******************************************************************************** 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/ztf-4.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIV:3645101-3645181 1.0000 80 chrX:4146200-4146280 1.0000 80 chrIII:12455832-12455912 1.0000 80 chrIII:5567610-5567690 1.0000 80 chrI:7081140-7081220 1.0000 80 chrII:8482199-8482279 1.0000 80 chrIV:13083001-13083081 1.0000 80 chrX:4143761-4143841 1.0000 80 chrX:3113336-3113416 1.0000 80 chrI:5378582-5378662 1.0000 80 chrV:8939789-8939869 1.0000 80 chrX:17482092-17482172 1.0000 80 chrV:13908494-13908574 1.0000 80 chrII:10300518-10300598 1.0000 80 chrI:5376226-5376306 1.0000 80 chrII:6288241-6288321 1.0000 80 chrI:14875674-14875754 1.0000 80 chrV:6226345-6226425 1.0000 80 chrX:12932079-12932159 1.0000 80 chrX:4148180-4148260 1.0000 80 chrX:4142784-4142864 1.0000 80 chrX:8032181-8032261 1.0000 80 chrIV:6751354-6751434 1.0000 80 chrIII:12607825-12607905 1.0000 80 chrI:2586323-2586403 1.0000 80 chrII:14407906-14407986 1.0000 80 chrX:17420134-17420214 1.0000 80 chrIII:8922180-8922260 1.0000 80 chrX:14979045-14979125 1.0000 80 chrII:11762059-11762139 1.0000 80 chrIII:9824660-9824740 1.0000 80 chrX:10057704-10057784 1.0000 80 chrIII:62612-62692 1.0000 80 chrII:12095226-12095306 1.0000 80 chrII:10557427-10557507 1.0000 80 chrII:6821306-6821386 1.0000 80 chrII:9285689-9285769 1.0000 80 chrIII:7152838-7152918 1.0000 80 chrIV:10295276-10295356 1.0000 80 chrI:999243-999323 1.0000 80 chrV:6221171-6221251 1.0000 80 chrII:10546212-10546292 1.0000 80 chrI:2418097-2418177 1.0000 80 chrIII:8732165-8732245 1.0000 80 chrIII:6820515-6820595 1.0000 80 chrII:14299725-14299805 1.0000 80 chrI:11940068-11940148 1.0000 80 chrIV:13083252-13083332 1.0000 80 chrX:9954746-9954826 1.0000 80 chrIII:9814000-9814080 1.0000 80 chrII:13279416-13279496 1.0000 80 chrIII:6988320-6988400 1.0000 80 chrIV:3026009-3026089 1.0000 80 chrX:6253901-6253981 1.0000 80 chrV:8039350-8039430 1.0000 80 chrX:6040555-6040635 1.0000 80 chrV:4824198-4824278 1.0000 80 chrX:13116324-13116404 1.0000 80 chrIV:11354202-11354282 1.0000 80 chrX:5940272-5940352 1.0000 80 chrIV:12033983-12034063 1.0000 80 chrI:8868445-8868525 1.0000 80 chrI:5375449-5375529 1.0000 80 chrV:3870485-3870565 1.0000 80 chrIII:6282617-6282697 1.0000 80 chrIII:6415445-6415525 1.0000 80 chrIV:14764533-14764613 1.0000 80 chrII:10546930-10547010 1.0000 80 chrV:20710298-20710378 1.0000 80 chrIII:5953553-5953633 1.0000 80 chrV:19520248-19520328 1.0000 80 chrX:4969456-4969536 1.0000 80 chrV:4820782-4820862 1.0000 80 chrIV:12037052-12037132 1.0000 80 chrI:7870571-7870651 1.0000 80 chrV:11822623-11822703 1.0000 80 chrIII:8449378-8449458 1.0000 80 chrX:1452273-1452353 1.0000 80 chrII:4902211-4902291 1.0000 80 chrX:3947354-3947434 1.0000 80 chrI:9095632-9095712 1.0000 80 chrII:10450468-10450548 1.0000 80 chrV:11889733-11889813 1.0000 80 chrIV:15722317-15722397 1.0000 80 chrV:10953817-10953897 1.0000 80 chrV:4794420-4794500 1.0000 80 chrII:10544149-10544229 1.0000 80 chrII:8820104-8820184 1.0000 80 chrIII:5853308-5853388 1.0000 80 chrII:11756976-11757056 1.0000 80 chrIII:3671145-3671225 1.0000 80 chrX:4147719-4147799 1.0000 80 chrIII:13716382-13716462 1.0000 80 chrX:13542829-13542909 1.0000 80 chrX:1445815-1445895 1.0000 80 chrIV:8790944-8791024 1.0000 80 chrX:4146903-4146983 1.0000 80 chrII:4859171-4859251 1.0000 80 chrX:3788706-3788786 1.0000 80 chrX:11474704-11474784 1.0000 80 chrX:430489-430569 1.0000 80 chrX:10233150-10233230 1.0000 80 chrV:13650258-13650338 1.0000 80 chrIII:10339535-10339615 1.0000 80 chrIII:8654746-8654826 1.0000 80 chrII:7887513-7887593 1.0000 80 chrV:11082632-11082712 1.0000 80 chrI:7087496-7087576 1.0000 80 chrV:11817416-11817496 1.0000 80 chrI:5376441-5376521 1.0000 80 chrX:4141121-4141201 1.0000 80 chrIV:4474288-4474368 1.0000 80 chrIII:5504314-5504394 1.0000 80 chrII:6889965-6890045 1.0000 80 chrIV:9668173-9668253 1.0000 80 chrV:11076526-11076606 1.0000 80 chrIV:11068486-11068566 1.0000 80 chrI:14938743-14938823 1.0000 80 chrII:9601825-9601905 1.0000 80 chrIV:10159402-10159482 1.0000 80 chrIII:8739886-8739966 1.0000 80 chrX:11469031-11469111 1.0000 80 chrV:4806935-4807015 1.0000 80 chrI:8011486-8011566 1.0000 80 chrX:6202973-6203053 1.0000 80 chrIV:13911099-13911179 1.0000 80 chrIII:9701397-9701477 1.0000 80 chrIII:5758814-5758894 1.0000 80 chrI:11662841-11662921 1.0000 80 chrIII:6405375-6405455 1.0000 80 chrIII:9457488-9457568 1.0000 80 chrX:8236204-8236284 1.0000 80 chrV:4157468-4157548 1.0000 80 chrIII:4100000-4100080 1.0000 80 chrII:7323440-7323520 1.0000 80 chrIII:5196517-5196597 1.0000 80 chrIII:5835710-5835790 1.0000 80 chrII:7891924-7892004 1.0000 80 chrI:3675810-3675890 1.0000 80 chrIV:5100247-5100327 1.0000 80 chrII:8020793-8020873 1.0000 80 chrIV:3647725-3647805 1.0000 80 chrIII:5025386-5025466 1.0000 80 chrII:5338404-5338484 1.0000 80 chrII:10390601-10390681 1.0000 80 chrI:4908255-4908335 1.0000 80 chrII:5945089-5945169 1.0000 80 chrII:8481077-8481157 1.0000 80 chrIII:7974248-7974328 1.0000 80 chrII:8789971-8790051 1.0000 80 chrIV:17470162-17470242 1.0000 80 chrX:14792928-14793008 1.0000 80 chrV:8607374-8607454 1.0000 80 chrII:8585430-8585510 