******************************************************************************** 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/nhr-102.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIII:13024437-13024517 1.0000 80 chrIV:13575822-13575902 1.0000 80 chrV:7145409-7145489 1.0000 80 chrV:16390793-16390873 1.0000 80 chrV:3468590-3468670 1.0000 80 chrV:519614-519694 1.0000 80 chrV:7163800-7163880 1.0000 80 chrIV:7258391-7258471 1.0000 80 chrIV:7260750-7260830 1.0000 80 chrV:332796-332876 1.0000 80 chrII:7457370-7457450 1.0000 80 chrIV:17174239-17174319 1.0000 80 chrV:7145611-7145691 1.0000 80 chrII:9807675-9807755 1.0000 80 chrX:15940002-15940082 1.0000 80 chrIV:12599301-12599381 1.0000 80 chrV:13529235-13529315 1.0000 80 chrII:3743863-3743943 1.0000 80 chrI:2686210-2686290 1.0000 80 chrV:7157189-7157269 1.0000 80 chrV:7142844-7142924 1.0000 80 chrV:5030368-5030448 1.0000 80 chrIV:4599129-4599209 1.0000 80 chrII:7277398-7277478 1.0000 80 chrX:575234-575314 1.0000 80 chrV:12937270-12937350 1.0000 80 chrII:7290129-7290209 1.0000 80 chrV:3841624-3841704 1.0000 80 chrII:2587149-2587229 1.0000 80 chrX:8248425-8248505 1.0000 80 chrV:5018241-5018321 1.0000 80 chrIV:6378579-6378659 1.0000 80 chrX:3256922-3257002 1.0000 80 chrII:7458947-7459027 1.0000 80 chrIII:9751260-9751340 1.0000 80 chrX:14743400-14743480 1.0000 80 chrV:1607997-1608077 1.0000 80 chrI:9849661-9849741 1.0000 80 chrII:12892595-12892675 1.0000 80 chrX:12518598-12518678 1.0000 80 chrV:333848-333928 1.0000 80 chrII:13956722-13956802 1.0000 80 chrII:14299510-14299590 1.0000 80 chrI:6497569-6497649 1.0000 80 chrV:16278066-16278146 1.0000 80 chrV:3784476-3784556 1.0000 80 chrX:10216999-10217079 1.0000 80 chrI:6499608-6499688 1.0000 80 chrV:13012054-13012134 1.0000 80 chrII:6526306-6526386 1.0000 80 chrV:7413907-7413987 1.0000 80 chrV:3632396-3632476 1.0000 80 chrV:12096013-12096093 1.0000 80 chrI:14104657-14104737 1.0000 80 chrIV:12601095-12601175 1.0000 80 chrV:9255642-9255722 1.0000 80 chrII:915392-915472 1.0000 80 chrIII:12658737-12658817 1.0000 80 chrIV:4817021-4817101 1.0000 80 chrV:2327263-2327343 1.0000 80 chrII:9791357-9791437 1.0000 80 chrX:15167851-15167931 1.0000 80 chrV:5192683-5192763 1.0000 80 chrV:12355011-12355091 1.0000 80 chrIV:4599358-4599438 1.0000 80 chrV:7095481-7095561 1.0000 80 chrII:8081375-8081455 1.0000 80 chrV:3970587-3970667 1.0000 80 chrII:8387096-8387176 1.0000 80 chrV:11067809-11067889 1.0000 80 chrX:15441170-15441250 1.0000 80 chrIV:12842268-12842348 1.0000 80 chrX:3150919-3150999 1.0000 80 chrV:20499094-20499174 1.0000 80 chrX:3290267-3290347 1.0000 80 chrV:10802218-10802298 1.0000 80 chrV:1456805-1456885 1.0000 80 chrIV:10463322-10463402 1.0000 80 chrIII:13607994-13608074 1.0000 80 chrIV:13708011-13708091 1.0000 80 chrV:11817372-11817452 1.0000 80 chrII:4871739-4871819 1.0000 80 chrIII:1392935-1393015 1.0000 80 chrIV:2618780-2618860 1.0000 80 chrII:14866947-14867027 1.0000 80 chrX:17255974-17256054 1.0000 80 chrV:2324436-2324516 1.0000 80 chrX:9261804-9261884 1.0000 80 chrX:8542540-8542620 1.0000 80 chrII:11614264-11614344 1.0000 80 chrIII:2760964-2761044 1.0000 80 chrV:7733174-7733254 1.0000 80 chrX:15075859-15075939 1.0000 80 chrIV:4083226-4083306 1.0000 80 chrIII:7758698-7758778 1.0000 80 chrIV:4014492-4014572 1.0000 80 chrIV:2796576-2796656 1.0000 80 chrV:8768603-8768683 1.0000 80 chrIV:7237959-7238039 1.0000 80 chrI:13333135-13333215 1.0000 80 chrII:14043356-14043436 1.0000 80 chrII:7166948-7167028 1.0000 80 chrI:6731875-6731955 1.0000 80 chrII:12980386-12980466 1.0000 80 chrV:16726108-16726188 1.0000 80 chrII:4770051-4770131 1.0000 80 chrX:11519252-11519332 1.0000 80 chrII:4881880-4881960 1.0000 80 chrII:1103849-1103929 1.0000 80 chrIV:13725335-13725415 1.0000 80 chrV:19672522-19672602 1.0000 80 chrII:4943801-4943881 1.0000 80 chrV:8922925-8923005 1.0000 80 chrV:2250304-2250384 1.0000 80 chrV:10693866-10693946 1.0000 80 chrX:2698620-2698700 1.0000 80 chrV:7150711-7150791 1.0000 80 chrV:4189749-4189829 1.0000 80 chrX:9233969-9234049 1.0000 80 chrV:6413215-6413295 1.0000 80 chrV:12744220-12744300 1.0000 80 chrII:9800433-9800513 1.0000 80 chrII:2610303-2610383 1.0000 80 chrII:15251734-15251814 1.0000 80 chrV:16046006-16046086 1.0000 80 chrV:12935117-12935197 1.0000 80 chrIII:10822677-10822757 1.0000 80 chrII:5323952-5324032 1.0000 80 chrI:10382084-10382164 1.0000 80 chrII:7877856-7877936 1.0000 80 chrI:3113766-3113846 1.0000 80 chrV:19437516-19437596 1.0000 80 chrX:10480722-10480802 1.0000 80 chrIII:13347245-13347325 1.0000 80 chrX:2663891-2663971 1.0000 80 chrX:440642-440722 1.0000 80 chrIV:7183041-7183121 1.0000 80 chrX:8089705-8089785 1.0000 80 chrX:14500793-14500873 1.0000 80 chrX:4698436-4698516 1.0000 80 chrIII:8733862-8733942 1.0000 80 chrV:9078986-9079066 1.0000 80 chrIV:10913594-10913674 1.0000 80 chrIV:12598552-12598632 1.0000 80 chrI:6727782-6727862 1.0000 80 chrI:9271062-9271142 1.0000 80 chrX:3153323-3153403 1.0000 80 chrX:8604334-8604414 1.0000 80 chrII:3911502-3911582 1.0000 80 chrX:14001624-14001704 1.0000 80 chrII:1233062-1233142 1.0000 80 chrX:10477705-10477785 1.0000 80 chrII:13465390-13465470 1.0000 80 chrX:6518733-6518813 