******************************************************************************** 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/madf-10.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:16299993-16300073 1.0000 80 chrV:10857060-10857140 1.0000 80 chrX:16409423-16409503 1.0000 80 chrV:6350281-6350361 1.0000 80 chrII:6843907-6843987 1.0000 80 chrIV:8758802-8758882 1.0000 80 chrIII:3619733-3619813 1.0000 80 chrIV:8757870-8757950 1.0000 80 chrV:6230837-6230917 1.0000 80 chrX:6533218-6533298 1.0000 80 chrI:12520508-12520588 1.0000 80 chrI:10437978-10438058 1.0000 80 chrIII:13625804-13625884 1.0000 80 chrX:16297268-16297348 1.0000 80 chrIII:11203094-11203174 1.0000 80 chrII:8784688-8784768 1.0000 80 chrIV:13877820-13877900 1.0000 80 chrIV:8266521-8266601 1.0000 80 chrIV:1739512-1739592 1.0000 80 chrV:20785535-20785615 1.0000 80 chrV:3634722-3634802 1.0000 80 chrX:5816466-5816546 1.0000 80 chrV:12004722-12004802 1.0000 80 chrV:6228587-6228667 1.0000 80 chrII:9285089-9285169 1.0000 80 chrIII:2535387-2535467 1.0000 80 chrI:10435821-10435901 1.0000 80 chrX:4147711-4147791 1.0000 80 chrX:6792808-6792888 1.0000 80 chrX:12904462-12904542 1.0000 80 chrIV:8762575-8762655 1.0000 80 chrIV:1915702-1915782 1.0000 80 chrII:10744984-10745064 1.0000 80 chrX:3408700-3408780 1.0000 80 chrX:15355830-15355910 1.0000 80 chrV:20779966-20780046 1.0000 80 chrV:20776933-20777013 1.0000 80 chrIV:2111604-2111684 1.0000 80 chrI:5378674-5378754 1.0000 80 chrX:6088932-6089012 1.0000 80 chrM:5257-5337 1.0000 80 chrV:12819259-12819339 1.0000 80 chrV:20782385-20782465 1.0000 80 chrV:7433021-7433101 1.0000 80 chrI:10446518-10446598 1.0000 80 chrV:10857264-10857344 1.0000 80 chrI:14940059-14940139 1.0000 80 chrIV:2998730-2998810 1.0000 80 chrX:11473206-11473286 1.0000 80 chrV:20163037-20163117 1.0000 80 chrV:20789232-20789312 1.0000 80 chrX:17434436-17434516 1.0000 80 chrIV:12689858-12689938 1.0000 80 chrM:1821-1901 1.0000 80 chrX:14783615-14783695 1.0000 80 chrIV:14822412-14822492 1.0000 80 chrIV:2709787-2709867 1.0000 80 chrX:12656825-12656905 1.0000 80 chrI:881585-881665 1.0000 80 chrII:12994267-12994347 1.0000 80 chrX:7681000-7681080 1.0000 80 chrIII:9060425-9060505 1.0000 80 chrX:7200578-7200658 1.0000 80 chrIV:10511618-10511698 1.0000 80 chrIV:296000-296080 1.0000 80 chrIV:2998930-2999010 1.0000 80 chrIII:11185678-11185758 1.0000 80 chrI:754679-754759 1.0000 80 chrX:4617039-4617119 1.0000 80 chrIV:15702098-15702178 1.0000 80 chrX:4007807-4007887 1.0000 80 chrX:12205619-12205699 1.0000 80 chrII:6943853-6943933 1.0000 80 chrM:3305-3385 1.0000 80 chrX:6609220-6609300 1.0000 80 chrIII:5196565-5196645 1.0000 80 chrI:6499632-6499712 1.0000 80 chrV:2308393-2308473 1.0000 80 chrV:20164670-20164750 1.0000 80 chrII:11731310-11731390 1.0000 80 chrI:14657250-14657330 1.0000 80 chrX:15842638-15842718 1.0000 80 chrV:9338674-9338754 1.0000 80 chrV:3697201-3697281 1.0000 80 chrIV:8261151-8261231 1.0000 80 chrV:20413579-20413659 1.0000 80 chrI:9671944-9672024 1.0000 80 chrX:16192701-16192781 1.0000 80 chrV:10802262-10802342 1.0000 80 chrX:11872296-11872376 1.0000 80 chrI:7660150-7660230 1.0000 80 chrIV:5654268-5654348 1.0000 80 chrV:6220977-6221057 1.0000 80 chrM:1532-1612 1.0000 80 chrIV:6555103-6555183 1.0000 80 chrV:6231038-6231118 1.0000 80 chrIV:12601142-12601222 1.0000 80 chrIV:4450049-4450129 1.0000 80 chrIV:15933229-15933309 1.0000 80 chrIV:13880928-13881008 1.0000 80 chrI:4597685-4597765 1.0000 80 chrV:20771027-20771107 1.0000 80 chrV:6243424-6243504 1.0000 80 chrV:16338626-16338706 1.0000 80 chrX:16617884-16617964 1.0000 80 chrV:8651490-8651570 1.0000 80 chrX:2569200-2569280 1.0000 80 chrIV:2993531-2993611 1.0000 80 chrX:8381817-8381897 1.0000 80 chrIII:5550994-5551074 1.0000 80 chrX:8939558-8939638 1.0000 80 chrX:10124488-10124568 1.0000 80 chrX:11473407-11473487 1.0000 80 chrV:2872301-2872381 1.0000 80 chrX:16554183-16554263 1.0000 80 chrI:1049236-1049316 1.0000 80 chrX:3567043-3567123 1.0000 80 chrII:12878882-12878962 1.0000 80 chrX:11792892-11792972 1.0000 80 chrV:3455294-3455374 1.0000 80 chrIV:13980259-13980339 1.0000 80 chrIII:12614765-12614845 1.0000 80 chrV:6251297-6251377 1.0000 80 chrI:7602332-7602412 1.0000 80 chrI:5377529-5377609 1.0000 80 chrII:9501073-9501153 1.0000 80 chrIII:13066975-13067055 1.0000 80 chrX:6533445-6533525 1.0000 80 chrII:13669005-13669085 1.0000 80 chrX:14539657-14539737 1.0000 80 chrIII:5762085-5762165 1.0000 80 chrV:19049467-19049547 1.0000 80 chrIV:12834103-12834183 1.0000 80 chrX:13782189-13782269 1.0000 80 chrV:3644425-3644505 1.0000 80 chrX:16024762-16024842 1.0000 80 chrIV:2990664-2990744 1.0000 80 chrIV:13701622-13701702 1.0000 80 chrX:13420124-13420204 1.0000 80 chrV:1132471-1132551 1.0000 80 chrX:16300585-16300665 1.0000 80 chrI:2996086-2996166 1.0000 80 chrV:6614502-6614582 1.0000 80 chrX:13261208-13261288 1.0000 80 chrII:9934055-9934135 1.0000 80 chrII:11151068-11151148 1.0000 80 