******************************************************************************** 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/hpl-2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:13269319-13269399 1.0000 80 chrX:4007890-4007970 1.0000 80 chrII:7147719-7147799 1.0000 80 chrI:1839801-1839881 1.0000 80 chrIV:12527439-12527519 1.0000 80 chrV:9516399-9516479 1.0000 80 chrV:16746755-16746835 1.0000 80 chrV:2008527-2008607 1.0000 80 chrII:14480048-14480128 1.0000 80 chrII:11916295-11916375 1.0000 80 chrV:5081068-5081148 1.0000 80 chrV:16045948-16046028 1.0000 80 chrX:15610623-15610703 1.0000 80 chrI:8134980-8135060 1.0000 80 chrIV:4401088-4401168 1.0000 80 chrV:11585366-11585446 1.0000 80 chrV:20162550-20162630 1.0000 80 chrIV:11364098-11364178 1.0000 80 chrI:11910055-11910135 1.0000 80 chrII:15120135-15120215 1.0000 80 chrIV:8431867-8431947 1.0000 80 chrV:19053517-19053597 1.0000 80 chrII:6888630-6888710 1.0000 80 chrIII:7945329-7945409 1.0000 80 chrII:11676116-11676196 1.0000 80 chrIII:1279359-1279439 1.0000 80 chrX:9838321-9838401 1.0000 80 chrX:4504393-4504473 1.0000 80 chrIV:6219605-6219685 1.0000 80 chrX:11007486-11007566 1.0000 80 chrII:6369426-6369506 1.0000 80 chrI:10106247-10106327 1.0000 80 chrIII:8355227-8355307 1.0000 80 chrIII:3736304-3736384 1.0000 80 chrX:3819297-3819377 1.0000 80 chrV:5576166-5576246 1.0000 80 chrIII:4191462-4191542 1.0000 80 chrX:17421166-17421246 1.0000 80 chrIII:7234278-7234358 1.0000 80 chrX:13396731-13396811 1.0000 80 chrX:6522873-6522953 1.0000 80 chrIII:12614700-12614780 1.0000 80 chrX:10576587-10576667 1.0000 80 chrX:10524627-10524707 1.0000 80 chrV:3391180-3391260 1.0000 80 chrI:7085717-7085797 1.0000 80 chrIV:9671092-9671172 1.0000 80 chrIV:16180998-16181078 1.0000 80 chrV:3803536-3803616 1.0000 80 chrII:12054233-12054313 1.0000 80 chrII:6374793-6374873 1.0000 80 chrX:15736621-15736701 1.0000 80 chrII:8091697-8091777 1.0000 80 chrV:12514112-12514192 1.0000 80 chrX:17419962-17420042 1.0000 80 chrIII:8868410-8868490 1.0000 80 chrIV:5591349-5591429 1.0000 80 chrIII:4018296-4018376 1.0000 80 chrI:11931923-11932003 1.0000 80 chrI:1628737-1628817 1.0000 80 chrV:10720008-10720088 1.0000 80 chrII:1820043-1820123 1.0000 80 chrIII:357517-357597 1.0000 80 chrV:7730606-7730686 1.0000 80 chrI:108490-108570 1.0000 80 chrIII:12549742-12549822 1.0000 80 chrV:20415366-20415446 1.0000 80 chrV:8760222-8760302 1.0000 80 chrX:17420166-17420246 1.0000 80 chrX:1504813-1504893 1.0000 80 chrI:15034047-15034127 1.0000 80 chrX:6808849-6808929 1.0000 80 chrIV:6555071-6555151 1.0000 80 chrII:8819934-8820014 1.0000 80 chrX:11792070-11792150 1.0000 80 chrI:3309746-3309826 1.0000 80 chrI:3680008-3680088 1.0000 80 chrIII:5839325-5839405 1.0000 80 chrV:17615995-17616075 1.0000 80 chrIV:10697311-10697391 1.0000 80 chrI:1251582-1251662 1.0000 80 chrIII:2876082-2876162 1.0000 80 chrV:8570069-8570149 1.0000 80 chrI:12970420-12970500 1.0000 80 chrII:13636472-13636552 1.0000 80 chrI:5261743-5261823 1.0000 80 chrI:7477148-7477228 1.0000 80 chrIII:7710250-7710330 1.0000 80 chrII:12058431-12058511 1.0000 80 chrIV:1496072-1496152 1.0000 80 chrI:13626384-13626464 1.0000 80 chrV:724223-724303 1.0000 80 chrV:13463128-13463208 1.0000 80 chrV:17659423-17659503 1.0000 80 chrII:506231-506311 1.0000 80 chrV:7854690-7854770 1.0000 80 chrIII:12327909-12327989 1.0000 80 chrIII:8749703-8749783 1.0000 80 chrIV:2774741-2774821 1.0000 80 chrV:6994127-6994207 1.0000 80 chrII:12425911-12425991 1.0000 80 chrI:7657503-7657583 1.0000 80 chrX:9113928-9114008 1.0000 80 chrI:1842100-1842180 1.0000 80 chrII:3129117-3129197 1.0000 80 chrX:14813507-14813587 1.0000 80 chrX:7181790-7181870 1.0000 80 chrV:1471674-1471754 1.0000 80 chrII:2420888-2420968 1.0000 80 chrV:5844512-5844592 1.0000 80 chrV:6656823-6656903 1.0000 80 chrV:10940867-10940947 1.0000 80 chrX:10772231-10772311 1.0000 80 chrX:1011237-1011317 1.0000 80 chrII:8817412-8817492 1.0000 80 chrIV:2390460-2390540 1.0000 80 chrII:2378770-2378850 1.0000 80 chrX:14214685-14214765 1.0000 80 chrIV:11955794-11955874 1.0000 80 chrII:6346870-6346950 1.0000 80 chrI:5358074-5358154 1.0000 80 chrIV:15398660-15398740 1.0000 80 chrIII:3540607-3540687 1.0000 80 chrX:15616580-15616660 1.0000 80 chrIV:12831776-12831856 1.0000 80 chrIII:12251328-12251408 1.0000 80 chrI:6092015-6092095 1.0000 80 chrX:13920587-13920667 1.0000 80 chrIV:292138-292218 1.0000 80 chrII:10100093-10100173 1.0000 80 chrII:12811102-12811182 1.0000 80 chrV:6785269-6785349 1.0000 80 chrII:10548689-10548769 1.0000 80 chrV:6229611-6229691 1.0000 80 chrI:2070875-2070955 1.0000 80 chrV:11534686-11534766 1.0000 80 chrI:3787743-3787823 1.0000 80 chrX:4529049-4529129 1.0000 80 chrIV:6786062-6786142 1.0000 80 chrV:18086927-18087007 1.0000 80 chrX:9540637-9540717 1.0000 80 chrV:10729583-10729663 1.0000 80 chrIV:393554-393634 1.0000 80 chrIV:9322583-9322663 1.0000 80 chrI:9095688-9095768 1.0000 80 chrIII:12313252-12313332 1.0000 80 chrIII:5943890-5943970 1.0000 80 chrX:14174000-14174080 1.0000 80 chrII:8016957-8017037 1.0000 80 chrV:7237259-7237339 1.0000 80 chrV:19158845-19158925 1.0000 80 chrI:7082267-7082347 