******************************************************************************** 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/lim-6.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrX:1073984-1074064 1.0000 80 chrX:6687841-6687921 1.0000 80 chrII:15254137-15254217 1.0000 80 chrI:8119345-8119425 1.0000 80 chrII:10804589-10804669 1.0000 80 chrX:1082089-1082169 1.0000 80 chrI:7374936-7375016 1.0000 80 chrIV:1687272-1687352 1.0000 80 chrII:8137465-8137545 1.0000 80 chrIII:6013145-6013225 1.0000 80 chrV:16553139-16553219 1.0000 80 chrII:10681967-10682047 1.0000 80 chrX:1064165-1064245 1.0000 80 chrI:10469107-10469187 1.0000 80 chrIV:14032725-14032805 1.0000 80 chrIII:10856996-10857076 1.0000 80 chrII:3482373-3482453 1.0000 80 chrV:3717813-3717893 1.0000 80 chrI:13421150-13421230 1.0000 80 chrIII:10436177-10436257 1.0000 80 chrI:3176598-3176678 1.0000 80 chrIII:10811214-10811294 1.0000 80 chrIII:12673516-12673596 1.0000 80 chrV:14443761-14443841 1.0000 80 chrIV:11872050-11872130 1.0000 80 chrIII:3499984-3500064 1.0000 80 chrIV:4702226-4702306 1.0000 80 chrIV:12621639-12621719 1.0000 80 chrI:7251587-7251667 1.0000 80 chrX:5056379-5056459 1.0000 80 chrV:7217947-7218027 1.0000 80 chrIII:11848458-11848538 1.0000 80 chrI:273727-273807 1.0000 80 chrIII:3476395-3476475 1.0000 80 chrII:7563780-7563860 1.0000 80 chrIII:13032584-13032664 1.0000 80 chrI:5659149-5659229 1.0000 80 chrII:4955562-4955642 1.0000 80 chrIV:13487165-13487245 1.0000 80 chrII:8945578-8945658 1.0000 80 chrIII:931569-931649 1.0000 80 chrIV:1845076-1845156 1.0000 80 chrIV:4401731-4401811 1.0000 80 chrI:933477-933557 1.0000 80 chrV:4181868-4181948 1.0000 80 chrIII:8588887-8588967 1.0000 80 chrIII:10016834-10016914 1.0000 80 chrII:5836520-5836600 1.0000 80 chrII:1134700-1134780 1.0000 80 chrV:16022751-16022831 1.0000 80 chrIII:11091834-11091914 1.0000 80 chrIV:6855111-6855191 1.0000 80 chrI:2487859-2487939 1.0000 80 chrIV:11179084-11179164 1.0000 80 chrX:13143348-13143428 1.0000 80 chrX:1058091-1058171 1.0000 80 chrII:10684889-10684969 1.0000 80 chrII:14428731-14428811 1.0000 80 chrIII:6551497-6551577 1.0000 80 chrII:12042357-12042437 1.0000 80 chrIII:3424057-3424137 1.0000 80 chrV:17548740-17548820 1.0000 80 chrIV:6887885-6887965 1.0000 80 chrII:476186-476266 1.0000 80 chrV:3218775-3218855 1.0000 80 chrII:12348868-12348948 1.0000 80 chrI:4967570-4967650 1.0000 80 chrIV:2824566-2824646 1.0000 80 chrI:15014009-15014089 1.0000 80 chrII:3527744-3527824 1.0000 80 chrV:5284756-5284836 1.0000 80 chrX:13598130-13598210 1.0000 80 chrI:10026050-10026130 1.0000 80 chrV:7728158-7728238 1.0000 80 chrIV:16995582-16995662 1.0000 80 chrX:601426-601506 1.0000 80 chrII:4038828-4038908 1.0000 80 chrIII:11093681-11093761 1.0000 80 chrIV:17108415-17108495 1.0000 80 chrV:1197397-1197477 1.0000 80 chrIII:4196712-4196792 1.0000 80 chrV:20424963-20425043 1.0000 80 chrIV:15561449-15561529 1.0000 80 chrIII:10262888-10262968 1.0000 80 chrIV:1824173-1824253 1.0000 80 chrIII:5308418-5308498 1.0000 80 chrI:6810471-6810551 1.0000 80 chrV:13111775-13111855 1.0000 80 chrI:1034339-1034419 1.0000 80 chrII:6741605-6741685 1.0000 80 chrV:11655171-11655251 1.0000 80 chrI:10232740-10232820 1.0000 80 chrIII:8144764-8144844 1.0000 80 chrV:18981156-18981236 1.0000 80 chrX:9997184-9997264 1.0000 80 chrI:1415965-1416045 1.0000 80 chrIII:10123779-10123859 1.0000 80 chrI:2710693-2710773 1.0000 80 chrII:15089558-15089638 1.0000 80 chrIII:4905466-4905546 1.0000 80 chrII:11751701-11751781 1.0000 80 chrIV:8973703-8973783 1.0000 80 chrIV:2033196-2033276 1.0000 80 chrII:14528484-14528564 1.0000 80 chrIII:8262747-8262827 1.0000 80 chrII:12175454-12175534 1.0000 80 chrIV:11310757-11310837 1.0000 80 chrI:7772639-7772719 1.0000 80 chrI:10642450-10642530 1.0000 80 chrI:8369761-8369841 1.0000 80 chrI:4247531-4247611 1.0000 80 chrI:10175464-10175544 1.0000 80 chrI:14756432-14756512 1.0000 80 chrX:7651311-7651391 1.0000 80 chrIII:7198999-7199079 1.0000 80 chrI:12899150-12899230 1.0000 80 chrIII:8529010-8529090 1.0000 80 chrII:4672685-4672765 1.0000 80 chrIII:5190302-5190382 1.0000 80 chrII:7676565-7676645 1.0000 80 chrIII:5069018-5069098 1.0000 80 chrX:1051272-1051352 1.0000 80 chrI:5164963-5165043 1.0000 80 chrII:6734840-6734920 1.0000 80 chrIII:11290718-11290798 1.0000 80 chrV:7820416-7820496 1.0000 80 chrV:9293530-9293610 1.0000 80 chrIII:159753-159833 1.0000 80 chrII:6838560-6838640 1.0000 80 chrV:11124090-11124170 1.0000 80 chrII:10547384-10547464 1.0000 80 chrX:2488775-2488855 1.0000 80 chrV:2638682-2638762 1.0000 80 chrI:27063-27143 1.0000 80 chrIV:6646282-6646362 1.0000 80 chrI:1823222-1823302 1.0000 80 chrIII:4912471-4912551 1.0000 80 chrII:5594391-5594471 1.0000 80 chrX:7798544-7798624 1.0000 80 chrI:9855538-9855618 1.0000 80 chrX:4125592-4125672 1.0000 80 chrIV:13533247-13533327 1.0000 80 chrIII:4930398-4930478 1.0000 80 chrI:788163-788243 1.0000 80 chrII:4456306-4456386 1.0000 80 chrV:11505134-11505214 1.0000 80 chrV:7084912-7084992 1.0000 80 chrI:3350051-3350131 1.0000 80 chrI:12921065-12921145 1.0000 80 chrIV:7817971-7818051 1.0000 80 chrIV:10085860-10085940 1.0000 80 chrV:10526107-10526187 1.0000 80 chrV:7465690-7465770 1.0000 80 chrIV:17099260-17099340 1.0000 80 chrV:8785775-8785855 1.0000 80 chrI:11585327-11585407 1.0000 80 chrV:13715491-13715571 1.0000 80 chrI:3822796-3822876 1.0000 80 chrV:15610522-15610602 1.0000 80 chrIII:10460716-10460796 1.0000 80 chrII:9497451-9497531 1.0000 80 chrIII:640557-640637 1.0000 80 chrIV:796710-796790 1.0000 80 chrI:2996333-2996413 1.0000 80 chrIV:410606-410686 1.0000 80 chrV:11039748-11039828 1.0000 80 chrV:1003901-1003981 1.0000 80 chrV:9980917-9980997 1.0000 80 chrI:6493925-6494005 1.0000 80 chrIV:11315034-11315114 1.0000 80 chrIV:9074415-9074495 1.0000 80 chrII:14143963-14144043 1.0000 80 chrV:10356092-10356172 1.0000 80 chrIV:11635777-11635857 1.0000 80 chrIV:8015966-8016046 1.0000 80 chrI:14787898-14787978 1.0000 80 chrII:4791445-4791525 1.0000 80 chrII:9307013-9307093 1.0000 80 chrX:12452326-12452406 1.0000 80 chrV:18723712-18723792 1.0000 80 chrI:8124509-8124589 1.0000 80 chrI:4224816-4224896 1.0000 80 chrIII:11142263-11142343 1.0000 80 chrIV:6648788-6648868 1.0000 80 chrIII:4506001-4506081 1.0000 80 chrIV:8629642-8629722 1.0000 80 chrII:10538119-10538199 1.0000 80 chrV:11644303-11644383 1.0000 80 chrII:14063234-14063314 1.0000 80 chrIV:8183500-8183580 1.0000 80 chrIII:5349405-5349485 1.0000 80 chrIII:8319285-8319365 1.0000 80 chrII:6913448-6913528 1.0000 80 chrIII:4656595-4656675 1.0000 80 chrI:5176389-5176469 1.0000 80 chrI:1416166-1416246 1.0000 80 chrII:7537793-7537873 1.0000 80 chrV:16401675-16401755 1.0000 80 chrI:1175831-1175911 1.0000 80 chrII:3502782-3502862 1.0000 80 chrII:11534715-11534795 1.0000 80 chrII:2752655-2752735 1.0000 80 chrX:14115659-14115739 1.0000 80 chrI:6446680-6446760 1.0000 80 chrIV:1858070-1858150 1.0000 