1.0000 80 chrX:8475276-8475356 1.0000 80 chrV:20713033-20713113 1.0000 80 chrII:4857880-4857960 1.0000 80 chrX:15541515-15541595 1.0000 80 chrX:13108731-13108811 1.0000 80 chrII:9120984-9121064 1.0000 80 chrX:5805224-5805304 1.0000 80 chrI:7147749-7147829 1.0000 80 chrX:13941287-13941367 1.0000 80 chrIII:3782034-3782114 1.0000 80 chrI:1695192-1695272 1.0000 80 chrX:7236963-7237043 1.0000 80 chrV:10861994-10862074 1.0000 80 chrX:5942260-5942340 1.0000 80 chrV:775128-775208 1.0000 80 chrX:16931411-16931491 1.0000 80 chrI:1877818-1877898 1.0000 80 chrII:6587447-6587527 1.0000 80 chrI:7597481-7597561 1.0000 80 chrII:12797166-12797246 1.0000 80 chrX:14562418-14562498 1.0000 80 chrII:4891552-4891632 1.0000 80 chrX:15608744-15608824 1.0000 80 chrV:10937455-10937535 1.0000 80 chrIV:11026808-11026888 1.0000 80 chrX:9343221-9343301 1.0000 80 chrV:3874515-3874595 1.0000 80 chrIV:5656074-5656154 1.0000 80 chrX:16931618-16931698 1.0000 80 chrV:13235505-13235585 1.0000 80 chrI:7085894-7085974 1.0000 80 chrX:12873759-12873839 1.0000 80 chrV:19519777-19519857 1.0000 80 chrI:6001193-6001273 1.0000 80 chrII:15212590-15212670 1.0000 80 chrIV:8978284-8978364 1.0000 80 chrI:4909116-4909196 1.0000 80 chrII:6888471-6888551 1.0000 80 chrIII:6362454-6362534 1.0000 80 chrV:11118457-11118537 1.0000 80 chrIV:1626899-1626979 1.0000 80 chrV:11638707-11638787 1.0000 80 chrI:9721133-9721213 1.0000 80 chrV:5812149-5812229 1.0000 80 chrIII:7369820-7369900 1.0000 80 chrV:20785493-20785573 1.0000 80 chrIII:5551010-5551090 1.0000 80 chrV:7432587-7432667 1.0000 80 chrI:9100956-9101036 1.0000 80 chrX:3111924-3112004 1.0000 80 chrII:11726701-11726781 1.0000 80 chrV:20777003-20777083 1.0000 80 chrII:8745178-8745258 1.0000 80 chrV:4823972-4824052 1.0000 80 chrV:8938332-8938412 1.0000 80 chrX:11472049-11472129 1.0000 80 chrV:10535578-10535658 1.0000 80 chrV:5848086-5848166 1.0000 80 chrIV:2709774-2709854 1.0000 80 chrIII:6123736-6123816 1.0000 80 chrIV:5602030-5602110 1.0000 80 chrV:5838923-5839003 1.0000 80 chrX:15355713-15355793 1.0000 80 chrIII:3800034-3800114 1.0000 80 chrV:14688635-14688715 1.0000 80 chrIII:10244954-10245034 1.0000 80 chrX:8015127-8015207 1.0000 80 chrV:1805970-1806050 1.0000 80 chrIII:6167327-6167407 1.0000 80 chrI:3754633-3754713 1.0000 80 chrI:5372620-5372700 1.0000 80 chrX:12877997-12878077 1.0000 80 chrV:9741084-9741164 1.0000 80 chrII:9117979-9118059 1.0000 80 chrII:10547694-10547774 1.0000 80 chrIII:8734547-8734627 1.0000 80 chrX:1504029-1504109 1.0000 80 chrII:7339243-7339323 1.0000 80 chrI:5599496-5599576 1.0000 80 chrIV:9212459-9212539 1.0000 80 chrII:4745432-4745512 1.0000 80 chrIII:7723030-7723110 1.0000 80 chrII:9683816-9683896 1.0000 80 chrV:14687091-14687171 1.0000 80 chrIV:13826516-13826596 1.0000 80 chrI:5389160-5389240 1.0000 80 chrI:12164768-12164848 1.0000 80 chrIII:8355264-8355344 1.0000 80 chrX:6743084-6743164 1.0000 80 chrIII:3955008-3955088 1.0000 80 chrV:11122636-11122716 1.0000 80 chrX:13220771-13220851 1.0000 80 chrIII:5622816-5622896 1.0000 80 chrII:9933872-9933952 1.0000 80 chrIII:9805137-9805217 1.0000 80 chrV:11226052-11226132 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_ztf-4/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/ztf-4.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 0.317 C 0.184 G 0.18 T 0.319 Background letter frequencies (from file dataset with add-one prior applied): A 0.317 C 0.184 G 0.18 T 0.319 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGAGCGCG MEME-1 width = 8 sites = 2 llr = 26 E-value = 6.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C ::::a:a: probability G aa:a:a:a matrix T :::::::: bits 2.5 ** ***** 2.2 ** ***** 2.0 ** ***** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (18.9 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGAGCGCG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:4902211-4902291 37 2.03e-06 ATTTCGTGTT GGAGCGCG TTTGCAACCA chrIII:12455832-12455912 19 2.03e-06 tgaagtcgtt ggagcgcg cttgcattat -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:4902211-4902291 2e-06 36_[+1]_36 chrIII:12455832-12455912 2e-06 18_[+1]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGCGCG width=8 seqs=2 chrII:4902211-4902291 ( 37) GGAGCGCG 1 chrIII:12455832-12455912 ( 19) GGAGCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.3073 E= 6.2e+003 -765 -765 247 -765 -765 -765 247 -765 165 -765 -765 -765 -765 -765 247 -765 -765 244 -765 -765 -765 -765 247 -765 -765 244 -765 -765 -765 -765 247 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.2e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCGCG MEME-1 regular expression -------------------------------------------------------------------------------- GGAGCGCG -------------------------------------------------------------------------------- Time 5.59 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTYTYTY MEME-2 width = 8 sites = 74 llr = 507 E-value = 6.