1.0000 80 chrIII:4918088-4918168 1.0000 80 chrV:8247925-8248005 1.0000 80 chrII:8990415-8990495 1.0000 80 chrII:10798660-10798740 1.0000 80 chrX:6841025-6841105 1.0000 80 chrIII:13256597-13256677 1.0000 80 chrII:5912323-5912403 1.0000 80 chrIII:3869628-3869708 1.0000 80 chrV:20493733-20493813 1.0000 80 chrIII:2090847-2090927 1.0000 80 chrIV:11635734-11635814 1.0000 80 chrII:5649598-5649678 1.0000 80 chrIII:13466391-13466471 1.0000 80 chrX:12018139-12018219 1.0000 80 chrI:7059342-7059422 1.0000 80 chrV:4820777-4820857 1.0000 80 chrI:13653967-13654047 1.0000 80 chrX:15779712-15779792 1.0000 80 chrV:8462283-8462363 1.0000 80 chrIII:7184188-7184268 1.0000 80 chrIV:4810605-4810685 1.0000 80 chrIII:12370067-12370147 1.0000 80 chrIV:6585559-6585639 1.0000 80 chrV:11824114-11824194 1.0000 80 chrIV:15932038-15932118 1.0000 80 chrX:7825853-7825933 1.0000 80 chrI:7867869-7867949 1.0000 80 chrI:13951827-13951907 1.0000 80 chrIV:4447075-4447155 1.0000 80 chrX:8243279-8243359 1.0000 80 chrI:3516389-3516469 1.0000 80 chrX:5018436-5018516 1.0000 80 chrII:7529229-7529309 1.0000 80 chrII:5886026-5886106 1.0000 80 chrIII:7573040-7573120 1.0000 80 chrIV:3233791-3233871 1.0000 80 chrII:11150135-11150215 1.0000 80 chrIV:3900024-3900104 1.0000 80 chrIV:8585305-8585385 1.0000 80 chrX:15607648-15607728 1.0000 80 chrIII:6173171-6173251 1.0000 80 chrII:5379739-5379819 1.0000 80 chrIII:11353610-11353690 1.0000 80 chrIV:5947910-5947990 1.0000 80 chrX:1503902-1503982 1.0000 80 chrIV:13881907-13881987 1.0000 80 chrIV:8527699-8527779 1.0000 80 chrI:7147667-7147747 1.0000 80 chrI:110702-110782 1.0000 80 chrII:13006443-13006523 1.0000 80 chrI:9422367-9422447 1.0000 80 chrIII:12978936-12979016 1.0000 80 chrI:4178670-4178750 1.0000 80 chrI:2928142-2928222 1.0000 80 chrII:11974712-11974792 1.0000 80 chrV:14468503-14468583 1.0000 80 chrV:19190194-19190274 1.0000 80 chrIII:10882148-10882228 1.0000 80 chrIII:7179853-7179933 1.0000 80 chrX:4395600-4395680 1.0000 80 chrX:13514558-13514638 1.0000 80 chrIV:17461451-17461531 1.0000 80 chrIII:7141371-7141451 1.0000 80 chrI:13475718-13475798 1.0000 80 chrX:1323162-1323242 1.0000 80 chrIV:4745598-4745678 1.0000 80 chrV:9583064-9583144 1.0000 80 chrIV:12724780-12724860 1.0000 80 chrIII:6895339-6895419 1.0000 80 chrIII:5228120-5228200 1.0000 80 chrX:11661715-11661795 1.0000 80 chrI:11893860-11893940 1.0000 80 chrX:16205975-16206055 1.0000 80 chrII:14383789-14383869 1.0000 80 chrI:12532320-12532400 1.0000 80 chrIV:247651-247731 1.0000 80 chrX:12872375-12872455 1.0000 80 chrV:13907893-13907973 1.0000 80 chrI:1273938-1274018 1.0000 80 chrII:13369393-13369473 1.0000 80 chrI:1444157-1444237 1.0000 80 chrX:13349568-13349648 1.0000 80 chrIII:1926524-1926604 1.0000 80 chrX:10197444-10197524 1.0000 80 chrIII:3505315-3505395 1.0000 80 chrX:2364849-2364929 1.0000 80 chrV:14028382-14028462 1.0000 80 chrIII:9467325-9467405 1.0000 80 chrV:14200166-14200246 1.0000 80 chrX:14946609-14946689 1.0000 80 chrX:7773944-7774024 1.0000 80 chrII:12006864-12006944 1.0000 80 chrIII:13061289-13061369 1.0000 80 chrX:6750313-6750393 1.0000 80 chrIV:866978-867058 1.0000 80 chrII:12339361-12339441 1.0000 80 chrV:13658774-13658854 1.0000 80 chrII:11097492-11097572 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_hpl-2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/hpl-2.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 250 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.292 C 0.208 G 0.205 T 0.294 Background letter frequencies (from file dataset with add-one prior applied): A 0.292 C 0.208 G 0.205 T 0.294 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTKCGMAA MEME-1 width = 8 sites = 35 llr = 303 E-value = 1.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::6aa pos.-specific C :1:8:4:: probability G ::3:a::: matrix T a972:::: bits 2.3 * 2.1 * 1.8 * * ** 1.6 * * ** Relative 1.4 ** ** ** Entropy 1.1 ** ** ** (12.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTCGAAA consensus GT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:7141371-7141451 62 2.70e-05 GAATTCGATC TTTCGAAA GAATGTGTCG chrII:7529229-7529309 27 2.70e-05 CAGCGATGAT TTTCGAAA ATTACAACTT chrIII:7184188-7184268 63 2.70e-05 AGTCTCTAGG TTTCGAAA CAAAATATTG chrX:11792070-11792150 64 2.70e-05 AGTCGAAAGA TTTCGAAA TGACAAAAT chrV:13269319-13269399 52 2.70e-05 AATTGAAACA TTTCGAAA TTCTTATCAC chrIII:9467325-9467405 65 4.62e-05 TTTTATTTTA TTTCGCAA CTATCTTT chrI:1444157-1444237 46 4.62e-05 CGCGCGCACT TTTCGCAA CCCCAGCGCA chrIII:4918088-4918168 56 4.62e-05 CGCGCGCGGG TTTCGCAA CGATTCTCTC chrII:6346870-6346950 12 4.62e-05 GAAAAAGTGA TTTCGCAA TGTGTATTGC chrV:13463128-13463208 36 4.62e-05 GGCGTCCCTC TTTCGCAA TACCAACACC chrIII:2876082-2876162 20 4.62e-05 GACCGTCTTG TTTCGCAa gaaaaagaaa chrII:1820043-1820123 9 4.62e-05 TTTTAAAA TTTCGCAA TATGGCGCCA chrX:10576587-10576667 69 4.62e-05 ACTCTATTCA TTTCGCAA CGCA chrII:15120135-15120215 57 4.62e-05 TCTGCGTACA TTTCGCAA CTCTCATTTA chrV:4820777-4820857 8 6.50e-05 GGCAGGG TTGCGAAA TTACGGTCCG chrV:10940867-10940947 48 6.50e-05 CGTGTTCCGA TTGCGAAA TATTGCGCAC chrV:6656823-6656903 28 6.50e-05 ATGAGAGATG TTGCGAAA