1.0000 80 chrIV:3012558-3012638 1.0000 80 chrI:6294076-6294156 1.0000 80 chrI:6416933-6417013 1.0000 80 chrV:6019292-6019372 1.0000 80 chrV:6665878-6665958 1.0000 80 chrIII:8161133-8161213 1.0000 80 chrIV:3739012-3739092 1.0000 80 chrIII:13604016-13604096 1.0000 80 chrX:6607245-6607325 1.0000 80 chrX:14815635-14815715 1.0000 80 chrIII:348240-348320 1.0000 80 chrV:14449818-14449898 1.0000 80 chrX:1478105-1478185 1.0000 80 chrX:4564955-4565035 1.0000 80 chrV:462379-462459 1.0000 80 chrIV:7915562-7915642 1.0000 80 chrV:7744198-7744278 1.0000 80 chrII:5575067-5575147 1.0000 80 chrV:17721887-17721967 1.0000 80 chrX:8473585-8473665 1.0000 80 chrX:11792883-11792963 1.0000 80 chrII:11538548-11538628 1.0000 80 chrX:2698412-2698492 1.0000 80 chrX:1443752-1443832 1.0000 80 chrII:7773567-7773647 1.0000 80 chrIV:6083786-6083866 1.0000 80 chrX:12197546-12197626 1.0000 80 chrV:8661740-8661820 1.0000 80 chrII:5917469-5917549 1.0000 80 chrV:5813231-5813311 1.0000 80 chrX:3117340-3117420 1.0000 80 chrIII:9930481-9930561 1.0000 80 chrIV:11123574-11123654 1.0000 80 chrV:5823149-5823229 1.0000 80 chrIV:9651315-9651395 1.0000 80 chrV:11069441-11069521 1.0000 80 chrI:11572653-11572733 1.0000 80 chrII:6919563-6919643 1.0000 80 chrX:14071088-14071168 1.0000 80 chrX:10142175-10142255 1.0000 80 chrIII:6396566-6396646 1.0000 80 chrX:4658795-4658875 1.0000 80 chrX:14166953-14167033 1.0000 80 chrX:11515586-11515666 1.0000 80 chrX:13339355-13339435 1.0000 80 chrV:18826610-18826690 1.0000 80 chrX:6088805-6088885 1.0000 80 chrX:16550737-16550817 1.0000 80 chrIV:2855484-2855564 1.0000 80 chrV:13043378-13043458 1.0000 80 chrI:5388660-5388740 1.0000 80 chrIV:10761461-10761541 1.0000 80 chrX:9833301-9833381 1.0000 80 chrX:1443955-1444035 1.0000 80 chrV:8270020-8270100 1.0000 80 chrV:5026606-5026686 1.0000 80 chrV:14422305-14422385 1.0000 80 chrIII:4654008-4654088 1.0000 80 chrX:1386960-1387040 1.0000 80 chrV:7761801-7761881 1.0000 80 chrV:3455318-3455398 1.0000 80 chrIV:11917004-11917084 1.0000 80 chrII:8413059-8413139 1.0000 80 chrV:8651499-8651579 1.0000 80 chrI:11571754-11571834 1.0000 80 chrV:16395258-16395338 1.0000 80 chrX:15076948-15077028 1.0000 80 chrIII:13626602-13626682 1.0000 80 chrV:3634688-3634768 1.0000 80 chrX:16192710-16192790 1.0000 80 chrII:13160620-13160700 1.0000 80 chrX:15748002-15748082 1.0000 80 chrX:14790865-14790945 1.0000 80 chrII:13077868-13077948 1.0000 80 chrX:13165839-13165919 1.0000 80 chrII:7264800-7264880 1.0000 80 chrII:7255813-7255893 1.0000 80 chrII:7287905-7287985 1.0000 80 chrI:5079459-5079539 1.0000 80 chrX:13310929-13311009 1.0000 80 chrII:9501097-9501177 1.0000 80 chrIV:14413491-14413571 1.0000 80 chrII:8384517-8384597 1.0000 80 chrV:534364-534444 1.0000 80 chrIII:7369788-7369868 1.0000 80 chrIII:10566130-10566210 1.0000 80 chrV:14421228-14421308 1.0000 80 chrV:17752499-17752579 1.0000 80 chrII:8988101-8988181 1.0000 80 chrII:13737904-13737984 1.0000 80 chrII:11336047-11336127 1.0000 80 chrX:2693262-2693342 1.0000 80 chrII:4710293-4710373 1.0000 80 chrV:3967928-3968008 1.0000 80 chrI:4382413-4382493 1.0000 80 chrIV:4479472-4479552 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_nhr-102/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-102.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 0.306 C 0.191 G 0.189 T 0.314 Background letter frequencies (from file dataset with add-one prior applied): A 0.306 C 0.191 G 0.189 T 0.314 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCTTATCA MEME-1 width = 8 sites = 42 llr = 359 E-value = 2.6e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::a::a pos.-specific C 16::::a: probability G :2:::::: matrix T 82aa:a:: bits 2.4 * 2.2 * 1.9 * 1.7 ** *** Relative 1.4 ****** Entropy 1.2 ****** (12.3 bits) 1.0 * ****** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCTTATCA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:9501097-9501177 13 3.32e-05 GCGCCGACGT TCTTATCA AACCGCTGGC chrX:13165839-13165919 49 3.32e-05 CTTATTATTA TCTTATCA CTTTCATCCG chrIII:6396566-6396646 28 3.32e-05 TTTCTGCCAA TCTTATCA TTGATATTAC chrI:3113766-3113846 34 3.32e-05 TCAACAGGCT TCTTATCA GTTTACTGCT chrII:5323952-5324032 52 3.32e-05 CCATAGTGTC TCTTATCA GCTGCGTGTT chrII:15251734-15251814 9 3.32e-05 ATAAAAAT TCTTATCA CACAATGTGT chrII:4770051-4770131 25 3.32e-05 GATTGACAGC TCTTATCA GGGAGGGTGT chrII:12980386-12980466 7 3.32e-05 TGTTCT TCTTATCA CCTATTGATA chrI:6731875-6731955 54 3.32e-05 CTAGTTTGAG TCTTATCA GTGTTTGCTA chrV:8768603-8768683 37 3.32e-05 CGCCAATTTT TCTTATCA CTAGTCAAGA chrV:2324436-2324516 18 3.32e-05 TTCTCATTCT TCTTATCA GTACTTTGTG chrIII:13607994-13608074 64 3.32e-05 AATTGGAAAC TCTTATCA TCATTGATG chrII:9791357-9791437 33 3.32e-05 ATGTGATCAG TCTTATCA TTTCACCTTA chrV:13012054-13012134 51 3.32e-05 GCAGTAGGTT TCTTATCA GTGGAATGTT chrI:6499608-6499688 31 3.32e-05 CAGTTATATT TCTTATCA CATATCGATG chrX:12518598-12518678 33 3.32e-05 AGCCAACAAT TCTTATCA GAGGGCAACG chrII:7277398-7277478 18 3.32e-05 CTTTTCACTG TCTTATCA GTGTCACCGA chrV:3634688-3634768 23 6.61e-05 TGAGAGCTCG TGTTATCA ATCGCTTGTG chrIV:2855484-2855564 39 6.61e-05 TGCCAACTTT TGTTATCA TTAAGCACGG chrX:8473585-8473665 34 6.61e-05 TACGTGAGCA TGTTATCA