80 chrV:5917883-5917963 1.0000 80 chrIII:11317208-11317288 1.0000 80 chrV:14347389-14347469 1.0000 80 chrIII:11119504-11119584 1.0000 80 chrV:15085563-15085643 1.0000 80 chrX:993074-993154 1.0000 80 chrV:12870085-12870165 1.0000 80 chrIII:783441-783521 1.0000 80 chrIII:8850818-8850898 1.0000 80 chrIV:6631977-6632057 1.0000 80 chrIV:16415221-16415301 1.0000 80 chrI:1435569-1435649 1.0000 80 chrIII:3175135-3175215 1.0000 80 chrIII:131857-131937 1.0000 80 chrI:13040730-13040810 1.0000 80 chrIV:4042402-4042482 1.0000 80 chrI:10474757-10474837 1.0000 80 chrIII:12273736-12273816 1.0000 80 chrIII:13721243-13721323 1.0000 80 chrIII:12351453-12351533 1.0000 80 chrII:14438169-14438249 1.0000 80 chrV:11375261-11375341 1.0000 80 chrIII:9703980-9704060 1.0000 80 chrV:1004104-1004184 1.0000 80 chrII:2889343-2889423 1.0000 80 chrII:5358379-5358459 1.0000 80 chrII:10033614-10033694 1.0000 80 chrX:8156138-8156218 1.0000 80 chrIV:8016173-8016253 1.0000 80 chrII:10872705-10872785 1.0000 80 chrII:8516929-8517009 1.0000 80 chrV:13468344-13468424 1.0000 80 chrV:1871930-1872010 1.0000 80 chrX:9347710-9347790 1.0000 80 chrIV:11605045-11605125 1.0000 80 chrII:4740137-4740217 1.0000 80 chrX:9337900-9337980 1.0000 80 chrIII:4568690-4568770 1.0000 80 chrII:5061940-5062020 1.0000 80 chrII:2451186-2451266 1.0000 80 chrIII:11946511-11946591 1.0000 80 chrIV:9316216-9316296 1.0000 80 chrIV:10481889-10481969 1.0000 80 chrI:14721600-14721680 1.0000 80 chrIV:10483881-10483961 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_lim-6/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/lim-6.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 0.257 C 0.237 G 0.231 T 0.276 Background letter frequencies (from file dataset with add-one prior applied): A 0.257 C 0.237 G 0.231 T 0.276 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTMGGCCA MEME-1 width = 8 sites = 45 llr = 405 E-value = 1.9e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :14::::7 pos.-specific C 9:6::aa: probability G 11:9a::3 matrix T :8:1:::: bits 2.1 *** 1.9 *** 1.7 * **** 1.5 * **** Relative 1.3 * **** Entropy 1.1 ******** (13.0 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTCGGCCA consensus A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:10483881-10483961 29 1.19e-05 AGCATAAATC CTCGGCCA CGGTTTGTGG chrV:11124090-11124170 55 1.19e-05 TCTCGGGTTC CTCGGCCA TTTTTATCGG chrIII:4905466-4905546 27 1.19e-05 TTCCGAGAGA CTCGGCCA CGAATTGGGT chrV:20424963-20425043 50 1.19e-05 CTCCATTGCA CTCGGCCA CCACTATTTA chrIII:12673516-12673596 65 1.19e-05 GAGACCCCGA CTCGGCCA GGCAAGtt chrII:4740137-4740217 47 2.49e-05 GTGCGAGTTT CTAGGCCA CGCGGAAATG chrV:13468344-13468424 28 2.49e-05 TGTGCGTTTT CTAGGCCA TTTTGGCGTG chrII:5358379-5358459 44 2.49e-05 GGTGCGATTT CTAGGCCA GCAGGGCTCT chrIII:12273736-12273816 70 2.49e-05 GTTGTGGTTT CTAGGCCA GGG chrI:10474757-10474837 49 2.49e-05 GTTCGAATTT CTAGGCCA CGACCATAAA chrIII:8850818-8850898 38 2.49e-05 CGTGGAAATT CTAGGCCA CGGATAACTA chrV:15085563-15085643 28 2.49e-05 ATGGAAGAAA CTAGGCCA GCAGGCCACG chrII:3502782-3502862 42 2.49e-05 TTGGAGTTTT CTAGGCCA CGAGTTGCAT chrIII:8319285-8319365 41 2.49e-05 CATCACAATT CTAGGCCA TTTTCAAAGA chrIII:5349405-5349485 57 2.49e-05 AAAAAGAAAG CTAGGCCA CCGATGCGGA chrV:10356092-10356172 46 2.49e-05 GAGGGATATT CTAGGCCA TATGTAGCAA chrI:4247531-4247611 66 2.49e-05 TAGTTACTTC CTAGGCCA CGCGGCC chrII:15089558-15089638 51 2.49e-05 CATTTGGTTC CTAGGCCA CGCGGCCGTG chrV:18981156-18981236 32 2.49e-05 TCAGAGTTTC CTAGGCCA CCGCCGGTGT chrIII:8144764-8144844 44 2.49e-05 GTTCTCAAAT CTAGGCCA TCTCAGTTTT chrI:1034339-1034419 52 2.49e-05 GCGCGGGTTT CTAGGCCA CGGCCACCGA chrI:15014009-15014089 26 2.49e-05 GGGTGGAATT CTAGGCCA CCAGATCATA chrI:5659149-5659229 24 2.49e-05 TTGTCGGTTC CTAGGCCA CCACCTCGTT chrII:8516929-8517009 72 3.56e-05 AAAGAAAAAG CTCGGCCG C chrII:10538119-10538199 30 3.56e-05 ATAATTATTT CTCGGCCG TGTACTCCTC chrII:4791445-4791525 26 3.56e-05 TAACATCCGA CTCGGCCG CCGGCCGTGT chrV:7084912-7084992 18 3.56e-05 AGAAACCAAC CTCGGCCG CACTGCGCCG chrIII:4912471-4912551 56 3.56e-05 CATTCGGATT CTCGGCCG TGGCCTAGAA chrII:11751701-11751781 54 3.56e-05 ATCTCTCTTC CTCGGCCG TGGAAGAGAA chrII:10872705-10872785 20 4.73e-05 ACACGAAAAC CTAGGCCG GCGGCCGCCA chrII:6913448-6913528 57 4.73e-05 GGAGAGTTTT CTAGGCCG TGTGTGCCGC chrII:2889343-2889423 62 5.73e-05 AATCGGTCGT CGCGGCCA CGGAGTCCTC chrIII:7198999-7199079 40 5.73e-05 TTCAAATGTG CGCGGCCA CGGCCACTGT chrI:14756432-14756512 42 7.92e-05 AAACCTCGGT CACGGCCA TGCCACTTTT chrIV:16995582-16995662 30 7.92e-05 TTTCCTCTTC CACGGCCA CGCGGCCCCC chrI:3176598-3176678 9 7.92e-05 AGTTAGGC CACGGCCA CCACGGCCCC chrV:16401675-16401755 39 9.98e-05 CTCTGGTGGC CGCGGCCG AGGTTTCTCC chrV:2638682-2638762 26 9.98e-05 TTGCGGTGGC CGCGGCCG TGAAAATGCG chrIV:8973703-8973783 37 9.98e-05 TCCTAGTCCG CGCGGCCG TGTAGTCCTC chrII:3482373-3482453 23 9.98e-05 AAGAACCCCC GTCGGCCA TGTGGTGCAA chrV:12870085-12870165 61 1.26e-04 CGCGCACTTC CTCTGCCA TTTCATTTGC chrV:18723712-18723792 65 1.26e-04 GCCATGTTTT CTCTGCCA CTCTCTCA chrV:7465690-7465770 66 1.26e-04 TTCTCTCTTT CTCTGCCA TCTCTCT chrIV:6631977-6632057 28 1.84e-04 TTTTTCTTCG GTCGGCCG TGGGTCGCGA chrII:10547384-10547464 36 1.84e-04 CGCGGAATCG GTCGGCCG GATGATTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:10483881-10483961 1.2e-05 28_[+1]_44 chrV:11124090-11124170 1.2e-05 54_[+1]_18 chrIII:4905466-4905546 1.2e-05 26_[+1]_46 chrV:20424963-20425043 1.2e-05 49_[+1]_23 chrIII:12673516-12673596 1.2e-05 64_[+1]_8 chrII:4740137-4740217 2.5e-05 46_[+1]_26 chrV:13468344-13468424 2.5e-05 27_[+1]_45 chrII:5358379-5358459 2.5e-05 43_[+1]_29 chrIII:12273736-12273816 2.5e-05 69_[+1]_3 chrI:10474757-10474837 2.5e-05 48_[+1]_24 chrIII:8850818-8850898 2.5e-05 37_[+1]_35 chrV:15085563-15085643 2.5e-05 27_[+1]_45 chrII:3502782-3502862 2.5e-05 41_[+1]_31 chrIII:8319285-8319365 2.5e-05 40_[+1]_32 chrIII:5349405-5349485 2.5e-05 56_[+1]_16 chrV:10356092-10356172 2.5e-05 45_[+1]_27 chrI:4247531-4247611 2.5e-05 65_[+1]_7 chrII:15089558-15089638 2.5e-05 50_[+1]_22 chrV:18981156-18981236 2.5e-05 31_[+1]_41 chrIII:8144764-8144844 2.5e-05 43_[+1]_29 chrI:1034339-1034419 2.5e-05 51_[+1]_21 chrI:15014009-15014089 2.5e-05 25_[+1]_47 chrI:5659149-5659229 2.5e-05 23_[+1]_49 chrII:8516929-8517009 3.6e-05 71_[+1]_1 chrII:10538119-10538199 3.6e-05 29_[+1]_43 chrII:4791445-4791525 3.6e-05 25_[+1]_47 chrV:7084912-7084992 3.6e-05 17_[+1]_55 chrIII:4912471-4912551 3.6e-05 55_[+1]_17 chrII:11751701-11751781 3.6e-05 53_[+1]_19 chrII:10872705-10872785 4.7e-05 19_[+1]_53 chrII:6913448-6913528 4.7e-05 56_[+1]_16 chrII:2889343-2889423 5.7e-05 61_[+1]_11 chrIII:7198999-7199079 5.7e-05 39_[+1]_33 chrI:14756432-14756512 7.9e-05 41_[+1]_31 chrIV:16995582-16995662 7.9e-05 29_[+1]_43 chrI:3176598-3176678 7.9e-05 8_[+1]_64 chrV:16401675-16401755 0.0001 38_[+1]_34 chrV:2638682-2638762 0.0001 25_[+1]_47 chrIV:8973703-8973783 0.0001 36_[+1]_36 