******************************************************************************** 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/worm/fasta/RankLinear2.0_40/gmeb-2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrI:3567651-3567731 1.0000 80 chrV:265487-265567 1.0000 80 chrI:3248619-3248699 1.0000 80 chrX:16944106-16944186 1.0000 80 chrV:13646102-13646182 1.0000 80 chrV:265691-265771 1.0000 80 chrII:2570543-2570623 1.0000 80 chrII:2570753-2570833 1.0000 80 chrX:5056378-5056458 1.0000 80 chrIII:3499984-3500064 1.0000 80 chrV:5284424-5284504 1.0000 80 chrIII:445726-445806 1.0000 80 chrX:8156139-8156219 1.0000 80 chrII:11974827-11974907 1.0000 80 chrI:3547037-3547117 1.0000 80 chrX:15668389-15668469 1.0000 80 chrV:20384814-20384894 1.0000 80 chrV:14689472-14689552 1.0000 80 chrIII:931568-931648 1.0000 80 chrIV:4399544-4399624 1.0000 80 chrV:5284761-5284841 1.0000 80 chrI:7535475-7535555 1.0000 80 chrI:933476-933556 1.0000 80 chrIII:13225182-13225262 1.0000 80 chrV:19722988-19723068 1.0000 80 chrIII:1327080-1327160 1.0000 80 chrV:16699814-16699894 1.0000 80 chrX:16602608-16602688 1.0000 80 chrV:1821464-1821544 1.0000 80 chrI:3564608-3564688 1.0000 80 chrIII:1616370-1616450 1.0000 80 chrX:3969503-3969583 1.0000 80 chrX:8638893-8638973 1.0000 80 chrI:3075084-3075164 1.0000 80 chrV:11345093-11345173 1.0000 80 chrI:9249382-9249462 1.0000 80 chrX:16551459-16551539 1.0000 80 chrIII:8650360-8650440 1.0000 80 chrII:4130238-4130318 1.0000 80 chrII:11636761-11636841 1.0000 80 chrV:13868888-13868968 1.0000 80 chrIII:4626321-4626401 1.0000 80 chrX:13415136-13415216 1.0000 80 chrX:12407400-12407480 1.0000 80 chrIV:1687368-1687448 1.0000 80 chrX:3994561-3994641 1.0000 80 chrX:8602859-8602939 1.0000 80 chrIII:8806376-8806456 1.0000 80 chrIII:6133434-6133514 1.0000 80 chrIII:5769872-5769952 1.0000 80 chrIV:4784984-4785064 1.0000 80 chrII:15218054-15218134 1.0000 80 chrIII:3664401-3664481 1.0000 80 chrV:15554009-15554089 1.0000 80 chrIII:11093617-11093697 1.0000 80 chrV:20061584-20061664 1.0000 80 chrI:3531525-3531605 1.0000 80 chrIII:13160809-13160889 1.0000 80 chrIV:5334685-5334765 1.0000 80 chrV:12510029-12510109 1.0000 80 chrII:4130441-4130521 1.0000 80 chrX:8818121-8818201 1.0000 80 chrII:7001599-7001679 1.0000 80 chrIII:12613639-12613719 1.0000 80 chrV:7745976-7746056 1.0000 80 chrII:4238045-4238125 1.0000 80 chrIII:1122411-1122491 1.0000 80 chrIII:12399828-12399908 1.0000 80 chrX:3914460-3914540 1.0000 80 chrV:19430713-19430793 1.0000 80 chrII:11884394-11884474 1.0000 80 chrI:11585403-11585483 1.0000 80 chrIV:5038925-5039005 1.0000 80 chrII:5341179-5341259 1.0000 80 chrV:2674008-2674088 1.0000 80 chrV:16553106-16553186 1.0000 80 chrV:7231023-7231103 1.0000 80 chrX:8944248-8944328 1.0000 80 chrIII:3175127-3175207 1.0000 80 chrIII:8653080-8653160 1.0000 80 chrV:3587802-3587882 1.0000 80 chrX:2216729-2216809 1.0000 80 chrIV:842833-842913 1.0000 80 chrV:15505239-15505319 1.0000 80 chrV:14524367-14524447 1.0000 80 chrII:8325293-8325373 1.0000 80 chrI:9855609-9855689 1.0000 80 chrIII:6805574-6805654 1.0000 80 chrIII:8529248-8529328 1.0000 80 chrX:12890296-12890376 1.0000 80 chrV:8039156-8039236 1.0000 80 chrX:9296778-9296858 1.0000 80 chrV:4510460-4510540 1.0000 80 chrI:13422032-13422112 1.0000 80 chrI:14614779-14614859 1.0000 80 chrV:4647997-4648077 1.0000 80 chrI:3873907-3873987 1.0000 80 chrI:11978761-11978841 1.0000 80 chrX:13781649-13781729 1.0000 80 chrIII:3620855-3620935 1.0000 80 chrX:15307727-15307807 1.0000 80 chrI:14708055-14708135 1.0000 80 chrI:9605761-9605841 1.0000 80 chrX:6252342-6252422 1.0000 80 chrV:9088888-9088968 1.0000 80 chrI:11266666-11266746 1.0000 80 chrV:20424422-20424502 1.0000 80 chrV:14855774-14855854 1.0000 80 chrIV:13549510-13549590 1.0000 80 chrX:17416729-17416809 1.0000 80 chrII:10304893-10304973 1.0000 80 chrI:11609205-11609285 1.0000 80 chrIII:13032766-13032846 1.0000 80 chrX:15340796-15340876 1.0000 80 chrIII:3812625-3812705 1.0000 80 chrII:7708751-7708831 1.0000 80 chrII:3567793-3567873 1.0000 80 chrIII:11935971-11936051 1.0000 80 chrV:19142855-19142935 1.0000 80 chrV:16022761-16022841 1.0000 80 chrI:7543698-7543778 1.0000 80 chrV:19622289-19622369 1.0000 80 chrIII:7030577-7030657 1.0000 80 chrX:5407389-5407469 1.0000 80 chrX:16271301-16271381 1.0000 80 chrI:4633644-4633724 1.0000 80 chrX:13730767-13730847 1.0000 80 chrX:9373124-9373204 1.0000 80 chrIV:14225032-14225112 1.0000 80 chrIV:3874590-3874670 1.0000 80 chrII:11535610-11535690 1.0000 80 chrIV:2639805-2639885 1.0000 80 chrIV:1056616-1056696 1.0000 80 chrIII:1601581-1601661 1.0000 80 chrIII:10432276-10432356 1.0000 80 chrIV:16776050-16776130 1.0000 80 chrI:4175890-4175970 1.0000 80 chrV:5576228-5576308 1.0000 80 chrIII:3916772-3916852 1.0000 80 chrII:14635374-14635454 1.0000 80 chrIII:535389-535469 1.0000 80 chrIII:1824689-1824769 1.0000 80 chrX:14115646-14115726 1.0000 80 chrX:2043409-2043489 1.0000 80 chrIII:3476310-3476390 1.0000 80 chrII:5836519-5836599 1.0000 80 chrIV:1388231-1388311 1.0000 80 chrI:8530126-8530206 1.0000 80 chrI:6136587-6136667 1.0000 80 chrV:12353451-12353531 1.0000 80 chrX:10821342-10821422 1.0000 80 chrII:11959408-11959488 1.0000 80 chrIV:3399222-3399302 1.0000 80 chrX:10900199-10900279 1.0000 80 chrIII:8971807-8971887 1.0000 80 