GTTCACAATC chrV:7744198-7744278 7 6.61e-05 AAAAAT TGTTATCA GTCGGGTCTT chrII:915392-915472 72 6.61e-05 AAATTGATCG TGTTATCA G chrIV:12599301-12599381 19 6.61e-05 GTCGGTGATG TGTTATCA AATTGATCAC chrV:332796-332876 39 6.61e-05 ACAATTTTCC TGTTATCA AACTGTGGTC chrX:16192710-16192790 3 8.63e-05 TT CCTTATCA GCTTCCTTAT chrV:17721887-17721967 49 8.63e-05 AAAACTTGCG CCTTATCA CTTGGGGTCA chrII:6526306-6526386 61 8.63e-05 CAGTAGCCTG CCTTATCA TCGACGATTG chrX:13339355-13339435 24 1.41e-04 CCTCGGAGGA TTTTATCA ACCAGTAGGA chrX:3117340-3117420 7 1.41e-04 TAAGTT TTTTATCA GTATTCGATA chrI:6727782-6727862 30 1.41e-04 TTTCCACGTT TTTTATCA ATTCATTCAA chrIV:12598552-12598632 32 1.41e-04 AATAATGTAG TTTTATCA TTTCGCTGTG chrIII:2760964-2761044 17 1.41e-04 ACACTCTACT TTTTATCA GTTTTTTGGA chrX:9261804-9261884 45 1.41e-04 TCCTAGTGGA TTTTATCA GCTTACTTTG chrIV:12601095-12601175 47 1.41e-04 CTTTGAACAT TTTTATCA TTATGGGTGA chrV:7145611-7145691 24 1.41e-04 TAGAAAGCGC TTTTATCA AACACTCCAT chrV:6413215-6413295 19 1.61e-04 AAAGAAAGCA CGTTATCA GTTCATCAGT chrX:13310929-13311009 18 1.81e-04 AAGCAACTGT GCTTATCA ATGACAACGC chrX:8542540-8542620 24 1.81e-04 TCGATGCAGA GCTTATCA AAACGGACTT chrII:6919563-6919643 62 2.35e-04 TAACCTGGCT TCTTGTCA AAGAAATTAT chrX:4698436-4698516 37 2.35e-04 CTTTGCTATC TCTTGTCA TCGACAATTT chrV:19437516-19437596 25 2.35e-04 ATTTTTTCAA CTTTATCA AAATGATGTA chrII:1103849-1103929 11 2.35e-04 CCCGCTAACT CTTTATCA GTGTTAAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:9501097-9501177 3.3e-05 12_[+1]_60 chrX:13165839-13165919 3.3e-05 48_[+1]_24 chrIII:6396566-6396646 3.3e-05 27_[+1]_45 chrI:3113766-3113846 3.3e-05 33_[+1]_39 chrII:5323952-5324032 3.3e-05 51_[+1]_21 chrII:15251734-15251814 3.3e-05 8_[+1]_64 chrII:4770051-4770131 3.3e-05 24_[+1]_48 chrII:12980386-12980466 3.3e-05 6_[+1]_66 chrI:6731875-6731955 3.3e-05 53_[+1]_19 chrV:8768603-8768683 3.3e-05 36_[+1]_36 chrV:2324436-2324516 3.3e-05 17_[+1]_55 chrIII:13607994-13608074 3.3e-05 63_[+1]_9 chrII:9791357-9791437 3.3e-05 32_[+1]_40 chrV:13012054-13012134 3.3e-05 50_[+1]_22 chrI:6499608-6499688 3.3e-05 30_[+1]_42 chrX:12518598-12518678 3.3e-05 32_[+1]_40 chrII:7277398-7277478 3.3e-05 17_[+1]_55 chrV:3634688-3634768 6.6e-05 22_[+1]_50 chrIV:2855484-2855564 6.6e-05 38_[+1]_34 chrX:8473585-8473665 6.6e-05 33_[+1]_39 chrV:7744198-7744278 6.6e-05 6_[+1]_66 chrII:915392-915472 6.6e-05 71_[+1]_1 chrIV:12599301-12599381 6.6e-05 18_[+1]_54 chrV:332796-332876 6.6e-05 38_[+1]_34 chrX:16192710-16192790 8.6e-05 2_[+1]_70 chrV:17721887-17721967 8.6e-05 48_[+1]_24 chrII:6526306-6526386 8.6e-05 60_[+1]_12 chrX:13339355-13339435 0.00014 23_[+1]_49 chrX:3117340-3117420 0.00014 6_[+1]_66 chrI:6727782-6727862 0.00014 29_[+1]_43 chrIV:12598552-12598632 0.00014 31_[+1]_41 chrIII:2760964-2761044 0.00014 16_[+1]_56 chrX:9261804-9261884 0.00014 44_[+1]_28 chrIV:12601095-12601175 0.00014 46_[+1]_26 chrV:7145611-7145691 0.00014 23_[+1]_49 chrV:6413215-6413295 0.00016 18_[+1]_54 chrX:13310929-13311009 0.00018 17_[+1]_55 chrX:8542540-8542620 0.00018 23_[+1]_49 chrII:6919563-6919643 0.00023 61_[+1]_11 chrX:4698436-4698516 0.00023 36_[+1]_36 chrV:19437516-19437596 0.00023 24_[+1]_48 chrII:1103849-1103929 0.00023 10_[+1]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTTATCA width=8 seqs=42 chrII:9501097-9501177 ( 13) TCTTATCA 1 chrX:13165839-13165919 ( 49) TCTTATCA 1 chrIII:6396566-6396646 ( 28) TCTTATCA 1 chrI:3113766-3113846 ( 34) TCTTATCA 1 chrII:5323952-5324032 ( 52) TCTTATCA 1 chrII:15251734-15251814 ( 9) TCTTATCA 1 chrII:4770051-4770131 ( 25) TCTTATCA 1 chrII:12980386-12980466 ( 7) TCTTATCA 1 chrI:6731875-6731955 ( 54) TCTTATCA 1 chrV:8768603-8768683 ( 37) TCTTATCA 1 chrV:2324436-2324516 ( 18) TCTTATCA 1 chrIII:13607994-13608074 ( 64) TCTTATCA 1 chrII:9791357-9791437 ( 33) TCTTATCA 1 chrV:13012054-13012134 ( 51) TCTTATCA 1 chrI:6499608-6499688 ( 31) TCTTATCA 1 chrX:12518598-12518678 ( 33) TCTTATCA 1 chrII:7277398-7277478 ( 18) TCTTATCA 1 chrV:3634688-3634768 ( 23) TGTTATCA 1 chrIV:2855484-2855564 ( 39) TGTTATCA 1 chrX:8473585-8473665 ( 34) TGTTATCA 1 chrV:7744198-7744278 ( 7) TGTTATCA 1 chrII:915392-915472 ( 72) TGTTATCA 1 chrIV:12599301-12599381 ( 19) TGTTATCA 1 chrV:332796-332876 ( 39) TGTTATCA 1 chrX:16192710-16192790 ( 3) CCTTATCA 1 chrV:17721887-17721967 ( 49) CCTTATCA 1 chrII:6526306-6526386 ( 61) CCTTATCA 1 chrX:13339355-13339435 ( 24) TTTTATCA 1 chrX:3117340-3117420 ( 7) TTTTATCA 1 chrI:6727782-6727862 ( 30) TTTTATCA 1 chrIV:12598552-12598632 ( 32) TTTTATCA 1 chrIII:2760964-2761044 ( 17) TTTTATCA 1 chrX:9261804-9261884 ( 45) TTTTATCA 1 chrIV:12601095-12601175 ( 47) TTTTATCA 1 chrV:7145611-7145691 ( 24) TTTTATCA 1 chrV:6413215-6413295 ( 19) CGTTATCA 1 chrX:13310929-13311009 ( 18) GCTTATCA 1 chrX:8542540-8542620 ( 24) GCTTATCA 1 chrII:6919563-6919643 ( 62) TCTTGTCA 1 chrX:4698436-4698516 ( 37) TCTTGTCA 1 chrV:19437516-19437596 ( 25) CTTTATCA 1 chrII:1103849-1103929 ( 11) CTTTATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.74794 E= 2.6e-012 -1204 -42 -199 137 -1204 158 1 -40 -1204 -1204 -1204 167 -1204 -1204 -1204 167 164 -1204 -199 -1204 -1204 -1204 -1204 167 -1204 239 -1204 -1204 171 -1204 -1204 -1204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 2.6e-012 0.000000 0.142857 0.047619 0.809524 0.000000 0.571429 0.190476 0.238095 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.952381 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTATCA MEME-1 regular expression -------------------------------------------------------------------------------- T[CT]TTATCA -------------------------------------------------------------------------------- Time 5.95 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTGTGDY MEME-2 width = 8 sites = 33 llr = 279 E-value = 7.