chrX:6536876-6536956 1.0000 80 chrIII:8639266-8639346 1.0000 80 chrV:16595480-16595560 1.0000 80 chrX:8440255-8440335 1.0000 80 chrIII:5937109-5937189 1.0000 80 chrX:14792924-14793004 1.0000 80 chrX:14127419-14127499 1.0000 80 chrII:8933876-8933956 1.0000 80 chrX:4453244-4453324 1.0000 80 chrX:11472143-11472223 1.0000 80 chrX:5106262-5106342 1.0000 80 chrIV:13919386-13919466 1.0000 80 chrII:7554997-7555077 1.0000 80 chrIII:5557329-5557409 1.0000 80 chrIV:9718560-9718640 1.0000 80 chrI:6745569-6745649 1.0000 80 chrV:11976861-11976941 1.0000 80 chrIV:13725355-13725435 1.0000 80 chrV:15298775-15298855 1.0000 80 chrII:13780886-13780966 1.0000 80 chrII:3062327-3062407 1.0000 80 chrIII:4018201-4018281 1.0000 80 chrV:20412330-20412410 1.0000 80 chrX:14438004-14438084 1.0000 80 chrV:20497729-20497809 1.0000 80 chrX:3290276-3290356 1.0000 80 chrIV:7402240-7402320 1.0000 80 chrI:3113754-3113834 1.0000 80 chrIII:2716422-2716502 1.0000 80 chrX:15146526-15146606 1.0000 80 chrII:5202062-5202142 1.0000 80 chrX:13714845-13714925 1.0000 80 chrV:6335406-6335486 1.0000 80 chrX:1445773-1445853 1.0000 80 chrIV:8133663-8133743 1.0000 80 chrX:3793542-3793622 1.0000 80 chrIII:11463950-11464030 1.0000 80 chrX:4193229-4193309 1.0000 80 chrII:5104235-5104315 1.0000 80 chrIII:6361605-6361685 1.0000 80 chrX:8640764-8640844 1.0000 80 chrM:10146-10226 1.0000 80 chrIV:2711449-2711529 1.0000 80 chrX:4409732-4409812 1.0000 80 chrII:11731512-11731592 1.0000 80 chrV:10855536-10855616 1.0000 80 chrII:11966807-11966887 1.0000 80 chrX:4410711-4410791 1.0000 80 chrII:12542797-12542877 1.0000 80 chrX:10148640-10148720 1.0000 80 chrX:14162073-14162153 1.0000 80 chrII:9617943-9618023 1.0000 80 chrX:3832169-3832249 1.0000 80 chrIV:12842293-12842373 1.0000 80 chrI:879857-879937 1.0000 80 chrM:3589-3669 1.0000 80 chrIV:1857902-1857982 1.0000 80 chrV:2008516-2008596 1.0000 80 chrI:10765843-10765923 1.0000 80 chrX:13969362-13969442 1.0000 80 chrI:6094414-6094494 1.0000 80 chrX:9561058-9561138 1.0000 80 chrX:4794168-4794248 1.0000 80 chrV:15547930-15548010 1.0000 80 chrX:4969440-4969520 1.0000 80 chrIII:8646154-8646234 1.0000 80 chrIV:9801627-9801707 1.0000 80 chrX:7244929-7245009 1.0000 80 chrV:185875-185955 1.0000 80 chrI:852187-852267 1.0000 80 chrIII:10354828-10354908 1.0000 80 chrIV:11955717-11955797 1.0000 80 chrII:13077853-13077933 1.0000 80 chrIII:10533506-10533586 1.0000 80 chrI:381683-381763 1.0000 80 chrI:6862199-6862279 1.0000 80 chrI:6949467-6949547 1.0000 80 chrI:5031167-5031247 1.0000 80 chrI:6163490-6163570 1.0000 80 chrV:6488095-6488175 1.0000 80 chrV:7093924-7094004 1.0000 80 chrIV:8530809-8530889 1.0000 80 chrIII:9824691-9824771 1.0000 80 chrX:5713631-5713711 1.0000 80 chrIII:5506226-5506306 1.0000 80 chrV:20792643-20792723 1.0000 80 chrX:11933734-11933814 1.0000 80 chrIII:6850364-6850444 1.0000 80 chrX:11482883-11482963 1.0000 80 chrX:3824043-3824123 1.0000 80 chrIV:292185-292265 1.0000 80 chrX:9024426-9024506 1.0000 80 chrIV:11871319-11871399 1.0000 80 chrIV:7710999-7711079 1.0000 80 chrIII:4449543-4449623 1.0000 80 chrX:8741940-8742020 1.0000 80 chrX:4008963-4009043 1.0000 80 chrX:9264884-9264964 1.0000 80 chrI:11579712-11579792 1.0000 80 chrI:6838223-6838303 1.0000 80 chrV:6559725-6559805 1.0000 80 chrV:6276316-6276396 1.0000 80 chrV:19527722-19527802 1.0000 80 chrV:20729135-20729215 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_madf-10/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/madf-10.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 0.273 C 0.229 G 0.223 T 0.275 Background letter frequencies (from file dataset with add-one prior applied): A 0.273 C 0.229 G 0.223 T 0.275 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF SGCSGCSG MEME-1 width = 8 sites = 36 llr = 316 E-value = 1.4e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1::::::2 pos.-specific C 6:a4:a32 probability G 4a:6a:76 matrix T :::::::: bits 2.2 ** ** 1.9 ** ** 1.7 ** ** 1.5 ** ** Relative 1.3 ** *** Entropy 1.1 ****** (12.7 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGCGGCGG consensus G C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:13969362-13969442 38 6.62e-06 TCGACTGAGG CGCGGCGG CGGGGACGCT chrIII:2716422-2716502 28 6.62e-06 ACGACGACGC CGCGGCGG CCCGCCGgag chrII:6843907-6843987 37 6.62e-06 CCTAAACGCG CGCGGCGG CGAACACACT chrIV:11871319-11871399 32 1.34e-05 TCGCCGACGC CGCCGCGG CTCTTGACTA chrIII:11185678-11185758 44 1.34e-05 TGGTGGTCGG CGCCGCGG CGCCGAGACG chrI:5378674-5378754 37 1.34e-05 TGCTGCGCGA CGCCGCGG CAAAAGTTGA chrII:13669005-13669085 11 1.99e-05 GTGTGTCGGC GGCGGCGG CAGCAGTGTG chrI:5377529-5377609 36 1.99e-05 TTTTGGCAGC GGCGGCGG CGACGGACCC chrIV:2998730-2998810 35 1.99e-05 cgaGTGCGGC GGCGGCGG TGGCCTCCGG chrV:10857264-10857344 56 1.99e-05 AAAAACGAGT GGCGGCGG AGCGCAGAGC chrIV:1915702-1915782 38 1.99e-05 TATcggctgc ggcggcgg cggcggcggc chrIII:3619733-3619813 32 1.99e-05 GGCGACGACC GGCGGCGG CGCCATGCAA chrIII:2535387-2535467 