chrIII:12599120-12599200 1.0000 80 chrX:8971606-8971686 1.0000 80 chrV:13176511-13176591 1.0000 80 chrI:6135835-6135915 1.0000 80 chrIII:6116570-6116650 1.0000 80 chrI:10807264-10807344 1.0000 80 chrIII:6133636-6133716 1.0000 80 chrI:4367905-4367985 1.0000 80 chrI:7195044-7195124 1.0000 80 chrX:4444219-4444299 1.0000 80 chrII:3439327-3439407 1.0000 80 chrIV:2802361-2802441 1.0000 80 chrI:13495259-13495339 1.0000 80 chrX:16928276-16928356 1.0000 80 chrIV:8334385-8334465 1.0000 80 chrIII:7642163-7642243 1.0000 80 chrV:11239330-11239410 1.0000 80 chrII:6721727-6721807 1.0000 80 chrV:53452-53532 1.0000 80 chrI:11505520-11505600 1.0000 80 chrIV:16399172-16399252 1.0000 80 chrIII:11091838-11091918 1.0000 80 chrX:8925620-8925700 1.0000 80 chrIV:14032702-14032782 1.0000 80 chrIII:1218372-1218452 1.0000 80 chrV:4731537-4731617 1.0000 80 chrI:6091104-6091184 1.0000 80 chrX:9078316-9078396 1.0000 80 chrI:12225444-12225524 1.0000 80 chrIII:7659569-7659649 1.0000 80 chrX:14804920-14805000 1.0000 80 chrX:12367634-12367714 1.0000 80 chrIV:16946911-16946991 1.0000 80 chrIII:1604723-1604803 1.0000 80 chrV:14876381-14876461 1.0000 80 chrX:12452276-12452356 1.0000 80 chrI:5164989-5165069 1.0000 80 chrI:6532054-6532134 1.0000 80 chrX:10555614-10555694 1.0000 80 chrI:14721595-14721675 1.0000 80 chrX:1837885-1837965 1.0000 80 chrV:7465716-7465796 1.0000 80 chrX:12843659-12843739 1.0000 80 chrI:6252940-6253020 1.0000 80 chrV:12780412-12780492 1.0000 80 chrIV:16388456-16388536 1.0000 80 chrI:1575687-1575767 1.0000 80 chrV:13962170-13962250 1.0000 80 chrIII:8768067-8768147 1.0000 80 chrII:10303876-10303956 1.0000 80 chrI:7094963-7095043 1.0000 80 chrX:5319378-5319458 1.0000 80 chrV:20694104-20694184 1.0000 80 chrIV:16382342-16382422 1.0000 80 chrV:15551824-15551904 1.0000 80 chrX:8386132-8386212 1.0000 80 chrIV:9191310-9191390 1.0000 80 chrIV:620455-620535 1.0000 80 chrX:6867883-6867963 1.0000 80 chrV:1197451-1197531 1.0000 80 chrIV:322628-322708 1.0000 80 chrI:9268958-9269038 1.0000 80 chrII:6383312-6383392 1.0000 80 chrX:6903078-6903158 1.0000 80 chrX:3348003-3348083 1.0000 80 chrIV:11310776-11310856 1.0000 80 chrIII:13721279-13721359 1.0000 80 chrI:13310318-13310398 1.0000 80 chrII:6913473-6913553 1.0000 80 chrIV:16863627-16863707 1.0000 80 chrIV:13980268-13980348 1.0000 80 chrI:13470412-13470492 1.0000 80 chrIV:1981109-1981189 1.0000 80 chrX:8608839-8608919 1.0000 80 chrIII:7199004-7199084 1.0000 80 chrIII:2576851-2576931 1.0000 80 chrIII:11236917-11236997 1.0000 80 chrI:10927483-10927563 1.0000 80 chrIII:3786658-3786738 1.0000 80 chrV:8631472-8631552 1.0000 80 chrIII:9104254-9104334 1.0000 80 chrV:9583067-9583147 1.0000 80 chrI:1175835-1175915 1.0000 80 chrIV:11928454-11928534 1.0000 80 chrII:5293409-5293489 1.0000 80 chrI:5176402-5176482 1.0000 80 chrIII:4378729-4378809 1.0000 80 chrX:8646456-8646536 1.0000 80 chrX:10145160-10145240 1.0000 80 chrX:6219950-6220030 1.0000 80 chrII:4942479-4942559 1.0000 80 chrX:16604710-16604790 1.0000 80 chrI:3265989-3266069 1.0000 80 chrV:13041788-13041868 1.0000 80 chrX:13264714-13264794 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/worm/inference_raw/MEME/RankLinear2.0_40_gmeb-2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/gmeb-2.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 0.253 C 0.249 G 0.25 T 0.249 Background letter frequencies (from file dataset with add-one prior applied): A 0.253 C 0.249 G 0.25 T 0.249 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCGAACCC MEME-1 width = 8 sites = 31 llr = 274 E-value = 1.3e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::a7::1 pos.-specific C :9:::7a9 probability G ::a:2::: matrix T a1::23:: bits 2.0 * ** 1.8 * ** * 1.6 * ** ** 1.4 **** ** Relative 1.2 **** ** Entropy 1.0 **** *** (12.8 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCGAACCC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:11928454-11928534 39 1.53e-05 GAAGTGGGAT TCGAACCC ACGCACCCAT chrX:6903078-6903158 51 1.53e-05 AGAGTGGGAT TCGAACCC ACGCCCCCGA chrX:12367634-12367714 23 1.53e-05 ATGCCGGGAA TCGAACCC GGGCCGCGTG chrIII:7642163-7642243 10 1.53e-05 TGCGGGGAA TCGAACCC CGGCCTTATG chrX:16928276-16928356 10 1.53e-05 gaccgggaa tcgaaccc gggccgcccg chrI:8530126-8530206 17 1.53e-05 TTGCGGGGAA TCGAACCC CGGCCTTATG chrX:16271301-16271381 10 1.53e-05 TGCGGGGAA TCGAACCC CGGCCTTATG chrI:9605761-9605841 58 1.53e-05 CCGCGTAGGT TCGAACCC TGCTCGCTGC chrV:20061584-20061664 3 1.53e-05 AC TCGAACCC GGTGGGGGGG chrIII:8650360-8650440 36 1.53e-05 GAACCGGGAA TCGAACCC GGGACCTCTC chrX:10145160-10145240 50 3.06e-05 GATTGTAGGT TCGAATCC TGCCGTGGTC chrI:6135835-6135915 60 3.06e-05 GGTCACTGGT TCGAATCC GGTTCGACGG chrX:8971606-8971686 57 3.06e-05 CCGCGTAGGT TCGAATCC TGCTGACTGC chrIII:535389-535469 58 3.06e-05 GGTCACTGGT TCGAATCC GGTTCGACGG chrII:11959408-11959488 21 6.08e-05 GGCCGCCGGT TCGATCCC GGCCAGGACC chrI:6136587-6136667 64 6.08e-05 TGTCGCGGGT TCGAGCCC CGCATTGGG chrX:13730767-13730847 65 6.08e-05 TGTCGCGGGT TCGAGCCC CGCATTGG chrX:13781649-13781729 45 6.08e-05 TGTCGCGGGT TCGAGCCC CGCATTGGGC chrIII:6805574-6805654 48 6.08e-05 GGTTGGTGGT TCGAGCCC ACCCGGGAGC chrX:16604710-16604790 25 7.62e-05 CGGCCGGGAA TTGAACCC GGGTCTCGCA chrIV:322628-322708 19 7.62e-05 cggccgggaa ttgaaccc gggtctcgca chrX:12890296-12890376 4 