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 32:6:5:5 probability G :2:::::: matrix T 76a4a5a5 bits 2.5 2.2 2.0 1.7 * * * Relative 1.5 * * * Entropy 1.2 *** * (9.9 bits) 1.0 * ****** 0.7 * ****** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTCTCTT consensus CC T T C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:1695192-1695272 14 2.06e-05 GTGAtctttc tttctctc tctctctctt chrV:20713033-20713113 34 2.06e-05 CCCTCCTCCT TTTCTCTC TCTTTCACTA chrX:8475276-8475356 3 2.06e-05 CA TTTCTCTC ATCTCTTATT chrI:3675810-3675890 53 2.06e-05 TTTTTCTCCT TTTCTCTC TGTGTATGTG chrIII:4100000-4100080 36 2.06e-05 cttttctatc tttctctc tctctctatc chrIII:9457488-9457568 50 2.06e-05 ACCTTGGCCT TTTCTCTC TGTCAGCTGT chrI:8011486-8011566 54 2.06e-05 TTTCTTTTCG TTTCTCTC TTCAATGCCA chrIII:5504314-5504394 26 2.06e-05 tttccctttc tttctctc cgtctctcCG chrX:4141121-4141201 59 2.06e-05 ATTCGTTTCC TTTCTCTC GCCTCACAAT chrIII:5622816-5622896 1 5.63e-05 . tttctctT TTTCAAATGA chrIV:9668173-9668253 14 5.63e-05 ATTGTAATCT TTTCTCTT TGATGCGACT chrX:4143761-4143841 62 5.63e-05 AATGTTTTAT TTTCTCTT AAATTTCCAT chrV:10861994-10862074 72 9.16e-05 ttctcttcac tctctctc t chrI:9095632-9095712 37 9.16e-05 GATTCGTCTG TGTCTCTC TGACTCAATC chrV:4820782-4820862 60 9.16e-05 CTATCTATCT CTTCTCTC AGTTCTTATC chrV:20710298-20710378 43 9.16e-05 AGTCTCTTTG TGTCTCTC TATATCTCGT chrII:11726701-11726781 64 1.27e-04 CCGTGTTTTA TTTCTTTC TACGCGAAA chrV:5848086-5848166 31 1.89e-04 AAGACGATGA CTTCTCTT TTTTCTTCTT chrX:13941287-13941367 14 1.89e-04 TTGGTGATTA TCTCTCTT ACACAAAGTC chrI:4908255-4908335 10 1.89e-04 CTAGTGTCT CTTCTCTT GAGTACACTC chrV:8039350-8039430 43 1.89e-04 TTCATTTTGA TCTCTCTT TTTTCCTTCT chrII:10390601-10390681 47 2.02e-04 TATCTCTATT CCTCTCTC AATCGTTCCA chrV:11082632-11082712 27 2.02e-04 AGATACTGCT CGTCTCTC GAGAAAGAAA chrIII:6820515-6820595 10 2.02e-04 TTATCTCTG CGTCTCTC CAATCCACAC chrX:6743084-6743164 30 3.00e-04 GCAAAGTGCC TTTCTTTT CTGTCCCGTT chrIII:6167327-6167407 22 3.00e-04 AACGTCTTCC TTTTTCTC AATTGATCCA chrIII:6362454-6362534 28 3.00e-04 CCCTTTTGAT TTTTTCTC GTCGTCGCCT chrX:12873759-12873839 8 3.00e-04 TATTGCC TTTCTTTT GAAACACACA chrI:5376441-5376521 43 3.00e-04 ACCTCCTTTT TTTCTTTT CAATGCTCTC chrV:11817416-11817496 22 3.00e-04 AAACATACGT TTTCTTTT CAGATATTTC chrX:1445815-1445895 57 3.00e-04 TCCCTATCCC TTTTTCTC GCGGAACCAG chrII:10450468-10450548 9 3.00e-04 gcgcatac tttttctc gttaaacata chrIV:12033983-12034063 11 3.00e-04 CTTGAGTGTT TTTCTTTT CATATCTCCG chrIV:11354202-11354282 16 3.00e-04 TTCCTCCGGT TTTCTTTT TGACTTTATA chrIII:9824660-9824740 6 3.00e-04 TTTGA TTTCTTTT CGATCATTTG chrI:14875674-14875754 30 3.00e-04 ATTTATGCTT TTTCTTTT TGTTAAAAAA chrV:1805970-1806050 56 3.61e-04 TATTGAATAC CTTCTTTC CAAAATAAAA chrV:20785493-20785573 67 3.61e-04 ttttgcaaaa tgtctttc agaaac chrI:7081140-7081220 40 3.61e-04 ATTAGTCATA TCTCTTTC GCGCCAATAT chrIV:13826516-13826596 52 3.84e-04 GAGATGTCTG CGTCTCTT GTGTGATATG chrIII:6405375-6405455 15 3.84e-04 GATAATCTGT CGTCTCTT CATTCACCAT chrII:8789971-8790051 14 4.46e-04 GAAATTTGTT TTTTTCTT CAAAAAAAAT chrX:13542829-13542909 11 4.46e-04 CTTCTTTTAT TTTTTCTT TGGTTCCGTC chrIII:6415445-6415525 47 4.46e-04 CTCGAGTTTT TTTTTCTT AAAAAATACC chrII:7339243-7339323 48 6.14e-04 AAGTGATTCC CTTTTCTC CTGCGAATTG chrV:19519777-19519857 10 6.14e-04 TCCGTCTGC TCTTTCTC AAAACCTTAT chrX:5942260-5942340 31 6.14e-04 GTCCGCCCAT TCTCTTTT CACAAGGTAC chrX:14792928-14793008 69 6.14e-04 TGAGTTTATA TCTCTTTT TATA chrIII:9701397-9701477 51 6.14e-04 ATGATttctt cttctttt ctatccgcac chrIII:8654746-8654826 19 6.14e-04 TTGTTTTTCA TCTCTTTT TTCACTGGTT chrX:430489-430569 41 6.14e-04 TTGATCGTTT TGTCTTTT GTCTCGTTTT chrX:11474704-11474784 7 6.14e-04 ATCTCA TCTCTTTT TTCCTCATTT chrV:6221171-6221251 37 6.14e-04 CAAATTTTGT TGTCTTTT TTGTTGCAGT chrII:9285689-9285769 4 6.14e-04 TAA TCTCTTTT AAATGAAGAT chrII:6821306-6821386 15 6.14e-04 CTGCTGTTCT CTTCTTTT TACTCAAATG chrV:11889733-11889813 30 6.37e-04 GTGACCTTCC CGTCTTTC ATTCGTTGAT chrI:14938743-14938823 47 6.99e-04 TAACACTATG TTTTTTTC CGGCTTGTGA chrIII:12455832-12455912 55 6.99e-04 ttattatgtt tttttttc tattgatttt chrV:9741084-9741164 64 8.05e-04 tacttttact cttttctt aattcatGT chrIV:4474288-4474368 18 8.05e-04 TAGTTGATAA CTTTTCTT GCAATGTTCT chrI:999243-999323 72 8.05e-04 TTCTCGATCC CTTTTCTT C chrX:4146903-4146983 37 8.70e-04 TTGCTCAAAC CCTTTCTC AATCGTCAAG chrV:13908494-13908574 57 8.70e-04 ACAACTTTTT CCTCTTTT TTAGCATTGT chrII:9933872-9933952 42 9.77e-04 AAAAAAAATG TTTTTTTT AATTTTTGAA chrIII:13716382-13716462 43 9.77e-04 CTTCGGGGTG TTTTTTTT ATTCTGGAAT chrIII:12607825-12607905 11 9.77e-04 CTTAAACTGA TTTTTTTT ATGATTTAAG chrI:9721133-9721213 69 1.08e-03 AGTTTCTCCG TCTTTTTC TATT chrII:12797166-12797246 29 1.08e-03 GGAGCAACGT TGTTTTTC CCCAACACAA chrIII:7152838-7152918 8 1.08e-03 TTATTCT TGTTTTTC ATGTTTTTGG chrX:4142784-4142864 61 1.08e-03 CGTCACGCCA TGTTTTTC GTCTGTTGTA chrV:4794420-4794500 50 1.12e-03 GGAGTTGCCA CCTTTCTT CAGAACTCCG chrII:9120984-9121064 20 1.31e-03 TGTATTTACA TGTTTTTT CAAAGAATTG chrX:12932079-12932159 64 1.31e-03 ACCCACCGGT TCTTTTTT TATGACATT chrIV:5656074-5656154 71 1.35e-03 TTCTGTACAC CGTTTTTC AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:1695192-1695272 2.1e-05 13_[+2]_59 chrV:20713033-20713113 2.1e-05 33_[+2]_39 chrX:8475276-8475356 2.1e-05 2_[+2]_70 chrI:3675810-3675890 2.1e-05 52_[+2]_20 chrIII:4100000-4100080 2.1e-05 35_[+2]_37 chrIII:9457488-9457568 2.1e-05 49_[+2]_23 chrI:8011486-8011566 2.1e-05 53_[+2]_19 chrIII:5504314-5504394 