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::::4: pos.-specific C :::::::4 probability G :3:a:a3: matrix T a7a:a:26 bits 2.4 * * 2.2 * * 1.9 * * 1.7 * **** Relative 1.4 * **** Entropy 1.2 * **** (12.2 bits) 1.0 ****** * 0.7 ****** * 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTGTGAT consensus G GC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:5823149-5823229 63 3.31e-05 GAAAATGTGT TTTGTGGT TAGTGAACGA chrII:14043356-14043436 36 3.31e-05 CTTATTGACG TTTGTGGT GTCTGTGCAC chrV:2324436-2324516 30 3.31e-05 TTATCAGTAC TTTGTGGT TTGGTTCAAT chrII:14866947-14867027 32 3.31e-05 TGGGTGATTT TTTGTGGT GGAAAATTTA chrV:1456805-1456885 68 3.31e-05 TTAAGCTTTG TTTGTGGT AGATC chrX:15441170-15441250 71 3.31e-05 TTACTCTACT TTTGTGGT CT chrV:3970587-3970667 69 3.31e-05 TTTAAAAAAC TTTGTGGT TTCA chrX:575234-575314 3 3.31e-05 GT TTTGTGGC TTATTCCCAT chrIV:3739012-3739092 57 8.68e-05 TCATCGCACA TTTGTGAC CACAGAAACG chrII:3911502-3911582 54 8.68e-05 CACAAAGGAG TTTGTGAC GGGGTCGGCA chrV:20499094-20499174 7 8.68e-05 AAAATG TTTGTGAC CGCATGCACT chrV:7095481-7095561 44 8.68e-05 ATAGCGGGGG TTTGTGAT CACCTAGCGT chrV:12096013-12096093 24 8.68e-05 GCTACAAAAT TTTGTGAC TACCGATGAC chrII:3743863-3743943 56 8.68e-05 AACGTCTAGG TTTGTGAT CTATGTTGTG chrIV:7260750-7260830 13 8.68e-05 TCACAAAATG TTTGTGAC TTTTACACCT chrV:7163800-7163880 59 8.68e-05 ACGTGAAGAT TTTGTGAC TTCTTTCTGT chrV:519614-519694 65 8.68e-05 TTGTGATCAA TTTGTGAC AACTATTT chrV:16390793-16390873 1 8.68e-05 . TTTGTGAT TTTATTGTGA chrIII:13024437-13024517 69 8.68e-05 GCAAATAACT TTTGTGAC CAAA chrII:11336047-11336127 70 1.07e-04 AATTGGAAAA TGTGTGGC CAC chrV:17752499-17752579 47 1.07e-04 CCATTCCGTT TGTGTGGT TTATGTCACT chrV:2250304-2250384 31 1.07e-04 CTTGCATTTT TGTGTGGT CTCTTCCCCG chrV:3634688-3634768 37 1.39e-04 ATCAATCGCT TGTGTGAT CGAGTAGGTG chrIV:10463322-10463402 7 1.39e-04 AGACTG TGTGTGAT GACACACCAG chrV:7145409-7145489 8 1.39e-04 TAAAGTG TGTGTGAC CATGTCTAGG chrV:6019292-6019372 68 1.94e-04 ACAGTAGATG TTTGTGTC CTCTT chrII:9800433-9800513 51 1.94e-04 GTCACTATGA TTTGTGTT TGAAAAATGG chrII:7166948-7167028 64 1.94e-04 TCACTTCGAT TTTGTGTT CACGGTTCA chrII:915392-915472 33 1.94e-04 TTTCTCCAGT TTTGTGTT GAATTTTTTT chrII:13956722-13956802 22 1.94e-04 GTCTGTGCAT TTTGTGTT GCTCTCACTC chrX:3153323-3153403 20 2.27e-04 GACTGACCTG TGTGTGTT GTACGCTTCA chrV:16046006-16046086 50 2.27e-04 TAATAGAACG TGTGTGTC AATTTTTAGA chrX:15940002-15940082 53 2.27e-04 ACAGCGCATT TGTGTGTT TTGAATGTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:5823149-5823229 3.3e-05 62_[+2]_10 chrII:14043356-14043436 3.3e-05 35_[+2]_37 chrV:2324436-2324516 3.3e-05 29_[+2]_43 chrII:14866947-14867027 3.3e-05 31_[+2]_41 chrV:1456805-1456885 3.3e-05 67_[+2]_5 chrX:15441170-15441250 3.3e-05 70_[+2]_2 chrV:3970587-3970667 3.3e-05 68_[+2]_4 chrX:575234-575314 3.3e-05 2_[+2]_70 chrIV:3739012-3739092 8.7e-05 56_[+2]_16 chrII:3911502-3911582 8.7e-05 53_[+2]_19 chrV:20499094-20499174 8.7e-05 6_[+2]_66 chrV:7095481-7095561 8.7e-05 43_[+2]_29 chrV:12096013-12096093 8.7e-05 23_[+2]_49 chrII:3743863-3743943 8.7e-05 55_[+2]_17 chrIV:7260750-7260830 8.7e-05 12_[+2]_60 chrV:7163800-7163880 8.7e-05 58_[+2]_14 chrV:519614-519694 8.7e-05 64_[+2]_8 chrV:16390793-16390873 8.7e-05 [+2]_72 chrIII:13024437-13024517 8.7e-05 68_[+2]_4 chrII:11336047-11336127 0.00011 69_[+2]_3 chrV:17752499-17752579 0.00011 46_[+2]_26 chrV:2250304-2250384 0.00011 30_[+2]_42 chrV:3634688-3634768 0.00014 36_[+2]_36 chrIV:10463322-10463402 0.00014 6_[+2]_66 chrV:7145409-7145489 0.00014 7_[+2]_65 chrV:6019292-6019372 0.00019 67_[+2]_5 chrII:9800433-9800513 0.00019 50_[+2]_22 chrII:7166948-7167028 0.00019 63_[+2]_9 chrII:915392-915472 0.00019 32_[+2]_40 chrII:13956722-13956802 0.00019 21_[+2]_51 chrX:3153323-3153403 0.00023 19_[+2]_53 chrV:16046006-16046086 0.00023 49_[+2]_23 chrX:15940002-15940082 0.00023 52_[+2]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTGTGDY width=8 seqs=33 chrV:5823149-5823229 ( 63) TTTGTGGT 1 chrII:14043356-14043436 ( 36) TTTGTGGT 1 chrV:2324436-2324516 ( 30) TTTGTGGT 1 chrII:14866947-14867027 ( 32) TTTGTGGT 1 chrV:1456805-1456885 ( 68) TTTGTGGT 1 chrX:15441170-15441250 ( 71) TTTGTGGT 1 chrV:3970587-3970667 ( 69) TTTGTGGT 1 chrX:575234-575314 ( 3) TTTGTGGC 1 chrIV:3739012-3739092 ( 57) TTTGTGAC 1 chrII:3911502-3911582 ( 54) TTTGTGAC 1 chrV:20499094-20499174 ( 7) TTTGTGAC 1 chrV:7095481-7095561 ( 44) TTTGTGAT 1 chrV:12096013-12096093 ( 24) TTTGTGAC 1 chrII:3743863-3743943 ( 56) TTTGTGAT 1 chrIV:7260750-7260830 ( 13) TTTGTGAC 1 chrV:7163800-7163880 ( 59) TTTGTGAC 1 chrV:519614-519694 ( 65) TTTGTGAC 1 chrV:16390793-16390873 ( 