7.62e-05 GAA TTGAACCC CGGACTTCTC chrIV:16388456-16388536 53 1.06e-04 CGACGCTGGT TCGATTCC AGCCGCAGGC chrI:11978761-11978841 56 1.06e-04 AGGCCGGGGT TCGATTCC CCGCAACGGA chrIV:842833-842913 29 1.06e-04 CGGCCCGGGT TCGATTCC CGGCATGGGA chrV:2674008-2674088 55 1.06e-04 GGTCGCTGGT TCGATTCC AGCATGAGGC chrIV:5038925-5039005 49 1.06e-04 GGTCAGGGGT TCGAGTCC CCTAGGTGGC chrIII:1601581-1601661 1 1.22e-04 . TCGAACCA GGGACCTATT chrX:16602608-16602688 41 1.22e-04 GGTGTGGGGG TCGAACCA TTAACCCCCC chrX:8925620-8925700 54 1.37e-04 ACTCATGACT TTGAATCC TGCGACCCGA chrX:8944248-8944328 26 1.98e-04 CGATCTGGAG TCGAACGC GCTACCATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:11928454-11928534 1.5e-05 38_[+1]_34 chrX:6903078-6903158 1.5e-05 50_[+1]_22 chrX:12367634-12367714 1.5e-05 22_[+1]_50 chrIII:7642163-7642243 1.5e-05 9_[+1]_63 chrX:16928276-16928356 1.5e-05 9_[+1]_63 chrI:8530126-8530206 1.5e-05 16_[+1]_56 chrX:16271301-16271381 1.5e-05 9_[+1]_63 chrI:9605761-9605841 1.5e-05 57_[+1]_15 chrV:20061584-20061664 1.5e-05 2_[+1]_70 chrIII:8650360-8650440 1.5e-05 35_[+1]_37 chrX:10145160-10145240 3.1e-05 49_[+1]_23 chrI:6135835-6135915 3.1e-05 59_[+1]_13 chrX:8971606-8971686 3.1e-05 56_[+1]_16 chrIII:535389-535469 3.1e-05 57_[+1]_15 chrII:11959408-11959488 6.1e-05 20_[+1]_52 chrI:6136587-6136667 6.1e-05 63_[+1]_9 chrX:13730767-13730847 6.1e-05 64_[+1]_8 chrX:13781649-13781729 6.1e-05 44_[+1]_28 chrIII:6805574-6805654 6.1e-05 47_[+1]_25 chrX:16604710-16604790 7.6e-05 24_[+1]_48 chrIV:322628-322708 7.6e-05 18_[+1]_54 chrX:12890296-12890376 7.6e-05 3_[+1]_69 chrIV:16388456-16388536 0.00011 52_[+1]_20 chrI:11978761-11978841 0.00011 55_[+1]_17 chrIV:842833-842913 0.00011 28_[+1]_44 chrV:2674008-2674088 0.00011 54_[+1]_18 chrIV:5038925-5039005 0.00011 48_[+1]_24 chrIII:1601581-1601661 0.00012 [+1]_72 chrX:16602608-16602688 0.00012 40_[+1]_32 chrX:8925620-8925700 0.00014 53_[+1]_19 chrX:8944248-8944328 0.0002 25_[+1]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCGAACCC width=8 seqs=31 chrIV:11928454-11928534 ( 39) TCGAACCC 1 chrX:6903078-6903158 ( 51) TCGAACCC 1 chrX:12367634-12367714 ( 23) TCGAACCC 1 chrIII:7642163-7642243 ( 10) TCGAACCC 1 chrX:16928276-16928356 ( 10) TCGAACCC 1 chrI:8530126-8530206 ( 17) TCGAACCC 1 chrX:16271301-16271381 ( 10) TCGAACCC 1 chrI:9605761-9605841 ( 58) TCGAACCC 1 chrV:20061584-20061664 ( 3) TCGAACCC 1 chrIII:8650360-8650440 ( 36) TCGAACCC 1 chrX:10145160-10145240 ( 50) TCGAATCC 1 chrI:6135835-6135915 ( 60) TCGAATCC 1 chrX:8971606-8971686 ( 57) TCGAATCC 1 chrIII:535389-535469 ( 58) TCGAATCC 1 chrII:11959408-11959488 ( 21) TCGATCCC 1 chrI:6136587-6136667 ( 64) TCGAGCCC 1 chrX:13730767-13730847 ( 65) TCGAGCCC 1 chrX:13781649-13781729 ( 45) TCGAGCCC 1 chrIII:6805574-6805654 ( 48) TCGAGCCC 1 chrX:16604710-16604790 ( 25) TTGAACCC 1 chrIV:322628-322708 ( 19) TTGAACCC 1 chrX:12890296-12890376 ( 4) TTGAACCC 1 chrIV:16388456-16388536 ( 53) TCGATTCC 1 chrI:11978761-11978841 ( 56) TCGATTCC 1 chrIV:842833-842913 ( 29) TCGATTCC 1 chrV:2674008-2674088 ( 55) TCGATTCC 1 chrIV:5038925-5039005 ( 49) TCGAGTCC 1 chrIII:1601581-1601661 ( 1) TCGAACCA 1 chrX:16602608-16602688 ( 41) TCGAACCA 1 chrX:8925620-8925700 ( 54) TTGAATCC 1 chrX:8944248-8944328 ( 26) TCGAACGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.16214 E= 1.3e-005 -1160 -1160 -1160 201 -1160 181 -1160 -95 -1160 -1160 200 -1160 198 -1160 -1160 -1160 142 -1160 -63 -63 -1160 144 -1160 37 -1160 196 -295 -1160 -197 191 -1160 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.3e-005 0.000000 0.000000 0.000000 1.000000 0.000000 0.870968 0.000000 0.129032 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.677419 0.000000 0.161290 0.161290 0.000000 0.677419 0.000000 0.322581 0.000000 0.967742 0.032258 0.000000 0.064516 0.935484 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGAACCC MEME-1 regular expression -------------------------------------------------------------------------------- TCGAA[CT]CC -------------------------------------------------------------------------------- Time 5.45 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTTGYW MEME-2 width = 8 sites = 33 llr = 281 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::3 pos.-specific C ::::234: probability G :::::7:: matrix T aaaa8:57 bits 2.0 **** 1.8 **** 1.6 **** 1.4 **** Relative 1.2 ****** Entropy 1.0 ****** * (12.3 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTTTTGTT consensus CCCA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:16863627-16863707 67 1.48e-05 GCCGCACACT TTTTTGTT GTTTTT chrX:14115646-14115726 8 1.48e-05 CCCTCTT TTTTTGTT ATAGGCAAAC chrV:7231023-7231103 58 1.48e-05 CCTCTCTCAG TTTTTGTT CCCTTTTTCT chrIV:5038925-5039005 72 1.48e-05 GTGGCTTGAT TTTTTGTT T chrIV:1687368-1687448 2 1.48e-05 A TTTTTGTT TTTATATTAA chrI:9249382-9249462 73 1.48e-05 TTAAGAGGGT TTTTTGTT chrIII:3476310-3476390 60 4.47e-05 AGTGGCATAG TTTTTGTA CTTAAATTCT chrI:5176402-5176482 4 5.95e-05 TCG TTTTTCTT GACAGAGAAA chrIV:11928454-11928534 5 5.95e-05 TTTC TTTTTCTT GCAAAAAGAT chrI:7094963-7095043 7 5.95e-05 ATAATT TTTTTCTT TCGAAAATCA chrI:14721595-14721675 69 5.95e-05 GTTGCCGTTA TTTTTCTT TTAC chrIV:4784984-4785064 5 5.95e-05 tCCT TTTTTCTT CTTCTATTTT chrII:11636761-11636841 25 5.95e-05 GCACTTTTTC TTTTTCTT ATCGGCGGGC chrV:20384814-20384894 