TCTGTGCAAA chrV:17659423-17659503 15 6.50e-05 CCAACACAAA TTGCGAAA TTTCGTTGTC chrI:1628737-1628817 26 6.50e-05 TGCCATTTCC TTGCGAAA TATTGCAGAA chrIII:4018296-4018376 57 6.50e-05 GGCAAATCTA TTGCGAAA CATACACAAA chrV:3803536-3803616 31 6.50e-05 CGAAAATATG TTGCGAAA TTGGGAGAGG chrIII:4191462-4191542 13 6.50e-05 GTTTGCCCTA TTGCGAAA GAAGTAAATG chrIII:8355227-8355307 38 6.50e-05 CGGCAAAACA TTGCGAAA TTTCGGAATA chrIV:11364098-11364178 20 6.50e-05 ACGAAATGTG TTGCGAAA TATATTCTGA chrIV:12527439-12527519 46 6.50e-05 GGTGACGGGA TTGCGAAA TCAAAGTGTT chrIII:6895339-6895419 67 1.17e-04 TTCGGTCACT TTTTGAAA GTTTTT chrI:5358074-5358154 26 1.17e-04 TTTTCACAAA TTTTGAAA CATTTTCGAT chrV:20162550-20162630 38 1.17e-04 TTTTCCACAT TTTTGAAA ATTTCATCAC chrII:11916295-11916375 38 1.17e-04 ACTTTAAAAT TTTTGAAA AGTTTGATGT chrV:9583064-9583144 55 1.44e-04 GCGCACGCTA TTTTGCAA GGTTGTCGCA chrV:7237259-7237339 20 1.44e-04 GGGCGCACTG TTTTGCAA TGGCACCGCG chrV:6785269-6785349 33 1.44e-04 GGCACGCAGT TTTTGCAA GGAGCGTGCA chrIV:4447075-4447155 29 1.70e-04 AAACAGTTGT TTGTGAAA TGAGTCAGGT chrII:5886026-5886106 10 2.08e-04 TTCTTTGCT TCTCGAAA CCCGTCAAAA chrII:10100093-10100173 6 2.22e-04 GCAGG TCTCGCAA CGACGAAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:7141371-7141451 2.7e-05 61_[+1]_11 chrII:7529229-7529309 2.7e-05 26_[+1]_46 chrIII:7184188-7184268 2.7e-05 62_[+1]_10 chrX:11792070-11792150 2.7e-05 63_[+1]_9 chrV:13269319-13269399 2.7e-05 51_[+1]_21 chrIII:9467325-9467405 4.6e-05 64_[+1]_8 chrI:1444157-1444237 4.6e-05 45_[+1]_27 chrIII:4918088-4918168 4.6e-05 55_[+1]_17 chrII:6346870-6346950 4.6e-05 11_[+1]_61 chrV:13463128-13463208 4.6e-05 35_[+1]_37 chrIII:2876082-2876162 4.6e-05 19_[+1]_53 chrII:1820043-1820123 4.6e-05 8_[+1]_64 chrX:10576587-10576667 4.6e-05 68_[+1]_4 chrII:15120135-15120215 4.6e-05 56_[+1]_16 chrV:4820777-4820857 6.5e-05 7_[+1]_65 chrV:10940867-10940947 6.5e-05 47_[+1]_25 chrV:6656823-6656903 6.5e-05 27_[+1]_45 chrV:17659423-17659503 6.5e-05 14_[+1]_58 chrI:1628737-1628817 6.5e-05 25_[+1]_47 chrIII:4018296-4018376 6.5e-05 56_[+1]_16 chrV:3803536-3803616 6.5e-05 30_[+1]_42 chrIII:4191462-4191542 6.5e-05 12_[+1]_60 chrIII:8355227-8355307 6.5e-05 37_[+1]_35 chrIV:11364098-11364178 6.5e-05 19_[+1]_53 chrIV:12527439-12527519 6.5e-05 45_[+1]_27 chrIII:6895339-6895419 0.00012 66_[+1]_6 chrI:5358074-5358154 0.00012 25_[+1]_47 chrV:20162550-20162630 0.00012 37_[+1]_35 chrII:11916295-11916375 0.00012 37_[+1]_35 chrV:9583064-9583144 0.00014 54_[+1]_18 chrV:7237259-7237339 0.00014 19_[+1]_53 chrV:6785269-6785349 0.00014 32_[+1]_40 chrIV:4447075-4447155 0.00017 28_[+1]_44 chrII:5886026-5886106 0.00021 9_[+1]_63 chrII:10100093-10100173 0.00022 5_[+1]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTKCGMAA width=8 seqs=35 chrIII:7141371-7141451 ( 62) TTTCGAAA 1 chrII:7529229-7529309 ( 27) TTTCGAAA 1 chrIII:7184188-7184268 ( 63) TTTCGAAA 1 chrX:11792070-11792150 ( 64) TTTCGAAA 1 chrV:13269319-13269399 ( 52) TTTCGAAA 1 chrIII:9467325-9467405 ( 65) TTTCGCAA 1 chrI:1444157-1444237 ( 46) TTTCGCAA 1 chrIII:4918088-4918168 ( 56) TTTCGCAA 1 chrII:6346870-6346950 ( 12) TTTCGCAA 1 chrV:13463128-13463208 ( 36) TTTCGCAA 1 chrIII:2876082-2876162 ( 20) TTTCGCAA 1 chrII:1820043-1820123 ( 9) TTTCGCAA 1 chrX:10576587-10576667 ( 69) TTTCGCAA 1 chrII:15120135-15120215 ( 57) TTTCGCAA 1 chrV:4820777-4820857 ( 8) TTGCGAAA 1 chrV:10940867-10940947 ( 48) TTGCGAAA 1 chrV:6656823-6656903 ( 28) TTGCGAAA 1 chrV:17659423-17659503 ( 15) TTGCGAAA 1 chrI:1628737-1628817 ( 26) TTGCGAAA 1 chrIII:4018296-4018376 ( 57) TTGCGAAA 1 chrV:3803536-3803616 ( 31) TTGCGAAA 1 chrIII:4191462-4191542 ( 13) TTGCGAAA 1 chrIII:8355227-8355307 ( 38) TTGCGAAA 1 chrIV:11364098-11364178 ( 20) TTGCGAAA 1 chrIV:12527439-12527519 ( 46) TTGCGAAA 1 chrIII:6895339-6895419 ( 67) TTTTGAAA 1 chrI:5358074-5358154 ( 26) TTTTGAAA 1 chrV:20162550-20162630 ( 38) TTTTGAAA 1 chrII:11916295-11916375 ( 38) TTTTGAAA 1 chrV:9583064-9583144 ( 55) TTTTGCAA 1 chrV:7237259-7237339 ( 20) TTTTGCAA 1 chrV:6785269-6785349 ( 33) TTTTGCAA 1 chrIV:4447075-4447155 ( 29) TTGTGAAA 1 chrII:5886026-5886106 ( 10) TCTCGAAA 1 chrII:10100093-10100173 ( 6) TCTCGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.12623 E= 1.5e-006 -1177 -1177 -1177 176 -1177 -187 -1177 168 -1177 -1177 74 116 -1177 189 -1177 -36 -1177 -1177 229 -1177 110 83 -1177 -1177 177 -1177 -1177 -1177 177 -1177 -1177 -1177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.5e-006 0.000000 0.000000 0.000000 1.000000 0.000000 0.057143 0.000000 0.942857 0.000000 0.000000 0.342857 0.657143 0.000000 0.771429 0.000000 0.228571 0.000000 0.000000 1.000000 0.000000 0.628571 0.371429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTKCGMAA MEME-1 regular expression -------------------------------------------------------------------------------- TT[TG][CT]G[AC]AA -------------------------------------------------------------------------------- Time 8.19 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGACGCA MEME-2 width = 8 sites = 23 llr = 216 E-value = 5.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:9:::8 pos.