chrII:3482373-3482453 0.0001 22_[+1]_50 chrV:12870085-12870165 0.00013 60_[+1]_12 chrV:18723712-18723792 0.00013 64_[+1]_8 chrV:7465690-7465770 0.00013 65_[+1]_7 chrIV:6631977-6632057 0.00018 27_[+1]_45 chrII:10547384-10547464 0.00018 35_[+1]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTMGGCCA width=8 seqs=45 chrIV:10483881-10483961 ( 29) CTCGGCCA 1 chrV:11124090-11124170 ( 55) CTCGGCCA 1 chrIII:4905466-4905546 ( 27) CTCGGCCA 1 chrV:20424963-20425043 ( 50) CTCGGCCA 1 chrIII:12673516-12673596 ( 65) CTCGGCCA 1 chrII:4740137-4740217 ( 47) CTAGGCCA 1 chrV:13468344-13468424 ( 28) CTAGGCCA 1 chrII:5358379-5358459 ( 44) CTAGGCCA 1 chrIII:12273736-12273816 ( 70) CTAGGCCA 1 chrI:10474757-10474837 ( 49) CTAGGCCA 1 chrIII:8850818-8850898 ( 38) CTAGGCCA 1 chrV:15085563-15085643 ( 28) CTAGGCCA 1 chrII:3502782-3502862 ( 42) CTAGGCCA 1 chrIII:8319285-8319365 ( 41) CTAGGCCA 1 chrIII:5349405-5349485 ( 57) CTAGGCCA 1 chrV:10356092-10356172 ( 46) CTAGGCCA 1 chrI:4247531-4247611 ( 66) CTAGGCCA 1 chrII:15089558-15089638 ( 51) CTAGGCCA 1 chrV:18981156-18981236 ( 32) CTAGGCCA 1 chrIII:8144764-8144844 ( 44) CTAGGCCA 1 chrI:1034339-1034419 ( 52) CTAGGCCA 1 chrI:15014009-15014089 ( 26) CTAGGCCA 1 chrI:5659149-5659229 ( 24) CTAGGCCA 1 chrII:8516929-8517009 ( 72) CTCGGCCG 1 chrII:10538119-10538199 ( 30) CTCGGCCG 1 chrII:4791445-4791525 ( 26) CTCGGCCG 1 chrV:7084912-7084992 ( 18) CTCGGCCG 1 chrIII:4912471-4912551 ( 56) CTCGGCCG 1 chrII:11751701-11751781 ( 54) CTCGGCCG 1 chrII:10872705-10872785 ( 20) CTAGGCCG 1 chrII:6913448-6913528 ( 57) CTAGGCCG 1 chrII:2889343-2889423 ( 62) CGCGGCCA 1 chrIII:7198999-7199079 ( 40) CGCGGCCA 1 chrI:14756432-14756512 ( 42) CACGGCCA 1 chrIV:16995582-16995662 ( 30) CACGGCCA 1 chrI:3176598-3176678 ( 9) CACGGCCA 1 chrV:16401675-16401755 ( 39) CGCGGCCG 1 chrV:2638682-2638762 ( 26) CGCGGCCG 1 chrIV:8973703-8973783 ( 37) CGCGGCCG 1 chrII:3482373-3482453 ( 23) GTCGGCCA 1 chrV:12870085-12870165 ( 61) CTCTGCCA 1 chrV:18723712-18723792 ( 65) CTCTGCCA 1 chrV:7465690-7465770 ( 66) CTCTGCCA 1 chrIV:6631977-6632057 ( 28) GTCGGCCG 1 chrII:10547384-10547464 ( 36) GTCGGCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.70763 E= 1.9e-025 -1214 198 -179 -1214 -194 -1214 -105 158 79 123 -1214 -1214 -1214 -1214 202 -205 -1214 -1214 212 -1214 -1214 208 -1214 -1214 -1214 208 -1214 -1214 147 -1214 33 -1214 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 1.9e-025 0.000000 0.933333 0.066667 0.000000 0.066667 0.000000 0.111111 0.822222 0.444444 0.555556 0.000000 0.000000 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.711111 0.000000 0.288889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTMGGCCA MEME-1 regular expression -------------------------------------------------------------------------------- CT[CA]GGCC[AG] -------------------------------------------------------------------------------- Time 7.86 secs. ******************************************************************************** ******************************************************************************** MOTIF TGGCCKAG MEME-2 width = 8 sites = 35 llr = 309 E-value = 2.2e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1::7: pos.-specific C 1::9a:1: probability G 1a9::6:a matrix T 9:1::41: bits 2.1 * * * 1.9 * * * 1.7 ** * * 1.5 **** * Relative 1.3 ***** * Entropy 1.1 ****** * (12.7 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGGCCGAG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:783441-783521 35 1.13e-05 TTGAAATTCG TGGCCGAG GCCTAGGATT chrIII:11290718-11290798 17 1.13e-05 ACACACCGGG TGGCCGAG TGGGGATTTC chrIII:5308418-5308498 38 1.13e-05 CGGGAGGCCA TGGCCGAG TTTTGACCTA chrIV:6887885-6887965 1 1.13e-05 . TGGCCGAG AATGTTTATG chrIII:12673516-12673596 50 1.13e-05 CACGGCGTGG TGGCCGAG ACCCCGACTC chrIV:10483881-10483961 3 2.49e-05 AA TGGCCTAG GTTCCACAAG chrIV:16415221-16415301 64 2.49e-05 CACGGCAGCG TGGCCTAG AAAACTCTT chrV:11644303-11644383 40 2.49e-05 CCAATGGCCG TGGCCTAG CTTTCTTGGT chrV:7465690-7465770 37 2.49e-05 GGCATGGACG TGGCCTAG AATTCCCCAA chrV:7084912-7084992 2 2.49e-05 C TGGCCTAG AAACCAACCT chrIII:4930398-4930478 37 2.49e-05 AAAACAGTGT TGGCCTAG TAAATGCGTG chrIII:4912471-4912551 64 2.49e-05 TTCTCGGCCG TGGCCTAG AATATTAGT chrI:5164963-5165043 52 2.49e-05 GTTTGCACCA TGGCCTAG AAACACAATG chrIII:7198999-7199079 18 2.49e-05 ATTGAACCAT TGGCCTAG AAAATTCAAA chrIII:4905466-4905546 7 2.49e-05 GGCATT TGGCCTAG CTTTCCGAGA chrV:20424963-20425043 11 2.49e-05 TTCCCAATGG TGGCCTAG AAAACCCCGA chrIII:4196712-4196792 42 2.49e-05 CAGGATCCAA TGGCCTAG CTTTACCCAG chrV:1871930-1872010 57 3.54e-05 CTGGTGGCCG TGGCCGCG AGCCGCGACG chrIV:4042402-4042482 43 3.54e-05 TCTTTTCTCG TGGCCGCG GCCTAGAAAT chrV:16022751-16022831 60 3.54e-05 GGTGGCCGCG TGGCCGCG GACTAAGTGA chrII:3482373-3482453 1 3.54e-05 . TGGCCGCG GCCTAAGAAC chrIII:12351453-12351533 65 6.02e-05 TTGCGCCGTG TGGACGAG AGAAACCT chrV:5917883-5917963 8 6.02e-05 GGTCGTG TGGACGAG GAAGCAAATG chrII:2451186-2451266 17 7.23e-05 TTGGCGCCGG TGGCCGTG GCCGGCGGCC chrX:14115659-14115739 31 7.23e-05 CCCACTTTCG TGGCCGTG TGGCCTAATG chrII:476186-476266 38 7.23e-05 TTGCCGACGA TGGCCGTG TGGGGGTTTC chrII:2889343-2889423 12 1.06e-04 TTGATTAACG CGGCCGAG AAATCGATTT chrII:3502782-3502862 24 1.06e-04 TTCCTCTTCG GGGCCGAG TTGGAGTTTT chrII:7537793-7537873 8 1.06e-04 TGGCCGC TGGACTAG TATTTGTACG chrIV:11315034-11315114 36 1.06e-04 ACACGCAACA TGGACTAG AATTTCGTGC chrII:6913448-6913528 18 1.34e-04 GAAAATTTAT TGTCCGAG AGGAGTACAC chrIII:5349405-5349485 17 1.34e-04 ACAAAAATGC TGTCCGAG AGGAGTCCGC chrIII:3175135-3175215 73 1.57e-04 CAAATGGGCG GGGCCTAG chrII:5358379-5358459 23 1.68e-04 ACCATTGCAG TGGCCGGG AGCGGTGCGA chrIII:159753-159833 62 2.39e-04 GCCTGAAAAC CGGCCGCG ATTTGTCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:783441-783521 1.1e-05 34_[+2]_38 chrIII:11290718-11290798 1.1e-05 16_[+2]_56 chrIII:5308418-5308498 1.1e-05 37_[+2]_35 chrIV:6887885-6887965 1.1e-05 [+2]_72 chrIII:12673516-12673596 1.1e-05 49_[+2]_23 chrIV:10483881-10483961 2.5e-05 2_[+2]_70 chrIV:16415221-16415301 2.5e-05 63_[+2]_9 chrV:11644303-11644383 2.5e-05 39_[+2]_33 chrV:7465690-7465770 2.5e-05 36_[+2]_36 chrV:7084912-7084992 2.5e-05 1_[+2]_71 chrIII:4930398-4930478 2.5e-05 36_[+2]_36 chrIII:4912471-4912551 2.5e-05 63_[+2]_9 chrI:5164963-5165043 2.5e-05 51_[+2]_21 chrIII:7198999-7199079 2.5e-05 17_[+2]_55 chrIII:4905466-4905546 2.5e-05 6_[+2]_66 chrV:20424963-20425043 2.5e-05 10_[+2]_62 chrIII:4196712-4196792 2.5e-05 41_[+2]_31 chrV:1871930-1872010 3.5e-05 56_[+2]_16 chrIV:4042402-4042482 3.5e-05 42_[+2]_30 chrV:16022751-16022831 3.5e-05 59_[+2]_13 chrII:3482373-3482453 3.5e-05 [+2]_72 chrIII:12351453-12351533 6e-05 64_[+2]_8 chrV:5917883-5917963 6e-05 7_[+2]_65 chrII:2451186-2451266 7.2e-05 16_[+2]_56 chrX:14115659-14115739 7.2e-05 30_[+2]_42 chrII:476186-476266 7.2e-05 37_[+2]_35 chrII:2889343-2889423 0.00011 11_[+2]_61 chrII:3502782-3502862 0.00011 23_[+2]_49 