4 5.95e-05 AGC TTTTTCTT CTGCTCCGCC chrII:10303876-10303956 69 7.46e-05 GTGCGCGCGC TTTTTGCA AGGT chrV:11239330-11239410 48 7.46e-05 GTGCGCGGGT TTTTTGCA ACCCCGCCGC chrI:4633644-4633724 33 7.46e-05 GCGTGCGCCG TTTTTGCA TAAAGTGTGT chrV:19142855-19142935 34 7.46e-05 TATTATCGAC TTTTTGCA GAACTTGGGC chrII:7708751-7708831 15 7.46e-05 GCGCGCACGG TTTTTGCA ATTCTCCCGC chrV:14524367-14524447 9 7.46e-05 CCCGCCCC TTTTTGCA AGATTGTGCG chrI:3547037-3547117 16 7.46e-05 TGGCACGGCA TTTTTGCA AGTGGTGCGC chrV:1197451-1197531 70 1.04e-04 CCAGCTCCCC TTTTCGTT GCT chrIII:6116570-6116650 49 1.04e-04 TTTTGAGGAA TTTTTCCT AATCACGAAA chrIII:11935971-11936051 40 1.04e-04 ACAACGAGCC TTTTCGTT GCCATAAATA chrX:15340796-15340876 59 1.04e-04 CACATTCTCA TTTTCGTT ACTGTTTGTT chrX:13781649-13781729 70 1.04e-04 GGCTTAGTTT TTTTTCCT TTT chrIII:3499984-3500064 6 1.04e-04 TCCCC TTTTCGTT CAGTTCCCGC chrII:5341179-5341259 23 1.19e-04 AGTATCAGCA TTTTCGCT AATTTGCCAG chrI:3248619-3248699 4 1.19e-04 CGA TTTTCGCT GTGGCGCCGC chrIII:1601581-1601661 17 1.64e-04 CAGGGACCTA TTTTTCCA AAAGCGAGGT chrX:12843659-12843739 10 1.94e-04 ACGCGCATC TTTTCGCA CTTTACTCAG chrV:1821464-1821544 3 1.94e-04 CG TTTTCGCA ATCTGCGCAC chrIII:8971807-8971887 50 2.39e-04 GCCACCTCAA TTTTTGGT TTTTATTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:16863627-16863707 1.5e-05 66_[+2]_6 chrX:14115646-14115726 1.5e-05 7_[+2]_65 chrV:7231023-7231103 1.5e-05 57_[+2]_15 chrIV:5038925-5039005 1.5e-05 71_[+2]_1 chrIV:1687368-1687448 1.5e-05 1_[+2]_71 chrI:9249382-9249462 1.5e-05 72_[+2] chrIII:3476310-3476390 4.5e-05 59_[+2]_13 chrI:5176402-5176482 6e-05 3_[+2]_69 chrIV:11928454-11928534 6e-05 4_[+2]_68 chrI:7094963-7095043 6e-05 6_[+2]_66 chrI:14721595-14721675 6e-05 68_[+2]_4 chrIV:4784984-4785064 6e-05 4_[+2]_68 chrII:11636761-11636841 6e-05 24_[+2]_48 chrV:20384814-20384894 6e-05 3_[+2]_69 chrII:10303876-10303956 7.5e-05 68_[+2]_4 chrV:11239330-11239410 7.5e-05 47_[+2]_25 chrI:4633644-4633724 7.5e-05 32_[+2]_40 chrV:19142855-19142935 7.5e-05 33_[+2]_39 chrII:7708751-7708831 7.5e-05 14_[+2]_58 chrV:14524367-14524447 7.5e-05 8_[+2]_64 chrI:3547037-3547117 7.5e-05 15_[+2]_57 chrV:1197451-1197531 0.0001 69_[+2]_3 chrIII:6116570-6116650 0.0001 48_[+2]_24 chrIII:11935971-11936051 0.0001 39_[+2]_33 chrX:15340796-15340876 0.0001 58_[+2]_14 chrX:13781649-13781729 0.0001 69_[+2]_3 chrIII:3499984-3500064 0.0001 5_[+2]_67 chrII:5341179-5341259 0.00012 22_[+2]_50 chrI:3248619-3248699 0.00012 3_[+2]_69 chrIII:1601581-1601661 0.00016 16_[+2]_56 chrX:12843659-12843739 0.00019 9_[+2]_63 chrV:1821464-1821544 0.00019 2_[+2]_70 chrIII:8971807-8971887 0.00024 49_[+2]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTTGYW width=8 seqs=33 chrIV:16863627-16863707 ( 67) TTTTTGTT 1 chrX:14115646-14115726 ( 8) TTTTTGTT 1 chrV:7231023-7231103 ( 58) TTTTTGTT 1 chrIV:5038925-5039005 ( 72) TTTTTGTT 1 chrIV:1687368-1687448 ( 2) TTTTTGTT 1 chrI:9249382-9249462 ( 73) TTTTTGTT 1 chrIII:3476310-3476390 ( 60) TTTTTGTA 1 chrI:5176402-5176482 ( 4) TTTTTCTT 1 chrIV:11928454-11928534 ( 5) TTTTTCTT 1 chrI:7094963-7095043 ( 7) TTTTTCTT 1 chrI:14721595-14721675 ( 69) TTTTTCTT 1 chrIV:4784984-4785064 ( 5) TTTTTCTT 1 chrII:11636761-11636841 ( 25) TTTTTCTT 1 chrV:20384814-20384894 ( 4) TTTTTCTT 1 chrII:10303876-10303956 ( 69) TTTTTGCA 1 chrV:11239330-11239410 ( 48) TTTTTGCA 1 chrI:4633644-4633724 ( 33) TTTTTGCA 1 chrV:19142855-19142935 ( 34) TTTTTGCA 1 chrII:7708751-7708831 ( 15) TTTTTGCA 1 chrV:14524367-14524447 ( 9) TTTTTGCA 1 chrI:3547037-3547117 ( 16) TTTTTGCA 1 chrV:1197451-1197531 ( 70) TTTTCGTT 1 chrIII:6116570-6116650 ( 49) TTTTTCCT 1 chrIII:11935971-11936051 ( 40) TTTTCGTT 1 chrX:15340796-15340876 ( 59) TTTTCGTT 1 chrX:13781649-13781729 ( 70) TTTTTCCT 1 chrIII:3499984-3500064 ( 6) TTTTCGTT 1 chrII:5341179-5341259 ( 23) TTTTCGCT 1 chrI:3248619-3248699 ( 4) TTTTCGCT 1 chrIII:1601581-1601661 ( 17) TTTTTCCA 1 chrX:12843659-12843739 ( 10) TTTTCGCA 1 chrV:1821464-1821544 ( 3) TTTTCGCA 1 chrIII:8971807-8971887 ( 50) TTTTTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.4541 E= 1.3e-002 -1169 -1169 -1169 201 -1169 -1169 -1169 201 -1169 -1169 -1169 201 -1169 -1169 -1169 201 -1169 -4 -1169 160 -1169 28 148 -1169 -1169 77 -304 113 40 -1169 -1169 142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 1.3e-002 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 0.242424 0.000000 0.757576 0.000000 0.303030 0.696970 0.000000 0.000000 0.424242 0.030303 0.545455 0.333333 0.000000 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTGYW MEME-2 regular expression -------------------------------------------------------------------------------- TTTT[TC][GC][TC][TA] -------------------------------------------------------------------------------- Time 10.26 secs. ******************************************************************************** ******************************************************************************** MOTIF CCACTAKA MEME-3 width = 8 sites = 15 llr = 156 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a::a:a pos.