-specific C ::::a3a: probability G a:91:7:1 matrix T ::1::::: bits 2.3 * * 2.1 * * * 1.8 * * * * 1.6 *** * * Relative 1.4 *** *** Entropy 1.1 ******** (13.6 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAGACGCA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:12018139-12018219 56 9.28e-06 GCATCCCGCT GAGACGCA CGTATTTATC chrII:5649598-5649678 2 9.28e-06 A GAGACGCA GAGAAAACCG chrII:5912323-5912403 65 9.28e-06 TTATCAGGTA GAGACGCA GATAACGT chrIII:12251328-12251408 38 9.28e-06 aaaaactaac gagacgca aattttggcg chrII:3129117-3129197 69 9.28e-06 CTCATGTACC GAGACGCA GGCG chrIV:10697311-10697391 23 9.28e-06 GCAGCTCTTG GAGACGCA GGCATAAAAT chrI:11931923-11932003 55 9.28e-06 tgagggaaaa gagacgca gacttttcaa chrV:3803536-3803616 52 9.28e-06 GGAGAGGGAG GAGACGCA GGTATGAGTC chrI:1839801-1839881 52 9.28e-06 gagagagtga gagacgca gagttgccaa chrIV:5947910-5947990 32 1.87e-05 GCGGCGCTGC GAGACCCA GTTGTGTAAA chrX:4504393-4504473 64 1.87e-05 ATTAACACTC GAGACCCA CGTGTCTTT chrIV:12527439-12527519 15 1.87e-05 GGGAAATCGT GAGACCCA GAGGGAAAAG chrI:2928142-2928222 9 3.17e-05 CACGAAAA GAGGCGCA GACAGTCATC chrV:19158845-19158925 70 3.17e-05 CTGGGTAGGA GAGGCGCA GAG chrII:11097492-11097572 53 4.49e-05 CTTTCGTTGC GAGACGCC AAAAGCGAAA chrIII:5228120-5228200 54 4.49e-05 ATTTCGTTGC GAGACCCG CTGCCCCGCT chrIV:15932038-15932118 14 4.49e-05 tgtcacatgc gagacccg ggttcaattc chrII:6888630-6888710 37 4.49e-05 GGATTTACAA GAGACCCG AAGCAATAGA chrIII:13061289-13061369 10 5.83e-05 CGGAGATGA GATACGCA GAGAAGCATA chrIII:3505315-3505395 41 5.83e-05 GTCTCGCCAC GATACGCA ATCAGACGTG chrIV:12831776-12831856 15 6.49e-05 CGCAAACACC GCGACGCA AAACCACACA chrIII:8749703-8749783 38 9.00e-05 ACAATTTGGA GAGACGGA GAGTTGAAAA chrV:3391180-3391260 52 9.00e-05 GACCAGTTTT GAGTCGCA GAGAAAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:12018139-12018219 9.3e-06 55_[+2]_17 chrII:5649598-5649678 9.3e-06 1_[+2]_71 chrII:5912323-5912403 9.3e-06 64_[+2]_8 chrIII:12251328-12251408 9.3e-06 37_[+2]_35 chrII:3129117-3129197 9.3e-06 68_[+2]_4 chrIV:10697311-10697391 9.3e-06 22_[+2]_50 chrI:11931923-11932003 9.3e-06 54_[+2]_18 chrV:3803536-3803616 9.3e-06 51_[+2]_21 chrI:1839801-1839881 9.3e-06 51_[+2]_21 chrIV:5947910-5947990 1.9e-05 31_[+2]_41 chrX:4504393-4504473 1.9e-05 63_[+2]_9 chrIV:12527439-12527519 1.9e-05 14_[+2]_58 chrI:2928142-2928222 3.2e-05 8_[+2]_64 chrV:19158845-19158925 3.2e-05 69_[+2]_3 chrII:11097492-11097572 4.5e-05 52_[+2]_20 chrIII:5228120-5228200 4.5e-05 53_[+2]_19 chrIV:15932038-15932118 4.5e-05 13_[+2]_59 chrII:6888630-6888710 4.5e-05 36_[+2]_36 chrIII:13061289-13061369 5.8e-05 9_[+2]_63 chrIII:3505315-3505395 5.8e-05 40_[+2]_32 chrIV:12831776-12831856 6.5e-05 14_[+2]_58 chrIII:8749703-8749783 9e-05 37_[+2]_35 chrV:3391180-3391260 9e-05 51_[+2]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGACGCA width=8 seqs=23 chrX:12018139-12018219 ( 56) GAGACGCA 1 chrII:5649598-5649678 ( 2) GAGACGCA 1 chrII:5912323-5912403 ( 65) GAGACGCA 1 chrIII:12251328-12251408 ( 38) GAGACGCA 1 chrII:3129117-3129197 ( 69) GAGACGCA 1 chrIV:10697311-10697391 ( 23) GAGACGCA 1 chrI:11931923-11932003 ( 55) GAGACGCA 1 chrV:3803536-3803616 ( 52) GAGACGCA 1 chrI:1839801-1839881 ( 52) GAGACGCA 1 chrIV:5947910-5947990 ( 32) GAGACCCA 1 chrX:4504393-4504473 ( 64) GAGACCCA 1 chrIV:12527439-12527519 ( 15) GAGACCCA 1 chrI:2928142-2928222 ( 9) GAGGCGCA 1 chrV:19158845-19158925 ( 70) GAGGCGCA 1 chrII:11097492-11097572 ( 53) GAGACGCC 1 chrIII:5228120-5228200 ( 54) GAGACCCG 1 chrIV:15932038-15932118 ( 14) GAGACCCG 1 chrII:6888630-6888710 ( 37) GAGACCCG 1 chrIII:13061289-13061369 ( 10) GATACGCA 1 chrIII:3505315-3505395 ( 41) GATACGCA 1 chrIV:12831776-12831856 ( 15) GCGACGCA 1 chrIII:8749703-8749783 ( 38) GAGACGGA 1 chrV:3391180-3391260 ( 52) GAGTCGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.6953 E= 5.0e-005 -1117 -1117 229 -1117 171 -226 -1117 -1117 -1117 -1117 215 -176 157 -1117 -124 -276 -1117 226 -1117 -1117 -1117 32 185 -1117 -1117 220 -223 -1117 150 -226 -65 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 5.0e-005 0.000000 0.000000 1.000000 0.000000 0.956522 0.043478 0.000000 0.000000 0.000000 0.000000 0.913043 0.086957 0.869565 0.000000 0.086957 0.043478 0.000000 1.000000 0.000000 0.000000 0.000000 0.260870 0.739130 0.000000 0.000000 0.956522 0.043478 0.000000 0.826087 0.043478 0.130435 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-2 regular expression -------------------------------------------------------------------------------- GAGAC[GC]CA -------------------------------------------------------------------------------- Time 11.95 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTGCGTC MEME-3 width = 8 sites = 12 llr = 127 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :9:1a::a probability G ::29:a:: matrix T a18:::a: bits 2.3 ** * 2.1 ** * 1.8 ** ***** 1.6 ** ***** Relative 1.4 ** ***** Entropy 1.1 ******** (15.2 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCTGCGTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:13061289-13061369 49 9.61e-06 TGTCAAGCTA TCTGCGTC TCTGTCGTTG chrIII:1926524-1926604 64 9.61e-06 CATCGTGCTC TCTGCGTC TCTCGAACC chrX:1323162-1323242 70 