e+00 80 chr6:71276691-71276771 5.98e-01 80 chr5:56205986-56206066 4.82e-01 80 chrX:130037051-130037131 5.96e-01 80 chrX:54070563-54070643 1.00e+00 80 chr5:159826902-159826982 9.02e-01 80 chr1:11322448-11322528 2.51e-01 47_[+2(4.13e-05)]_25 chr21:33765545-33765625 9.92e-01 80 chr15:42264621-42264701 9.99e-01 80 chr1:92764401-92764481 8.22e-01 80 chr15:102264486-10226456 9.99e-01 80 chr16:25078333-25078413 9.98e-01 80 chr19:40503040-40503120 1.30e-02 80 chr15:80215933-80216013 9.17e-01 80 chr12:74931697-74931777 2.82e-03 2_[+4(8.91e-06)]_70 chr5:89705408-89705488 1.65e-02 64_[+2(2.17e-05)]_8 chr6:90348325-90348405 3.75e-01 80 chr20:56884860-56884940 1.00e+00 80 chr19:50979843-50979923 9.92e-01 80 chr7:143599095-143599175 3.18e-02 18_[+2(6.08e-05)]_54 chr15:90645558-90645638 1.00e+00 80 chr12:105629751-10562983 9.73e-01 80 chr2:61921672-61921752 2.33e-01 80 chr6:8435616-8435696 9.95e-01 80 chr5:138533832-138533912 2.36e-01 80 chr15:75199019-75199099 9.72e-01 80 chr14:73525299-73525379 8.89e-04 34_[+5(2.26e-06)]_38 chr15:40226428-40226508 8.50e-01 80 chr2:27651635-27651715 6.97e-01 80 chr10:7830206-7830286 8.27e-01 80 chr9:115512686-115512766 5.81e-01 80 chr11:126173776-12617385 9.23e-01 80 chr20:1306157-1306237 2.46e-03 1_[+1(2.17e-06)]_71 chr22:21996223-21996303 9.15e-02 70_[+2(4.13e-05)]_2 chr6:76311763-76311843 5.00e-01 80 chr3:58419409-58419489 9.79e-02 80 chr7:134001499-134001579 4.89e-01 80 chr20:30795757-30795837 1.00e+00 80 chr17:42766981-42767061 7.49e-01 80 chr2:99952641-99952721 1.62e-01 39_[+2(6.57e-05)]_33 chr1:202858092-202858172 5.45e-02 16_[+3(8.58e-06)]_56 chr19:33667625-33667705 9.98e-01 80 chr5:81267923-81268003 9.31e-01 80 chr3:49977656-49977736 9.02e-01 80 chr7:98741893-98741973 5.84e-01 80 chr19:18942838-18942918 1.00e+00 80 chr11:67806246-67806326 8.56e-01 80 chr17:58041942-58042022 6.15e-01 80 chr1:46664277-46664357 4.01e-01 80 chr6:52442126-52442206 1.45e-01 80 chr11:34938253-34938333 9.36e-01 80 chr5:114961583-114961663 2.71e-02 80 chr14:51707046-51707126 7.05e-01 80 chr1:227127534-227127614 9.39e-01 80 chr9:123605409-123605489 3.86e-01 80 chr1:9294917-9294997 9.97e-01 80 chr19:9649161-9649241 8.02e-01 80 chr7:23339029-23339109 1.00e+00 80 chr1:47069772-47069852 3.57e-01 80 chr18:12884046-12884126 2.14e-02 19_[+2(9.73e-06)]_53 chr3:169490995-169491075 9.86e-01 80 chr22:39928607-39928687 9.59e-01 80 chr14:23398413-23398493 9.90e-01 80 chr11:67798228-67798308 1.00e+00 80 chr18:33767539-33767619 9.99e-01 80 chr15:68521866-68521946 1.00e+00 80 chr4:99182135-99182215 5.82e-01 80 chr20:37377193-37377273 1.00e+00 80 chr2:128051605-128051685 3.18e-03 68_[+3(8.58e-06)]_4 chr4:37828377-37828457 6.18e-01 80 chr20:35234249-35234329 9.95e-01 80 chr8:42698228-42698308 5.73e-01 80 chr17:57970545-57970625 7.96e-01 80 chr13:26796254-26796334 2.58e-02 35_[+3(8.58e-06)]_37 chr22:43411427-43411507 9.87e-01 80 