-specific C aa:a:::: probability G ::::::6: matrix T ::::a:4: bits 2.0 ****** * 1.8 ****** * 1.6 ****** * 1.4 ****** * Relative 1.2 ****** * Entropy 1.0 ******** (15.0 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCACTAGA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:9268958-9269038 24 1.56e-05 GAGAATCATA CCACTAGA CCACTCAGCC chrIII:1604723-1604803 33 1.56e-05 TAAATCCTAA CCACTAGA CCACAACGGA chrX:12367634-12367714 62 1.56e-05 CGAATCCTAA CCACTAGA CCACATGGGA chrIII:7642163-7642243 49 1.56e-05 TAAATCCTAA CCACTAGA CCACAACGGA chrX:10821342-10821422 39 1.56e-05 CGAATCCTAA CCACTAGA CCACATGGGA chrI:8530126-8530206 56 1.56e-05 TAAATCCTAA CCACTAGA CCACAACGGA chrIV:1388231-1388311 39 1.56e-05 CGAATCCTAA CCACTAGA CCACATGGGA chrIV:2639805-2639885 58 1.56e-05 CGAATCCTAA CCACTAGA CCACATAGGA chrX:16271301-16271381 49 1.56e-05 TAAATCCTAA CCACTAGA CCACAACGGA chrX:16604710-16604790 64 3.11e-05 CGGATACTCA CCACTATA CTACCGAGG chrIV:322628-322708 58 3.11e-05 cggatactca ccactata ctaccgaGGA chrV:15551824-15551904 29 3.11e-05 cggatactca ccactata ctaccgaGGA chrII:11535610-11535690 9 3.11e-05 TATCTGAC CCACTATA ATGAGGGGAC chrI:933476-933556 52 3.11e-05 CTGtggcttc ccactata ttttactctc chrX:5056378-5056458 51 3.11e-05 CTctggcttc ccactata ttttactctc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:9268958-9269038 1.6e-05 23_[+3]_49 chrIII:1604723-1604803 1.6e-05 32_[+3]_40 chrX:12367634-12367714 1.6e-05 61_[+3]_11 chrIII:7642163-7642243 1.6e-05 48_[+3]_24 chrX:10821342-10821422 1.6e-05 38_[+3]_34 chrI:8530126-8530206 1.6e-05 55_[+3]_17 chrIV:1388231-1388311 1.6e-05 38_[+3]_34 chrIV:2639805-2639885 1.6e-05 57_[+3]_15 chrX:16271301-16271381 1.6e-05 48_[+3]_24 chrX:16604710-16604790 3.1e-05 63_[+3]_9 chrIV:322628-322708 3.1e-05 57_[+3]_15 chrV:15551824-15551904 3.1e-05 28_[+3]_44 chrII:11535610-11535690 3.1e-05 8_[+3]_64 chrI:933476-933556 3.1e-05 51_[+3]_21 chrX:5056378-5056458 3.1e-05 50_[+3]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCACTAKA width=8 seqs=15 chrI:9268958-9269038 ( 24) CCACTAGA 1 chrIII:1604723-1604803 ( 33) CCACTAGA 1 chrX:12367634-12367714 ( 62) CCACTAGA 1 chrIII:7642163-7642243 ( 49) CCACTAGA 1 chrX:10821342-10821422 ( 39) CCACTAGA 1 chrI:8530126-8530206 ( 56) CCACTAGA 1 chrIV:1388231-1388311 ( 39) CCACTAGA 1 chrIV:2639805-2639885 ( 58) CCACTAGA 1 chrX:16271301-16271381 ( 49) CCACTAGA 1 chrX:16604710-16604790 ( 64) CCACTATA 1 chrIV:322628-322708 ( 58) CCACTATA 1 chrV:15551824-15551904 ( 29) CCACTATA 1 chrII:11535610-11535690 ( 9) CCACTATA 1 chrI:933476-933556 ( 52) CCACTATA 1 chrX:5056378-5056458 ( 51) CCACTATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.1725 E= 1.4e-001 -1055 201 -1055 -1055 -1055 201 -1055 -1055 198 -1055 -1055 -1055 -1055 201 -1055 -1055 -1055 -1055 -1055 200 198 -1055 -1055 -1055 -1055 -1055 127 68 198 -1055 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 1.4e-001 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACTAKA MEME-3 regular expression -------------------------------------------------------------------------------- CCACTA[GT]A -------------------------------------------------------------------------------- Time 13.86 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGTGTGY MEME-4 width = 8 sites = 18 llr = 169 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 2::::::4 probability G 8:a:8:a: matrix T :a:a2a:6 bits 2.0 *** ** 1.8 *** ** 1.6 *** ** 1.4 *** ** Relative 1.2 ******* Entropy 1.0 ******** (13.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GTGTGTGT consensus C T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:4130441-4130521 15 1.50e-05 gtgtgtgtgt gtgtgtgt TGTCCCATCA chrIII:6133434-6133514 34 1.50e-05 CCCCgtgtgt gtgtgtgt gtgtgtgtgt chrX:12407400-12407480 62 1.50e-05 gagtatgtgt gtgtgtgt atgtgtgtgt chrII:4130238-4130318 34 1.50e-05 AATtgtgtgt gtgtgtgt gtgtgtgtgt chrV:14689472-14689552 29 1.50e-05 CTTCAGTTTT GTGTGTGT CAGCGGCATC chrIII:445726-445806 38 1.50e-05 gtgtgtgtgt gtgtgtgt gtgtgtAGGT chrI:3567651-3567731 35 1.50e-05 gtgtgtgtgt gtgtgtgt gtgtgtgtgt chrII:6913473-6913553 39 3.00e-05 TTTCTAGGCC GTGTGTGC CGCAAATTGG chrIII:3916772-3916852 34 3.00e-05 AAAACCTAAA GTGTGTGC GGCGACTTTG chrI:4633644-4633724 45 3.00e-05 TTTGCATAAA GTGTGTGC CAGGGTTGCA chrIV:4399544-4399624 15 3.00e-05 GGTGGTGTCT GTGTGTGC GCACCGTCCC chrI:9855609-9855689 7 5.99e-05 GCCTGA CTGTGTGT CCTTGCCAGC chrX:8156139-8156219 16 5.99e-05 GTTGTATAGG CTGTGTGT TCTCCTATTA chrII:4942479-4942559 31 8.99e-05 TCTCGACTTT CTGTGTGC ATTGAGAATC chrIII:8768067-8768147 23 8.99e-05 ACTGTGCGGC GTGTTTGC GGAAATCGCG chrI:5164989-5165069 14 8.99e-05 ATTGCGCGCC GTGTTTGC ACCATGGCCT chrIII:1616370-1616450 22 8.99e-05 AAAAACTGcg gtgtttgc gtacttttga chrX:15340796-15340876 68 1.05e-04 ATTTTCGTTA CTGTTTGT TAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:4130441-4130521 1.5e-05 14_[+4]_58 chrIII:6133434-6133514 1.5e-05 33_[+4]_39 chrX:12407400-12407480 1.5e-05 61_[+4]_11 chrII:4130238-4130318 1.5e-05 33_[+4]_39 chrV:14689472-14689552 1.5e-05 28_[+4]_44 chrIII:445726-445806 1.5e-05 37_[+4]_35 chrI:3567651-3567731 1.5e-05 34_[+4]_38 chrII:6913473-6913553 3e-05 38_[+4]_34 chrIII:3916772-3916852 3e-05 33_[+4]_39 chrI:4633644-4633724 3e-05 44_[+4]_28 chrIV:4399544-4399624 3e-05 14_[+4]_58 chrI:9855609-9855689 6e-05 6_[+4]_66 chrX:8156139-8156219 6e-05 15_[+4]_57 chrII:4942479-4942559 9e-05 30_[+4]_42 chrIII:8768067-8768147 9e-05 22_[+4]_50 chrI:5164989-5165069 9e-05 13_[+4]_59 chrIII:1616370-1616450 9e-05 21_[+4]_51 chrX:15340796-15340876 0.0001 