9.61e-06 AACCTAGTGT TCTGCGTC TCT chrII:7529229-7529309 45 9.61e-06 ATTACAACTT TCTGCGTC TCTAGATCTT chrIII:7184188-7184268 31 9.61e-06 GCAAATGTTC TCTGCGTC TCTGAGTTAC chrX:15616580-15616660 68 9.61e-06 TTAATTCGTC TCTGCGTC ACTAT chrIV:16180998-16181078 36 9.61e-06 TCCGAGTTTC TCTGCGTC TCTTCAATTT chrV:5081068-5081148 44 9.61e-06 TGTGTAGCCG TCTGCGTC TATTCCTTAA chrIV:13881907-13881987 7 1.63e-05 AACTAG TCGGCGTC TCCTCTTTTC chrV:13463128-13463208 24 1.63e-05 CGTCGCGTGA TCGGCGTC CCTCTTTCGC chrIV:6585559-6585639 23 2.61e-05 TTGCATTGTG TCTCCGTC TCCATAATTT chrIV:12831776-12831856 63 3.96e-05 TTTGTGCATG TTTGCGTC ACCGTGTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:13061289-13061369 9.6e-06 48_[+3]_24 chrIII:1926524-1926604 9.6e-06 63_[+3]_9 chrX:1323162-1323242 9.6e-06 69_[+3]_3 chrII:7529229-7529309 9.6e-06 44_[+3]_28 chrIII:7184188-7184268 9.6e-06 30_[+3]_42 chrX:15616580-15616660 9.6e-06 67_[+3]_5 chrIV:16180998-16181078 9.6e-06 35_[+3]_37 chrV:5081068-5081148 9.6e-06 43_[+3]_29 chrIV:13881907-13881987 1.6e-05 6_[+3]_66 chrV:13463128-13463208 1.6e-05 23_[+3]_49 chrIV:6585559-6585639 2.6e-05 22_[+3]_50 chrIV:12831776-12831856 4e-05 62_[+3]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTGCGTC width=8 seqs=12 chrIII:13061289-13061369 ( 49) TCTGCGTC 1 chrIII:1926524-1926604 ( 64) TCTGCGTC 1 chrX:1323162-1323242 ( 70) TCTGCGTC 1 chrII:7529229-7529309 ( 45) TCTGCGTC 1 chrIII:7184188-7184268 ( 31) TCTGCGTC 1 chrX:15616580-15616660 ( 68) TCTGCGTC 1 chrIV:16180998-16181078 ( 36) TCTGCGTC 1 chrV:5081068-5081148 ( 44) TCTGCGTC 1 chrIV:13881907-13881987 ( 7) TCGGCGTC 1 chrV:13463128-13463208 ( 24) TCGGCGTC 1 chrIV:6585559-6585639 ( 23) TCTCCGTC 1 chrIV:12831776-12831856 ( 63) TTTGCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.0174 E= 1.2e+000 -1023 -1023 -1023 176 -1023 214 -1023 -182 -1023 -1023 -30 150 -1023 -132 216 -1023 -1023 226 -1023 -1023 -1023 -1023 229 -1023 -1023 -1023 -1023 176 -1023 226 -1023 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 1.2e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.916667 0.000000 0.083333 0.000000 0.000000 0.166667 0.833333 0.000000 0.083333 0.916667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-3 regular expression -------------------------------------------------------------------------------- TCTGCGTC -------------------------------------------------------------------------------- Time 17.24 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCGCGC MEME-4 width = 8 sites = 23 llr = 207 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A 1:::2:1: pos.-specific C :a:7:a:a probability G 7:a:8:7: matrix T 1::3::3: bits 2.3 * * 2.1 ** * * 1.8 ** * * 1.6 ** ** * Relative 1.4 ** ** * Entropy 1.1 ***** * (13.0 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCGCGCGC consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:1444157-1444237 35 3.31e-06 TTTGCAACCA GCGCGCGC ACTTTTCGCA chrV:7237259-7237339 35 3.31e-06 CAATGGCACC GCGCGCGC TATTTTTTTA chrI:15034047-15034127 56 3.31e-06 TTGATTCTCA GCGCGCGC AACCAAATTT chrIV:17461451-17461531 55 8.05e-06 TTTGGGTTTC GCGCGCTC GTTCAAACGC chrX:12018139-12018219 28 8.05e-06 AGGTCTGCAA GCGCGCTC TATTGACAAA chrII:11097492-11097572 73 1.27e-05 AAGCGAAAGT GCGTGCGC chrII:12339361-12339441 22 1.27e-05 gtgggggtga gcgtgCGC GCATCACACA chrI:13951827-13951907 47 1.27e-05 GCCACGAAGG GCGTGCGC CTTTAAACTG chrV:9583064-9583144 45 1.74e-05 TTTGCAAGCC GCGCACGC TATTTTGCAA chrV:18086927-18087007 25 2.22e-05 AATTCGAATT TCGCGCGC ATTTCACCGT chrV:8570069-8570149 27 2.69e-05 CTGACACTTG GCGCGCAC TAAGTTTTTC chrIII:4918088-4918168 45 3.83e-05 GCAAACATTT ACGCGCGC GGGTTTCGCA chrV:14468503-14468583 73 4.16e-05 TTTTTTAGGG CCGCGCGC chrII:12006864-12006944 26 5.28e-05 GAGCGCGATT GCGCGGGC ATGACGTCAC chrV:19158845-19158925 47 5.28e-05 ATTTGCGGTG GGGCGCGC TTGCACTGGG chrX:13396731-13396811 7 5.28e-05 TAGTGT GCGAGCGC AAGAGGATGC chrV:10940867-10940947 60 5.96e-05 GCGAAATATT GCGCACTC GGATTCTGTA chrII:11676116-11676196 34 5.96e-05 GTGTGTGTTG GCGCACTC GCGGTTGTTG chrV:2008527-2008607 17 6.62e-05 aattaaatgc gcgtacgc aaagtacgca chrX:10197444-10197524 42 7.30e-05 CTACGACACT TCGCGCTC TTTGTTTATT chrIII:8355227-8355307 70 7.97e-05 ATCACTCGTC TCGTGCGC GAT chrV:6785269-6785349 44 8.64e-05 TTTGCAAGGA GCGTGCAC GCAGTTGCCT chrX:15607648-15607728 30 9.31e-05 TCTCATCGCC ACGCGCTC TCTTCCGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:1444157-1444237 3.3e-06 34_[+4]_38 chrV:7237259-7237339 3.3e-06 34_[+4]_38 chrI:15034047-15034127 3.3e-06 55_[+4]_17 chrIV:17461451-17461531 8e-06 54_[+4]_18 chrX:12018139-12018219 8e-06 27_[+4]_45 chrII:11097492-11097572 1.3e-05 72_[+4] chrII:12339361-12339441 1.3e-05 21_[+4]_51 chrI:13951827-13951907 1.3e-05 46_[+4]_26 chrV:9583064-9583144 1.7e-05 44_[+4]_28 chrV:18086927-18087007 2.2e-05 24_[+4]_48 chrV:8570069-8570149 2.7e-05 26_[+4]_46 chrIII:4918088-4918168 3.8e-05 44_[+4]_28 chrV:14468503-14468583 4.2e-05 72_[+4] chrII:12006864-12006944 5.3e-05 25_[+4]_47 chrV:19158845-19158925 5.3e-05 46_[+4]_26 chrX:13396731-13396811 5.3e-05 6_[+4]_66 chrV:10940867-10940947 6e-05 59_[+4]_13 chrII:11676116-11676196 6e-05 33_[+4]_39 