2.1e-05 25_[+2]_47 chrX:4141121-4141201 2.1e-05 58_[+2]_14 chrIII:5622816-5622896 5.6e-05 [+2]_72 chrIV:9668173-9668253 5.6e-05 13_[+2]_59 chrX:4143761-4143841 5.6e-05 61_[+2]_11 chrV:10861994-10862074 9.2e-05 71_[+2]_1 chrI:9095632-9095712 9.2e-05 36_[+2]_36 chrV:4820782-4820862 9.2e-05 59_[+2]_13 chrV:20710298-20710378 9.2e-05 42_[+2]_30 chrII:11726701-11726781 0.00013 63_[+2]_9 chrV:5848086-5848166 0.00019 30_[+2]_42 chrX:13941287-13941367 0.00019 13_[+2]_59 chrI:4908255-4908335 0.00019 9_[+2]_63 chrV:8039350-8039430 0.00019 42_[+2]_30 chrII:10390601-10390681 0.0002 46_[+2]_26 chrV:11082632-11082712 0.0002 26_[+2]_46 chrIII:6820515-6820595 0.0002 9_[+2]_63 chrX:6743084-6743164 0.0003 29_[+2]_43 chrIII:6167327-6167407 0.0003 21_[+2]_51 chrIII:6362454-6362534 0.0003 27_[+2]_45 chrX:12873759-12873839 0.0003 7_[+2]_65 chrI:5376441-5376521 0.0003 42_[+2]_30 chrV:11817416-11817496 0.0003 21_[+2]_51 chrX:1445815-1445895 0.0003 56_[+2]_16 chrII:10450468-10450548 0.0003 8_[+2]_64 chrIV:12033983-12034063 0.0003 10_[+2]_62 chrIV:11354202-11354282 0.0003 15_[+2]_57 chrIII:9824660-9824740 0.0003 5_[+2]_67 chrI:14875674-14875754 0.0003 29_[+2]_43 chrV:1805970-1806050 0.00036 55_[+2]_17 chrV:20785493-20785573 0.00036 66_[+2]_6 chrI:7081140-7081220 0.00036 39_[+2]_33 chrIV:13826516-13826596 0.00038 51_[+2]_21 chrIII:6405375-6405455 0.00038 14_[+2]_58 chrII:8789971-8790051 0.00045 13_[+2]_59 chrX:13542829-13542909 0.00045 10_[+2]_62 chrIII:6415445-6415525 0.00045 46_[+2]_26 chrII:7339243-7339323 0.00061 47_[+2]_25 chrV:19519777-19519857 0.00061 9_[+2]_63 chrX:5942260-5942340 0.00061 30_[+2]_42 chrX:14792928-14793008 0.00061 68_[+2]_4 chrIII:9701397-9701477 0.00061 50_[+2]_22 chrIII:8654746-8654826 0.00061 18_[+2]_54 chrX:430489-430569 0.00061 40_[+2]_32 chrX:11474704-11474784 0.00061 6_[+2]_66 chrV:6221171-6221251 0.00061 36_[+2]_36 chrII:9285689-9285769 0.00061 3_[+2]_69 chrII:6821306-6821386 0.00061 14_[+2]_58 chrV:11889733-11889813 0.00064 29_[+2]_43 chrI:14938743-14938823 0.0007 46_[+2]_26 chrIII:12455832-12455912 0.0007 54_[+2]_18 chrV:9741084-9741164 0.00081 63_[+2]_9 chrIV:4474288-4474368 0.00081 17_[+2]_55 chrI:999243-999323 0.00081 71_[+2]_1 chrX:4146903-4146983 0.00087 36_[+2]_36 chrV:13908494-13908574 0.00087 56_[+2]_16 chrII:9933872-9933952 0.00098 41_[+2]_31 chrIII:13716382-13716462 0.00098 42_[+2]_30 chrIII:12607825-12607905 0.00098 10_[+2]_62 chrI:9721133-9721213 0.0011 68_[+2]_4 chrII:12797166-12797246 0.0011 28_[+2]_44 chrIII:7152838-7152918 0.0011 7_[+2]_65 chrX:4142784-4142864 0.0011 60_[+2]_12 chrV:4794420-4794500 0.0011 49_[+2]_23 chrII:9120984-9121064 0.0013 19_[+2]_53 chrX:12932079-12932159 0.0013 63_[+2]_9 chrIV:5656074-5656154 0.0013 70_[+2]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTYTYTY width=8 seqs=74 chrI:1695192-1695272 ( 14) TTTCTCTC 1 chrV:20713033-20713113 ( 34) TTTCTCTC 1 chrX:8475276-8475356 ( 3) TTTCTCTC 1 chrI:3675810-3675890 ( 53) TTTCTCTC 1 chrIII:4100000-4100080 ( 36) TTTCTCTC 1 chrIII:9457488-9457568 ( 50) TTTCTCTC 1 chrI:8011486-8011566 ( 54) TTTCTCTC 1 chrIII:5504314-5504394 ( 26) TTTCTCTC 1 chrX:4141121-4141201 ( 59) TTTCTCTC 1 chrIII:5622816-5622896 ( 1) TTTCTCTT 1 chrIV:9668173-9668253 ( 14) TTTCTCTT 1 chrX:4143761-4143841 ( 62) TTTCTCTT 1 chrV:10861994-10862074 ( 72) TCTCTCTC 1 chrI:9095632-9095712 ( 37) TGTCTCTC 1 chrV:4820782-4820862 ( 60) CTTCTCTC 1 chrV:20710298-20710378 ( 43) TGTCTCTC 1 chrII:11726701-11726781 ( 64) TTTCTTTC 1 chrV:5848086-5848166 ( 31) CTTCTCTT 1 chrX:13941287-13941367 ( 14) TCTCTCTT 1 chrI:4908255-4908335 ( 10) CTTCTCTT 1 chrV:8039350-8039430 ( 43) TCTCTCTT 1 chrII:10390601-10390681 ( 47) CCTCTCTC 1 chrV:11082632-11082712 ( 27) CGTCTCTC 1 chrIII:6820515-6820595 ( 10) CGTCTCTC 1 chrX:6743084-6743164 ( 30) TTTCTTTT 1 chrIII:6167327-6167407 ( 22) TTTTTCTC 1 chrIII:6362454-6362534 ( 28) TTTTTCTC 1 chrX:12873759-12873839 ( 8) TTTCTTTT 1 chrI:5376441-5376521 ( 43) TTTCTTTT 1 chrV:11817416-11817496 ( 22) TTTCTTTT 1 chrX:1445815-1445895 ( 57) TTTTTCTC 1 chrII:10450468-10450548 ( 9) TTTTTCTC 1 chrIV:12033983-12034063 ( 11) TTTCTTTT 1 chrIV:11354202-11354282 ( 16) TTTCTTTT 1 chrIII:9824660-9824740 ( 6) TTTCTTTT 1 chrI:14875674-14875754 ( 30) TTTCTTTT 1 chrV:1805970-1806050 ( 56) CTTCTTTC 1 chrV:20785493-20785573 ( 67) TGTCTTTC 1 chrI:7081140-7081220 ( 40) TCTCTTTC 1 chrIV:13826516-13826596 ( 52) CGTCTCTT 1 chrIII:6405375-6405455 ( 15) CGTCTCTT 1 chrII:8789971-8790051 ( 14) TTTTTCTT 1 chrX:13542829-13542909 ( 11) TTTTTCTT 1 chrIII:6415445-6415525 ( 47) TTTTTCTT 1 chrII:7339243-7339323 ( 48) CTTTTCTC 1 chrV:19519777-19519857 ( 10) TCTTTCTC 1 chrX:5942260-5942340 ( 31) TCTCTTTT 1 chrX:14792928-14793008 ( 69) TCTCTTTT 1 chrIII:9701397-9701477 ( 51) CTTCTTTT 1 chrIII:8654746-8654826 ( 19) TCTCTTTT 1 chrX:430489-430569 ( 41) TGTCTTTT 1 chrX:11474704-11474784 ( 7) TCTCTTTT 1 chrV:6221171-6221251 ( 37) TGTCTTTT 1 chrII:9285689-9285769 ( 4) TCTCTTTT 1 chrII:6821306-6821386 ( 15) CTTCTTTT 1 chrV:11889733-11889813 ( 30) CGTCTTTC 1 chrI:14938743-14938823 ( 47) TTTTTTTC 1 chrIII:12455832-12455912 ( 55) TTTTTTTC 1 chrV:9741084-9741164 ( 64) CTTTTCTT 1 chrIV:4474288-4474368 ( 18) CTTTTCTT 1 chrI:999243-999323 ( 