67_[+4]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGTGTGY width=8 seqs=18 chrII:4130441-4130521 ( 15) GTGTGTGT 1 chrIII:6133434-6133514 ( 34) GTGTGTGT 1 chrX:12407400-12407480 ( 62) GTGTGTGT 1 chrII:4130238-4130318 ( 34) GTGTGTGT 1 chrV:14689472-14689552 ( 29) GTGTGTGT 1 chrIII:445726-445806 ( 38) GTGTGTGT 1 chrI:3567651-3567731 ( 35) GTGTGTGT 1 chrII:6913473-6913553 ( 39) GTGTGTGC 1 chrIII:3916772-3916852 ( 34) GTGTGTGC 1 chrI:4633644-4633724 ( 45) GTGTGTGC 1 chrIV:4399544-4399624 ( 15) GTGTGTGC 1 chrI:9855609-9855689 ( 7) CTGTGTGT 1 chrX:8156139-8156219 ( 16) CTGTGTGT 1 chrII:4942479-4942559 ( 31) CTGTGTGC 1 chrIII:8768067-8768147 ( 23) GTGTTTGC 1 chrI:5164989-5165069 ( 14) GTGTTTGC 1 chrIII:1616370-1616450 ( 22) GTGTTTGC 1 chrX:15340796-15340876 ( 68) CTGTTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.7767 E= 1.5e+003 -1081 -16 164 -1081 -1081 -1081 -1081 200 -1081 -1081 200 -1081 -1081 -1081 -1081 200 -1081 -1081 164 -16 -1081 -1081 -1081 200 -1081 -1081 200 -1081 -1081 84 -1081 116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 1.5e+003 0.000000 0.222222 0.777778 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.444444 0.000000 0.555556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGTGTGY MEME-4 regular expression -------------------------------------------------------------------------------- [GC]TGT[GT]TG[TC] -------------------------------------------------------------------------------- Time 17.45 secs. ******************************************************************************** ******************************************************************************** MOTIF AGTGGTTA MEME-5 width = 8 sites = 15 llr = 155 E-value = 2.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::::::a pos.-specific C ::1::1:: probability G :a:aa::: matrix T ::9::9a: bits 2.0 ** ** ** 1.8 ** ** ** 1.6 ** ** ** 1.4 ******** Relative 1.2 ******** Entropy 1.0 ******** (14.9 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AGTGGTTA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:8646456-8646536 37 1.54e-05 CATGTGGTCT AGTGGTTA GGATTCGTGG chrII:5293409-5293489 56 1.54e-05 GTTGTGGTCT AGTGGTTA GGATTTATGG chrIV:620455-620535 40 1.54e-05 CCTCTGGTGT AGTGGTTA TCACGTCTGC chrIV:16388456-16388536 13 1.54e-05 TGCGTAGTAT AGTGGTTA GTACTCCACG chrX:12843659-12843739 42 1.54e-05 CTCGTGGTGT AGTGGTTA TCACATCTGT chrV:53452-53532 37 1.54e-05 cgcatggccg agtggtta gtacgtatgc chrX:4444219-4444299 56 1.54e-05 CATGTGGTCT AGTGGTTA GGATTCGTGG chrX:8971606-8971686 7 1.54e-05 TGTCCG AGTGGTTA AGGAGATTGA chrI:9605761-9605841 8 1.54e-05 ATGTCCG AGTGGTTA AGGAGTTGGA chrI:11978761-11978841 16 1.54e-05 GTTGTGGTCT AGTGGTTA GGATTTATGG chrV:15554009-15554089 34 1.54e-05 TGCTTAGTAT AGTGGTTA GTACTCCACG chrX:8925620-8925700 34 4.63e-05 TCCATGGTGT AGCGGTTA GCACTCATGA chrI:4175890-4175970 45 4.63e-05 GTAGTGGTCT AGTGGCTA GCAGGCACAC chrI:11609205-11609285 41 4.63e-05 ACCGTGGCCT AGTGGCTA GTAACACAGG chrIV:5334685-5334765 40 4.63e-05 TCCATGGTGT AGCGGTTA GCACTCAGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:8646456-8646536 1.5e-05 36_[+5]_36 chrII:5293409-5293489 1.5e-05 55_[+5]_17 chrIV:620455-620535 1.5e-05 39_[+5]_33 chrIV:16388456-16388536 1.5e-05 12_[+5]_60 chrX:12843659-12843739 1.5e-05 41_[+5]_31 chrV:53452-53532 1.5e-05 36_[+5]_36 chrX:4444219-4444299 1.5e-05 55_[+5]_17 chrX:8971606-8971686 1.5e-05 6_[+5]_66 chrI:9605761-9605841 1.5e-05 7_[+5]_65 chrI:11978761-11978841 1.5e-05 15_[+5]_57 chrV:15554009-15554089 1.5e-05 33_[+5]_39 chrX:8925620-8925700 4.6e-05 33_[+5]_39 chrI:4175890-4175970 4.6e-05 44_[+5]_28 chrI:11609205-11609285 4.6e-05 40_[+5]_32 chrIV:5334685-5334765 4.6e-05 39_[+5]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGTGGTTA width=8 seqs=15 chrX:8646456-8646536 ( 37) AGTGGTTA 1 chrII:5293409-5293489 ( 56) AGTGGTTA 1 chrIV:620455-620535 ( 40) AGTGGTTA 1 chrIV:16388456-16388536 ( 13) AGTGGTTA 1 chrX:12843659-12843739 ( 42) AGTGGTTA 1 chrV:53452-53532 ( 37) AGTGGTTA 1 chrX:4444219-4444299 ( 56) AGTGGTTA 1 chrX:8971606-8971686 ( 7) AGTGGTTA 1 chrI:9605761-9605841 ( 8) AGTGGTTA 1 chrI:11978761-11978841 ( 16) AGTGGTTA 1 chrV:15554009-15554089 ( 34) AGTGGTTA 1 chrX:8925620-8925700 ( 34) AGCGGTTA 1 chrI:4175890-4175970 ( 45) AGTGGCTA 1 chrI:11609205-11609285 ( 41) AGTGGCTA 1 chrIV:5334685-5334765 ( 40) AGCGGTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.1725 E= 2.3e-001 198 -1055 -1055 -1055 -1055 -1055 200 -1055 -1055 -90 -1055 180 -1055 -1055 200 -1055 -1055 -1055 200 -1055 -1055 -90 -1055 180 -1055 -1055 -1055 200 198 -1055 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 2.3e-001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.133333 0.000000 0.866667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.133333 0.000000 0.866667 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGGTTA MEME-5 regular expression -------------------------------------------------------------------------------- AGTGGTTA -------------------------------------------------------------------------------- Time 20.88 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:3567651-3567731 6.45e-03 2_[+4(1.50e-05)]_[+4(1.50e-05)]_\ [+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_30 chrV:265487-265567 8.75e-01 80 chrI:3248619-3248699 1.81e-01 80 