16 2.65e-05 GGCTCTCCGC GGCCGCGG CGACGTCGTG chrX:8741940-8742020 57 4.03e-05 cggcgtgagg cgccgccg ccgcgccgct chrI:1049236-1049316 49 4.03e-05 ACGTCATTGT CGCCGCCG TTTCTCTTTT chrX:17434436-17434516 31 4.03e-05 GCCCAGCCAC CGCCGCCG CACGTCACCC chrIII:11203094-11203174 72 4.03e-05 TCGACGTCGC CGCCGCCG C chrX:16409423-16409503 43 4.03e-05 ccgtcgccgc cgccgccg ccATTCCGAA chrI:852187-852267 26 5.37e-05 TTGGGCTGTG CGCGGCGC CTTAGACTAC chrIII:11463950-11464030 7 5.37e-05 GGCCCA GGCGGCCG ACGTCTCACG chrIII:4018201-4018281 3 5.37e-05 CG CGCGGCGC CCGCTCGCAT chrI:10446518-10446598 38 5.37e-05 ATTCGCGACC GGCGGCCG ACGTCAAATG chrIV:1739512-1739592 66 5.37e-05 CTCGTGTCAC CGCGGCGC AGCGCCC chrX:14127419-14127499 27 6.75e-05 CTGTTTTATC GGCCGCCG CTGCTATTCT chrV:10857060-10857140 48 6.75e-05 cagccgccgt cgccgcgc cAAACCAAAA chrV:16299993-16300073 51 6.75e-05 GGCGACGCCG CGCCGCGC TGCTATTACA chrI:6745569-6745649 71 8.22e-05 AGGACGAACG CGCGGCGA TG chrX:5816466-5816546 25 8.22e-05 GATTCAGCGT GGCGGCGC CGCACAGCGA chrIII:5557329-5557409 57 9.73e-05 CCAAGTGAAC GGCCGCGC TCGCATAAAA chrI:11579712-11579792 64 1.12e-04 GAGCTAACCG GGCGGCGA TCACAGTTA chrIII:4449543-4449623 56 1.43e-04 CATTGCGCCA CGCGGCCA CAGTTTGAAG chrIV:5654268-5654348 33 1.51e-04 AGTACGTCAG AGCGGCGG GTCGTTGAAT chrV:6350281-6350361 53 1.51e-04 CGTCTCGACC AGCGGCGG GCGCGGCGTC chrIV:9718560-9718640 23 1.66e-04 CCTCGGCCAC CGCCGCCA CCTTTTCAAT chrIV:2990664-2990744 15 1.66e-04 GGGGGAGAGG CGCCGCCA AGAGAACGCA chrI:6163490-6163570 49 1.74e-04 ACTGAGCTAT GGCGGCCA ACACATGTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:13969362-13969442 6.6e-06 37_[+1]_35 chrIII:2716422-2716502 6.6e-06 27_[+1]_45 chrII:6843907-6843987 6.6e-06 36_[+1]_36 chrIV:11871319-11871399 1.3e-05 31_[+1]_41 chrIII:11185678-11185758 1.3e-05 43_[+1]_29 chrI:5378674-5378754 1.3e-05 36_[+1]_36 chrII:13669005-13669085 2e-05 10_[+1]_62 chrI:5377529-5377609 2e-05 35_[+1]_37 chrIV:2998730-2998810 2e-05 34_[+1]_38 chrV:10857264-10857344 2e-05 55_[+1]_17 chrIV:1915702-1915782 2e-05 37_[+1]_35 chrIII:3619733-3619813 2e-05 31_[+1]_41 chrIII:2535387-2535467 2.6e-05 15_[+1]_57 chrX:8741940-8742020 4e-05 56_[+1]_16 chrI:1049236-1049316 4e-05 48_[+1]_24 chrX:17434436-17434516 4e-05 30_[+1]_42 chrIII:11203094-11203174 4e-05 71_[+1]_1 chrX:16409423-16409503 4e-05 42_[+1]_30 chrI:852187-852267 5.4e-05 25_[+1]_47 chrIII:11463950-11464030 5.4e-05 6_[+1]_66 chrIII:4018201-4018281 5.4e-05 2_[+1]_70 chrI:10446518-10446598 5.4e-05 37_[+1]_35 chrIV:1739512-1739592 5.4e-05 65_[+1]_7 chrX:14127419-14127499 6.7e-05 26_[+1]_46 chrV:10857060-10857140 6.7e-05 47_[+1]_25 chrV:16299993-16300073 6.7e-05 50_[+1]_22 chrI:6745569-6745649 8.2e-05 70_[+1]_2 chrX:5816466-5816546 8.2e-05 24_[+1]_48 chrIII:5557329-5557409 9.7e-05 56_[+1]_16 chrI:11579712-11579792 0.00011 63_[+1]_9 chrIII:4449543-4449623 0.00014 55_[+1]_17 chrIV:5654268-5654348 0.00015 32_[+1]_40 chrV:6350281-6350361 0.00015 52_[+1]_20 chrIV:9718560-9718640 0.00017 22_[+1]_50 chrIV:2990664-2990744 0.00017 14_[+1]_58 chrI:6163490-6163570 0.00017 48_[+1]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SGCSGCSG width=8 seqs=36 chrX:13969362-13969442 ( 38) CGCGGCGG 1 chrIII:2716422-2716502 ( 28) CGCGGCGG 1 chrII:6843907-6843987 ( 37) CGCGGCGG 1 chrIV:11871319-11871399 ( 32) CGCCGCGG 1 chrIII:11185678-11185758 ( 44) CGCCGCGG 1 chrI:5378674-5378754 ( 37) CGCCGCGG 1 chrII:13669005-13669085 ( 11) GGCGGCGG 1 chrI:5377529-5377609 ( 36) GGCGGCGG 1 chrIV:2998730-2998810 ( 35) GGCGGCGG 1 chrV:10857264-10857344 ( 56) GGCGGCGG 1 chrIV:1915702-1915782 ( 38) GGCGGCGG 1 chrIII:3619733-3619813 ( 32) GGCGGCGG 1 chrIII:2535387-2535467 ( 16) GGCCGCGG 1 chrX:8741940-8742020 ( 57) CGCCGCCG 1 chrI:1049236-1049316 ( 49) CGCCGCCG 1 chrX:17434436-17434516 ( 31) CGCCGCCG 1 chrIII:11203094-11203174 ( 72) CGCCGCCG 1 chrX:16409423-16409503 ( 43) CGCCGCCG 1 chrI:852187-852267 ( 26) CGCGGCGC 1 chrIII:11463950-11464030 ( 7) GGCGGCCG 1 chrIII:4018201-4018281 ( 3) CGCGGCGC 1 chrI:10446518-10446598 ( 38) GGCGGCCG 1 chrIV:1739512-1739592 ( 66) CGCGGCGC 1 chrX:14127419-14127499 ( 27) GGCCGCCG 1 chrV:10857060-10857140 ( 48) CGCCGCGC 1 chrV:16299993-16300073 ( 51) CGCCGCGC 1 chrI:6745569-6745649 ( 71) CGCGGCGA 1 chrX:5816466-5816546 ( 25) GGCGGCGC 1 chrIII:5557329-5557409 ( 57) GGCCGCGC 1 chrI:11579712-11579792 ( 64) GGCGGCGA 1 chrIII:4449543-4449623 ( 56) CGCGGCCA 1 chrIV:5654268-5654348 ( 33) AGCGGCGG 1 chrV:6350281-6350361 ( 53) AGCGGCGG 1 chrIV:9718560-9718640 ( 23) CGCCGCCA 1 chrIV:2990664-2990744 ( 15) CGCCGCCA 1 chrI:6163490-6163570 ( 49) GGCGGCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.0174 E= 1.4e-010 -229 128 80 -1181 -1181 -1181 216 -1181 -1181 212 -1181 -1181 -1181 86 139 -1181 -1181 -1181 216 -1181 -1181 212 -1181 -1181 -1181 54 158 -1181 -71 -24 152 -1181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 1.4e-010 0.055556 0.555556 0.388889 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.416667 0.583333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.166667 0.194444 0.638889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGCSGCSG MEME-1 regular expression -------------------------------------------------------------------------------- [CG]GC[GC]GC[GC]G -------------------------------------------------------------------------------- Time 9.28 secs. ******************************************************************************** ******************************************************************************** MOTIF CGVCGWCG MEME-2 width = 8 sites = 20 llr = 193 E-value = 1.