72) CTTTTCTT 1 chrX:4146903-4146983 ( 37) CCTTTCTC 1 chrV:13908494-13908574 ( 57) CCTCTTTT 1 chrII:9933872-9933952 ( 42) TTTTTTTT 1 chrIII:13716382-13716462 ( 43) TTTTTTTT 1 chrIII:12607825-12607905 ( 11) TTTTTTTT 1 chrI:9721133-9721213 ( 69) TCTTTTTC 1 chrII:12797166-12797246 ( 29) TGTTTTTC 1 chrIII:7152838-7152918 ( 8) TGTTTTTC 1 chrX:4142784-4142864 ( 61) TGTTTTTC 1 chrV:4794420-4794500 ( 50) CCTTTCTT 1 chrII:9120984-9121064 ( 20) TGTTTTTT 1 chrX:12932079-12932159 ( 64) TCTTTTTT 1 chrIV:5656074-5656154 ( 71) CGTTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.74794 E= 6.5e+003 -1285 55 -1285 119 -1285 23 17 87 -1285 -1285 -1285 165 -1285 182 -1285 14 -1285 -1285 -1285 165 -1285 152 -1285 57 -1285 -1285 -1285 165 -1285 136 -1285 73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 74 E= 6.5e+003 0.000000 0.270270 0.000000 0.729730 0.000000 0.216216 0.202703 0.581081 0.000000 0.000000 0.000000 1.000000 0.000000 0.648649 0.000000 0.351351 0.000000 0.000000 0.000000 1.000000 0.000000 0.527027 0.000000 0.472973 0.000000 0.000000 0.000000 1.000000 0.000000 0.472973 0.000000 0.527027 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYTYTY MEME-2 regular expression -------------------------------------------------------------------------------- [TC][TCG]T[CT]T[CT]T[TC] -------------------------------------------------------------------------------- Time 9.48 secs. ******************************************************************************** ******************************************************************************** MOTIF YCACRTGA MEME-3 width = 8 sites = 24 llr = 205 E-value = 1.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 2:a:4::6 pos.-specific C 3a:a:::: probability G 2:::6:a2 matrix T 4::::a:2 bits 2.5 * * * 2.2 * * * 2.0 * * * 1.7 *** ** Relative 1.5 *** ** Entropy 1.2 ****** (12.3 bits) 1.0 ****** 0.7 ****** 0.5 ******* 0.2 ******* 0.0 -------- Multilevel TCACGTGA consensus C A G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:4745432-4745512 28 1.77e-05 CATGTTGGAA TCACGTGA AGCCCGTGAG chrX:15355713-15355793 35 1.77e-05 AGCACGACAT TCACGTGA TGAATTTTTC chrII:10390601-10390681 62 1.77e-05 CTCAATCGTT CCACGTGA TTGTTGTGTG chrIV:13911099-13911179 17 1.77e-05 GCCCAAATTT TCACGTGA GTGATACTTT chrII:10557427-10557507 34 1.77e-05 TCGTTTCTAA CCACGTGA CATATATTCT chrX:12877997-12878077 57 3.77e-05 TTAATAAACG GCACGTGG CAGTTCGCTT chrX:5942260-5942340 5 3.77e-05 GCGA GCACGTGG TGGCCTTGGT chrII:10546212-10546292 52 3.77e-05 TGATCGACTT GCACGTGG TCACCGATCC chrII:15212590-15212670 48 6.88e-05 CTACTCATCA TCACATGA TGATCGTCGT chrV:10937455-10937535 22 6.88e-05 AATCTCACTC TCACATGA TTCAATTCCT chrIV:11068486-11068566 41 6.88e-05 GATACGTGTG TCACATGA TTAGTTGAGA chrV:11822623-11822703 45 6.88e-05 AGAGGTCACA CCACATGA GAGTGAGTGT chrII:10546930-10547010 22 6.88e-05 TATCAAATTT TCACATGA GAATCACTAG chrII:6288241-6288321 72 6.88e-05 CTTCAGTCTT CCACATGA T chrX:17482092-17482172 20 6.88e-05 GATATGACTT TCACATGA CTAAGCATTT chrV:10535578-10535658 17 9.77e-05 CTGGCAGAAC ACACGTGA AGTCATCGAA chrI:6001193-6001273 49 9.77e-05 CTCTAGTTTG CCACGTGT TGTCACCTGT chrII:10300518-10300598 23 9.77e-05 ATGACAAATT ACACGTGA CGTCAGCCAC chrIII:9814000-9814080 68 1.27e-04 GATTCGTACC TCACATGG TGGAA chrIII:3782034-3782114 25 1.39e-04 CAATAATGTG ACACGTGG CAGAGGGTAA chrI:5378582-5378662 72 1.39e-04 ACTTAAAAGA GCACGTGT C chrII:9683816-9683896 69 1.97e-04 CTCCCCATCT TCACATGT GTAC chrII:7891924-7892004 69 1.97e-04 TCCCAATCCG CCACATGT TCGT chrIII:8922180-8922260 14 2.08e-04 GTCTCTATTC ACACGTGT TGGCAGGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:4745432-4745512 1.8e-05 27_[+3]_45 chrX:15355713-15355793 1.8e-05 34_[+3]_38 chrII:10390601-10390681 1.8e-05 61_[+3]_11 chrIV:13911099-13911179 1.8e-05 16_[+3]_56 chrII:10557427-10557507 1.8e-05 33_[+3]_39 chrX:12877997-12878077 3.8e-05 56_[+3]_16 chrX:5942260-5942340 3.8e-05 4_[+3]_68 chrII:10546212-10546292 3.8e-05 51_[+3]_21 chrII:15212590-15212670 6.9e-05 47_[+3]_25 chrV:10937455-10937535 6.9e-05 21_[+3]_51 chrIV:11068486-11068566 6.9e-05 40_[+3]_32 chrV:11822623-11822703 6.9e-05 44_[+3]_28 chrII:10546930-10547010 6.9e-05 21_[+3]_51 chrII:6288241-6288321 6.9e-05 71_[+3]_1 chrX:17482092-17482172 6.9e-05 19_[+3]_53 chrV:10535578-10535658 9.8e-05 16_[+3]_56 chrI:6001193-6001273 9.8e-05 48_[+3]_24 chrII:10300518-10300598 9.8e-05 22_[+3]_50 chrIII:9814000-9814080 0.00013 67_[+3]_5 chrIII:3782034-3782114 0.00014 24_[+3]_48 chrI:5378582-5378662 0.00014 71_[+3]_1 chrII:9683816-9683896 0.0002 68_[+3]_4 chrII:7891924-7892004 0.0002 68_[+3]_4 chrIII:8922180-8922260 0.00021 13_[+3]_59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YCACRTGA width=8 seqs=24 chrII:4745432-4745512 ( 28) TCACGTGA 1 chrX:15355713-15355793 ( 35) TCACGTGA 1 chrII:10390601-10390681 ( 62) CCACGTGA 1 chrIV:13911099-13911179 ( 17) TCACGTGA 1 chrII:10557427-10557507 ( 34) CCACGTGA 1 chrX:12877997-12878077 ( 57) GCACGTGG 1 chrX:5942260-5942340 ( 5) GCACGTGG 1 chrII:10546212-10546292 ( 52) GCACGTGG 1 chrII:15212590-15212670 ( 48) TCACATGA 1 chrV:10937455-10937535 ( 22) TCACATGA 1 chrIV:11068486-11068566 ( 41) TCACATGA 1 chrV:11822623-11822703 ( 45) CCACATGA 1 chrII:10546930-10547010 ( 