chrII:7537793-7537873 0.00011 7_[+2]_65 chrIV:11315034-11315114 0.00011 35_[+2]_37 chrII:6913448-6913528 0.00013 17_[+2]_55 chrIII:5349405-5349485 0.00013 16_[+2]_56 chrIII:3175135-3175215 0.00016 72_[+2] chrII:5358379-5358459 0.00017 22_[+2]_50 chrIII:159753-159833 0.00024 61_[+2]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGGCCKAG width=8 seqs=35 chrIII:783441-783521 ( 35) TGGCCGAG 1 chrIII:11290718-11290798 ( 17) TGGCCGAG 1 chrIII:5308418-5308498 ( 38) TGGCCGAG 1 chrIV:6887885-6887965 ( 1) TGGCCGAG 1 chrIII:12673516-12673596 ( 50) TGGCCGAG 1 chrIV:10483881-10483961 ( 3) TGGCCTAG 1 chrIV:16415221-16415301 ( 64) TGGCCTAG 1 chrV:11644303-11644383 ( 40) TGGCCTAG 1 chrV:7465690-7465770 ( 37) TGGCCTAG 1 chrV:7084912-7084992 ( 2) TGGCCTAG 1 chrIII:4930398-4930478 ( 37) TGGCCTAG 1 chrIII:4912471-4912551 ( 64) TGGCCTAG 1 chrI:5164963-5165043 ( 52) TGGCCTAG 1 chrIII:7198999-7199079 ( 18) TGGCCTAG 1 chrIII:4905466-4905546 ( 7) TGGCCTAG 1 chrV:20424963-20425043 ( 11) TGGCCTAG 1 chrIII:4196712-4196792 ( 42) TGGCCTAG 1 chrV:1871930-1872010 ( 57) TGGCCGCG 1 chrIV:4042402-4042482 ( 43) TGGCCGCG 1 chrV:16022751-16022831 ( 60) TGGCCGCG 1 chrII:3482373-3482453 ( 1) TGGCCGCG 1 chrIII:12351453-12351533 ( 65) TGGACGAG 1 chrV:5917883-5917963 ( 8) TGGACGAG 1 chrII:2451186-2451266 ( 17) TGGCCGTG 1 chrX:14115659-14115739 ( 31) TGGCCGTG 1 chrII:476186-476266 ( 38) TGGCCGTG 1 chrII:2889343-2889423 ( 12) CGGCCGAG 1 chrII:3502782-3502862 ( 24) GGGCCGAG 1 chrII:7537793-7537873 ( 8) TGGACTAG 1 chrIV:11315034-11315114 ( 36) TGGACTAG 1 chrII:6913448-6913528 ( 18) TGTCCGAG 1 chrIII:5349405-5349485 ( 17) TGTCCGAG 1 chrIII:3175135-3175215 ( 73) GGGCCTAG 1 chrII:5358379-5358459 ( 23) TGGCCGGG 1 chrIII:159753-159833 ( 62) CGGCCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.84661 E= 2.2e-010 -1177 -205 -201 168 -1177 -1177 212 -1177 -1177 -1177 203 -227 -117 190 -1177 -1177 -1177 208 -1177 -1177 -1177 -1177 131 64 153 -73 -301 -169 -1177 -1177 212 -1177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 2.2e-010 0.000000 0.057143 0.057143 0.885714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.942857 0.057143 0.114286 0.885714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.742857 0.142857 0.028571 0.085714 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGCCKAG MEME-2 regular expression -------------------------------------------------------------------------------- TGGCC[GT]AG -------------------------------------------------------------------------------- Time 11.58 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARAAAA MEME-3 width = 8 sites = 40 llr = 343 E-value = 1.1e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 67a4a8aa pos.-specific C :::::::: probability G 43:6:2:: matrix T :::::::: bits 2.1 1.9 * * ** 1.7 * * ** 1.5 * * ** Relative 1.3 * **** Entropy 1.1 ******** (12.4 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAGAAAA consensus GG A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:8516929-8517009 62 1.71e-05 TGCATACCAT AAAGAAAA AGCTCGGCCG chrII:11534715-11534795 48 1.71e-05 TATTTTTCTC AAAGAAAA CAATACAACG chrII:6913448-6913528 5 1.71e-05 TTCG AAAGAAAA TTTATTGTCC chrIII:8319285-8319365 54 1.71e-05 GGCCATTTTC AAAGAAAA CGGAGGGAGG chrII:15089558-15089638 8 1.71e-05 TAATTTC AAAGAAAA AGTTAAATAT chrIV:11179084-11179164 26 1.71e-05 TATTTTTCTC AAAGAAAA CGATACAACG chrIV:10481889-10481969 7 3.25e-05 TTGAAT GAAGAAAA TGAGGGGGGA chrII:2752655-2752735 11 3.25e-05 CAGAAAAAAT GAAGAAAA TCCATGGAAA chrIV:8015966-8016046 18 3.25e-05 TATTTTTCTC GAAGAAAA CGATACAACG chrV:1197397-1197477 47 3.25e-05 GTATCTTCTA GAAGAAAA TTTCAAAAAT chrIV:4702226-4702306 46 3.25e-05 GTATCTTCTA GAAGAAAA TTTCAAAAAT chrIII:10811214-10811294 52 3.25e-05 GTATCTTCTA GAAGAAAA TTTCAAAAAT chrI:10469107-10469187 48 3.25e-05 GTATCTTCTA GAAGAAAA TTTCAAAAAT chrI:27063-27143 9 5.15e-05 TAAAACTT AAAAAAAA CTACAAAATT chrIV:15561449-15561529 24 5.15e-05 ACAAAACTGC AAAAAAAA ACGCGATGAG chrII:8137465-8137545 13 5.15e-05 AGATTCGCTG AAAAAAAA TGAAGTTGTC chrI:7374936-7375016 69 5.15e-05 TCTGAAATGA AAAAAAAA CAAG chrIII:4506001-4506081 39 6.86e-05 AAGGAAACGG GAAAAAAA TGGAAGGAAA chrI:11585327-11585407 31 6.86e-05 TTAAAAAAGG GAAAAAAA GAACTGAAGA chrI:14756432-14756512 8 6.86e-05 GGACTAG GAAAAAAA TGGAGCCGCT chrII:14428731-14428811 35 6.86e-05 TGATGGGTGT GAAAAAAA TTTTCAAAAA chrII:4955562-4955642 70 6.86e-05 GACAGAACAT GAAAAAAA TTA chrIII:12273736-12273816 47 8.40e-05 AGGAGAGCGC AGAGAAAA ACAGGGTTGT chrV:12870085-12870165 41 8.40e-05 GCGGGATGGA AGAGAAAA CGCGCGCACT chrX:993074-993154 61 8.40e-05 GAAACGCCGG AGAGAAAA CGCACAAAGA chrI:5176389-5176469 28 8.40e-05 TTTTCTTGAC AGAGAAAA AGTGTGCGCA chrI:4247531-4247611 8 8.40e-05 AATTGAC AGAGAAAA ATGGAAAACA chrX:9997184-9997264 47 8.40e-05 AAGCGAAAGG AGAGAAAA ACATTTCAAA chrI:8124509-8124589 46 9.94e-05 ACGCAGATAT AAAGAGAA CATAGAGGAG chrV:9980917-9980997 58 1.44e-04 AGAATTAACA AGAAAAAA TAATTTTAAA chrIV:8973703-8973783 6 1.44e-04 ATATG GAAGAGAA ATCAATTGGG chrII:11751701-11751781 64 1.44e-04 CTCGGCCGTG GAAGAGAA GACGGAGGA chrIII:8144764-8144844 64 1.44e-04 TCAGTTTTTG AGAAAAAA GTTAAAAAA chrII:1134700-1134780 47 1.44e-04 GCGTTGCGTG AGAAAAAA TGCGTTTTGT chrIII:5349405-5349485 47 1.61e-04 GAGATGGACG AAAAAGAA AGCTAGGCCA chrV:7084912-7084992 63 1.61e-04 CGGCAATTCA AAAAAGAA TAACAAGGGT chrIII:12673516-12673596 3 1.61e-04 aa aaaaagaa tTGTTTGTCC chrIV:13487165-13487245 53 1.92e-04 GAAGATCTAC GAAAAGAA GATCTACGAA chrIII:4656595-4656675 66 2.06e-04 AACGACGATA AGAGAGAA AGAAATG chrII:14438169-14438249 52 2.18e-04 CGGTAGACAA GGAGAGAA CGTGGTAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:8516929-8517009 1.7e-05 61_[+3]_11 chrII:11534715-11534795 1.7e-05 47_[+3]_25 chrII:6913448-6913528 1.7e-05 4_[+3]_68 chrIII:8319285-8319365 1.7e-05 53_[+3]_19 chrII:15089558-15089638 1.7e-05 7_[+3]_65 chrIV:11179084-11179164 1.7e-05 25_[+3]_47 chrIV:10481889-10481969 3.2e-05 6_[+3]_66 chrII:2752655-2752735 3.2e-05 10_[+3]_62 chrIV:8015966-8016046 3.2e-05 17_[+3]_55 chrV:1197397-1197477 3.2e-05 46_[+3]_26 chrIV:4702226-4702306 3.2e-05 45_[+3]_27 chrIII:10811214-10811294 3.2e-05 51_[+3]_21 chrI:10469107-10469187 3.2e-05 47_[+3]_25 chrI:27063-27143 5.2e-05 8_[+3]_64 chrIV:15561449-15561529 5.2e-05 23_[+3]_49 chrII:8137465-8137545 5.2e-05 12_[+3]_60 chrI:7374936-7375016 5.2e-05 68_[+3]_4 chrIII:4506001-4506081 6.9e-05 38_[+3]_34 chrI:11585327-11585407 6.9e-05 30_[+3]_42 chrI:14756432-14756512 6.9e-05 7_[+3]_65 chrII:14428731-14428811 6.9e-05 34_[+3]_38 chrII:4955562-4955642 6.9e-05 69_[+3]_3 chrIII:12273736-12273816 8.4e-05 46_[+3]_26 chrV:12870085-12870165 8.4e-05 40_[+3]_32 chrX:993074-993154 8.4e-05 60_[+3]_12 chrI:5176389-5176469 8.4e-05 27_[+3]_45 chrI:4247531-4247611 8.4e-05 7_[+3]_65 chrX:9997184-9997264 8.4e-05 46_[+3]_26 chrI:8124509-8124589 9.9e-05 45_[+3]_27 chrV:9980917-9980997 0.00014 57_[+3]_15 chrIV:8973703-8973783 0.00014 