chrV:2008527-2008607 6.6e-05 16_[+4]_56 chrX:10197444-10197524 7.3e-05 41_[+4]_31 chrIII:8355227-8355307 8e-05 69_[+4]_3 chrV:6785269-6785349 8.6e-05 43_[+4]_29 chrX:15607648-15607728 9.3e-05 29_[+4]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCGCGC width=8 seqs=23 chrI:1444157-1444237 ( 35) GCGCGCGC 1 chrV:7237259-7237339 ( 35) GCGCGCGC 1 chrI:15034047-15034127 ( 56) GCGCGCGC 1 chrIV:17461451-17461531 ( 55) GCGCGCTC 1 chrX:12018139-12018219 ( 28) GCGCGCTC 1 chrII:11097492-11097572 ( 73) GCGTGCGC 1 chrII:12339361-12339441 ( 22) GCGTGCGC 1 chrI:13951827-13951907 ( 47) GCGTGCGC 1 chrV:9583064-9583144 ( 45) GCGCACGC 1 chrV:18086927-18087007 ( 25) TCGCGCGC 1 chrV:8570069-8570149 ( 27) GCGCGCAC 1 chrIII:4918088-4918168 ( 45) ACGCGCGC 1 chrV:14468503-14468583 ( 73) CCGCGCGC 1 chrII:12006864-12006944 ( 26) GCGCGGGC 1 chrV:19158845-19158925 ( 47) GGGCGCGC 1 chrX:13396731-13396811 ( 7) GCGAGCGC 1 chrV:10940867-10940947 ( 60) GCGCACTC 1 chrII:11676116-11676196 ( 34) GCGCACTC 1 chrV:2008527-2008607 ( 17) GCGTACGC 1 chrX:10197444-10197524 ( 42) TCGCGCTC 1 chrIII:8355227-8355307 ( 70) TCGTGCGC 1 chrV:6785269-6785349 ( 44) GCGTGCAC 1 chrX:15607648-15607728 ( 30) ACGCGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.5229 E= 1.6e+000 -175 -226 185 -117 -1117 220 -223 -1117 -1117 -1117 229 -1117 -275 174 -1117 -17 -75 -1117 201 -1117 -1117 220 -223 -1117 -175 -1117 167 -17 -1117 226 -1117 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 1.6e+000 0.086957 0.043478 0.739130 0.130435 0.000000 0.956522 0.043478 0.000000 0.000000 0.000000 1.000000 0.000000 0.043478 0.695652 0.000000 0.260870 0.173913 0.000000 0.826087 0.000000 0.000000 0.956522 0.043478 0.000000 0.086957 0.000000 0.652174 0.260870 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 regular expression -------------------------------------------------------------------------------- GCG[CT]GC[GT]C -------------------------------------------------------------------------------- Time 22.50 secs. ******************************************************************************** ******************************************************************************** MOTIF TGGAGCGC MEME-5 width = 8 sites = 9 llr = 96 E-value = 4.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :2:8:::: pos.-specific C :::1:a:a probability G :8a1a:a: matrix T a::::::: bits 2.3 * **** 2.1 * **** 1.8 * * **** 1.6 * * **** Relative 1.4 *** **** Entropy 1.1 *** **** (15.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGGAGCGC consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:12006864-12006944 14 6.56e-06 TCTGTCGCGA TGGAGCGC GATTGCGCGG chrV:18086927-18087007 54 6.56e-06 tcgagtccaa tggagcgc acttgcatta chrIII:12251328-12251408 57 6.56e-06 attttggcga tggagcgC GATTGCATTT chrII:14480048-14480128 6 6.56e-06 ATCAG TGGAGCGC AGTTTCACCA chrII:7147719-7147799 52 6.56e-06 AAATTAGCCA TGGAGCGC ACTTGAAAAT chrI:9422367-9422447 27 2.52e-05 CTGTCTTGAT TAGAGCGC GTTTGCACTA chrI:3516389-3516469 32 2.52e-05 AATTGTGCGG TAGAGCGC GAATGCGTTT chrV:7237259-7237339 64 2.52e-05 GATTTGAACC TGGCGCGC TTTCTGGCG chrI:10106247-10106327 47 2.52e-05 GAGTTCTCCA TGGGGCGC AACTGCAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:12006864-12006944 6.6e-06 13_[+5]_59 chrV:18086927-18087007 6.6e-06 53_[+5]_19 chrIII:12251328-12251408 6.6e-06 56_[+5]_16 chrII:14480048-14480128 6.6e-06 5_[+5]_67 chrII:7147719-7147799 6.6e-06 51_[+5]_21 chrI:9422367-9422447 2.5e-05 26_[+5]_46 chrI:3516389-3516469 2.5e-05 31_[+5]_41 chrV:7237259-7237339 2.5e-05 63_[+5]_9 chrI:10106247-10106327 2.5e-05 46_[+5]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGGAGCGC width=8 seqs=9 chrII:12006864-12006944 ( 14) TGGAGCGC 1 chrV:18086927-18087007 ( 54) TGGAGCGC 1 chrIII:12251328-12251408 ( 57) TGGAGCGC 1 chrII:14480048-14480128 ( 6) TGGAGCGC 1 chrII:7147719-7147799 ( 52) TGGAGCGC 1 chrI:9422367-9422447 ( 27) TAGAGCGC 1 chrI:3516389-3516469 ( 32) TAGAGCGC 1 chrV:7237259-7237339 ( 64) TGGCGCGC 1 chrI:10106247-10106327 ( 47) TGGGGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.8333 E= 4.8e+002 -982 -982 -982 176 -39 -982 192 -982 -982 -982 229 -982 141 -91 -88 -982 -982 -982 229 -982 -982 226 -982 -982 -982 -982 229 -982 -982 226 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 4.8e+002 0.000000 0.000000 0.000000 1.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.777778 0.111111 0.111111 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGAGCGC MEME-5 regular expression -------------------------------------------------------------------------------- T[GA]GAGCGC -------------------------------------------------------------------------------- Time 26.