22) TCACATGA 1 chrII:6288241-6288321 ( 72) CCACATGA 1 chrX:17482092-17482172 ( 20) TCACATGA 1 chrV:10535578-10535658 ( 17) ACACGTGA 1 chrI:6001193-6001273 ( 49) CCACGTGT 1 chrII:10300518-10300598 ( 23) ACACGTGA 1 chrIII:9814000-9814080 ( 68) TCACATGG 1 chrIII:3782034-3782114 ( 25) ACACGTGG 1 chrI:5378582-5378662 ( 72) GCACGTGT 1 chrII:9683816-9683896 ( 69) TCACATGT 1 chrII:7891924-7892004 ( 69) CCACATGT 1 chrIII:8922180-8922260 ( 14) ACACGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.0167 E= 1.3e+004 -93 44 -11 39 -1123 244 -1123 -1123 166 -1123 -1123 -1123 -1123 244 -1123 -1123 39 -1123 169 -1123 -1123 -1123 -1123 165 -1123 -1123 247 -1123 88 -1123 21 -61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.3e+004 0.166667 0.250000 0.166667 0.416667 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.416667 0.000000 0.583333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.583333 0.000000 0.208333 0.208333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACRTGA MEME-3 regular expression -------------------------------------------------------------------------------- [TC]CAC[GA]TG[AGT] -------------------------------------------------------------------------------- Time 13.44 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGGGCAM MEME-4 width = 8 sites = 3 llr = 36 E-value = 3.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::a7 pos.-specific C :::::a:3 probability G aaaaa::: matrix T :::::::: bits 2.5 ****** 2.2 ****** 2.0 ****** 1.7 ******* Relative 1.5 ******* Entropy 1.2 ******* (17.5 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGGGCAA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:6362454-6362534 53 3.49e-06 CCTCCGACCT GGGGGCAA ACGTAGACAC chrI:4909116-4909196 60 3.49e-06 CTCACGAACA GGGGGCAA TAACAACTTT chrIV:5100247-5100327 69 5.52e-06 TAGAGCGACC GGGGGCAC ATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:6362454-6362534 3.5e-06 52_[+4]_20 chrI:4909116-4909196 3.5e-06 59_[+4]_13 chrIV:5100247-5100327 5.5e-06 68_[+4]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGGGCAM width=8 seqs=3 chrIII:6362454-6362534 ( 53) GGGGGCAA 1 chrI:4909116-4909196 ( 60) GGGGGCAA 1 chrIV:5100247-5100327 ( 69) GGGGGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.0179 E= 3.2e+004 -823 -823 247 -823 -823 -823 247 -823 -823 -823 247 -823 -823 -823 247 -823 -823 -823 247 -823 -823 244 -823 -823 165 -823 -823 -823 107 85 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 3.2e+004 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 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGCAM MEME-4 regular expression -------------------------------------------------------------------------------- GGGGGCA[AC] -------------------------------------------------------------------------------- Time 17.16 secs. ******************************************************************************** ******************************************************************************** MOTIF GGSGGGAT MEME-5 width = 8 sites = 10 llr = 98 E-value = 3.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::::81 pos.-specific C 116::::1 probability G 994aaa:2 matrix T ::::::26 bits 2.5 *** 2.2 *** 2.0 ** *** 1.7 ** *** Relative 1.5 ****** Entropy 1.2 ****** (14.2 bits) 1.0 ******* 0.7 ******* 0.5 ******* 0.2 ******** 0.0 -------- Multilevel GGCGGGAT consensus G TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:5599496-5599576 22 3.52e-06 ATCGTCCTGC GGCGGGAT CCCATCAGAA chrX:1452273-1452353 61 6.96e-06 CACATGTTCA GGGGGGAT AGGTTTTCAG chrI:2586323-2586403 32 8.94e-06 GAAATAGAAA GGCGGGAG AATGAGGCGA chrII:12797166-12797246 15 1.09e-05 TTGACGTGGG GGGGGGAG CAACGTTGTT chrIII:3782034-3782114 3 1.64e-05 TC GGCGGGTT ACCGCAATAA chrIII:3800034-3800114 4 1.84e-05 CAT GGGGGGAC CTGTTATGTC chrIII:62612-62692 53 2.19e-05 TTGAACAATA GGCGGGAA ATTTTGTTTC chrIV:3647725-3647805 65 2.54e-05 GGGCTTTCCA GGGGGGTT TGGGACCA chrII:6587447-6587527 61 3.80e-05 TTAGCTTTCC GCCGGGAT GAAATCACAG chrIII:6405375-6405455 60 3.80e-05 GACTAAGACG CGCGGGAT TCGGACTACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:5599496-5599576 3.5e-06 21_[+5]_51 chrX:1452273-1452353 7e-06 60_[+5]_12 chrI:2586323-2586403 8.9e-06 31_[+5]_41 chrII:12797166-12797246 1.1e-05 14_[+5]_58 chrIII:3782034-3782114 1.6e-05 2_[+5]_70 chrIII:3800034-3800114 1.8e-05 3_[+5]_69 chrIII:62612-62692 2.2e-05 52_[+5]_20 chrIV:3647725-3647805 2.5e-05 64_[+5]_8 chrII:6587447-6587527 3.8e-05 60_[+5]_12 chrIII:6405375-6405455 3.8e-05 59_[+5]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGSGGGAT width=8 seqs=10 chrI:5599496-5599576 ( 22) GGCGGGAT 1 chrX:1452273-1452353 ( 61) GGGGGGAT 1 chrI:2586323-2586403 ( 32) GGCGGGAG 1 chrII:12797166-12797246 ( 15) GGGGGGAG 1 chrIII:3782034-3782114 ( 3) GGCGGGTT 1 chrIII:3800034-3800114 ( 4) GGGGGGAC 1 chrIII:62612-62692 ( 53) GGCGGGAA 1 chrIV:3647725-3647805 ( 65) GGGGGGTT 1 chrII:6587447-6587527 ( 61) GCCGGGAT 1 chrIII:6405375-6405455 ( 60) CGCGGGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.3073 E= 3.4e+004 -997 -88 232 -997 -997 -88 232 -997 -997 170 115 -997 -997 -997 247 -997 -997 -997 247 -997 -997 -997 247 -997 134 -997 -997 -67 -166 -88 15 91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 3.4e+004 0.000000 0.100000 0.900000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 0.600000 0.400000 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 0.800000 0.000000 0.000000 0.200000 0.100000 0.100000 0.200000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGSGGGAT MEME-5 regular expression -------------------------------------------------------------------------------- GG[CG]GGG[AT][TG] -------------------------------------------------------------------------------- Time 20.