1) TTTGTGAT 1 chrIII:13024437-13024517 ( 69) TTTGTGAC 1 chrII:11336047-11336127 ( 70) TGTGTGGC 1 chrV:17752499-17752579 ( 47) TGTGTGGT 1 chrV:2250304-2250384 ( 31) TGTGTGGT 1 chrV:3634688-3634768 ( 37) TGTGTGAT 1 chrIV:10463322-10463402 ( 7) TGTGTGAT 1 chrV:7145409-7145489 ( 8) TGTGTGAC 1 chrV:6019292-6019372 ( 68) TTTGTGTC 1 chrII:9800433-9800513 ( 51) TTTGTGTT 1 chrII:7166948-7167028 ( 64) TTTGTGTT 1 chrII:915392-915472 ( 33) TTTGTGTT 1 chrII:13956722-13956802 ( 22) TTTGTGTT 1 chrX:3153323-3153403 ( 20) TGTGTGTT 1 chrV:16046006-16046086 ( 50) TGTGTGTC 1 chrX:15940002-15940082 ( 53) TGTGTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.4541 E= 7.6e-002 -1169 -1169 -1169 167 -1169 -1169 53 121 -1169 -1169 -1169 167 -1169 -1169 240 -1169 -1169 -1169 -1169 167 -1169 -1169 240 -1169 47 -1169 82 -37 -1169 105 -1169 95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 7.6e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.272727 0.727273 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 0.424242 0.000000 0.333333 0.242424 0.000000 0.393939 0.000000 0.606061 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTGDY MEME-2 regular expression -------------------------------------------------------------------------------- T[TG]TGTG[AGT][TC] -------------------------------------------------------------------------------- Time 9.57 secs. ******************************************************************************** ******************************************************************************** MOTIF GATAAGAA MEME-3 width = 8 sites = 26 llr = 226 E-value = 9.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a3aa3a9 pos.-specific C :::::::1 probability G a::::7:: matrix T ::7::::: bits 2.4 * 2.2 * 1.9 * 1.7 ** ** * Relative 1.4 ** ** * Entropy 1.2 ** ***** (12.5 bits) 1.0 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GATAAGAA consensus A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:5026606-5026686 14 3.01e-05 TAGTCTTCCT GATAAGAA ACGAAAACAT chrI:5388660-5388740 48 3.01e-05 GAGACTAAAT GATAAGAA CGAGACAAGC chrIV:9651315-9651395 47 3.01e-05 TATCTAGTCC GATAAGAA GGCATGATGC chrX:4564955-4565035 9 3.01e-05 CTCTTAAA GATAAGAA GAATTCATAA chrIII:8733862-8733942 50 3.01e-05 GATAGCTGCT GATAAGAA ATGAAAACTG chrX:14500793-14500873 46 3.01e-05 ATTACCACTT GATAAGAA CTGATTGTGC chrII:2610303-2610383 59 3.01e-05 CCAATTATTA GATAAGAA ACGCAGTGAG chrV:3970587-3970667 24 3.01e-05 CGAGTGATAA GATAAGAA ACTACAAAAT chrV:2327263-2327343 73 3.01e-05 ACAAAGTACT GATAAGAA chrV:3784476-3784556 68 3.01e-05 TTTTATTCGA GATAAGAA CGCAT chrII:2587149-2587229 63 3.01e-05 GCAGTTAATT GATAAGAA ACATAGCGTG chrII:9807675-9807755 67 3.01e-05 AAGTTTTGAC GATAAGAA AGTTTC chrII:8988101-8988181 61 5.94e-05 AATTAATTTT GAAAAGAA ACGCCAATTA chrV:8661740-8661820 14 5.94e-05 ATCAATTAGT GAAAAGAA GAGCATTGAG chrX:10477705-10477785 71 5.94e-05 AAGACGAACT GAAAAGAA TG chrV:17752499-17752579 23 1.08e-04 ATAAACAATT GATAAAAA GTTACACCAT chrIII:13604016-13604096 30 1.08e-04 ATTGCAACAA GATAAAAA TTATGGAAGT chrV:7150711-7150791 52 1.08e-04 TTTGTAAATA GATAAAAA TGAGAAATTC chrV:10693866-10693946 25 1.08e-04 GCAGTGTACT GATAAAAA TTGATAAAAC chrX:10142175-10142255 64 1.27e-04 ACTATTGGTC GATAAGAC ACTTTCGGG chrX:15940002-15940082 15 1.27e-04 ACGGTGATGA GATAAGAC AGACTGAGGA chrIII:7369788-7369868 66 1.74e-04 GCGAAGAAAC GAAAAAAA AACTATA chrV:17721887-17721967 33 1.74e-04 TCCTGTAATC GAAAAAAA AACTTGCGCC chrX:1478105-1478185 27 1.74e-04 ACCTCAGCGA GAAAAAAA GTGGGAACAC chrIII:13347245-13347325 15 1.74e-04 CTCGTCACCC GAAAAAAA GTACGCAAAA chrIV:7237959-7238039 43 1.93e-04 TAGTTAAACT GATAAGAG TTTTAGCTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:5026606-5026686 3e-05 13_[+3]_59 chrI:5388660-5388740 3e-05 47_[+3]_25 chrIV:9651315-9651395 3e-05 46_[+3]_26 chrX:4564955-4565035 3e-05 8_[+3]_64 chrIII:8733862-8733942 3e-05 49_[+3]_23 chrX:14500793-14500873 3e-05 45_[+3]_27 chrII:2610303-2610383 3e-05 58_[+3]_14 chrV:3970587-3970667 3e-05 23_[+3]_49 chrV:2327263-2327343 3e-05 72_[+3] chrV:3784476-3784556 3e-05 67_[+3]_5 chrII:2587149-2587229 3e-05 62_[+3]_10 chrII:9807675-9807755 3e-05 66_[+3]_6 chrII:8988101-8988181 5.9e-05 60_[+3]_12 chrV:8661740-8661820 5.9e-05 13_[+3]_59 chrX:10477705-10477785 5.9e-05 70_[+3]_2 chrV:17752499-17752579 0.00011 22_[+3]_50 chrIII:13604016-13604096 0.00011 29_[+3]_43 chrV:7150711-7150791 0.00011 51_[+3]_21 chrV:10693866-10693946 0.00011 24_[+3]_48 chrX:10142175-10142255 0.00013 63_[+3]_9 chrX:15940002-15940082 0.00013 14_[+3]_58 chrIII:7369788-7369868 0.00017 65_[+3]_7 chrV:17721887-17721967 0.00017 32_[+3]_40 chrX:1478105-1478185 0.00017 26_[+3]_46 chrIII:13347245-13347325 0.00017 14_[+3]_58 chrIV:7237959-7238039 0.00019 42_[+3]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GATAAGAA width=8 seqs=26 chrV:5026606-5026686 ( 14) GATAAGAA 1 chrI:5388660-5388740 ( 48) GATAAGAA 1 chrIV:9651315-9651395 ( 47) GATAAGAA 1 chrX:4564955-4565035 ( 9) GATAAGAA 1 chrIII:8733862-8733942 ( 50) GATAAGAA 1 chrX:14500793-14500873 ( 46) GATAAGAA 1 chrII:2610303-2610383 ( 59) GATAAGAA 1 chrV:3970587-3970667 ( 24) GATAAGAA 1 chrV:2327263-2327343 ( 73) GATAAGAA 1 chrV:3784476-3784556 ( 68) GATAAGAA 