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:13269319-13269399 6.49e-02 51_[+1(2.70e-05)]_21 chrX:4007890-4007970 7.30e-01 80 chrII:7147719-7147799 3.47e-03 51_[+5(6.56e-06)]_21 chrI:1839801-1839881 1.40e-03 51_[+2(9.28e-06)]_21 chrIV:12527439-12527519 3.07e-03 14_[+2(1.87e-05)]_23_[+1(6.50e-05)]_\ 27 chrV:9516399-9516479 6.24e-01 80 chrV:16746755-16746835 1.80e-01 80 chrV:2008527-2008607 5.31e-02 16_[+4(6.62e-05)]_56 chrII:14480048-14480128 5.42e-03 5_[+5(6.56e-06)]_67 chrII:11916295-11916375 1.82e-01 80 chrV:5081068-5081148 3.37e-02 43_[+3(9.61e-06)]_29 chrV:16045948-16046028 9.99e-01 80 chrX:15610623-15610703 9.68e-01 80 chrI:8134980-8135060 6.24e-01 80 chrIV:4401088-4401168 2.44e-01 80 chrV:11585366-11585446 6.60e-01 80 chrV:20162550-20162630 3.38e-01 80 chrIV:11364098-11364178 1.41e-01 19_[+1(6.50e-05)]_53 chrI:11910055-11910135 5.46e-01 80 chrII:15120135-15120215 9.96e-03 56_[+1(4.62e-05)]_16 chrIV:8431867-8431947 1.46e-01 80 chrV:19053517-19053597 5.02e-01 80 chrII:6888630-6888710 1.47e-01 36_[+2(4.49e-05)]_36 chrIII:7945329-7945409 8.28e-01 80 chrII:11676116-11676196 2.91e-02 33_[+4(5.96e-05)]_39 chrIII:1279359-1279439 3.24e-01 80 chrX:9838321-9838401 8.07e-01 80 chrX:4504393-4504473 5.94e-02 63_[+2(1.87e-05)]_9 chrIV:6219605-6219685 4.33e-01 80 chrX:11007486-11007566 1.31e-01 80 chrII:6369426-6369506 9.93e-01 80 chrI:10106247-10106327 1.36e-02 46_[+5(2.52e-05)]_26 chrIII:8355227-8355307 1.32e-03 37_[+1(6.50e-05)]_24_[+4(7.97e-05)]_\ 3 chrIII:3736304-3736384 9.44e-01 80 chrX:3819297-3819377 9.02e-01 80 chrV:5576166-5576246 8.57e-01 80 chrIII:4191462-4191542 2.68e-01 12_[+1(6.50e-05)]_60 chrX:17421166-17421246 9.44e-01 80 chrIII:7234278-7234358 2.40e-01 80 chrX:13396731-13396811 1.98e-03 6_[+4(5.28e-05)]_66 chrX:6522873-6522953 8.78e-01 80 chrIII:12614700-12614780 1.61e-01 80 chrX:10576587-10576667 6.24e-04 68_[+1(4.62e-05)]_4 chrX:10524627-10524707 1.30e-01 80 chrV:3391180-3391260 1.47e-02 51_[+2(9.00e-05)]_21 chrI:7085717-7085797 1.07e-01 80 chrIV:9671092-9671172 6.82e-01 80 chrIV:16180998-16181078 1.06e-01 35_[+3(9.61e-06)]_37 chrV:3803536-3803616 7.53e-04 30_[+1(6.50e-05)]_13_[+2(9.28e-06)]_\ 21 chrII:12054233-12054313 2.82e-01 13_[+3(6.97e-05)]_59 chrII:6374793-6374873 8.11e-01 80 chrX:15736621-15736701 2.90e-01 80 chrII:8091697-8091777 7.42e-02 80 chrV:12514112-12514192 5.77e-01 80 chrX:17419962-17420042 2.82e-01 80 chrIII:8868410-8868490 4.43e-01 80 chrIV:5591349-5591429 8.28e-01 80 chrIII:4018296-4018376 9.34e-02 56_[+1(6.50e-05)]_16 chrI:11931923-11932003 2.95e-03 54_[+2(9.28e-06)]_18 chrI:1628737-1628817 2.38e-01 25_[+1(6.50e-05)]_47 chrV:10720008-10720088 7.63e-01 80 chrII:1820043-1820123 1.29e-02 8_[+1(4.62e-05)]_64 chrIII:357517-357597 8.31e-01 80 chrV:7730606-7730686 5.65e-01 80 chrI:108490-108570 9.51e-01 80 chrIII:12549742-12549822 9.16e-01 80 chrV:20415366-20415446 5.85e-01 80 chrV:8760222-8760302 9.71e-01 80 chrX:17420166-17420246 6.94e-01 80 chrX:1504813-1504893 6.38e-01 80 chrI:15034047-15034127 1.15e-03 23_[+4(9.31e-05)]_24_[+4(3.31e-06)]_\ 17 chrX:6808849-6808929 8.69e-01 80 chrIV:6555071-6555151 3.29e-01 80 chrII:8819934-8820014 8.83e-01 80 chrX:11792070-11792150 1.73e-02 63_[+1(2.70e-05)]_9 chrI:3309746-3309826 8.17e-01 80 chrI:3680008-3680088 3.10e-01 80 chrIII:5839325-5839405 9.88e-01 80 chrV:17615995-17616075 9.47e-01 80 chrIV:10697311-10697391 3.66e-03 22_[+2(9.28e-06)]_50 chrI:1251582-1251662 7.52e-01 80 chrIII:2876082-2876162 9.11e-03 19_[+1(4.62e-05)]_53 chrV:8570069-8570149 7.35e-04 24_[+5(2.52e-05)]_48 chrI:12970420-12970500 4.93e-01 80 chrII:13636472-13636552 1.00e+00 80 chrI:5261743-5261823 7.38e-02 80 chrI:7477148-7477228 1.48e-01 35_[+3(6.97e-05)]_37 chrIII:7710250-7710330 1.45e-01 80 chrII:12058431-12058511 5.82e-01 80 chrIV:1496072-1496152 2.31e-01 80 chrI:13626384-13626464 3.92e-02 80 chrV:724223-724303 3.42e-01 80 chrV:13463128-13463208 6.71e-04 23_[+3(1.63e-05)]_4_[+1(4.62e-05)]_\ 37 chrV:17659423-17659503 1.48e-01 14_[+1(6.50e-05)]_58 chrII:506231-506311 1.59e-01 80 chrV:7854690-7854770 4.38e-02 80 chrIII:12327909-12327989 7.64e-01 80 chrIII:8749703-8749783 4.14e-02 37_[+2(9.00e-05)]_35 chrIV:2774741-2774821 5.99e-01 80 chrV:6994127-6994207 8.72e-01 80 chrII:12425911-12425991 7.43e-01 80 chrI:7657503-7657583 9.80e-01 80 chrX:9113928-9114008 1.64e-02 80 chrI:1842100-1842180 4.24e-02 [+3(4.64e-05)]_72 chrII:3129117-3129197 3.47e-03 68_[+2(9.28e-06)]_4 chrX:14813507-14813587 2.62e-01 80 chrX:7181790-7181870 5.05e-01 80 chrV:1471674-1471754 4.09e-01 80 chrII:2420888-2420968 9.40e-01 80 chrV:5844512-5844592 5.61e-02 80 chrV:6656823-6656903 3.07e-02 27_[+1(6.50e-05)]_45 chrV:10940867-10940947 1.77e-03 47_[+1(6.50e-05)]_4_[+4(5.96e-05)]_\ 13 chrX:10772231-10772311 3.07e-01 80 chrX:1011237-1011317 5.42e-01 80 chrII:8817412-8817492 9.61e-01 80 chrIV:2390460-2390540 6.09e-01 80 chrII:2378770-2378850 8.84e-01 80 chrX:14214685-14214765 4.45e-02 80 chrIV:11955794-11955874 8.07e-02 80 chrII:6346870-6346950 5.38e-02 11_[+1(4.62e-05)]_61 chrI:5358074-5358154 3.40e-01 80 chrIV:15398660-15398740 3.51e-01 80 chrIII:3540607-3540687 9.76e-01 80 chrX:15616580-15616660 1.64e-02 67_[+3(9.61e-06)]_5 chrIV:12831776-12831856 2.32e-03 14_[+2(6.49e-05)]_40_[+3(3.96e-05)]_\ 10 chrIII:12251328-12251408 9.27e-06 37_[+2(9.28e-06)]_11_[+5(6.56e-06)]_\ 16 chrI:6092015-6092095 7.82e-01 80 chrX:13920587-13920667 6.13e-01 80 chrIV:292138-292218 9.25e-01 80 chrII:10100093-10100173 7.95e-02 80 chrII:12811102-12811182 1.16e-01 80 chrV:6785269-6785349 1.80e-03 43_[+4(8.64e-05)]_29 chrII:10548689-10548769 6.21e-01 80 