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:3645101-3645181 1.90e-01 80 chrX:4146200-4146280 4.96e-01 80 chrIII:12455832-12455912 1.86e-03 18_[+1(2.03e-06)]_54 chrIII:5567610-5567690 9.61e-01 80 chrI:7081140-7081220 4.86e-01 80 chrII:8482199-8482279 7.18e-01 80 chrIV:13083001-13083081 8.39e-01 80 chrX:4143761-4143841 1.72e-01 61_[+2(5.63e-05)]_11 chrX:3113336-3113416 9.85e-01 80 chrI:5378582-5378662 8.95e-02 80 chrV:8939789-8939869 3.08e-01 80 chrX:17482092-17482172 2.50e-01 19_[+3(6.88e-05)]_53 chrV:13908494-13908574 2.03e-01 80 chrII:10300518-10300598 1.86e-03 22_[+3(9.77e-05)]_50 chrI:5376226-5376306 9.71e-01 80 chrII:6288241-6288321 3.55e-01 71_[+3(6.88e-05)]_1 chrI:14875674-14875754 4.68e-01 80 chrV:6226345-6226425 9.28e-01 80 chrX:12932079-12932159 4.90e-01 80 chrX:4148180-4148260 9.93e-01 80 chrX:4142784-4142864 2.91e-01 80 chrX:8032181-8032261 9.99e-01 80 chrIV:6751354-6751434 9.95e-01 80 chrIII:12607825-12607905 7.90e-02 80 chrI:2586323-2586403 1.16e-02 31_[+5(8.94e-06)]_41 chrII:14407906-14407986 6.85e-01 80 chrX:17420134-17420214 9.97e-01 80 chrIII:8922180-8922260 6.07e-02 80 chrX:14979045-14979125 9.34e-01 80 chrII:11762059-11762139 8.04e-01 80 chrIII:9824660-9824740 1.61e-01 80 chrX:10057704-10057784 1.07e-01 80 chrIII:62612-62692 9.03e-03 52_[+5(2.19e-05)]_20 chrII:12095226-12095306 1.44e-01 80 chrII:10557427-10557507 4.37e-02 33_[+3(1.77e-05)]_39 chrII:6821306-6821386 4.42e-01 80 chrII:9285689-9285769 5.98e-01 80 chrIII:7152838-7152918 5.47e-01 80 chrIV:10295276-10295356 9.99e-01 80 chrI:999243-999323 1.38e-02 80 chrV:6221171-6221251 4.83e-01 80 chrII:10546212-10546292 9.29e-02 51_[+3(3.77e-05)]_21 chrI:2418097-2418177 9.90e-01 80 chrIII:8732165-8732245 9.16e-01 80 chrIII:6820515-6820595 1.39e-01 80 chrII:14299725-14299805 8.91e-01 80 chrI:11940068-11940148 7.69e-01 80 chrIV:13083252-13083332 9.75e-01 80 chrX:9954746-9954826 1.71e-01 80 chrIII:9814000-9814080 1.06e-01 80 chrII:13279416-13279496 9.30e-01 80 chrIII:6988320-6988400 5.72e-01 80 chrIV:3026009-3026089 1.46e-03 68_[+1(7.06e-05)]_4 chrX:6253901-6253981 2.61e-01 80 chrV:8039350-8039430 3.64e-01 80 chrX:6040555-6040635 7.60e-01 80 chrV:4824198-4824278 8.92e-01 80 chrX:13116324-13116404 9.48e-01 80 chrIV:11354202-11354282 4.48e-01 80 chrX:5940272-5940352 9.96e-01 80 chrIV:12033983-12034063 4.15e-01 80 chrI:8868445-8868525 8.71e-01 80 chrI:5375449-5375529 9.51e-01 80 chrV:3870485-3870565 7.92e-01 80 chrIII:6282617-6282697 6.10e-01 80 chrIII:6415445-6415525 1.92e-01 80 chrIV:14764533-14764613 9.13e-01 80 chrII:10546930-10547010 2.32e-01 21_[+3(6.88e-05)]_51 chrV:20710298-20710378 3.05e-02 42_[+2(9.16e-05)]_30 chrIII:5953553-5953633 8.13e-01 80 chrV:19520248-19520328 4.54e-03 80 chrX:4969456-4969536 9.60e-01 80 chrV:4820782-4820862 8.89e-03 59_[+2(9.16e-05)]_13 chrIV:12037052-12037132 9.80e-01 80 chrI:7870571-7870651 1.25e-01 80 chrV:11822623-11822703 1.06e-01 44_[+3(6.88e-05)]_28 chrIII:8449378-8449458 6.88e-01 80 chrX:1452273-1452353 5.79e-04 60_[+5(6.96e-06)]_12 chrII:4902211-4902291 4.74e-04 36_[+1(2.03e-06)]_36 chrX:3947354-3947434 8.23e-01 80 chrI:9095632-9095712 4.19e-01 36_[+2(9.16e-05)]_36 chrII:10450468-10450548 2.61e-01 80 chrV:11889733-11889813 3.12e-01 80 chrIV:15722317-15722397 9.48e-01 80 chrV:10953817-10953897 8.49e-01 80 chrV:4794420-4794500 6.64e-01 80 chrII:10544149-10544229 7.94e-01 80 chrII:8820104-8820184 1.18e-01 80 chrIII:5853308-5853388 9.92e-01 80 chrII:11756976-11757056 9.75e-01 80 chrIII:3671145-3671225 7.38e-01 80 chrX:4147719-4147799 6.97e-01 80 chrIII:13716382-13716462 2.94e-01 80 chrX:13542829-13542909 4.06e-01 80 chrX:1445815-1445895 1.00e-01 80 chrIV:8790944-8791024 7.60e-01 80 chrX:4146903-4146983 7.60e-01 80 chrII:4859171-4859251 8.00e-01 80 chrX:3788706-3788786 7.68e-02 80 chrX:11474704-11474784 1.88e-01 80 chrX:430489-430569 9.55e-03 80 chrX:10233150-10233230 9.97e-01 80 chrV:13650258-13650338 1.00e+00 80 chrIII:10339535-10339615 2.30e-01 80 chrIII:8654746-8654826 8.28e-02 80 chrII:7887513-7887593 2.59e-01 80 chrV:11082632-11082712 2.77e-01 80 chrI:7087496-7087576 9.99e-01 80 chrV:11817416-11817496 6.39e-01 80 chrI:5376441-5376521 1.16e-01 80 chrX:4141121-4141201 1.40e-01 58_[+2(2.06e-05)]_14 chrIV:4474288-4474368 7.02e-01 80 chrIII:5504314-5504394 1.34e-01 25_[+2(2.06e-05)]_47 chrII:6889965-6890045 1.56e-01 80 chrIV:9668173-9668253 2.15e-01 13_[+2(5.63e-05)]_59 chrV:11076526-11076606 1.88e-02 37_[+5(8.86e-05)]_35 chrIV:11068486-11068566 2.14e-01 40_[+3(6.88e-05)]_32 chrI:14938743-14938823 1.19e-01 80 chrII:9601825-9601905 1.57e-02 80 chrIV:10159402-10159482 9.02e-01 80 chrIII:8739886-8739966 5.95e-01 80 chrX:11469031-11469111 7.82e-04 