1 chrII:2587149-2587229 ( 63) GATAAGAA 1 chrII:9807675-9807755 ( 67) GATAAGAA 1 chrII:8988101-8988181 ( 61) GAAAAGAA 1 chrV:8661740-8661820 ( 14) GAAAAGAA 1 chrX:10477705-10477785 ( 71) GAAAAGAA 1 chrV:17752499-17752579 ( 23) GATAAAAA 1 chrIII:13604016-13604096 ( 30) GATAAAAA 1 chrV:7150711-7150791 ( 52) GATAAAAA 1 chrV:10693866-10693946 ( 25) GATAAAAA 1 chrX:10142175-10142255 ( 64) GATAAGAC 1 chrX:15940002-15940082 ( 15) GATAAGAC 1 chrIII:7369788-7369868 ( 66) GAAAAAAA 1 chrV:17721887-17721967 ( 33) GAAAAAAA 1 chrX:1478105-1478185 ( 27) GAAAAAAA 1 chrIII:13347245-13347325 ( 15) GAAAAAAA 1 chrIV:7237959-7238039 ( 43) GATAAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.98426 E= 9.6e+000 -1134 -1134 240 -1134 171 -1134 -1134 -1134 -19 -1134 -1134 122 171 -1134 -1134 -1134 171 -1134 -1134 -1134 1 -1134 187 -1134 171 -1134 -1134 -1134 153 -131 -230 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 9.6e+000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.269231 0.000000 0.000000 0.730769 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.307692 0.000000 0.692308 0.000000 1.000000 0.000000 0.000000 0.000000 0.884615 0.076923 0.038462 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 regular expression -------------------------------------------------------------------------------- GA[TA]AA[GA]AA -------------------------------------------------------------------------------- Time 13.14 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGAGGGR MEME-4 width = 8 sites = 7 llr = 76 E-value = 8.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::9:::3 pos.-specific C :1:1:::: probability G a9a:aaa6 matrix T :::::::1 bits 2.4 * * *** 2.2 * * *** 1.9 *** *** 1.7 *** *** Relative 1.4 *** *** Entropy 1.2 ******* (15.8 bits) 1.0 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGAGGGG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:18826610-18826690 46 2.64e-06 CGTGTCAGCA GGGAGGGG GTGCCACCAG chrIV:13708011-13708091 6 2.64e-06 ACAAG GGGAGGGG GAAGGGGTAG chrV:5813231-5813311 7 6.90e-06 GAAGTA GGGAGGGA GAATGATGAC chrIV:6378579-6378659 42 6.90e-06 CCGAATAGTT GGGAGGGA TGATTTCAGA chrI:4382413-4382493 27 8.55e-06 ACGGTTCTGT GGGCGGGG TCAATCCCCC chrV:5823149-5823229 15 1.12e-05 GAAGTTTAGT GCGAGGGG GTAGCTAGAG chrII:4770051-4770131 33 1.56e-05 GCTCTTATCA GGGAGGGT GTGATCGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:18826610-18826690 2.6e-06 45_[+4]_27 chrIV:13708011-13708091 2.6e-06 5_[+4]_67 chrV:5813231-5813311 6.9e-06 6_[+4]_66 chrIV:6378579-6378659 6.9e-06 41_[+4]_31 chrI:4382413-4382493 8.5e-06 26_[+4]_46 chrV:5823149-5823229 1.1e-05 14_[+4]_58 chrII:4770051-4770131 1.6e-05 32_[+4]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGAGGGR width=8 seqs=7 chrV:18826610-18826690 ( 46) GGGAGGGG 1 chrIV:13708011-13708091 ( 6) GGGAGGGG 1 chrV:5813231-5813311 ( 7) GGGAGGGA 1 chrIV:6378579-6378659 ( 42) GGGAGGGA 1 chrI:4382413-4382493 ( 27) GGGCGGGG 1 chrV:5823149-5823229 ( 15) GCGAGGGG 1 chrII:4770051-4770131 ( 33) GGGAGGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.5704 E= 8.5e+002 -945 -945 240 -945 -945 -41 218 -945 -945 -945 240 -945 148 -41 -945 -945 -945 -945 240 -945 -945 -945 240 -945 -945 -945 240 -945 -10 -945 159 -113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 8.5e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.571429 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGAGGGR MEME-4 regular expression -------------------------------------------------------------------------------- GGGAGGG[GA] -------------------------------------------------------------------------------- Time 16.67 secs. ******************************************************************************** ******************************************************************************** MOTIF AGACGCAG MEME-5 width = 8 sites = 4 llr = 47 E-value = 4.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A a:a:::a: pos.-specific C :::a:a:: probability G :a::a::a matrix T :::::::: bits 2.4 * *** * 2.2 * *** * 1.9 * *** * 1.7 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.1 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AGACGCAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:10566130-10566210 9 7.06e-06 ATCAGTGG AGACGCAG ACGTATGTCT chrII:7255813-7255893 48 7.06e-06 TTTTACAACG AGACGCAG AGACAGGACA chrIV:6083786-6083866 41 7.06e-06 AGAGAGTTTT AGACGCAG ACTGCATAAG chrII:3743863-3743943 20 7.06e-06 TGTCCACTGG AGACGCAG ACAGTTGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:10566130-10566210 7.1e-06 8_[+5]_64 chrII:7255813-7255893 7.1e-06 47_[+5]_25 chrIV:6083786-6083866 7.1e-06 40_[+5]_32 chrII:3743863-3743943 7.1e-06 19_[+5]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGACGCAG width=8 seqs=4 chrIII:10566130-10566210 ( 9) AGACGCAG 1 chrII:7255813-7255893 ( 48) AGACGCAG 1 chrIV:6083786-6083866 ( 41) AGACGCAG 1 chrII:3743863-3743943 ( 20) AGACGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.1553 E= 4.9e+003 171 -865 -865 -865 -865 -865 240 -865 171 -865 -865 -865 -865 239 -865 -865 -865 -865 240 -865 -865 239 -865 -865 171 -865 -865 -865 -865 -865 240 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 4.9e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGCAG MEME-5 regular expression -------------------------------------------------------------------------------- AGACGCAG -------------------------------------------------------------------------------- Time 20.