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::4::6:: pos.-specific C a:4a::a: probability G :a3:a1:a matrix T :::::4:: bits 2.2 ** ** ** 1.9 ** ** ** 1.7 ** ** ** 1.5 ** ** ** Relative 1.3 ** ** ** Entropy 1.1 ** ** ** (13.9 bits) 0.9 ** ** ** 0.6 ** ***** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGACGACG consensus C T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:11871319-11871399 23 8.33e-06 CCGTTGCTGT CGCCGACG CCGCCGCGGC chrII:9501073-9501153 28 8.33e-06 AACGTTCTGG CGCCGACG TTCTTATCAA chrII:9285089-9285169 22 8.33e-06 TGACGATATT CGCCGACG TCTCTTTCCG chrX:8741940-8742020 27 1.64e-05 gcgcggcgac cggcgacg gcgaaggccg chrX:12904462-12904542 43 1.64e-05 TTGGCGACTG CGGCGACG CATTTCTGCC chrIII:3619733-3619813 21 1.64e-05 TGCAGCTTCG CGGCGACG ACCGGCGGCG chrV:16299993-16300073 40 1.64e-05 GCGCGGCGAT CGGCGACG CCGCGCCGCG chrIII:2716422-2716502 19 2.64e-05 AAGACGAGGA CGACGACG CCGCGGCGGC chrIV:2993531-2993611 33 2.64e-05 GGGCGCGcga cgacgacg acggcgtcga chrIV:2998730-2998810 13 2.64e-05 acgacaacga cgacgacg acaacgaGTG chrII:10744984-10745064 34 2.64e-05 GCCGCTGCGA CGACGACG ACTACACGCG chrX:16024762-16024842 53 3.47e-05 GACGCGCGAC CGCCGTCG AGACATGCAC chrX:16409423-16409503 31 3.47e-05 CCATcgtcgc cgccgtcg ccgccgccgc chrV:10857060-10857140 26 3.47e-05 CAACGGTGTA cgccgtcg gtcgcagccg chrV:6350281-6350361 64 4.29e-05 GCGGCGGGCG CGGCGTCG TTGAACACA chrIII:2535387-2535467 24 5.29e-05 GCGGCCGCGG CGACGTCG TGTGCAACTC chrX:5816466-5816546 40 5.29e-05 CGCCGCACAG CGACGTCG CATAAAACAC chrIII:11203094-11203174 63 5.29e-05 CTACTTCTAT CGACGTCG CCGCCGCCGC chrV:20776933-20777013 39 5.97e-05 TGGACTTGGA CGCCGGCG CCACCGCGCG chrIV:1915702-1915782 49 6.63e-05 gcggcggcgg cggcggcg tgcgTGCCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:11871319-11871399 8.3e-06 22_[+2]_50 chrII:9501073-9501153 8.3e-06 27_[+2]_45 chrII:9285089-9285169 8.3e-06 21_[+2]_51 chrX:8741940-8742020 1.6e-05 26_[+2]_46 chrX:12904462-12904542 1.6e-05 42_[+2]_30 chrIII:3619733-3619813 1.6e-05 20_[+2]_52 chrV:16299993-16300073 1.6e-05 39_[+2]_33 chrIII:2716422-2716502 2.6e-05 18_[+2]_54 chrIV:2993531-2993611 2.6e-05 32_[+2]_40 chrIV:2998730-2998810 2.6e-05 12_[+2]_60 chrII:10744984-10745064 2.6e-05 33_[+2]_39 chrX:16024762-16024842 3.5e-05 52_[+2]_20 chrX:16409423-16409503 3.5e-05 30_[+2]_42 chrV:10857060-10857140 3.5e-05 25_[+2]_47 chrV:6350281-6350361 4.3e-05 63_[+2]_9 chrIII:2535387-2535467 5.3e-05 23_[+2]_49 chrX:5816466-5816546 5.3e-05 39_[+2]_33 chrIII:11203094-11203174 5.3e-05 62_[+2]_10 chrV:20776933-20777013 6e-05 38_[+2]_34 chrIV:1915702-1915782 6.6e-05 48_[+2]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGVCGWCG width=8 seqs=20 chrIV:11871319-11871399 ( 23) CGCCGACG 1 chrII:9501073-9501153 ( 28) CGCCGACG 1 chrII:9285089-9285169 ( 22) CGCCGACG 1 chrX:8741940-8742020 ( 27) CGGCGACG 1 chrX:12904462-12904542 ( 43) CGGCGACG 1 chrIII:3619733-3619813 ( 21) CGGCGACG 1 chrV:16299993-16300073 ( 40) CGGCGACG 1 chrIII:2716422-2716502 ( 19) CGACGACG 1 chrIV:2993531-2993611 ( 33) CGACGACG 1 chrIV:2998730-2998810 ( 13) CGACGACG 1 chrII:10744984-10745064 ( 34) CGACGACG 1 chrX:16024762-16024842 ( 53) CGCCGTCG 1 chrX:16409423-16409503 ( 31) CGCCGTCG 1 chrV:10857060-10857140 ( 26) CGCCGTCG 1 chrV:6350281-6350361 ( 64) CGGCGTCG 1 chrIII:2535387-2535467 ( 24) CGACGTCG 1 chrX:5816466-5816546 ( 40) CGACGTCG 1 chrIII:11203094-11203174 ( 63) CGACGTCG 1 chrV:20776933-20777013 ( 39) CGCCGGCG 1 chrIV:1915702-1915782 ( 49) CGGCGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.307 E= 1.1e-003 -1097 212 -1097 -1097 -1097 -1097 216 -1097 36 61 43 -1097 -1097 212 -1097 -1097 -1097 -1097 216 -1097 101 -1097 -116 35 -1097 212 -1097 -1097 -1097 -1097 216 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.350000 0.350000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.550000 0.000000 0.100000 0.350000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGVCGWCG MEME-2 regular expression -------------------------------------------------------------------------------- CG[ACG]CG[AT]CG -------------------------------------------------------------------------------- Time 13.01 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGAGACG MEME-3 width = 8 sites = 25 llr = 217 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 23:a:a3: pos.