5_[+3]_67 chrII:11751701-11751781 0.00014 63_[+3]_9 chrIII:8144764-8144844 0.00014 63_[+3]_9 chrII:1134700-1134780 0.00014 46_[+3]_26 chrIII:5349405-5349485 0.00016 46_[+3]_26 chrV:7084912-7084992 0.00016 62_[+3]_10 chrIII:12673516-12673596 0.00016 2_[+3]_70 chrIV:13487165-13487245 0.00019 52_[+3]_20 chrIII:4656595-4656675 0.00021 65_[+3]_7 chrII:14438169-14438249 0.00022 51_[+3]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAARAAAA width=8 seqs=40 chrII:8516929-8517009 ( 62) AAAGAAAA 1 chrII:11534715-11534795 ( 48) AAAGAAAA 1 chrII:6913448-6913528 ( 5) AAAGAAAA 1 chrIII:8319285-8319365 ( 54) AAAGAAAA 1 chrII:15089558-15089638 ( 8) AAAGAAAA 1 chrIV:11179084-11179164 ( 26) AAAGAAAA 1 chrIV:10481889-10481969 ( 7) GAAGAAAA 1 chrII:2752655-2752735 ( 11) GAAGAAAA 1 chrIV:8015966-8016046 ( 18) GAAGAAAA 1 chrV:1197397-1197477 ( 47) GAAGAAAA 1 chrIV:4702226-4702306 ( 46) GAAGAAAA 1 chrIII:10811214-10811294 ( 52) GAAGAAAA 1 chrI:10469107-10469187 ( 48) GAAGAAAA 1 chrI:27063-27143 ( 9) AAAAAAAA 1 chrIV:15561449-15561529 ( 24) AAAAAAAA 1 chrII:8137465-8137545 ( 13) AAAAAAAA 1 chrI:7374936-7375016 ( 69) AAAAAAAA 1 chrIII:4506001-4506081 ( 39) GAAAAAAA 1 chrI:11585327-11585407 ( 31) GAAAAAAA 1 chrI:14756432-14756512 ( 8) GAAAAAAA 1 chrII:14428731-14428811 ( 35) GAAAAAAA 1 chrII:4955562-4955642 ( 70) GAAAAAAA 1 chrIII:12273736-12273816 ( 47) AGAGAAAA 1 chrV:12870085-12870165 ( 41) AGAGAAAA 1 chrX:993074-993154 ( 61) AGAGAAAA 1 chrI:5176389-5176469 ( 28) AGAGAAAA 1 chrI:4247531-4247611 ( 8) AGAGAAAA 1 chrX:9997184-9997264 ( 47) AGAGAAAA 1 chrI:8124509-8124589 ( 46) AAAGAGAA 1 chrV:9980917-9980997 ( 58) AGAAAAAA 1 chrIV:8973703-8973783 ( 6) GAAGAGAA 1 chrII:11751701-11751781 ( 64) GAAGAGAA 1 chrIII:8144764-8144844 ( 64) AGAAAAAA 1 chrII:1134700-1134780 ( 47) AGAAAAAA 1 chrIII:5349405-5349485 ( 47) AAAAAGAA 1 chrV:7084912-7084992 ( 63) AAAAAGAA 1 chrIII:12673516-12673596 ( 3) AAAAAGAA 1 chrIV:13487165-13487245 ( 53) GAAAAGAA 1 chrIII:4656595-4656675 ( 66) AGAGAGAA 1 chrII:14438169-14438249 ( 52) GGAGAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.8918 E= 1.1e-011 122 -1197 79 -1197 150 -1197 25 -1197 196 -1197 -1197 -1197 64 -1197 138 -1197 196 -1197 -1197 -1197 159 -1197 -4 -1197 196 -1197 -1197 -1197 196 -1197 -1197 -1197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.1e-011 0.600000 0.000000 0.400000 0.000000 0.725000 0.000000 0.275000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.775000 0.000000 0.225000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAAAA MEME-3 regular expression -------------------------------------------------------------------------------- [AG][AG]A[GA]A[AG]AA -------------------------------------------------------------------------------- Time 15.17 secs. ******************************************************************************** ******************************************************************************** MOTIF CTTYTCTC MEME-4 width = 8 sites = 38 llr = 319 E-value = 1.3e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 7237:9:a probability G :::::::: matrix T 3873a1a: bits 2.1 * 1.9 * ** 1.7 **** 1.5 **** Relative 1.3 * **** Entropy 1.1 ******** (12.1 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTTCTCTC consensus T CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:4224816-4224896 34 1.83e-05 TTCAACCCGT CTTCTCTC CCATCTAACC chrI:14787898-14787978 15 1.83e-05 TACTGCGCCT CTTCTCTC TCACGCGTGA chrIV:17099260-17099340 16 1.83e-05 TCGACGAGAT CTTCTCTC CGTGGTGTCT chrIV:10085860-10085940 72 1.83e-05 TCAAATGTGA CTTCTCTC T chrI:12921065-12921145 69 1.83e-05 TCTTTCTCTT CTTCTCTC TATT chrI:1823222-1823302 44 1.83e-05 CGTGAACAAT CTTCTCTC GAATCGCGAG chrIV:6887885-6887965 42 1.83e-05 GGACGCGCAA CTTCTCTC TCTACGTCTC chrI:8119345-8119425 64 1.83e-05 ATTGGATGCT CTTCTCTC GTCTCACAC chrIV:10483881-10483961 48 5.53e-05 GGTTTGTGGA CTCCTCTC GGATAAACAG chrIV:4042402-4042482 34 5.53e-05 AACTCGCGCT CTTTTCTC GTGGCCGCGG chrV:16401675-16401755 66 5.53e-05 CGCGCTCGGA CTCCTCTC GGAGGAG chrI:1416166-1416246 34 5.53e-05 GATGCATTGC CTCCTCTC AAGCGCGCCC chrII:10538119-10538199 42 5.53e-05 CGGCCGTGTA CTCCTCTC GGGCAATTAA chrII:4791445-4791525 45 5.53e-05 CGGCCGTGTA CTCCTCTC GGACAATATA chrV:2638682-2638762 53 5.53e-05 GCGCTGCGGA CTCCTCTC AGACAACGTT chrIII:5069018-5069098 3 5.53e-05 TA CTCCTCTC GGACTAACCC chrII:7676565-7676645 34 5.53e-05 CCACACACTT CTCCTCTC GTTGGTATTC chrV:18981156-18981236 51 5.53e-05 CGCCGGTGTA CTCCTCTC CGACAACGGG chrII:10684889-10684969 9 5.53e-05 CAAGCCCC CTTTTCTC AATTGCTAAT chrIV:8629642-8629722 58 7.67e-05 CATCCGTCTC TTTCTCTC AAATCCAGGA chrV:7465690-7465770 55 7.67e-05 AATTCCCCAA TTTCTCTC TTTCTCTGCC chrIV:13533247-13533327 57 7.67e-05 GCGTCTCCCG TTTCTCTC ATCTCGATTT chrI:933477-933557 34 7.67e-05 ACCAATTATC TTTCTCTC TGtggcttcc chrX:1064165-1064245 30 9.24e-05 CACATCTCTC CCTCTCTC TGCTCCTTCG chrX:993074-993154 15 1.11e-04 CTTGCCCCTA CTCTTCTC TTTCTTGATT chrII:11534715-11534795 40 1.54e-04 CCAAACGCTA TTTTTCTC AAAGAAAACA chrIV:8015966-8016046 10 1.54e-04 CAAACGCTA TTTTTCTC GAAGAAAACG chrV:9980917-9980997 31 1.54e-04 TAAAACTGTA TTTTTCTC AATAGAGCGA chrIII:6551497-6551577 67 1.54e-04 CAAAACGCAT TTTTTCTC ACGCAA chrIV:11179084-11179164 18 1.54e-04 CCAAACGCTA TTTTTCTC AAAGAAAACG chrIV:4401731-4401811 54 1.54e-04 CAAAACGCAA TTTTTCTC ACGCAACGCA chrIII:10460716-10460796 67 1.86e-04 CGTCACAGAA CCTTTCTC TACAGA chrV:10526107-10526187 24 1.86e-04 GTTAGGCCAT CCTTTCTC ATCCTACTCT chrX:13598130-13598210 73 1.86e-04 TCTGCCATTT Cctttctc chrII:15254137-15254217 24 1.86e-04 CAACTGACTG CCTTTCTC CCCTCATCAC chrI:1435569-1435649 2 2.04e-04 C TCTCTCTC TATGATAATG chrI:9855538-9855618 13 2.47e-04 GATGGCTTTC CTTCTTTC GTTTCCTTCT chrI:7772639-7772719 13 3.67e-04 ATTGAACGCA TTTCTTTC AAACTTTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:4224816-4224896 1.8e-05 33_[+4]_39 chrI:14787898-14787978 1.8e-05 14_[+4]_58 chrIV:17099260-17099340 1.8e-05 15_[+4]_57 chrIV:10085860-10085940 1.8e-05 71_[+4]_1 chrI:12921065-12921145 1.8e-05 68_[+4]_4 chrI:1823222-1823302 1.8e-05 43_[+4]_29 chrIV:6887885-6887965 1.8e-05 41_[+4]_31 chrI:8119345-8119425 1.8e-05 63_[+4]_9 chrIV:10483881-10483961 5.5e-05 47_[+4]_25 chrIV:4042402-4042482 5.5e-05 33_[+4]_39 chrV:16401675-16401755 5.5e-05 65_[+4]_7 chrI:1416166-1416246 5.5e-05 33_[+4]_39 chrII:10538119-10538199 5.5e-05 41_[+4]_31 chrII:4791445-4791525 5.5e-05 44_[+4]_28 chrV:2638682-2638762 5.5e-05 52_[+4]_20 chrIII:5069018-5069098 5.5e-05 2_[+4]_70 chrII:7676565-7676645 5.5e-05 33_[+4]_39 chrV:18981156-18981236 5.5e-05 50_[+4]_22 chrII:10684889-10684969 5.5e-05 8_[+4]_64 chrIV:8629642-8629722 7.7e-05 57_[+4]_15 chrV:7465690-7465770 7.7e-05 54_[+4]_18 chrIV:13533247-13533327 7.7e-05 56_[+4]_16 chrI:933477-933557 7.7e-05 33_[+4]_39 chrX:1064165-1064245 9.2e-05 29_[+4]_43 chrX:993074-993154 0.00011 14_[+4]_58 chrII:11534715-11534795 0.00015 39_[+4]_33 