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:13024437-13024517 7.74e-02 68_[+2(8.68e-05)]_4 chrIV:13575822-13575902 5.89e-01 80 chrV:7145409-7145489 2.70e-01 80 chrV:16390793-16390873 7.93e-02 [+2(8.68e-05)]_72 chrV:3468590-3468670 3.59e-01 80 chrV:519614-519694 9.43e-02 53_[+2(8.68e-05)]_3_[+2(8.68e-05)]_\ 8 chrV:7163800-7163880 5.54e-02 58_[+2(8.68e-05)]_14 chrIV:7258391-7258471 1.97e-01 80 chrIV:7260750-7260830 8.30e-02 12_[+2(8.68e-05)]_60 chrV:332796-332876 3.74e-02 38_[+1(6.61e-05)]_34 chrII:7457370-7457450 8.62e-01 80 chrIV:17174239-17174319 7.94e-01 80 chrV:7145611-7145691 3.08e-01 80 chrII:9807675-9807755 4.04e-02 66_[+3(3.01e-05)]_6 chrX:15940002-15940082 1.24e-02 80 chrIV:12599301-12599381 1.55e-02 18_[+1(6.61e-05)]_54 chrV:13529235-13529315 7.74e-01 80 chrII:3743863-3743943 1.30e-03 19_[+5(7.06e-06)]_28_[+2(8.68e-05)]_\ 17 chrI:2686210-2686290 8.87e-01 80 chrV:7157189-7157269 9.93e-01 80 chrV:7142844-7142924 9.88e-01 80 chrV:5030368-5030448 9.66e-01 80 chrIV:4599129-4599209 3.18e-01 80 chrII:7277398-7277478 7.89e-02 17_[+1(3.32e-05)]_55 chrX:575234-575314 4.95e-02 2_[+2(3.31e-05)]_70 chrV:12937270-12937350 6.99e-01 80 chrII:7290129-7290209 7.74e-01 80 chrV:3841624-3841704 5.43e-01 80 chrII:2587149-2587229 6.47e-02 62_[+3(3.01e-05)]_10 chrX:8248425-8248505 5.67e-01 80 chrV:5018241-5018321 1.64e-01 80 chrIV:6378579-6378659 1.14e-02 41_[+4(6.90e-06)]_31 chrX:3256922-3257002 1.07e-01 80 chrII:7458947-7459027 6.17e-01 80 chrIII:9751260-9751340 1.86e-01 80 chrX:14743400-14743480 5.54e-01 80 chrV:1607997-1608077 2.95e-01 80 chrI:9849661-9849741 8.84e-01 80 chrII:12892595-12892675 2.83e-02 80 chrX:12518598-12518678 7.04e-02 32_[+1(3.32e-05)]_40 chrV:333848-333928 9.93e-02 80 chrII:13956722-13956802 7.85e-02 80 chrII:14299510-14299590 4.82e-01 80 chrI:6497569-6497649 9.20e-01 80 chrV:16278066-16278146 3.76e-01 80 chrV:3784476-3784556 3.01e-02 67_[+3(3.01e-05)]_5 chrX:10216999-10217079 8.17e-01 80 chrI:6499608-6499688 4.71e-02 30_[+1(3.32e-05)]_42 chrV:13012054-13012134 6.03e-02 50_[+1(3.32e-05)]_22 chrII:6526306-6526386 3.21e-01 60_[+1(8.63e-05)]_12 chrV:7413907-7413987 5.03e-01 80 chrV:3632396-3632476 9.88e-01 80 chrV:12096013-12096093 1.02e-01 23_[+2(8.68e-05)]_49 chrI:14104657-14104737 7.59e-02 80 chrIV:12601095-12601175 4.09e-02 80 chrV:9255642-9255722 9.52e-02 80 chrII:915392-915472 2.13e-02 71_[+1(6.61e-05)]_1 chrIII:12658737-12658817 7.97e-01 80 chrIV:4817021-4817101 3.31e-01 80 chrV:2327263-2327343 6.90e-02 72_[+3(3.01e-05)] chrII:9791357-9791437 1.58e-01 1_[+1(8.63e-05)]_23_[+1(3.32e-05)]_\ 40 chrX:15167851-15167931 4.01e-01 80 chrV:5192683-5192763 1.67e-01 80 chrV:12355011-12355091 8.31e-01 80 chrIV:4599358-4599438 4.38e-01 80 chrV:7095481-7095561 4.82e-03 43_[+2(8.68e-05)]_29 chrII:8081375-8081455 5.83e-01 80 chrV:3970587-3970667 2.07e-03 23_[+3(3.01e-05)]_14_[+3(5.94e-05)]_\ 15_[+2(3.31e-05)]_4 chrII:8387096-8387176 8.37e-01 80 chrV:11067809-11067889 7.73e-01 80 chrX:15441170-15441250 9.09e-02 70_[+2(3.31e-05)]_2 chrIV:12842268-12842348 8.75e-01 80 chrX:3150919-3150999 9.44e-01 80 chrV:20499094-20499174 4.81e-02 6_[+2(8.68e-05)]_66 chrX:3290267-3290347 4.34e-01 80 chrV:10802218-10802298 8.79e-01 80 chrV:1456805-1456885 1.59e-02 67_[+2(3.31e-05)]_5 chrIV:10463322-10463402 1.15e-01 80 chrIII:13607994-13608074 2.74e-01 63_[+1(3.32e-05)]_9 chrIV:13708011-13708091 4.72e-03 5_[+4(2.64e-06)]_67 chrV:11817372-11817452 5.42e-01 80 chrII:4871739-4871819 3.29e-01 80 chrIII:1392935-1393015 6.44e-01 80 chrIV:2618780-2618860 1.11e-01 80 chrII:14866947-14867027 3.52e-02 31_[+2(3.31e-05)]_41 chrX:17255974-17256054 3.96e-01 80 chrV:2324436-2324516 1.93e-03 17_[+1(3.32e-05)]_4_[+2(3.31e-05)]_\ 43 chrX:9261804-9261884 1.52e-01 80 chrX:8542540-8542620 7.14e-02 80 chrII:11614264-11614344 9.87e-01 80 chrIII:2760964-2761044 1.02e-01 80 chrV:7733174-7733254 4.11e-01 80 chrX:15075859-15075939 8.23e-01 80 chrIV:4083226-4083306 4.92e-01 80 chrIII:7758698-7758778 5.82e-01 80 chrIV:4014492-4014572 6.37e-01 80 chrIV:2796576-2796656 7.71e-01 80 chrV:8768603-8768683 2.01e-01 36_[+1(3.32e-05)]_36 chrIV:7237959-7238039 2.80e-02 80 chrI:13333135-13333215 7.53e-01 80 chrII:14043356-14043436 8.16e-02 35_[+2(3.31e-05)]_37 chrII:7166948-7167028 2.74e-01 80 chrI:6731875-6731955 4.27e-02 53_[+1(3.32e-05)]_19 chrII:12980386-12980466 3.22e-02 6_[+1(3.32e-05)]_66 chrV:16726108-16726188 1.63e-01 80 chrII:4770051-4770131 1.07e-03 24_[+1(3.32e-05)]_[+4(1.56e-05)]_40 chrX:11519252-11519332 4.97e-03 80 chrII:4881880-4881960 4.66e-01 80 chrII:1103849-1103929 3.11e-01 80 chrIV:13725335-13725415 1.42e-01 80 chrV:19672522-19672602 7.29e-02 80 chrII:4943801-4943881 7.96e-01 80 chrV:8922925-8923005 2.89e-01 80 chrV:2250304-2250384 3.66e-01 80 chrV:10693866-10693946 2.21e-01 80 chrX:2698620-2698700 9.20e-01 80 chrV:7150711-7150791 8.00e-02 80 chrV:4189749-4189829 4.85e-01 80 chrX:9233969-9234049 9.92e-01 