-specific C ::3:::6: probability G 877:a:1a matrix T :::::::: bits 2.2 * * 1.9 *** * 1.7 *** * 1.5 *** * Relative 1.3 * **** * Entropy 1.1 ****** * (12.5 bits) 0.9 ****** * 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GGGAGACG consensus AAC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:2709787-2709867 16 9.41e-06 cacgctctct gggagacg agaaaaaata chrIII:4449543-4449623 31 1.91e-05 CTGCTCCGTA GGCAGACG CGTTATCCAT chrX:10148640-10148720 50 1.91e-05 CTGCTCCGTA GGCAGACG CGTTATCCAT chrX:8640764-8640844 71 1.91e-05 CTGCTCCGTA GGCAGACG CG chrX:17434436-17434516 8 1.91e-05 CGAACGC GGCAGACG TTCTTGCCCA chrIII:2716422-2716502 70 4.18e-05 gaattgcaga gagagacg cag chrV:20771027-20771107 9 4.18e-05 AGACAAAT GGGAGAAG GGAGGTGTCA chrV:20413579-20413659 41 4.18e-05 TGATgagaga gagagacg gagagacgga chrIV:2998930-2999010 37 4.18e-05 GAACGGAATG GGGAGAAG AGGGCGACCA chrV:12819259-12819339 19 4.18e-05 GCAAAATATA GGGAGAAG AGGAGGACGA chrX:5816466-5816546 8 4.18e-05 TCGAATT GAGAGACG ATTCAGCGTG chrIV:13980259-13980339 68 5.33e-05 TCATGTTTTG AGGAGACG CAACG chrX:2569200-2569280 10 5.33e-05 TGTATGACA AGGAGACG AACTAAAACG chrIV:1915702-1915782 70 5.33e-05 gTGCCGCAGA AGGAGACG AGT chrIV:2990664-2990744 7 6.25e-05 AATCGG GGGAGAGG CGCCGCCAAG chrV:20164670-20164750 72 6.25e-05 TACTGTTTTA GGGAGAGG A chrIV:13877820-13877900 10 6.25e-05 GCAAAAAGT GGGAGAGG CTCAGACGGC chrIV:1857902-1857982 39 8.59e-05 CAACACACCC GGCAGAAG AAGAAAAAGC chrX:16617884-16617964 44 8.59e-05 TCTCGCATGT GACAGACG CGGATACTCA chrV:20782385-20782465 32 9.96e-05 TAGAAAATTG GAGAGAAG TAGAGAAGCA chrI:5378674-5378754 12 9.96e-05 CAAAACGGAT GAGAGAAG GAAGAGCTGC chrIV:8762575-8762655 32 9.96e-05 TAGAGAGTTT GAGAGAAG GAGACTTCTG chrX:3793542-3793622 63 1.11e-04 CTGCGTGTAA AGCAGACG TGATAACCAC chrV:10857264-10857344 71 1.11e-04 CGGAGCGCAG AGCAGACG GA chrV:185875-185955 26 1.39e-04 CTGTAGCGGT AAGAGACG CAGAGAAGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:2709787-2709867 9.4e-06 15_[+3]_57 chrIII:4449543-4449623 1.9e-05 30_[+3]_42 chrX:10148640-10148720 1.9e-05 49_[+3]_23 chrX:8640764-8640844 1.9e-05 70_[+3]_2 chrX:17434436-17434516 1.9e-05 7_[+3]_65 chrIII:2716422-2716502 4.2e-05 69_[+3]_3 chrV:20771027-20771107 4.2e-05 8_[+3]_64 chrV:20413579-20413659 4.2e-05 40_[+3]_32 chrIV:2998930-2999010 4.2e-05 36_[+3]_36 chrV:12819259-12819339 4.2e-05 18_[+3]_54 chrX:5816466-5816546 4.2e-05 7_[+3]_65 chrIV:13980259-13980339 5.3e-05 67_[+3]_5 chrX:2569200-2569280 5.3e-05 9_[+3]_63 chrIV:1915702-1915782 5.3e-05 69_[+3]_3 chrIV:2990664-2990744 6.3e-05 6_[+3]_66 chrV:20164670-20164750 6.3e-05 71_[+3]_1 chrIV:13877820-13877900 6.3e-05 9_[+3]_63 chrIV:1857902-1857982 8.6e-05 38_[+3]_34 chrX:16617884-16617964 8.6e-05 43_[+3]_29 chrV:20782385-20782465 0.0001 31_[+3]_41 chrI:5378674-5378754 0.0001 11_[+3]_61 chrIV:8762575-8762655 0.0001 31_[+3]_41 chrX:3793542-3793622 0.00011 62_[+3]_10 chrV:10857264-10857344 0.00011 70_[+3]_2 chrV:185875-185955 0.00014 25_[+3]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGAGACG width=8 seqs=25 chrIV:2709787-2709867 ( 16) GGGAGACG 1 chrIII:4449543-4449623 ( 31) GGCAGACG 1 chrX:10148640-10148720 ( 50) GGCAGACG 1 chrX:8640764-8640844 ( 71) GGCAGACG 1 chrX:17434436-17434516 ( 8) GGCAGACG 1 chrIII:2716422-2716502 ( 70) GAGAGACG 1 chrV:20771027-20771107 ( 9) GGGAGAAG 1 chrV:20413579-20413659 ( 41) GAGAGACG 1 chrIV:2998930-2999010 ( 37) GGGAGAAG 1 chrV:12819259-12819339 ( 19) GGGAGAAG 1 chrX:5816466-5816546 ( 8) GAGAGACG 1 chrIV:13980259-13980339 ( 68) AGGAGACG 1 chrX:2569200-2569280 ( 10) AGGAGACG 1 chrIV:1915702-1915782 ( 70) AGGAGACG 1 chrIV:2990664-2990744 ( 7) GGGAGAGG 1 chrV:20164670-20164750 ( 72) GGGAGAGG 1 chrIV:13877820-13877900 ( 10) GGGAGAGG 1 chrIV:1857902-1857982 ( 39) GGCAGAAG 1 chrX:16617884-16617964 ( 44) GACAGACG 1 chrV:20782385-20782465 ( 32) GAGAGAAG 1 chrI:5378674-5378754 ( 12) GAGAGAAG 1 chrIV:8762575-8762655 ( 32) GAGAGAAG 1 chrX:3793542-3793622 ( 63) AGCAGACG 1 chrV:10857264-10857344 ( 71) AGCAGACG 1 chrV:185875-185955 ( 26) AAGAGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.1193 E= 1.5e+002 -18 -1129 177 -1129 23 -1129 161 -1129 -1129 48 161 -1129 188 -1129 -1129 -1129 -1129 -1129 216 -1129 188 -1129 -1129 -1129 4 139 -89 -1129 -1129 -1129 216 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.5e+002 0.240000 0.000000 0.760000 0.000000 0.320000 0.000000 0.680000 0.000000 0.000000 0.320000 0.680000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.280000 0.600000 0.120000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGACG MEME-3 regular expression -------------------------------------------------------------------------------- [GA][GA][GC]AGA[CA]G -------------------------------------------------------------------------------- Time 16.64 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAGAAAA MEME-4 width = 8 sites = 14 llr = 133 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A aaa1a9aa pos.