chrIV:8015966-8016046 0.00015 9_[+4]_63 chrV:9980917-9980997 0.00015 30_[+4]_42 chrIII:6551497-6551577 0.00015 66_[+4]_6 chrIV:11179084-11179164 0.00015 17_[+4]_55 chrIV:4401731-4401811 0.00015 53_[+4]_19 chrIII:10460716-10460796 0.00019 66_[+4]_6 chrV:10526107-10526187 0.00019 23_[+4]_49 chrX:13598130-13598210 0.00019 72_[+4] chrII:15254137-15254217 0.00019 23_[+4]_49 chrI:1435569-1435649 0.0002 1_[+4]_71 chrI:9855538-9855618 0.00025 12_[+4]_60 chrI:7772639-7772719 0.00037 12_[+4]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTTYTCTC width=8 seqs=38 chrI:4224816-4224896 ( 34) CTTCTCTC 1 chrI:14787898-14787978 ( 15) CTTCTCTC 1 chrIV:17099260-17099340 ( 16) CTTCTCTC 1 chrIV:10085860-10085940 ( 72) CTTCTCTC 1 chrI:12921065-12921145 ( 69) CTTCTCTC 1 chrI:1823222-1823302 ( 44) CTTCTCTC 1 chrIV:6887885-6887965 ( 42) CTTCTCTC 1 chrI:8119345-8119425 ( 64) CTTCTCTC 1 chrIV:10483881-10483961 ( 48) CTCCTCTC 1 chrIV:4042402-4042482 ( 34) CTTTTCTC 1 chrV:16401675-16401755 ( 66) CTCCTCTC 1 chrI:1416166-1416246 ( 34) CTCCTCTC 1 chrII:10538119-10538199 ( 42) CTCCTCTC 1 chrII:4791445-4791525 ( 45) CTCCTCTC 1 chrV:2638682-2638762 ( 53) CTCCTCTC 1 chrIII:5069018-5069098 ( 3) CTCCTCTC 1 chrII:7676565-7676645 ( 34) CTCCTCTC 1 chrV:18981156-18981236 ( 51) CTCCTCTC 1 chrII:10684889-10684969 ( 9) CTTTTCTC 1 chrIV:8629642-8629722 ( 58) TTTCTCTC 1 chrV:7465690-7465770 ( 55) TTTCTCTC 1 chrIV:13533247-13533327 ( 57) TTTCTCTC 1 chrI:933477-933557 ( 34) TTTCTCTC 1 chrX:1064165-1064245 ( 30) CCTCTCTC 1 chrX:993074-993154 ( 15) CTCTTCTC 1 chrII:11534715-11534795 ( 40) TTTTTCTC 1 chrIV:8015966-8016046 ( 10) TTTTTCTC 1 chrV:9980917-9980997 ( 31) TTTTTCTC 1 chrIII:6551497-6551577 ( 67) TTTTTCTC 1 chrIV:11179084-11179164 ( 18) TTTTTCTC 1 chrIV:4401731-4401811 ( 54) TTTTTCTC 1 chrIII:10460716-10460796 ( 67) CCTTTCTC 1 chrV:10526107-10526187 ( 24) CCTTTCTC 1 chrX:13598130-13598210 ( 73) CCTTTCTC 1 chrII:15254137-15254217 ( 24) CCTTTCTC 1 chrI:1435569-1435649 ( 2) TCTCTCTC 1 chrI:9855538-9855618 ( 13) CTTCTTTC 1 chrI:7772639-7772719 ( 13) TTTCTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.8035 E= 1.3e-005 -1189 153 -1189 19 -1189 -58 -1189 161 -1189 15 -1189 142 -1189 147 -1189 31 -1189 -1189 -1189 186 -1189 200 -1189 -239 -1189 -1189 -1189 186 -1189 208 -1189 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.3e-005 0.000000 0.684211 0.000000 0.315789 0.000000 0.157895 0.000000 0.842105 0.000000 0.263158 0.000000 0.736842 0.000000 0.657895 0.000000 0.342105 0.000000 0.000000 0.000000 1.000000 0.000000 0.947368 0.000000 0.052632 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTYTCTC MEME-4 regular expression -------------------------------------------------------------------------------- [CT]T[TC][CT]TCTC -------------------------------------------------------------------------------- Time 18.71 secs. ******************************************************************************** ******************************************************************************** MOTIF GRRARGAG MEME-5 width = 8 sites = 38 llr = 314 E-value = 1.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :7687:7: pos.-specific C :::::::: probability G a3423a3a matrix T :::::::: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 ******** (11.9 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAAAGAG consensus GGGG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:9307013-9307093 4 1.38e-05 AAT GAAAAGAG CATCAGTCAA chrII:10804589-10804669 8 1.38e-05 TTTTCGA GAAAAGAG TAGATTTCTA chrX:9997184-9997264 23 2.62e-05 AGACGAGAGG GAGAAGAG AAAAATAAGC chrIV:10481889-10481969 22 5.11e-05 AAATGAGGGG GGAAAGAG GGGTTAGAGA chrIV:8629642-8629722 73 5.11e-05 CTCAAATCCA GGAAAGAG chrI:3350051-3350131 33 5.11e-05 ACTCTCGATG GAAAGGAG ACGGAGAAAC chrIII:3499984-3500064 64 5.11e-05 GAGGCCCCAC GGAAAGAG GATCTGCGA chrI:8119345-8119425 19 5.11e-05 GGAAGATGAG GGAAAGAG AGAGGAAGCG chrI:10474757-10474837 1 8.58e-05 . GAGAGGAG TACACATCCG chrIV:16415221-16415301 44 8.58e-05 CCCATTGTCC GAGAGGAG TACACGGCAG chrII:11534715-11534795 8 8.58e-05 GAGCAAC GAAAAGGG GATCTGGCAC chrII:10538119-10538199 2 8.58e-05 C GAGAGGAG TACATGGCCG chrV:15610522-15610602 65 8.58e-05 AGAGGAGGGG GAGAGGAG CGGTCAAA chrI:12921065-12921145 16 8.58e-05 TGTTCGGGTT GAAAAGGG GAAGAAGGAG chrIII:4912471-4912551 31 8.58e-05 TGTCTTGTCC GAGAGGAG TACACGACAT chrI:12899150-12899230 53 8.58e-05 GGGGATCTGC GAAAAGGG GATCGGCAAA chrX:7651311-7651391 54 8.58e-05 GAGGCGTCCG GAGAGGAG AGGGCGGCAG chrV:11655171-11655251 28 8.58e-05 CGGACGTGTG GAAAAGGG GCGGGCGCTC chrV:13111775-13111855 39 8.58e-05 GACGGGCGGT GGGAAGAG GACGATGAGC chrIV:15561449-15561529 47 8.58e-05 ATGAGGAAGA GAAAAGGG GGAAGAAACG chrIII:6551497-6551577 26 8.58e-05 GGGGAGATAC GAAAAGGG GAGCTGGCAC chrV:4181868-4181948 10 8.58e-05 AGGCCCCAC GAAAAGGG GATCTGCGAG chrIV:4401731-4401811 13 8.58e-05 GGGGAGCAAC GAAAAGGG GAGCTGGCAC chrIII:11848458-11848538 68 8.58e-05 CCCCACCACG GAAAAGGG ATCTG chrX:1082089-1082169 10 8.58e-05 GAAGGGCGG GAGAGGAG TCGCTGTGGC chrI:11585327-11585407 44 1.09e-04 AAAAAGAACT GAAGAGAG TGGGATTCGA chrI:15014009-15014089 52 1.21e-04 TAAAATGGAG GGAAGGAG CAGAATTTGA chrIII:12273736-12273816 36 1.32e-04 TGTGGAGAAC GAGGAGAG CGCAGAGAAA chrI:8124509-8124589 58 1.32e-04 AGAGAACATA GAGGAGAG TGTCGCGATT chrIV:1824173-1824253 69 1.32e-04 GGTTGGCAAG GAGGAGAG AGGG chrIII:10016834-10016914 37 1.32e-04 ggggactcgt gaggagag tgtgagtgCG chrII:4038828-4038908 2 1.64e-04 A GGGAGGAG CCGCCCTTTT chrI:788163-788243 50 1.84e-04 AAGAAGCGGG GGGAAGGG GAGCCCCCCT chrII:4456306-4456386 5 2.07e-04 AGAC GGAGAGAG ACACTCACGC chrX:4125592-4125672 3 2.07e-04 AG GGAGAGAG CACTCCGCAA chrII:3527744-3527824 5 2.67e-04 TTGC GGGAGGGG GAGTGACACT chrIII:8319285-8319365 63 2.77e-04 CAAAGAAAAC GGAGGGAG GTTCAAAATT chrIII:8588887-8588967 2 2.77e-04 C GGAGGGAG CCGAGCACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:9307013-9307093 1.4e-05 3_[+5]_69 chrII:10804589-10804669 1.4e-05 7_[+5]_65 chrX:9997184-9997264 2.6e-05 22_[+5]_50 chrIV:10481889-10481969 5.1e-05 21_[+5]_51 chrIV:8629642-8629722 5.1e-05 72_[+5] chrI:3350051-3350131 5.1e-05 32_[+5]_40 chrIII:3499984-3500064 5.1e-05 63_[+5]_9 chrI:8119345-8119425 5.1e-05 18_[+5]_54 chrI:10474757-10474837 8.6e-05 [+5]_72 chrIV:16415221-16415301 8.6e-05 43_[+5]_29 chrII:11534715-11534795 8.6e-05 7_[+5]_65 chrII:10538119-10538199 8.6e-05 1_[+5]_71 chrV:15610522-15610602 8.6e-05 64_[+5]_8 chrI:12921065-12921145 8.6e-05 15_[+5]_57 chrIII:4912471-4912551 8.6e-05 30_[+5]_42 chrI:12899150-12899230 8.6e-05 52_[+5]_20 chrX:7651311-7651391 8.6e-05 53_[+5]_19 chrV:11655171-11655251 8.6e-05 27_[+5]_45 chrV:13111775-13111855 8.6e-05 38_[+5]_34 chrIV:15561449-15561529 8.6e-05 46_[+5]_26 chrIII:6551497-6551577 8.6e-05 25_[+5]_47 chrV:4181868-4181948 8.6e-05 9_[+5]_63 chrIV:4401731-4401811 8.6e-05 12_[+5]_60 chrIII:11848458-11848538 8.6e-05 67_[+5]_5 chrX:1082089-1082169 8.6e-05 