52_[+1(7.06e-05)]_20 chrV:4806935-4807015 7.39e-01 80 chrI:8011486-8011566 2.18e-01 53_[+2(2.06e-05)]_19 chrX:6202973-6203053 7.50e-01 80 chrIV:13911099-13911179 9.10e-02 16_[+3(1.77e-05)]_56 chrIII:9701397-9701477 6.92e-01 80 chrIII:5758814-5758894 1.12e-01 80 chrI:11662841-11662921 7.26e-01 80 chrIII:6405375-6405455 9.06e-04 59_[+5(3.80e-05)]_13 chrIII:9457488-9457568 1.43e-01 49_[+2(2.06e-05)]_23 chrX:8236204-8236284 7.03e-03 71_[+1(6.40e-06)]_1 chrV:4157468-4157548 5.93e-01 80 chrIII:4100000-4100080 8.89e-02 20_[+2(5.63e-05)]_7_[+2(2.06e-05)]_\ 37 chrII:7323440-7323520 2.25e-01 80 chrIII:5196517-5196597 8.79e-01 80 chrIII:5835710-5835790 7.34e-01 80 chrII:7891924-7892004 2.30e-01 80 chrI:3675810-3675890 1.04e-01 52_[+2(2.06e-05)]_20 chrIV:5100247-5100327 1.02e-03 68_[+4(5.52e-06)]_4 chrII:8020793-8020873 9.97e-01 80 chrIV:3647725-3647805 9.63e-03 64_[+5(2.54e-05)]_8 chrIII:5025386-5025466 5.87e-02 80 chrII:5338404-5338484 6.58e-01 80 chrII:10390601-10390681 9.47e-03 61_[+3(1.77e-05)]_11 chrI:4908255-4908335 7.23e-02 80 chrII:5945089-5945169 8.44e-01 80 chrII:8481077-8481157 9.85e-01 80 chrIII:7974248-7974328 1.11e-01 80 chrII:8789971-8790051 4.77e-01 80 chrIV:17470162-17470242 6.23e-01 80 chrX:14792928-14793008 7.57e-01 80 chrV:8607374-8607454 4.22e-01 80 chrII:8585430-8585510 4.05e-01 80 chrX:8475276-8475356 8.81e-03 2_[+2(2.06e-05)]_70 chrV:20713033-20713113 1.40e-01 33_[+2(2.06e-05)]_39 chrII:4857880-4857960 3.99e-01 80 chrX:15541515-15541595 9.90e-01 80 chrX:13108731-13108811 7.01e-01 80 chrII:9120984-9121064 1.99e-01 80 chrX:5805224-5805304 9.95e-01 80 chrI:7147749-7147829 1.75e-02 80 chrX:13941287-13941367 2.68e-01 80 chrIII:3782034-3782114 1.63e-03 2_[+5(1.64e-05)]_70 chrI:1695192-1695272 9.68e-02 13_[+2(2.06e-05)]_[+2(9.16e-05)]_51 chrX:7236963-7237043 9.29e-01 80 chrV:10861994-10862074 2.22e-02 60_[+2(5.63e-05)]_3_[+2(9.16e-05)]_\ 1 chrX:5942260-5942340 2.27e-03 4_[+3(3.77e-05)]_68 chrV:775128-775208 2.78e-01 80 chrX:16931411-16931491 8.78e-01 80 chrI:1877818-1877898 2.40e-01 80 chrII:6587447-6587527 1.74e-01 60_[+5(3.80e-05)]_12 chrI:7597481-7597561 9.94e-01 80 chrII:12797166-12797246 5.79e-05 14_[+5(1.09e-05)]_58 chrX:14562418-14562498 5.50e-01 80 chrII:4891552-4891632 4.44e-01 80 chrX:15608744-15608824 9.03e-01 80 chrV:10937455-10937535 1.67e-01 21_[+3(6.88e-05)]_51 chrIV:11026808-11026888 8.23e-01 80 chrX:9343221-9343301 9.60e-01 80 chrV:3874515-3874595 9.96e-01 80 chrIV:5656074-5656154 2.69e-01 80 chrX:16931618-16931698 9.81e-01 80 chrV:13235505-13235585 9.52e-01 80 chrI:7085894-7085974 2.37e-01 80 chrX:12873759-12873839 2.46e-02 80 chrV:19519777-19519857 4.43e-01 80 chrI:6001193-6001273 4.97e-02 48_[+3(9.77e-05)]_24 chrII:15212590-15212670 1.89e-01 47_[+3(6.88e-05)]_25 chrIV:8978284-8978364 9.51e-01 80 chrI:4909116-4909196 3.28e-03 59_[+4(3.49e-06)]_13 chrII:6888471-6888551 7.45e-01 80 chrIII:6362454-6362534 5.39e-04 52_[+4(3.49e-06)]_20 chrV:11118457-11118537 3.98e-01 80 chrIV:1626899-1626979 9.66e-01 80 chrV:11638707-11638787 4.27e-01 80 chrI:9721133-9721213 7.11e-01 80 chrV:5812149-5812229 8.56e-01 80 chrIII:7369820-7369900 7.22e-01 80 chrV:20785493-20785573 5.15e-01 80 chrIII:5551010-5551090 9.84e-01 80 chrV:7432587-7432667 9.73e-01 80 chrI:9100956-9101036 2.97e-03 58_[+4(2.29e-05)]_14 chrX:3111924-3112004 9.20e-01 80 chrII:11726701-11726781 6.25e-02 80 chrV:20777003-20777083 5.99e-01 80 chrII:8745178-8745258 8.87e-01 80 chrV:4823972-4824052 9.31e-01 80 chrV:8938332-8938412 5.13e-01 80 chrX:11472049-11472129 9.69e-03 80 chrV:10535578-10535658 1.33e-01 16_[+3(9.77e-05)]_56 chrV:5848086-5848166 1.75e-01 80 chrIV:2709774-2709854 8.95e-01 80 chrIII:6123736-6123816 4.31e-01 80 chrIV:5602030-5602110 3.96e-01 80 chrV:5838923-5839003 6.50e-01 80 chrX:15355713-15355793 4.42e-02 34_[+3(1.77e-05)]_38 chrIII:3800034-3800114 1.04e-02 3_[+5(1.84e-05)]_69 chrV:14688635-14688715 8.28e-01 80 chrIII:10244954-10245034 8.88e-01 80 chrX:8015127-8015207 9.98e-01 80 chrV:1805970-1806050 4.85e-01 80 chrIII:6167327-6167407 1.23e-01 80 chrI:3754633-3754713 2.41e-01 80 chrI:5372620-5372700 9.92e-01 80 chrX:12877997-12878077 3.62e-02 56_[+3(3.77e-05)]_16 chrV:9741084-9741164 3.54e-01 80 chrII:9117979-9118059 9.58e-01 80 chrII:10547694-10547774 8.93e-01 80 chrIII:8734547-8734627 3.61e-02 80 chrX:1504029-1504109 6.02e-01 80 chrII:7339243-7339323 4.37e-01 80 chrI:5599496-5599576 8.46e-04 21_[+5(3.52e-06)]_51 chrIV:9212459-9212539 9.97e-01 80 chrII:4745432-4745512 1.29e-02 27_[+3(1.77e-05)]_45 chrIII:7723030-7723110 9.79e-01 80 chrII:9683816-9683896 3.12e-01 80 chrV:14687091-14687171 6.92e-01 80 chrIV:13826516-13826596 5.00e-02 80 chrI:5389160-5389240 1.93e-01 80 chrI:12164768-12164848 9.03e-02 80 chrIII:8355264-8355344 1.41e-02 80 chrX:6743084-6743164 4.69e-01 80 chrIII:3955008-3955088 8.94e-01 80 chrV:11122636-11122716 8.35e-01 80 chrX:13220771-13220851 2.41e-01 80 chrIII:5622816-5622896 1.32e-01 [+2(5.63e-05)]_72 chrII:9933872-9933952 8.45e-01 80 chrIII:9805137-9805217 9.41e-01 80 chrV:11226052-11226132 9.98e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n09.farnam.hpc.yale.internal ********************************************************************************