-specific C :::3:::: probability G :::6:1:: matrix T :::::::: bits 2.2 1.9 *** * ** 1.7 *** * ** 1.5 *** **** Relative 1.3 *** **** Entropy 1.1 *** **** (13.7 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAGAAAA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:9264884-9264964 72 2.52e-05 ACGAAGTAAC AAAGAAAA A chrV:6488095-6488175 65 2.52e-05 CGAACGTTTG AAAGAAAA TGGAGAGC chrX:7244929-7245009 25 2.52e-05 AAAGGAGGAA AAAGAAAA AGGGCAAATA chrX:3793542-3793622 5 2.52e-05 ATTA AAAGAAAA CAGAACAGTA chrII:7554997-7555077 13 2.52e-05 ACACAAAACC AAAGAAAA TAGGGTGACA chrX:13782189-13782269 32 2.52e-05 CAGGTATCTT AAAGAAAA GAAAGTAATC chrV:3697201-3697281 56 2.52e-05 GGGAACAGAA AAAGAAAA TGATTATAAT chrX:15355830-15355910 8 2.52e-05 GGAAACC AAAGAAAA AGATGAAGAA chrX:15146526-15146606 23 5.11e-05 acctaatttg aaacaaaa cattTTGACC chrX:16554183-16554263 2 5.11e-05 T AAACAAAA GGTGGAAAGT chrV:10857264-10857344 41 5.11e-05 GTGACGAATG AAACAAAA AACGAGTGGC chrV:20785535-20785615 71 5.11e-05 atggaatcct aaacaaaa aa chrIII:5762085-5762165 66 7.17e-05 TTTTCGATCA AAAGAGAA CGGCGGA chrIII:3619733-3619813 48 1.03e-04 GGCGCCATGC AAAAAAAA TCGGGGCGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:9264884-9264964 2.5e-05 71_[+4]_1 chrV:6488095-6488175 2.5e-05 64_[+4]_8 chrX:7244929-7245009 2.5e-05 24_[+4]_48 chrX:3793542-3793622 2.5e-05 4_[+4]_68 chrII:7554997-7555077 2.5e-05 12_[+4]_60 chrX:13782189-13782269 2.5e-05 31_[+4]_41 chrV:3697201-3697281 2.5e-05 55_[+4]_17 chrX:15355830-15355910 2.5e-05 7_[+4]_65 chrX:15146526-15146606 5.1e-05 22_[+4]_50 chrX:16554183-16554263 5.1e-05 1_[+4]_71 chrV:10857264-10857344 5.1e-05 40_[+4]_32 chrV:20785535-20785615 5.1e-05 70_[+4]_2 chrIII:5762085-5762165 7.2e-05 65_[+4]_7 chrIII:3619733-3619813 0.0001 47_[+4]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAGAAAA width=8 seqs=14 chrX:9264884-9264964 ( 72) AAAGAAAA 1 chrV:6488095-6488175 ( 65) AAAGAAAA 1 chrX:7244929-7245009 ( 25) AAAGAAAA 1 chrX:3793542-3793622 ( 5) AAAGAAAA 1 chrII:7554997-7555077 ( 13) AAAGAAAA 1 chrX:13782189-13782269 ( 32) AAAGAAAA 1 chrV:3697201-3697281 ( 56) AAAGAAAA 1 chrX:15355830-15355910 ( 8) AAAGAAAA 1 chrX:15146526-15146606 ( 23) AAACAAAA 1 chrX:16554183-16554263 ( 2) AAACAAAA 1 chrV:10857264-10857344 ( 41) AAACAAAA 1 chrV:20785535-20785615 ( 71) AAACAAAA 1 chrIII:5762085-5762165 ( 66) AAAGAGAA 1 chrIII:3619733-3619813 ( 48) AAAAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.9532 E= 1.7e+003 187 -1045 -1045 -1045 187 -1045 -1045 -1045 187 -1045 -1045 -1045 -193 32 153 -1045 187 -1045 -1045 -1045 177 -1045 -164 -1045 187 -1045 -1045 -1045 187 -1045 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 1.7e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.071429 0.285714 0.642857 0.000000 1.000000 0.000000 0.000000 0.000000 0.928571 0.000000 0.071429 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGAAAA MEME-4 regular expression -------------------------------------------------------------------------------- AAA[GC]AAAA -------------------------------------------------------------------------------- Time 20.24 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGGGGGC MEME-5 width = 8 sites = 2 llr = 24 E-value = 2.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a::::::a probability G :aaaaaa: matrix T :::::::: bits 2.2 ******** 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (17.2 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGGGGGGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:6243424-6243504 38 6.45e-06 GTGTGATCGA CGGGGGGC TCGAAGCCTT chrIV:2998730-2998810 50 6.45e-06 CGGTGGCCTC CGGGGGGC GAAATAGACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:6243424-6243504 6.4e-06 37_[+5]_35 chrIV:2998730-2998810 6.4e-06 49_[+5]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGGGGGGC width=8 seqs=2 chrV:6243424-6243504 ( 38) CGGGGGGC 1 chrIV:2998730-2998810 ( 50) CGGGGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 2.0e+004 -765 212 -765 -765 -765 -765 216 -765 -765 -765 216 -765 -765 -765 216 -765 -765 -765 216 -765 -765 -765 216 -765 -765 -765 216 -765 -765 212 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.0e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGGGGGC MEME-5 regular expression -------------------------------------------------------------------------------- CGGGGGGC -------------------------------------------------------------------------------- Time 23.81 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:16299993-16300073 2.03e-03 30_[+1(8.22e-05)]_1_[+2(1.64e-05)]_\ 33 chrV:10857060-10857140 8.30e-04 25_[+2(3.47e-05)]_8_[+2(3.47e-05)]_\ 31 chrX:16409423-16409503 1.26e-03 27_[+1(4.03e-05)]_1_[+1(4.03e-05)]_\ 36 chrV:6350281-6350361 6.48e-04 63_[+2(4.29e-05)]_9 chrII:6843907-6843987 1.63e-05 36_[+1(6.62e-06)]_36 chrIV:8758802-8758882 2.46e-01 80 chrIII:3619733-3619813 4.68e-07 20_[+2(1.64e-05)]_3_[+1(1.99e-05)]_\ 41 chrIV:8757870-8757950 7.27e-02 51_[+4(7.17e-05)]_21 