80 chrV:6413215-6413295 9.69e-02 80 chrV:12744220-12744300 3.06e-01 80 chrII:9800433-9800513 6.71e-02 80 chrII:2610303-2610383 4.58e-03 58_[+3(3.01e-05)]_14 chrII:15251734-15251814 7.80e-02 8_[+1(3.32e-05)]_64 chrV:16046006-16046086 1.85e-01 80 chrV:12935117-12935197 8.08e-02 80 chrIII:10822677-10822757 9.47e-01 80 chrII:5323952-5324032 9.45e-02 51_[+1(3.32e-05)]_21 chrI:10382084-10382164 3.63e-01 80 chrII:7877856-7877936 2.60e-01 80 chrI:3113766-3113846 7.38e-02 33_[+1(3.32e-05)]_39 chrV:19437516-19437596 1.38e-01 80 chrX:10480722-10480802 6.19e-01 80 chrIII:13347245-13347325 1.47e-01 80 chrX:2663891-2663971 2.97e-01 80 chrX:440642-440722 9.95e-02 80 chrIV:7183041-7183121 5.89e-01 80 chrX:8089705-8089785 7.22e-01 80 chrX:14500793-14500873 2.44e-02 45_[+3(3.01e-05)]_27 chrX:4698436-4698516 4.24e-02 80 chrIII:8733862-8733942 1.19e-02 49_[+3(3.01e-05)]_23 chrV:9078986-9079066 4.53e-01 80 chrIV:10913594-10913674 5.21e-01 80 chrIV:12598552-12598632 1.59e-01 80 chrI:6727782-6727862 7.94e-02 80 chrI:9271062-9271142 2.79e-01 80 chrX:3153323-3153403 5.05e-02 80 chrX:8604334-8604414 5.38e-01 80 chrII:3911502-3911582 1.87e-02 53_[+2(8.68e-05)]_19 chrX:14001624-14001704 7.45e-01 80 chrII:1233062-1233142 7.97e-01 80 chrX:10477705-10477785 1.55e-02 70_[+3(5.94e-05)]_2 chrII:13465390-13465470 9.84e-01 80 chrX:6518733-6518813 2.20e-01 80 chrIV:3012558-3012638 4.94e-01 80 chrI:6294076-6294156 4.92e-01 80 chrI:6416933-6417013 8.49e-02 80 chrV:6019292-6019372 2.58e-01 80 chrV:6665878-6665958 7.17e-03 80 chrIII:8161133-8161213 9.06e-01 80 chrIV:3739012-3739092 9.65e-02 56_[+2(8.68e-05)]_16 chrIII:13604016-13604096 1.79e-01 80 chrX:6607245-6607325 4.86e-01 80 chrX:14815635-14815715 9.42e-01 80 chrIII:348240-348320 8.05e-01 80 chrV:14449818-14449898 1.30e-01 80 chrX:1478105-1478185 9.98e-02 80 chrX:4564955-4565035 3.78e-02 8_[+3(3.01e-05)]_64 chrV:462379-462459 7.72e-01 80 chrIV:7915562-7915642 4.87e-01 80 chrV:7744198-7744278 5.74e-02 6_[+1(6.61e-05)]_66 chrII:5575067-5575147 6.26e-02 80 chrV:17721887-17721967 1.47e-02 48_[+1(8.63e-05)]_24 chrX:8473585-8473665 3.45e-01 33_[+1(6.61e-05)]_39 chrX:11792883-11792963 8.14e-01 80 chrII:11538548-11538628 9.42e-01 80 chrX:2698412-2698492 1.13e-02 80 chrX:1443752-1443832 9.81e-01 80 chrII:7773567-7773647 9.98e-01 80 chrIV:6083786-6083866 3.68e-03 40_[+5(7.06e-06)]_32 chrX:12197546-12197626 3.16e-01 80 chrV:8661740-8661820 6.05e-03 13_[+3(5.94e-05)]_59 chrII:5917469-5917549 6.99e-01 80 chrV:5813231-5813311 4.21e-02 6_[+4(6.90e-06)]_66 chrX:3117340-3117420 3.22e-01 80 chrIII:9930481-9930561 5.91e-01 80 chrIV:11123574-11123654 6.18e-01 80 chrV:5823149-5823229 1.23e-04 14_[+4(1.12e-05)]_40_[+2(3.31e-05)]_\ 10 chrIV:9651315-9651395 1.29e-01 46_[+3(3.01e-05)]_26 chrV:11069441-11069521 8.51e-01 80 chrI:11572653-11572733 7.40e-01 80 chrII:6919563-6919643 2.62e-01 80 chrX:14071088-14071168 3.51e-01 80 chrX:10142175-10142255 7.06e-02 80 chrIII:6396566-6396646 2.49e-02 27_[+1(3.32e-05)]_45 chrX:4658795-4658875 1.00e+00 80 chrX:14166953-14167033 2.00e-01 80 chrX:11515586-11515666 4.45e-01 80 chrX:13339355-13339435 1.27e-01 80 chrV:18826610-18826690 2.08e-02 45_[+4(2.64e-06)]_27 chrX:6088805-6088885 2.83e-01 80 chrX:16550737-16550817 1.95e-01 80 chrIV:2855484-2855564 2.54e-02 38_[+1(6.61e-05)]_34 chrV:13043378-13043458 4.19e-01 80 chrI:5388660-5388740 1.58e-01 47_[+3(3.01e-05)]_25 chrIV:10761461-10761541 8.68e-01 80 chrX:9833301-9833381 9.01e-01 80 chrX:1443955-1444035 9.97e-01 80 chrV:8270020-8270100 9.29e-01 80 chrV:5026606-5026686 4.26e-02 13_[+3(3.01e-05)]_59 chrV:14422305-14422385 7.59e-02 80 chrIII:4654008-4654088 5.11e-01 80 chrX:1386960-1387040 3.15e-01 80 chrV:7761801-7761881 7.34e-01 80 chrV:3455318-3455398 6.81e-01 80 chrIV:11917004-11917084 9.98e-01 80 chrII:8413059-8413139 6.09e-01 80 chrV:8651499-8651579 3.76e-01 80 chrI:11571754-11571834 9.98e-01 80 chrV:16395258-16395338 2.58e-01 80 chrX:15076948-15077028 7.60e-01 80 chrIII:13626602-13626682 9.83e-01 80 chrV:3634688-3634768 1.35e-03 22_[+1(6.61e-05)]_50 chrX:16192710-16192790 1.13e-01 2_[+1(8.63e-05)]_4_[+1(8.63e-05)]_\ 58 chrII:13160620-13160700 8.40e-01 80 chrX:15748002-15748082 4.40e-01 80 chrX:14790865-14790945 9.62e-01 80 chrII:13077868-13077948 3.22e-01 80 chrX:13165839-13165919 1.08e-01 48_[+1(3.32e-05)]_24 chrII:7264800-7264880 9.23e-01 80 chrII:7255813-7255893 4.71e-02 47_[+5(7.06e-06)]_25 chrII:7287905-7287985 1.54e-01 80 chrI:5079459-5079539 4.58e-01 80 chrX:13310929-13311009 3.98e-02 80 chrII:9501097-9501177 5.10e-03 12_[+1(3.32e-05)]_60 chrIV:14413491-14413571 2.97e-01 80 chrII:8384517-8384597 7.58e-02 80 chrV:534364-534444 7.64e-01 80 chrIII:7369788-7369868 2.90e-01 80 chrIII:10566130-10566210 1.84e-02 8_[+5(7.06e-06)]_64 chrV:14421228-14421308 9.82e-01 80 chrV:17752499-17752579 9.17e-03 80 chrII:8988101-8988181 4.90e-02 60_[+3(5.94e-05)]_12 chrII:13737904-13737984 6.32e-01 80 chrII:11336047-11336127 2.83e-02 80 chrX:2693262-2693342 5.42e-01 80 chrII:4710293-4710373 2.16e-01 80 chrV:3967928-3968008 8.71e-01 80 chrI:4382413-4382493 3.00e-02 26_[+4(8.55e-06)]_46 chrIV:4479472-4479552 2.80e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************