chrV:6229611-6229691 8.03e-01 80 chrI:2070875-2070955 6.12e-02 80 chrV:11534686-11534766 2.94e-01 80 chrI:3787743-3787823 2.36e-01 80 chrX:4529049-4529129 7.10e-01 80 chrIV:6786062-6786142 3.52e-01 80 chrV:18086927-18087007 2.21e-05 24_[+4(2.22e-05)]_21_[+5(6.56e-06)]_\ 19 chrX:9540637-9540717 2.43e-01 80 chrV:10729583-10729663 2.53e-01 80 chrIV:393554-393634 2.99e-01 80 chrIV:9322583-9322663 8.22e-01 80 chrI:9095688-9095768 5.70e-01 80 chrIII:12313252-12313332 9.58e-01 80 chrIII:5943890-5943970 6.32e-02 71_[+3(5.59e-05)]_1 chrX:14174000-14174080 7.17e-02 80 chrII:8016957-8017037 9.87e-01 80 chrV:7237259-7237339 1.66e-05 34_[+4(3.31e-06)]_21_[+5(2.52e-05)]_\ 9 chrV:19158845-19158925 9.64e-06 44_[+5(2.52e-05)]_17_[+2(3.17e-05)]_\ 3 chrI:7082267-7082347 6.44e-02 80 chrIII:4918088-4918168 1.28e-03 44_[+4(3.83e-05)]_3_[+1(4.62e-05)]_\ 17 chrV:8247925-8248005 7.85e-01 80 chrII:8990415-8990495 2.84e-01 80 chrII:10798660-10798740 7.55e-02 80 chrX:6841025-6841105 3.21e-01 80 chrIII:13256597-13256677 4.13e-01 80 chrII:5912323-5912403 2.98e-02 64_[+2(9.28e-06)]_8 chrIII:3869628-3869708 7.92e-01 80 chrV:20493733-20493813 6.02e-01 80 chrIII:2090847-2090927 9.37e-01 80 chrIV:11635734-11635814 2.32e-01 80 chrII:5649598-5649678 1.39e-02 1_[+2(9.28e-06)]_71 chrIII:13466391-13466471 1.52e-01 80 chrX:12018139-12018219 5.19e-05 27_[+4(8.05e-06)]_20_[+2(9.28e-06)]_\ 17 chrI:7059342-7059422 6.74e-01 80 chrV:4820777-4820857 3.41e-02 7_[+1(6.50e-05)]_65 chrI:13653967-13654047 5.46e-01 80 chrX:15779712-15779792 8.79e-01 80 chrV:8462283-8462363 6.90e-01 80 chrIII:7184188-7184268 5.55e-04 30_[+3(9.61e-06)]_24_[+1(2.70e-05)]_\ 10 chrIV:4810605-4810685 7.80e-01 80 chrIII:12370067-12370147 7.58e-01 80 chrIV:6585559-6585639 1.09e-03 22_[+3(2.61e-05)]_50 chrV:11824114-11824194 2.89e-01 80 chrIV:15932038-15932118 2.81e-02 13_[+2(4.49e-05)]_59 chrX:7825853-7825933 3.82e-01 80 chrI:7867869-7867949 9.38e-01 80 chrI:13951827-13951907 1.11e-03 46_[+4(1.27e-05)]_26 chrIV:4447075-4447155 3.35e-01 80 chrX:8243279-8243359 3.32e-01 80 chrI:3516389-3516469 8.53e-02 31_[+5(2.52e-05)]_41 chrX:5018436-5018516 3.87e-01 80 chrII:7529229-7529309 4.32e-04 26_[+1(2.70e-05)]_10_[+3(9.61e-06)]_\ 28 chrII:5886026-5886106 7.94e-03 80 chrIII:7573040-7573120 7.01e-02 80 chrIV:3233791-3233871 4.53e-01 80 chrII:11150135-11150215 7.36e-01 80 chrIV:3900024-3900104 1.81e-01 80 chrIV:8585305-8585385 4.57e-01 80 chrX:15607648-15607728 7.65e-02 29_[+4(9.31e-05)]_43 chrIII:6173171-6173251 6.50e-01 80 chrII:5379739-5379819 1.22e-01 80 chrIII:11353610-11353690 1.57e-01 80 chrIV:5947910-5947990 1.31e-03 31_[+2(1.87e-05)]_41 chrX:1503902-1503982 6.91e-01 80 chrIV:13881907-13881987 2.20e-02 6_[+3(1.63e-05)]_66 chrIV:8527699-8527779 1.47e-01 80 chrI:7147667-7147747 8.29e-01 80 chrI:110702-110782 9.27e-03 80 chrII:13006443-13006523 8.28e-01 80 chrI:9422367-9422447 3.50e-03 26_[+5(2.52e-05)]_46 chrIII:12978936-12979016 6.16e-02 80 chrI:4178670-4178750 4.92e-01 80 chrI:2928142-2928222 5.04e-03 8_[+2(3.17e-05)]_64 chrII:11974712-11974792 8.28e-01 80 chrV:14468503-14468583 4.68e-02 72_[+4(4.16e-05)] chrV:19190194-19190274 8.87e-01 80 chrIII:10882148-10882228 6.49e-02 80 chrIII:7179853-7179933 7.61e-01 80 chrX:4395600-4395680 4.24e-01 80 chrX:13514558-13514638 8.98e-01 80 chrIV:17461451-17461531 1.44e-03 54_[+4(8.05e-06)]_8_[+4(6.62e-05)]_\ 2 chrIII:7141371-7141451 1.74e-01 61_[+1(2.70e-05)]_11 chrI:13475718-13475798 7.30e-01 80 chrX:1323162-1323242 7.60e-02 69_[+3(9.61e-06)]_3 chrIV:4745598-4745678 9.76e-02 80 chrV:9583064-9583144 1.38e-03 44_[+4(1.74e-05)]_28 chrIV:12724780-12724860 2.82e-01 80 chrIII:6895339-6895419 1.36e-01 80 chrIII:5228120-5228200 1.56e-02 53_[+2(4.49e-05)]_19 chrX:11661715-11661795 4.94e-01 80 chrI:11893860-11893940 5.16e-01 80 chrX:16205975-16206055 3.96e-01 80 chrII:14383789-14383869 2.22e-02 57_[+5(3.84e-05)]_15 chrI:12532320-12532400 1.39e-01 80 chrIV:247651-247731 1.69e-02 80 chrX:12872375-12872455 2.08e-01 80 chrV:13907893-13907973 4.76e-01 80 chrI:1273938-1274018 9.81e-01 80 chrII:13369393-13369473 2.45e-02 80 chrI:1444157-1444237 3.37e-05 34_[+4(3.31e-06)]_3_[+1(4.62e-05)]_\ 27 chrX:13349568-13349648 2.79e-01 80 chrIII:1926524-1926604 1.46e-03 63_[+3(9.61e-06)]_9 chrX:10197444-10197524 2.17e-02 41_[+4(7.30e-05)]_31 chrIII:3505315-3505395 5.76e-02 40_[+2(5.83e-05)]_32 chrX:2364849-2364929 5.17e-01 80 chrV:14028382-14028462 8.65e-01 80 chrIII:9467325-9467405 5.11e-02 64_[+1(4.62e-05)]_8 chrV:14200166-14200246 2.26e-02 11_[+1(4.62e-05)]_39_[+1(4.62e-05)]_\ 14 chrX:14946609-14946689 3.70e-01 80 chrX:7773944-7774024 3.32e-01 80 chrII:12006864-12006944 5.66e-04 13_[+5(6.56e-06)]_4_[+4(5.28e-05)]_\ 47 chrIII:13061289-13061369 3.42e-03 9_[+2(5.83e-05)]_31_[+3(9.61e-06)]_\ 24 chrX:6750313-6750393 8.46e-01 80 chrIV:866978-867058 9.91e-01 80 chrII:12339361-12339441 4.55e-03 21_[+4(1.27e-05)]_51 chrV:13658774-13658854 5.30e-02 80 chrII:11097492-11097572 3.69e-04 52_[+2(4.49e-05)]_12_[+4(1.27e-05)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n12.farnam.hpc.yale.internal ********************************************************************************