chrV:6230837-6230917 9.59e-01 80 chrX:6533218-6533298 2.52e-01 80 chrI:12520508-12520588 3.80e-01 80 chrI:10437978-10438058 1.19e-01 80 chrIII:13625804-13625884 6.44e-01 80 chrX:16297268-16297348 2.27e-01 80 chrIII:11203094-11203174 1.87e-03 68_[+1(4.03e-05)]_4 chrII:8784688-8784768 2.87e-01 80 chrIV:13877820-13877900 3.63e-03 9_[+3(6.25e-05)]_63 chrIV:8266521-8266601 8.78e-01 80 chrIV:1739512-1739592 3.35e-02 65_[+1(5.37e-05)]_7 chrV:20785535-20785615 3.18e-01 70_[+4(5.11e-05)]_2 chrV:3634722-3634802 2.82e-01 80 chrX:5816466-5816546 1.66e-04 7_[+3(4.18e-05)]_9_[+1(8.22e-05)]_7_\ [+2(5.29e-05)]_33 chrV:12004722-12004802 6.75e-01 80 chrV:6228587-6228667 1.72e-01 80 chrII:9285089-9285169 1.15e-03 21_[+2(8.33e-06)]_51 chrIII:2535387-2535467 1.37e-03 20_[+2(1.64e-05)]_52 chrI:10435821-10435901 2.38e-01 80 chrX:4147711-4147791 1.00e+00 80 chrX:6792808-6792888 9.94e-01 80 chrX:12904462-12904542 1.52e-02 42_[+2(1.64e-05)]_30 chrIV:8762575-8762655 1.58e-01 31_[+3(9.96e-05)]_41 chrIV:1915702-1915782 2.12e-05 37_[+1(1.99e-05)]_1_[+1(1.99e-05)]_\ 15_[+3(5.33e-05)]_3 chrII:10744984-10745064 3.81e-03 30_[+2(2.64e-05)]_42 chrX:3408700-3408780 4.99e-01 80 chrX:15355830-15355910 1.70e-02 7_[+4(2.52e-05)]_65 chrV:20779966-20780046 1.00e+00 80 chrV:20776933-20777013 8.28e-02 38_[+2(5.97e-05)]_34 chrIV:2111604-2111684 8.24e-01 80 chrI:5378674-5378754 6.53e-05 11_[+3(9.96e-05)]_17_[+1(1.34e-05)]_\ 36 chrX:6088932-6089012 1.00e+00 80 chrM:5257-5337 1.00e+00 80 chrV:12819259-12819339 1.37e-02 18_[+3(4.18e-05)]_54 chrV:20782385-20782465 6.56e-02 31_[+3(9.96e-05)]_41 chrV:7433021-7433101 8.65e-01 80 chrI:10446518-10446598 1.37e-04 37_[+1(5.37e-05)]_35 chrV:10857264-10857344 7.09e-06 40_[+4(5.11e-05)]_7_[+1(1.99e-05)]_\ 17 chrI:14940059-14940139 3.24e-01 80 chrIV:2998730-2998810 3.08e-06 9_[+2(2.64e-05)]_14_[+1(1.99e-05)]_\ 10_[+5(6.45e-06)]_23 chrX:11473206-11473286 6.24e-01 80 chrV:20163037-20163117 9.99e-01 80 chrV:20789232-20789312 3.92e-02 80 chrX:17434436-17434516 1.02e-04 7_[+3(1.91e-05)]_15_[+1(4.03e-05)]_\ 42 chrIV:12689858-12689938 9.72e-01 80 chrM:1821-1901 2.38e-01 80 chrX:14783615-14783695 4.71e-01 80 chrIV:14822412-14822492 1.00e+00 80 chrIV:2709787-2709867 1.56e-02 15_[+3(9.41e-06)]_57 chrX:12656825-12656905 3.35e-01 80 chrI:881585-881665 9.96e-01 80 chrII:12994267-12994347 1.14e-02 80 chrX:7681000-7681080 8.74e-01 80 chrIII:9060425-9060505 9.99e-01 80 chrX:7200578-7200658 9.60e-01 80 chrIV:10511618-10511698 2.15e-01 80 chrIV:296000-296080 2.60e-01 80 chrIV:2998930-2999010 5.34e-03 36_[+3(4.18e-05)]_36 chrIII:11185678-11185758 6.83e-04 43_[+1(1.34e-05)]_29 chrI:754679-754759 1.85e-01 80 chrX:4617039-4617119 9.69e-02 80 chrIV:15702098-15702178 7.33e-01 80 chrX:4007807-4007887 6.42e-01 80 chrX:12205619-12205699 2.80e-01 80 chrII:6943853-6943933 7.88e-02 80 chrM:3305-3385 7.97e-01 80 chrX:6609220-6609300 6.17e-01 80 chrIII:5196565-5196645 9.27e-01 80 chrI:6499632-6499712 9.84e-01 80 chrV:2308393-2308473 9.22e-01 80 chrV:20164670-20164750 5.44e-02 71_[+3(6.25e-05)]_1 chrII:11731310-11731390 1.05e-01 80 chrI:14657250-14657330 1.95e-01 80 chrX:15842638-15842718 8.62e-01 80 chrV:9338674-9338754 7.40e-01 80 chrV:3697201-3697281 3.55e-02 55_[+4(2.52e-05)]_17 chrIV:8261151-8261231 4.66e-01 80 chrV:20413579-20413659 5.54e-02 40_[+3(4.18e-05)]_[+3(4.18e-05)]_24 chrI:9671944-9672024 5.99e-01 80 chrX:16192701-16192781 9.02e-01 80 chrV:10802262-10802342 9.99e-01 80 chrX:11872296-11872376 9.95e-01 80 chrI:7660150-7660230 5.83e-01 80 chrIV:5654268-5654348 1.21e-01 80 chrV:6220977-6221057 9.97e-01 80 chrM:1532-1612 9.02e-01 80 chrIV:6555103-6555183 9.99e-01 80 chrV:6231038-6231118 9.18e-01 80 chrIV:12601142-12601222 9.39e-01 80 chrIV:4450049-4450129 9.97e-01 80 chrIV:15933229-15933309 8.92e-01 80 chrIV:13880928-13881008 6.00e-01 80 chrI:4597685-4597765 5.08e-01 80 chrV:20771027-20771107 5.03e-02 8_[+3(4.18e-05)]_64 chrV:6243424-6243504 1.60e-03 37_[+5(6.45e-06)]_35 chrV:16338626-16338706 9.77e-01 80 chrX:16617884-16617964 6.84e-02 43_[+3(8.59e-05)]_29 chrV:8651490-8651570 9.64e-01 80 chrX:2569200-2569280 2.26e-02 9_[+3(5.33e-05)]_63 chrIV:2993531-2993611 1.25e-02 29_[+2(2.64e-05)]_4_[+2(4.29e-05)]_\ 31 chrX:8381817-8381897 1.19e-01 80 chrIII:5550994-5551074 6.39e-01 80 chrX:8939558-8939638 3.61e-01 80 chrX:10124488-10124568 7.88e-01 80 chrX:11473407-11473487 7.21e-02 80 chrV:2872301-2872381 6.91e-01 80 chrX:16554183-16554263 1.53e-01 1_[+4(5.11e-05)]_71 chrI:1049236-1049316 1.49e-02 48_[+1(4.03e-05)]_24 chrX:3567043-3567123 6.50e-01 80 chrII:12878882-12878962 1.66e-02 80 chrX:11792892-11792972 1.79e-01 80 chrV:3455294-3455374 2.26e-01 80 chrIV:13980259-13980339 7.10e-02 67_[+3(5.33e-05)]_5 chrIII:12614765-12614845 5.30e-01 80 chrV:6251297-6251377 9.80e-01 80 chrI:7602332-7602412 9.99e-01 80 chrI:5377529-5377609 6.68e-04 40_[+2(1.64e-05)]_32 chrII:9501073-9501153 5.55e-03 27_[+2(8.33e-06)]_45 chrIII:13066975-13067055 9.07e-01 80 