chr16:3355563-3355643 2.86e-01 80 chr12:44200263-44200343 9.52e-01 80 chr8:91997325-91997405 3.69e-02 80 chr14:92506239-92506319 7.90e-01 80 chr19:57831943-57832023 9.99e-01 80 chr6:13328593-13328673 8.79e-01 80 chr11:107992374-10799245 5.17e-01 80 chr11:27528465-27528545 9.94e-01 80 chr2:114514063-114514143 5.38e-01 80 chr11:47587208-47587288 8.97e-01 80 chr19:14640481-14640561 7.75e-02 80 chr8:87520741-87520821 5.01e-01 80 chr14:75230124-75230204 9.07e-01 80 chr11:114271040-11427112 2.84e-01 80 chr7:130353424-130353504 5.80e-01 80 chr8:71581242-71581322 7.99e-01 80 chr3:33482631-33482711 1.72e-05 72_[+5(2.26e-06)] chr7:77325841-77325921 1.09e-02 80 chr16:66864687-66864767 9.55e-01 80 chr17:11900990-11901070 5.58e-02 [+2(1.45e-05)]_72 chr1:43233012-43233092 3.07e-01 80 chr6:127588090-127588170 3.10e-01 80 chr4:108911083-108911163 4.20e-01 80 chr10:122610953-12261103 6.00e-01 80 chr8:82598383-82598463 1.85e-01 80 chr6:33217418-33217498 1.74e-01 80 chr3:140950356-140950436 9.96e-01 80 chr11:85375931-85376011 9.36e-01 80 chr5:89825249-89825329 7.07e-02 80 chr10:38146722-38146802 9.59e-01 80 chr3:180707356-180707436 1.72e-02 25_[+2(9.73e-06)]_47 chr12:95397325-95397405 1.78e-03 48_[+4(1.33e-05)]_24 chr22:41047972-41048052 9.79e-01 80 chr8:110346649-110346729 9.98e-01 80 chr6:28129623-28129703 7.44e-01 80 chr7:77166053-77166133 2.76e-02 80 chr16:74640843-74640923 8.42e-02 80 chr11:76155556-76155636 2.56e-03 80 chr2:61698576-61698656 9.94e-01 80 chr1:161359587-161359667 9.60e-01 80 chr2:27294374-27294454 6.71e-01 80 chrX:71496917-71496997 5.21e-01 80 chr3:196594850-196594930 1.00e+00 80 chr7:142960624-142960704 9.55e-01 80 chr7:23145178-23145258 8.51e-04 1_[+5(7.98e-05)]_71 chr12:62860673-62860753 9.96e-01 80 chr7:73097581-73097661 4.11e-01 80 chr10:38265213-38265293 9.66e-01 80 chr15:76603575-76603655 7.87e-01 80 chr22:42486619-42486699 2.83e-01 80 chr2:183581063-183581143 8.42e-01 80 chr12:53846249-53846329 8.81e-01 80 chr3:186284941-186285021 5.70e-01 80 chr19:11485469-11485549 3.86e-01 80 chr19:46850413-46850493 4.25e-01 80 chr1:90460793-90460873 9.85e-01 80 chr13:22178140-22178220 9.83e-01 80 chr1:3816664-3816744 6.63e-01 80 chr11:107879858-10787993 9.42e-03 24_[+3(2.58e-05)]_48 chr6:111280018-111280098 6.63e-01 80 chr11:17229698-17229778 5.92e-01 80 chr16:87351186-87351266 1.71e-01 13_[+2(1.93e-05)]_59 chr6:117923540-117923620 6.30e-01 80 chr15:41624649-41624729 3.64e-04 47_[+1(8.06e-05)]_25 chr1:183604740-183604820 9.61e-01 80 chr5:143550036-143550116 1.05e-05 21_[+3(8.58e-06)]_27_[+2(9.73e-06)]_\ 16 chr4:113153026-113153106 7.05e-01 80 chr3:186857094-186857174 8.13e-01 80 chr1:161147156-161147236 8.58e-01 80 chr4:84376840-84376920 4.17e-01 80 chr1:21113974-21114054 9.86e-01 80 chr17:58603424-58603504 2.98e-01 80 chr8:145911475-145911555 1.95e-01 80 chr15:41099468-41099548 4.20e-02 80 chr19:2476197-2476277 7.80e-01 