chrX:16944106-16944186 9.26e-01 80 chrV:13646102-13646182 9.75e-01 80 chrV:265691-265771 1.79e-01 80 chrII:2570543-2570623 9.57e-01 80 chrII:2570753-2570833 9.68e-01 80 chrX:5056378-5056458 7.30e-02 50_[+3(3.11e-05)]_22 chrIII:3499984-3500064 6.06e-02 80 chrV:5284424-5284504 4.26e-01 80 chrIII:445726-445806 6.43e-02 1_[+4(1.50e-05)]_[+4(1.50e-05)]_\ [+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_31 chrX:8156139-8156219 1.49e-01 15_[+4(5.99e-05)]_57 chrII:11974827-11974907 4.80e-01 80 chrI:3547037-3547117 6.29e-02 15_[+2(7.46e-05)]_57 chrX:15668389-15668469 7.54e-01 80 chrV:20384814-20384894 2.79e-01 3_[+2(5.95e-05)]_69 chrV:14689472-14689552 8.19e-03 28_[+4(1.50e-05)]_44 chrIII:931568-931648 9.56e-01 80 chrIV:4399544-4399624 1.63e-01 14_[+4(3.00e-05)]_58 chrV:5284761-5284841 4.26e-01 80 chrI:7535475-7535555 1.00e-01 80 chrI:933476-933556 7.30e-02 51_[+3(3.11e-05)]_21 chrIII:13225182-13225262 5.93e-01 80 chrV:19722988-19723068 9.90e-01 80 chrIII:1327080-1327160 8.59e-01 80 chrV:16699814-16699894 7.51e-01 80 chrX:16602608-16602688 1.81e-02 80 chrV:1821464-1821544 2.49e-01 80 chrI:3564608-3564688 6.98e-01 80 chrIII:1616370-1616450 8.88e-02 21_[+4(8.99e-05)]_51 chrX:3969503-3969583 7.47e-01 80 chrX:8638893-8638973 4.73e-01 80 chrI:3075084-3075164 4.30e-01 80 chrV:11345093-11345173 6.95e-01 80 chrI:9249382-9249462 6.81e-02 72_[+2(1.48e-05)] chrX:16551459-16551539 6.62e-01 80 chrIII:8650360-8650440 9.70e-02 35_[+1(1.53e-05)]_37 chrII:4130238-4130318 1.24e-01 27_[+4(1.50e-05)]_[+4(1.50e-05)]_\ [+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_5 chrII:11636761-11636841 1.31e-01 18_[+2(5.95e-05)]_54 chrV:13868888-13868968 1.00e+00 80 chrIII:4626321-4626401 1.00e+00 80 chrX:13415136-13415216 8.67e-01 80 chrX:12407400-12407480 9.02e-02 57_[+4(1.50e-05)]_6_[+4(1.50e-05)]_\ 1 chrIV:1687368-1687448 7.60e-02 1_[+2(1.48e-05)]_71 chrX:3994561-3994641 8.63e-01 80 chrX:8602859-8602939 1.00e+00 80 chrIII:8806376-8806456 4.67e-01 80 chrIII:6133434-6133514 1.08e-02 27_[+4(1.50e-05)]_[+4(1.50e-05)]_\ [+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_[+4(1.50e-05)]_5 chrIII:5769872-5769952 4.17e-01 80 chrIV:4784984-4785064 2.13e-01 4_[+2(5.95e-05)]_68 chrII:15218054-15218134 5.91e-01 80 chrIII:3664401-3664481 4.81e-01 80 chrV:15554009-15554089 1.24e-01 33_[+5(1.54e-05)]_39 chrIII:11093617-11093697 9.31e-01 80 chrV:20061584-20061664 5.81e-02 2_[+1(1.53e-05)]_70 chrI:3531525-3531605 1.66e-01 80 chrIII:13160809-13160889 9.70e-01 80 chrIV:5334685-5334765 5.22e-02 39_[+5(4.63e-05)]_33 chrV:12510029-12510109 1.00e+00 80 chrII:4130441-4130521 3.00e-02 [+4(1.50e-05)]_[+4(1.50e-05)]_64 chrX:8818121-8818201 3.73e-01 80 chrII:7001599-7001679 5.52e-01 80 chrIII:12613639-12613719 9.06e-01 80 chrV:7745976-7746056 4.57e-01 80 chrII:4238045-4238125 9.60e-01 80 chrIII:1122411-1122491 7.65e-01 80 chrIII:12399828-12399908 9.10e-01 80 chrX:3914460-3914540 1.46e-01 80 chrV:19430713-19430793 9.79e-01 80 chrII:11884394-11884474 6.48e-01 80 chrI:11585403-11585483 9.29e-01 80 chrIV:5038925-5039005 5.91e-04 71_[+2(1.48e-05)]_1 chrII:5341179-5341259 3.09e-01 80 chrV:2674008-2674088 1.25e-01 80 chrV:16553106-16553186 1.34e-01 28_[+2(7.46e-05)]_7_[+2(7.46e-05)]_\ 29 chrV:7231023-7231103 1.15e-02 57_[+2(1.48e-05)]_3_[+2(5.95e-05)]_\ 4 chrX:8944248-8944328 3.16e-02 80 chrIII:3175127-3175207 4.28e-01 80 chrIII:8653080-8653160 2.00e-01 80 chrV:3587802-3587882 5.98e-01 80 chrX:2216729-2216809 5.44e-01 80 chrIV:842833-842913 1.01e-02 80 chrV:15505239-15505319 5.49e-01 80 chrV:14524367-14524447 2.02e-02 8_[+2(7.46e-05)]_64 chrII:8325293-8325373 8.25e-01 80 chrI:9855609-9855689 7.11e-02 6_[+4(5.99e-05)]_66 chrIII:6805574-6805654 2.68e-02 47_[+1(6.08e-05)]_25 chrIII:8529248-8529328 8.03e-01 80 chrX:12890296-12890376 1.55e-01 3_[+1(7.62e-05)]_69 chrV:8039156-8039236 2.80e-01 80 chrX:9296778-9296858 2.71e-01 80 chrV:4510460-4510540 9.99e-01 80 chrI:13422032-13422112 8.68e-01 80 chrI:14614779-14614859 3.34e-01 80 chrV:4647997-4648077 9.93e-01 80 chrI:3873907-3873987 3.80e-01 80 chrI:11978761-11978841 5.20e-03 15_[+5(1.54e-05)]_57 chrX:13781649-13781729 6.44e-04 44_[+1(6.08e-05)]_28 chrIII:3620855-3620935 6.47e-01 80 chrX:15307727-15307807 9.86e-01 80 chrI:14708055-14708135 9.50e-01 80 chrI:9605761-9605841 1.42e-03 7_[+5(1.54e-05)]_42_[+1(1.53e-05)]_\ 15 chrX:6252342-6252422 6.11e-01 80 chrV:9088888-9088968 8.83e-01 80 chrI:11266666-11266746 9.87e-01 80 chrV:20424422-20424502 6.28e-01 80 chrV:14855774-14855854 2.22e-01 80 chrIV:13549510-13549590 3.13e-01 80 chrX:17416729-17416809 5.99e-01 80 chrII:10304893-10304973 8.15e-01 80 chrI:11609205-11609285 6.97e-02 40_[+5(4.63e-05)]_32 chrIII:13032766-13032846 9.94e-01 80 chrX:15340796-15340876 2.31e-02 80 chrIII:3812625-3812705 5.27e-01 80 chrII:7708751-7708831 2.17e-02 14_[+2(7.46e-05)]_58 chrII:3567793-3567873 9.58e-01 80 chrIII:11935971-11936051 1.92e-01 80 chrV:19142855-19142935 7.84e-02 9_[+2(7.46e-05)]_16_[+2(7.46e-05)]_\ 39 chrV:16022761-16022841 8.66e-01 80 chrI:7543698-7543778 7.75e-01 80 chrV:19622289-19622369 6.99e-01 80 chrIII:7030577-7030657 2.98e-01 80 chrX:5407389-5407469 7.23e-01 80 chrX:16271301-16271381 1.01e-03 9_[+1(1.53e-05)]_31_[+3(1.56e-05)]_\ 24 chrI:4633644-4633724 5.30e-03 32_[+2(7.46e-05)]_4_[+4(3.00e-05)]_\ 28 