chrX:6533445-6533525 9.99e-01 80 chrII:13669005-13669085 3.90e-04 7_[+1(1.99e-05)]_46_[+1(6.75e-05)]_\ 11 chrX:14539657-14539737 6.84e-01 80 chrIII:5762085-5762165 3.46e-03 65_[+4(7.17e-05)]_7 chrV:19049467-19049547 9.47e-01 80 chrIV:12834103-12834183 9.98e-01 80 chrX:13782189-13782269 1.80e-02 31_[+4(2.52e-05)]_41 chrV:3644425-3644505 1.00e+00 80 chrX:16024762-16024842 7.28e-04 52_[+2(3.47e-05)]_20 chrIV:2990664-2990744 4.27e-04 6_[+3(6.25e-05)]_66 chrIV:13701622-13701702 5.96e-01 80 chrX:13420124-13420204 9.96e-01 80 chrV:1132471-1132551 9.11e-01 80 chrX:16300585-16300665 1.23e-01 80 chrI:2996086-2996166 2.65e-01 80 chrV:6614502-6614582 8.57e-01 80 chrX:13261208-13261288 3.08e-02 80 chrII:9934055-9934135 5.43e-01 80 chrII:11151068-11151148 9.35e-01 80 chrX:6536876-6536956 1.76e-01 80 chrIII:8639266-8639346 5.87e-01 80 chrV:16595480-16595560 7.98e-02 80 chrX:8440255-8440335 9.33e-01 80 chrIII:5937109-5937189 1.35e-01 80 chrX:14792924-14793004 9.75e-01 80 chrX:14127419-14127499 3.06e-02 26_[+1(6.75e-05)]_46 chrII:8933876-8933956 1.92e-01 80 chrX:4453244-4453324 2.65e-02 80 chrX:11472143-11472223 8.88e-01 80 chrX:5106262-5106342 9.96e-01 80 chrIV:13919386-13919466 5.57e-01 80 chrII:7554997-7555077 8.52e-02 12_[+4(2.52e-05)]_60 chrIII:5557329-5557409 1.11e-01 56_[+1(9.73e-05)]_16 chrIV:9718560-9718640 2.02e-01 80 chrI:6745569-6745649 9.41e-03 70_[+1(8.22e-05)]_2 chrV:11976861-11976941 3.20e-01 80 chrIV:13725355-13725435 2.55e-01 80 chrV:15298775-15298855 7.49e-01 80 chrII:13780886-13780966 7.54e-01 80 chrII:3062327-3062407 9.76e-02 80 chrIII:4018201-4018281 8.64e-03 2_[+1(5.37e-05)]_70 chrV:20412330-20412410 6.31e-01 80 chrX:14438004-14438084 5.85e-01 80 chrV:20497729-20497809 9.31e-01 80 chrX:3290276-3290356 8.49e-01 80 chrIV:7402240-7402320 9.15e-01 80 chrI:3113754-3113834 7.69e-01 80 chrIII:2716422-2716502 9.21e-07 18_[+2(2.64e-05)]_1_[+1(6.62e-06)]_\ 34_[+3(4.18e-05)]_3 chrX:15146526-15146606 1.74e-02 22_[+4(5.11e-05)]_50 chrII:5202062-5202142 9.94e-01 80 chrX:13714845-13714925 6.95e-01 80 chrV:6335406-6335486 5.95e-01 80 chrX:1445773-1445853 2.83e-01 80 chrIV:8133663-8133743 8.48e-01 80 chrX:3793542-3793622 1.20e-03 4_[+4(2.52e-05)]_68 chrIII:11463950-11464030 1.47e-03 6_[+1(5.37e-05)]_66 chrX:4193229-4193309 9.80e-01 80 chrII:5104235-5104315 9.83e-01 80 chrIII:6361605-6361685 5.28e-01 80 chrX:8640764-8640844 1.20e-02 70_[+3(1.91e-05)]_2 chrM:10146-10226 9.94e-01 80 chrIV:2711449-2711529 6.88e-01 80 chrX:4409732-4409812 8.99e-01 80 chrII:11731512-11731592 8.92e-01 80 chrV:10855536-10855616 7.73e-01 80 chrII:11966807-11966887 9.05e-01 80 chrX:4410711-4410791 2.44e-01 80 chrII:12542797-12542877 8.33e-01 80 chrX:10148640-10148720 6.88e-03 49_[+3(1.91e-05)]_23 chrX:14162073-14162153 9.41e-01 80 chrII:9617943-9618023 3.54e-01 80 chrX:3832169-3832249 5.92e-01 80 chrIV:12842293-12842373 9.01e-01 80 chrI:879857-879937 6.14e-01 80 chrM:3589-3669 9.50e-01 80 chrIV:1857902-1857982 4.47e-02 38_[+3(8.59e-05)]_34 chrV:2008516-2008596 7.27e-01 80 chrI:10765843-10765923 5.46e-03 80 chrX:13969362-13969442 8.82e-05 37_[+1(6.62e-06)]_35 chrI:6094414-6094494 5.62e-01 80 chrX:9561058-9561138 8.51e-02 80 chrX:4794168-4794248 7.97e-01 80 chrV:15547930-15548010 7.45e-01 80 chrX:4969440-4969520 4.49e-01 80 chrIII:8646154-8646234 8.43e-01 80 chrIV:9801627-9801707 9.36e-01 80 chrX:7244929-7245009 1.74e-01 24_[+4(2.52e-05)]_48 chrV:185875-185955 1.22e-01 80 chrI:852187-852267 7.72e-03 25_[+1(5.37e-05)]_47 chrIII:10354828-10354908 1.00e+00 80 chrIV:11955717-11955797 9.59e-01 80 chrII:13077853-13077933 9.92e-01 80 chrIII:10533506-10533586 4.43e-01 80 chrI:381683-381763 6.69e-01 80 chrI:6862199-6862279 2.36e-01 80 chrI:6949467-6949547 3.53e-01 80 chrI:5031167-5031247 4.64e-01 80 chrI:6163490-6163570 2.47e-01 80 chrV:6488095-6488175 1.60e-01 64_[+4(2.52e-05)]_8 chrV:7093924-7094004 6.80e-01 80 chrIV:8530809-8530889 9.95e-01 80 chrIII:9824691-9824771 4.20e-01 80 chrX:5713631-5713711 7.39e-01 80 chrIII:5506226-5506306 9.94e-01 80 chrV:20792643-20792723 1.57e-01 80 chrX:11933734-11933814 1.47e-03 80 chrIII:6850364-6850444 8.49e-01 80 chrX:11482883-11482963 3.71e-01 80 chrX:3824043-3824123 3.12e-01 80 chrIV:292185-292265 1.00e+00 80 chrX:9024426-9024506 9.99e-01 80 chrIV:11871319-11871399 3.57e-04 22_[+2(8.33e-06)]_1_[+1(1.34e-05)]_\ 41 chrIV:7710999-7711079 9.86e-01 80 chrIII:4449543-4449623 2.10e-03 30_[+3(1.91e-05)]_42 chrX:8741940-8742020 5.90e-04 17_[+1(8.22e-05)]_1_[+2(1.64e-05)]_\ 22_[+1(4.03e-05)]_16 chrX:4008963-4009043 2.10e-01 80 chrX:9264884-9264964 4.20e-02 71_[+4(2.52e-05)]_1 chrI:11579712-11579792 4.69e-03 80 chrI:6838223-6838303 1.30e-01 80 chrV:6559725-6559805 7.32e-01 80 chrV:6276316-6276396 9.79e-01 80 chrV:19527722-19527802 5.24e-01 80 chrV:20729135-20729215 9.96e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n07.farnam.hpc.yale.internal ********************************************************************************