80 chr10:102295772-10229585 7.49e-01 80 chr18:33552296-33552376 5.52e-02 80 chr1:1209085-1209165 5.99e-01 80 chr5:141348836-141348916 9.12e-01 80 chr5:43313394-43313474 1.10e-01 57_[+2(9.73e-06)]_15 chr14:55518477-55518557 9.96e-01 80 chr20:3451407-3451487 1.13e-01 80 chr12:123011370-12301145 9.60e-01 80 chr3:38180245-38180325 5.03e-01 80 chr6:88299551-88299631 9.77e-01 80 chr6:136611219-136611299 6.77e-01 80 chr16:50186881-50186961 5.27e-01 80 chr7:43966146-43966226 6.09e-01 80 chr3:141457229-141457309 2.63e-01 80 chr15:59225642-59225722 9.58e-01 80 chr7:103848335-103848415 8.15e-01 80 chr2:58468335-58468415 5.00e-02 80 chr9:132816237-132816317 1.00e+00 80 chr4:25378968-25379048 7.41e-01 80 chr5:16466083-16466163 5.72e-01 80 chr1:40204635-40204715 8.90e-01 80 chr19:19843750-19843830 5.47e-02 8_[+2(9.73e-06)]_64 chr1:214454621-214454701 9.73e-01 80 chr2:187454810-187454890 8.22e-02 80 chr6:146135747-146135827 1.00e+00 80 chr15:77223727-77223807 6.66e-01 80 chr12:121648023-12164810 7.92e-01 80 chr2:27851988-27852068 4.02e-01 80 chr20:44044835-44044915 4.17e-01 80 chr19:42900947-42901027 2.10e-01 80 chr12:32908674-32908754 1.68e-01 80 chr11:27528188-27528268 3.48e-01 80 chr16:71495990-71496070 9.18e-01 80 chr10:60145247-60145327 7.16e-01 80 chr12:95867987-95868067 1.57e-01 80 chr1:236030496-236030576 6.44e-01 80 chr2:74056187-74056267 9.44e-01 80 chr7:155437396-155437476 9.93e-01 80 chr18:21166578-21166658 5.07e-01 80 chr22:22336992-22337072 1.96e-05 68_[+1(2.17e-06)]_4 chr1:28696342-28696422 4.72e-01 80 chr16:3767692-3767772 9.94e-01 80 chr6:36515055-36515135 5.99e-01 80 chr5:167913553-167913633 9.14e-02 80 chr6:13328910-13328990 1.59e-01 80 chr12:2921933-2922013 5.93e-01 80 chr11:62494776-62494856 9.78e-01 80 chr19:9251171-9251251 8.26e-01 80 chr2:74007075-74007155 6.28e-01 80 chr5:108084232-108084312 1.61e-02 3_[+2(6.08e-05)]_69 chr11:108338029-10833810 1.06e-02 15_[+4(8.91e-06)]_57 chr12:100536480-10053656 5.69e-01 80 chr11:17229381-17229461 9.35e-01 80 chr1:33430281-33430361 9.52e-01 80 chr6:41039898-41039978 5.61e-03 29_[+3(2.58e-05)]_43 chr10:32345191-32345271 9.21e-01 80 chr8:9912362-9912442 1.47e-02 45_[+5(7.98e-05)]_27 chr22:21356236-21356316 8.57e-01 80 chr5:178977665-178977745 2.45e-02 [+3(2.58e-05)]_72 chr6:88182792-88182872 9.98e-01 80 chr12:122150432-12215051 1.49e-02 80 chr11:118868555-11886863 7.90e-01 80 chr1:172502347-172502427 8.57e-01 80 chr6:13574926-13575006 8.16e-01 80 chr3:113464911-113464991 8.03e-01 80 chr5:150080418-150080498 2.51e-01 69_[+2(4.13e-05)]_3 chr3:47204910-47204990 7.96e-01 80 chr17:60005107-60005187 4.93e-01 80 chr7:132937920-132938000 9.13e-01 80 chr7:99517017-99517097 2.29e-01 80 chr8:124085032-124085112 5.38e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n07.farnam.hpc.yale.internal ********************************************************************************