chrX:13730767-13730847 1.74e-02 64_[+1(6.08e-05)]_8 chrX:9373124-9373204 1.99e-02 80 chrIV:14225032-14225112 4.01e-01 80 chrIV:3874590-3874670 9.88e-01 80 chrII:11535610-11535690 6.12e-02 8_[+3(3.11e-05)]_64 chrIV:2639805-2639885 9.07e-03 57_[+3(1.56e-05)]_15 chrIV:1056616-1056696 4.45e-01 80 chrIII:1601581-1601661 5.86e-03 80 chrIII:10432276-10432356 5.62e-02 80 chrIV:16776050-16776130 4.95e-01 80 chrI:4175890-4175970 1.33e-01 44_[+5(4.63e-05)]_28 chrV:5576228-5576308 7.42e-01 80 chrIII:3916772-3916852 1.16e-01 33_[+4(3.00e-05)]_39 chrII:14635374-14635454 7.48e-01 80 chrIII:535389-535469 7.16e-02 57_[+1(3.06e-05)]_15 chrIII:1824689-1824769 9.28e-01 80 chrX:14115646-14115726 1.76e-02 7_[+2(1.48e-05)]_65 chrX:2043409-2043489 9.75e-01 80 chrIII:3476310-3476390 5.76e-02 59_[+2(4.47e-05)]_13 chrII:5836519-5836599 6.61e-01 80 chrIV:1388231-1388311 1.40e-02 38_[+3(1.56e-05)]_34 chrI:8530126-8530206 9.07e-04 16_[+1(1.53e-05)]_31_[+3(1.56e-05)]_\ 17 chrI:6136587-6136667 1.74e-02 63_[+1(6.08e-05)]_9 chrV:12353451-12353531 7.00e-01 80 chrX:10821342-10821422 1.23e-02 38_[+3(1.56e-05)]_34 chrII:11959408-11959488 4.59e-02 20_[+1(6.08e-05)]_52 chrIV:3399222-3399302 6.63e-01 80 chrX:10900199-10900279 2.98e-01 80 chrIII:8971807-8971887 6.09e-02 80 chrIII:12599120-12599200 4.09e-01 80 chrX:8971606-8971686 9.64e-04 6_[+5(1.54e-05)]_42_[+1(3.06e-05)]_\ 16 chrV:13176511-13176591 6.87e-01 80 chrI:6135835-6135915 7.16e-02 59_[+1(3.06e-05)]_13 chrIII:6116570-6116650 2.02e-01 80 chrI:10807264-10807344 9.11e-01 80 chrIII:6133636-6133716 9.76e-01 80 chrI:4367905-4367985 7.95e-01 80 chrI:7195044-7195124 6.91e-01 80 chrX:4444219-4444299 5.94e-02 55_[+5(1.54e-05)]_17 chrII:3439327-3439407 9.08e-01 80 chrIV:2802361-2802441 4.45e-01 80 chrI:13495259-13495339 9.93e-01 80 chrX:16928276-16928356 2.68e-02 9_[+1(1.53e-05)]_63 chrIV:8334385-8334465 9.79e-01 80 chrIII:7642163-7642243 2.47e-04 9_[+1(1.53e-05)]_31_[+3(1.56e-05)]_\ 24 chrV:11239330-11239410 1.11e-01 47_[+2(7.46e-05)]_25 chrII:6721727-6721807 8.35e-01 80 chrV:53452-53532 2.44e-02 36_[+5(1.54e-05)]_36 chrI:11505520-11505600 5.54e-01 80 chrIV:16399172-16399252 7.54e-01 80 chrIII:11091838-11091918 3.28e-01 80 chrX:8925620-8925700 7.65e-03 33_[+5(4.63e-05)]_39 chrIV:14032702-14032782 8.91e-01 80 chrIII:1218372-1218452 7.46e-01 80 chrV:4731537-4731617 2.61e-01 80 chrI:6091104-6091184 3.38e-01 80 chrX:9078316-9078396 9.09e-01 80 chrI:12225444-12225524 5.59e-01 80 chrIII:7659569-7659649 3.16e-01 80 chrX:14804920-14805000 9.38e-02 80 chrX:12367634-12367714 5.56e-04 22_[+1(1.53e-05)]_31_[+3(1.56e-05)]_\ 11 chrIV:16946911-16946991 9.31e-01 80 chrIII:1604723-1604803 7.83e-02 32_[+3(1.56e-05)]_40 chrV:14876381-14876461 7.82e-01 80 chrX:12452276-12452356 9.50e-01 80 chrI:5164989-5165069 5.36e-02 13_[+4(8.99e-05)]_59 chrI:6532054-6532134 2.50e-01 80 chrX:10555614-10555694 7.75e-01 80 chrI:14721595-14721675 1.96e-01 68_[+2(5.95e-05)]_4 chrX:1837885-1837965 9.90e-01 80 chrV:7465716-7465796 8.42e-01 80 chrX:12843659-12843739 3.91e-03 41_[+5(1.54e-05)]_31 chrI:6252940-6253020 4.84e-01 80 chrV:12780412-12780492 7.54e-01 80 chrIV:16388456-16388536 7.24e-03 12_[+5(1.54e-05)]_60 chrI:1575687-1575767 4.81e-01 80 chrV:13962170-13962250 7.47e-01 80 chrIII:8768067-8768147 1.40e-01 22_[+4(8.99e-05)]_50 chrII:10303876-10303956 4.61e-02 68_[+2(7.46e-05)]_4 chrI:7094963-7095043 9.81e-02 6_[+2(5.95e-05)]_66 chrX:5319378-5319458 8.32e-01 80 chrV:20694104-20694184 2.22e-01 80 chrIV:16382342-16382422 9.15e-01 80 chrV:15551824-15551904 8.88e-03 28_[+3(3.11e-05)]_44 chrX:8386132-8386212 5.74e-01 80 chrIV:9191310-9191390 6.33e-01 80 chrIV:620455-620535 1.57e-02 39_[+5(1.54e-05)]_33 chrX:6867883-6867963 8.69e-02 80 chrV:1197451-1197531 1.95e-01 80 chrIV:322628-322708 4.59e-03 18_[+1(7.62e-05)]_31_[+3(3.11e-05)]_\ 15 chrI:9268958-9269038 1.10e-02 23_[+3(1.56e-05)]_49 chrII:6383312-6383392 4.48e-01 80 chrX:6903078-6903158 1.96e-02 50_[+1(1.53e-05)]_22 chrX:3348003-3348083 9.59e-02 80 chrIV:11310776-11310856 9.73e-01 80 chrIII:13721279-13721359 9.50e-01 80 chrI:13310318-13310398 8.56e-01 80 chrII:6913473-6913553 7.04e-02 38_[+4(3.00e-05)]_34 chrIV:16863627-16863707 3.48e-02 66_[+2(1.48e-05)]_6 chrIV:13980268-13980348 9.38e-01 80 chrI:13470412-13470492 9.26e-01 80 chrIV:1981109-1981189 1.68e-01 80 chrX:8608839-8608919 1.17e-01 80 chrIII:7199004-7199084 1.39e-01 80 chrIII:2576851-2576931 8.27e-01 80 chrIII:11236917-11236997 8.84e-01 80 chrI:10927483-10927563 2.58e-01 80 chrIII:3786658-3786738 3.73e-01 80 chrV:8631472-8631552 9.99e-01 80 chrIII:9104254-9104334 7.66e-01 80 chrV:9583067-9583147 4.24e-01 80 chrI:1175835-1175915 6.55e-01 80 chrIV:11928454-11928534 1.68e-03 4_[+2(5.95e-05)]_26_[+1(1.53e-05)]_\ 34 chrII:5293409-5293489 1.69e-02 55_[+5(1.54e-05)]_17 chrI:5176402-5176482 6.92e-02 3_[+2(5.95e-05)]_69 chrIII:4378729-4378809 6.01e-01 80 chrX:8646456-8646536 2.68e-02 36_[+5(1.54e-05)]_36 chrX:10145160-10145240 2.87e-02 49_[+1(3.06e-05)]_23 chrX:6219950-6220030 5.78e-01 80 chrII:4942479-4942559 8.49e-02 30_[+4(8.99e-05)]_42 chrX:16604710-16604790 4.59e-03 24_[+1(7.62e-05)]_31_[+3(3.11e-05)]_\ 9 chrI:3265989-3266069 6.07e-01 80 chrV:13041788-13041868 3.74e-01 80 chrX:13264714-13264794 9.65e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************