9_[+5]_63 chrI:11585327-11585407 0.00011 43_[+5]_29 chrI:15014009-15014089 0.00012 51_[+5]_21 chrIII:12273736-12273816 0.00013 35_[+5]_37 chrI:8124509-8124589 0.00013 57_[+5]_15 chrIV:1824173-1824253 0.00013 68_[+5]_4 chrIII:10016834-10016914 0.00013 36_[+5]_36 chrII:4038828-4038908 0.00016 1_[+5]_71 chrI:788163-788243 0.00018 49_[+5]_23 chrII:4456306-4456386 0.00021 4_[+5]_68 chrX:4125592-4125672 0.00021 2_[+5]_70 chrII:3527744-3527824 0.00027 4_[+5]_68 chrIII:8319285-8319365 0.00028 62_[+5]_10 chrIII:8588887-8588967 0.00028 1_[+5]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GRRARGAG width=8 seqs=38 chrII:9307013-9307093 ( 4) GAAAAGAG 1 chrII:10804589-10804669 ( 8) GAAAAGAG 1 chrX:9997184-9997264 ( 23) GAGAAGAG 1 chrIV:10481889-10481969 ( 22) GGAAAGAG 1 chrIV:8629642-8629722 ( 73) GGAAAGAG 1 chrI:3350051-3350131 ( 33) GAAAGGAG 1 chrIII:3499984-3500064 ( 64) GGAAAGAG 1 chrI:8119345-8119425 ( 19) GGAAAGAG 1 chrI:10474757-10474837 ( 1) GAGAGGAG 1 chrIV:16415221-16415301 ( 44) GAGAGGAG 1 chrII:11534715-11534795 ( 8) GAAAAGGG 1 chrII:10538119-10538199 ( 2) GAGAGGAG 1 chrV:15610522-15610602 ( 65) GAGAGGAG 1 chrI:12921065-12921145 ( 16) GAAAAGGG 1 chrIII:4912471-4912551 ( 31) GAGAGGAG 1 chrI:12899150-12899230 ( 53) GAAAAGGG 1 chrX:7651311-7651391 ( 54) GAGAGGAG 1 chrV:11655171-11655251 ( 28) GAAAAGGG 1 chrV:13111775-13111855 ( 39) GGGAAGAG 1 chrIV:15561449-15561529 ( 47) GAAAAGGG 1 chrIII:6551497-6551577 ( 26) GAAAAGGG 1 chrV:4181868-4181948 ( 10) GAAAAGGG 1 chrIV:4401731-4401811 ( 13) GAAAAGGG 1 chrIII:11848458-11848538 ( 68) GAAAAGGG 1 chrX:1082089-1082169 ( 10) GAGAGGAG 1 chrI:11585327-11585407 ( 44) GAAGAGAG 1 chrI:15014009-15014089 ( 52) GGAAGGAG 1 chrIII:12273736-12273816 ( 36) GAGGAGAG 1 chrI:8124509-8124589 ( 58) GAGGAGAG 1 chrIV:1824173-1824253 ( 69) GAGGAGAG 1 chrIII:10016834-10016914 ( 37) GAGGAGAG 1 chrII:4038828-4038908 ( 2) GGGAGGAG 1 chrI:788163-788243 ( 50) GGGAAGGG 1 chrII:4456306-4456386 ( 5) GGAGAGAG 1 chrX:4125592-4125672 ( 3) GGAGAGAG 1 chrII:3527744-3527824 ( 5) GGGAGGGG 1 chrIII:8319285-8319365 ( 63) GGAGGGAG 1 chrIII:8588887-8588967 ( 2) GGAGGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.9532 E= 1.0e-003 -1189 -1189 212 -1189 136 -1189 57 -1189 117 -1189 87 -1189 157 -1189 4 -1189 136 -1189 57 -1189 -1189 -1189 212 -1189 147 -1189 33 -1189 -1189 -1189 212 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.0e-003 0.000000 0.000000 1.000000 0.000000 0.657895 0.000000 0.342105 0.000000 0.578947 0.000000 0.421053 0.000000 0.763158 0.000000 0.236842 0.000000 0.657895 0.000000 0.342105 0.000000 0.000000 0.000000 1.000000 0.000000 0.710526 0.000000 0.289474 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRRARGAG MEME-5 regular expression -------------------------------------------------------------------------------- G[AG][AG][AG][AG]G[AG]G -------------------------------------------------------------------------------- Time 22.18 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1073984-1074064 2.60e-01 80 chrX:6687841-6687921 3.43e-01 80 chrII:15254137-15254217 1.57e-01 80 chrI:8119345-8119425 1.33e-03 18_[+5(5.11e-05)]_37_[+4(1.83e-05)]_\ 9 chrII:10804589-10804669 6.26e-03 7_[+5(1.38e-05)]_65 chrX:1082089-1082169 2.73e-02 9_[+5(8.58e-05)]_63 chrI:7374936-7375016 5.26e-02 67_[+3(5.15e-05)]_5 chrIV:1687272-1687352 1.81e-02 80 chrII:8137465-8137545 1.43e-01 12_[+3(5.15e-05)]_60 chrIII:6013145-6013225 7.89e-01 80 chrV:16553139-16553219 1.23e-01 80 chrII:10681967-10682047 7.58e-01 80 chrX:1064165-1064245 4.57e-02 29_[+4(9.24e-05)]_43 chrI:10469107-10469187 1.59e-01 47_[+3(3.25e-05)]_25 chrIV:14032725-14032805 8.61e-01 80 chrIII:10856996-10857076 9.78e-01 80 chrII:3482373-3482453 1.38e-02 [+2(3.54e-05)]_14_[+1(9.98e-05)]_50 chrV:3717813-3717893 1.39e-01 80 chrI:13421150-13421230 9.83e-01 80 chrIII:10436177-10436257 9.61e-01 80 chrI:3176598-3176678 6.63e-02 8_[+1(7.92e-05)]_64 chrIII:10811214-10811294 1.59e-01 51_[+3(3.25e-05)]_21 chrIII:12673516-12673596 9.65e-06 49_[+2(1.13e-05)]_7_[+1(1.19e-05)]_\ 8 chrV:14443761-14443841 8.92e-01 80 chrIV:11872050-11872130 8.34e-02 80 chrIII:3499984-3500064 7.12e-03 63_[+5(5.11e-05)]_9 chrIV:4702226-4702306 1.61e-01 45_[+3(3.25e-05)]_27 chrIV:12621639-12621719 7.89e-01 80 chrI:7251587-7251667 9.58e-01 80 chrX:5056379-5056459 8.27e-01 80 chrV:7217947-7218027 1.90e-02 80 chrIII:11848458-11848538 7.32e-02 48_[+5(5.11e-05)]_11_[+5(8.58e-05)]_\ 5 chrI:273727-273807 1.58e-01 80 chrIII:3476395-3476475 3.66e-01 80 chrII:7563780-7563860 7.09e-01 80 chrIII:13032584-13032664 9.05e-01 80 chrI:5659149-5659229 1.03e-02 23_[+1(2.49e-05)]_49 chrII:4955562-4955642 6.89e-02 69_[+3(6.86e-05)]_3 chrIV:13487165-13487245 1.15e-01 80 chrII:8945578-8945658 9.08e-01 80 chrIII:931569-931649 5.08e-01 80 chrIV:1845076-1845156 3.57e-01 80 chrIV:4401731-4401811 9.88e-04 12_[+5(8.58e-05)]_60 chrI:933477-933557 3.51e-01 33_[+4(7.67e-05)]_39 chrV:4181868-4181948 1.86e-01 9_[+5(8.58e-05)]_63 chrIII:8588887-8588967 1.27e-01 80 chrIII:10016834-10016914 7.55e-02 80 chrII:5836520-5836600 2.51e-01 80 chrII:1134700-1134780 1.77e-01 80 chrV:16022751-16022831 1.52e-02 51_[+2(3.54e-05)]_[+2(3.54e-05)]_13 chrIII:11091834-11091914 6.76e-01 80 chrIV:6855111-6855191 5.62e-01 80 chrI:2487859-2487939 9.81e-01 80 chrIV:11179084-11179164 2.09e-03 25_[+3(1.71e-05)]_47 chrX:13143348-13143428 8.36e-01 80 chrX:1058091-1058171 1.31e-01 80 chrII:10684889-10684969 7.56e-02 8_[+4(5.53e-05)]_64 chrII:14428731-14428811 3.92e-02 34_[+3(6.86e-05)]_38 chrIII:6551497-6551577 3.68e-03 10_[+5(8.58e-05)]_7_[+5(8.58e-05)]_\ 47 chrII:12042357-12042437 5.84e-01 80 chrIII:3424057-3424137 1.76e-01 80 chrV:17548740-17548820 5.96e-01 80 chrIV:6887885-6887965 8.93e-04 [+2(1.13e-05)]_33_[+4(1.83e-05)]_31 chrII:476186-476266 9.40e-02 37_[+2(7.23e-05)]_35 chrV:3218775-3218855 4.90e-01 80 chrII:12348868-12348948 3.56e-01 80 chrI:4967570-4967650 3.41e-01 80 chrIV:2824566-2824646 8.75e-01 80 chrI:15014009-15014089 1.22e-03 25_[+1(2.49e-05)]_47 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chrI:10232740-10232820 3.56e-01 80 chrIII:8144764-8144844 1.57e-04 43_[+1(2.49e-05)]_29 chrV:18981156-18981236 3.07e-04 31_[+1(2.49e-05)]_11_[+4(5.53e-05)]_\ 22 chrX:9997184-9997264 3.16e-03 22_[+5(2.62e-05)]_10_[+5(5.11e-05)]_\ 32 chrI:1415965-1416045 6.40e-01 80 chrIII:10123779-10123859 3.23e-01 80 chrI:2710693-2710773 9.25e-01 80 chrII:15089558-15089638 1.76e-04 7_[+3(1.71e-05)]_35_[+1(2.49e-05)]_\ [+1(9.98e-05)]_14 chrIII:4905466-4905546 9.87e-04 6_[+2(2.49e-05)]_12_[+1(1.19e-05)]_\ 46 chrII:11751701-11751781 1.01e-05 53_[+1(3.56e-05)]_19 chrIV:8973703-8973783 6.01e-04 36_[+1(9.98e-05)]_36 chrIV:2033196-2033276 7.38e-01 80 chrII:14528484-14528564 9.73e-01 80 chrIII:8262747-8262827 5.69e-01 80 chrII:12175454-12175534 6.52e-01 80 chrIV:11310757-11310837 1.44e-02 80 chrI:7772639-7772719 1.67e-01 80 chrI:10642450-10642530 1.54e-01 80 chrI:8369761-8369841 8.23e-01 80 chrI:4247531-4247611 1.12e-03 7_[+3(8.40e-05)]_50_[+1(2.49e-05)]_\ 7 chrI:10175464-10175544 5.88e-01 80 chrI:14756432-14756512 3.09e-03 7_[+3(6.86e-05)]_26_[+1(7.92e-05)]_\ 31 chrX:7651311-7651391 4.87e-02 53_[+5(8.58e-05)]_19 chrIII:7198999-7199079 1.07e-03 17_[+2(2.49e-05)]_14_[+1(5.73e-05)]_\ 33 chrI:12899150-12899230 1.50e-01 22_[+5(8.58e-05)]_22_[+5(8.58e-05)]_\ 20 chrIII:8529010-8529090 4.09e-01 80 chrII:4672685-4672765 9.22e-01 80 chrIII:5190302-5190382 9.44e-01 80 chrII:7676565-7676645 4.72e-02 33_[+4(5.53e-05)]_39 chrIII:5069018-5069098 1.06e-01 2_[+4(5.53e-05)]_70 chrX:1051272-1051352 8.41e-02 80 chrI:5164963-5165043 7.54e-02 51_[+2(2.49e-05)]_8_[+2(7.23e-05)]_\ 5 chrII:6734840-6734920 1.77e-01 80 chrIII:11290718-11290798 6.87e-03 16_[+2(1.13e-05)]_56 chrV:7820416-7820496 9.72e-01 80 chrV:9293530-9293610 4.53e-01 80 chrIII:159753-159833 1.46e-01 80 chrII:6838560-6838640 1.69e-01 80 chrV:11124090-11124170 5.68e-03 54_[+1(1.19e-05)]_18 chrII:10547384-10547464 2.36e-01 80 chrX:2488775-2488855 5.33e-01 80 chrV:2638682-2638762 1.60e-04 21_[+2(3.54e-05)]_23_[+4(5.53e-05)]_\ 20 chrI:27063-27143 4.29e-02 8_[+3(5.15e-05)]_64 chrIV:6646282-6646362 4.64e-02 80 chrI:1823222-1823302 1.44e-02 43_[+4(1.83e-05)]_29 chrIII:4912471-4912551 5.37e-05 30_[+5(8.58e-05)]_17_[+1(3.56e-05)]_\ [+2(2.49e-05)]_9 chrII:5594391-5594471 1.93e-01 80 chrX:7798544-7798624 4.58e-01 80 chrI:9855538-9855618 3.08e-01 80 chrX:4125592-4125672 5.58e-02 80 chrIV:13533247-13533327 6.11e-02 56_[+4(7.67e-05)]_16 chrIII:4930398-4930478 7.50e-03 36_[+2(2.49e-05)]_36 chrI:788163-788243 2.52e-01 80 chrII:4456306-4456386 2.27e-02 80 chrV:11505134-11505214 5.88e-01 80 chrV:7084912-7084992 4.26e-05 1_[+2(2.49e-05)]_8_[+1(3.56e-05)]_\ 55 chrI:3350051-3350131 8.12e-02 32_[+5(5.11e-05)]_40 chrI:12921065-12921145 1.97e-03 15_[+5(8.58e-05)]_45_[+4(1.83e-05)]_\ 4 chrIV:7817971-7818051 4.36e-01 80 chrIV:10085860-10085940 8.07e-02 71_[+4(1.83e-05)]_1 chrV:10526107-10526187 1.87e-02 80 chrV:7465690-7465770 1.81e-04 36_[+2(2.49e-05)]_10_[+4(7.67e-05)]_\ 18 chrIV:17099260-17099340 1.16e-02 15_[+4(1.83e-05)]_57 chrV:8785775-8785855 9.72e-01 80 chrI:11585327-11585407 1.45e-02 30_[+3(6.86e-05)]_42 chrV:13715491-13715571 4.66e-01 80 chrI:3822796-3822876 7.34e-01 80 chrV:15610522-15610602 1.48e-01 53_[+5(8.58e-05)]_3_[+5(8.58e-05)]_\ 8 chrIII:10460716-10460796 5.51e-02 80 chrII:9497451-9497531 4.37e-02 80 chrIII:640557-640637 7.45e-01 80 chrIV:796710-796790 4.20e-01 80 chrI:2996333-2996413 4.49e-01 80 chrIV:410606-410686 1.62e-01 80 chrV:11039748-11039828 3.16e-01 80 chrV:1003901-1003981 9.38e-01 80 chrV:9980917-9980997 1.71e-02 80 chrI:6493925-6494005 7.94e-01 80 chrIV:11315034-11315114 2.84e-02 80 chrIV:9074415-9074495 7.96e-01 80 chrII:14143963-14144043 7.60e-02 80 chrV:10356092-10356172 8.72e-02 45_[+1(2.49e-05)]_27 chrIV:11635777-11635857 9.58e-01 80 chrIV:8015966-8016046 1.32e-02 17_[+3(3.25e-05)]_55 chrI:14787898-14787978 1.03e-01 14_[+4(1.83e-05)]_58 chrII:4791445-4791525 5.70e-04 25_[+1(3.56e-05)]_11_[+4(5.53e-05)]_\ 28 chrII:9307013-9307093 1.72e-03 3_[+5(1.38e-05)]_69 chrX:12452326-12452406 3.12e-01 80 chrV:18723712-18723792 9.74e-02 80 chrI:8124509-8124589 1.35e-02 45_[+3(9.94e-05)]_27 chrI:4224816-4224896 7.71e-02 33_[+4(1.83e-05)]_39 chrIII:11142263-11142343 4.54e-01 80 chrIV:6648788-6648868 3.50e-01 20_[+4(5.53e-05)]_52 chrIII:4506001-4506081 2.17e-02 38_[+3(6.86e-05)]_34 chrIV:8629642-8629722 3.67e-03 57_[+4(7.67e-05)]_7_[+5(5.11e-05)] chrII:10538119-10538199 1.15e-05 1_[+5(8.58e-05)]_20_[+1(3.56e-05)]_\ 4_[+4(5.53e-05)]_31 chrV:11644303-11644383 1.60e-01 39_[+2(2.49e-05)]_33 chrII:14063234-14063314 6.26e-01 80 chrIV:8183500-8183580 4.50e-01 80 chrIII:5349405-5349485 1.15e-05 21_[+5(8.58e-05)]_27_[+1(2.49e-05)]_\ 16 chrIII:8319285-8319365 5.65e-05 24_[+1(7.92e-05)]_8_[+1(2.49e-05)]_\ 5_[+3(1.71e-05)]_19 chrII:6913448-6913528 2.28e-06 4_[+3(1.71e-05)]_10_[+5(8.58e-05)]_\ 26_[+1(4.73e-05)]_16 chrIII:4656595-4656675 5.36e-02 80 chrI:5176389-5176469 1.03e-02 27_[+3(8.40e-05)]_45 chrI:1416166-1416246 2.05e-01 33_[+4(5.53e-05)]_39 chrII:7537793-7537873 1.85e-01 80 chrV:16401675-16401755 8.68e-05 34_[+2(3.54e-05)]_23_[+4(5.53e-05)]_\ 7 chrI:1175831-1175911 3.23e-01 80 chrII:3502782-3502862 2.62e-03 41_[+1(2.49e-05)]_31 chrII:11534715-11534795 5.55e-05 7_[+5(8.58e-05)]_32_[+3(1.71e-05)]_\ 25 chrII:2752655-2752735 3.82e-02 10_[+3(3.25e-05)]_62 chrX:14115659-14115739 2.03e-02 30_[+2(7.23e-05)]_42 chrI:6446680-6446760 2.32e-01 80 chrIV:1858070-1858150 2.56e-01 80 chrV:5917883-5917963 7.72e-03 7_[+2(6.02e-05)]_65 chrIII:11317208-11317288 2.26e-01 80 chrV:14347389-14347469 5.82e-01 80 chrIII:11119504-11119584 6.01e-01 80 chrV:15085563-15085643 2.21e-02 27_[+1(2.49e-05)]_45 chrX:993074-993154 1.04e-02 60_[+3(8.40e-05)]_12 chrV:12870085-12870165 4.34e-04 40_[+3(8.40e-05)]_32 chrIII:783441-783521 3.43e-02 34_[+2(1.13e-05)]_19_[+2(2.49e-05)]_\ 11 chrIII:8850818-8850898 6.16e-02 37_[+1(2.49e-05)]_35 chrIV:6631977-6632057 4.24e-03 80 chrIV:16415221-16415301 4.59e-04 43_[+5(8.58e-05)]_12_[+2(2.49e-05)]_\ 9 chrI:1435569-1435649 2.44e-01 80 chrIII:3175135-3175215 1.77e-01 80 chrIII:131857-131937 8.65e-01 80 chrI:13040730-13040810 7.08e-01 80 chrIV:4042402-4042482 1.97e-03 33_[+4(5.53e-05)]_1_[+2(3.54e-05)]_\ 30 chrI:10474757-10474837 2.15e-03 [+5(8.58e-05)]_40_[+1(2.49e-05)]_24 chrIII:12273736-12273816 2.89e-04 46_[+3(8.40e-05)]_15_[+1(2.49e-05)]_\ 3 chrIII:13721243-13721323 1.28e-01 80 chrIII:12351453-12351533 1.84e-02 64_[+2(6.02e-05)]_8 chrII:14438169-14438249 4.78e-02 80 chrV:11375261-11375341 3.84e-01 80 chrIII:9703980-9704060 3.59e-01 80 chrV:1004104-1004184 8.73e-01 80 chrII:2889343-2889423 8.52e-03 9_[+1(9.98e-05)]_44_[+1(5.73e-05)]_\ 11 chrII:5358379-5358459 1.82e-03 43_[+1(2.49e-05)]_29 chrII:10033614-10033694 5.49e-01 80 chrX:8156138-8156218 8.00e-01 80 chrIV:8016173-8016253 4.51e-01 80 chrII:10872705-10872785 9.58e-02 19_[+1(4.73e-05)]_53 chrII:8516929-8517009 8.31e-04 61_[+3(1.71e-05)]_2_[+1(3.56e-05)]_\ 1 chrV:13468344-13468424 4.90e-02 27_[+1(2.49e-05)]_45 chrV:1871930-1872010 4.78e-02 56_[+2(3.54e-05)]_16 chrX:9347710-9347790 9.18e-02 80 chrIV:11605045-11605125 1.92e-01 80 chrII:4740137-4740217 1.11e-02 46_[+1(2.49e-05)]_26 chrX:9337900-9337980 1.27e-01 80 chrIII:4568690-4568770 3.03e-01 80 chrII:5061940-5062020 4.82e-01 80 chrII:2451186-2451266 3.37e-02 16_[+2(7.23e-05)]_56 chrIII:11946511-11946591 2.03e-01 80 chrIV:9316216-9316296 7.26e-01 80 chrIV:10481889-10481969 7.32e-04 6_[+3(3.25e-05)]_7_[+5(5.11e-05)]_\ 51 chrI:14721600-14721680 7.16e-01 80 chrIV:10483881-10483961 3.15e-05 2_[+2(2.49e-05)]_18_[+1(1.19e-05)]_\ 11_[+4(5.53e-05)]_25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n11.farnam.hpc.yale.internal ********************************************************************************