******************************************************************************** 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/fkh-2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrII:5046404-5046484 1.0000 80 chrIV:9538359-9538439 1.0000 80 chrI:12164788-12164868 1.0000 80 chrII:7887456-7887536 1.0000 80 chrX:16391227-16391307 1.0000 80 chrV:5330077-5330157 1.0000 80 chrII:5092562-5092642 1.0000 80 chrIV:5594045-5594125 1.0000 80 chrI:5140475-5140555 1.0000 80 chrI:12548183-12548263 1.0000 80 chrI:7396604-7396684 1.0000 80 chrIII:3560472-3560552 1.0000 80 chrIV:4033692-4033772 1.0000 80 chrX:3257994-3258074 1.0000 80 chrV:19897710-19897790 1.0000 80 chrII:7838804-7838884 1.0000 80 chrIV:1105304-1105384 1.0000 80 chrX:9347767-9347847 1.0000 80 chrII:14598523-14598603 1.0000 80 chrIV:7815901-7815981 1.0000 80 chrI:9375291-9375371 1.0000 80 chrX:14557601-14557681 1.0000 80 chrI:14902827-14902907 1.0000 80 chrX:14983409-14983489 1.0000 80 chrI:14845636-14845716 1.0000 80 chrIII:2804635-2804715 1.0000 80 chrX:8206051-8206131 1.0000 80 chrIV:14033644-14033724 1.0000 80 chrV:20646387-20646467 1.0000 80 chrV:14366669-14366749 1.0000 80 chrV:14393229-14393309 1.0000 80 chrII:13195329-13195409 1.0000 80 chrIII:12583574-12583654 1.0000 80 chrII:13447867-13447947 1.0000 80 chrX:535975-536055 1.0000 80 chrIII:7217321-7217401 1.0000 80 chrV:8001044-8001124 1.0000 80 chrX:8724061-8724141 1.0000 80 chrI:6745493-6745573 1.0000 80 chrI:10539293-10539373 1.0000 80 chrI:12675370-12675450 1.0000 80 chrIV:3161026-3161106 1.0000 80 chrII:11464650-11464730 1.0000 80 chrIV:5530667-5530747 1.0000 80 chrV:13107873-13107953 1.0000 80 chrIII:86412-86492 1.0000 80 chrI:7321587-7321667 1.0000 80 chrV:14200261-14200341 1.0000 80 chrX:7234992-7235072 1.0000 80 chrI:7867730-7867810 1.0000 80 chrIV:11744507-11744587 1.0000 80 chrII:9603600-9603680 1.0000 80 chrII:8787510-8787590 1.0000 80 chrII:12102575-12102655 1.0000 80 chrIV:6881315-6881395 1.0000 80 chrV:1471207-1471287 1.0000 80 chrX:1479296-1479376 1.0000 80 chrV:18712415-18712495 1.0000 80 chrIV:14032953-14033033 1.0000 80 chrX:10901192-10901272 1.0000 80 chrI:8409929-8410009 1.0000 80 chrIV:5209569-5209649 1.0000 80 chrIII:13061213-13061293 1.0000 80 chrIV:8431889-8431969 1.0000 80 chrI:8426861-8426941 1.0000 80 chrV:18723770-18723850 1.0000 80 chrIV:6879077-6879157 1.0000 80 chrV:9212748-9212828 1.0000 80 chrX:16931500-16931580 1.0000 80 chrV:5917874-5917954 1.0000 80 chrII:5593655-5593735 1.0000 80 chrX:11473523-11473603 1.0000 80 chrIII:25636-25716 1.0000 80 chrII:9062033-9062113 1.0000 80 chrIII:8904264-8904344 1.0000 80 chrV:8828-8908 1.0000 80 chrX:5812109-5812189 1.0000 80 chrX:1909551-1909631 1.0000 80 chrX:1093246-1093326 1.0000 80 chrV:12814546-12814626 1.0000 80 chrIV:10936963-10937043 1.0000 80 chrIV:5607480-5607560 1.0000 80 chrII:14018352-14018432 1.0000 80 chrIII:4552048-4552128 1.0000 80 chrIV:15472525-15472605 1.0000 80 chrI:7492029-7492109 1.0000 80 chrX:13969454-13969534 1.0000 80 chrV:18079307-18079387 1.0000 80 chrX:9441644-9441724 1.0000 80 chrI:13337228-13337308 1.0000 80 chrIII:3677521-3677601 1.0000 80 chrI:13663321-13663401 1.0000 80 chrIII:8658559-8658639 1.0000 80 chrIII:8447129-8447209 1.0000 80 chrII:410996-411076 1.0000 80 chrX:949586-949666 1.0000 80 chrX:7823185-7823265 1.0000 80 chrIII:8417606-8417686 1.0000 80 chrV:6224694-6224774 1.0000 80 chrIII:4223848-4223928 1.0000 80 chrV:10871619-10871699 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_fkh-2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/fkh-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= 101 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= 8080 N= 101 sample: seed= 0 hsfrac= 0 searchsize= 8080 norand= no csites= 1000 Letter frequencies in dataset: A 0.28 C 0.226 G 0.224 T 0.27 Background letter frequencies (from file dataset with add-one prior applied): A 0.28 C 0.226 G 0.224 T 0.27 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF BTCTCTBY MEME-1 width = 8 sites = 56 llr = 370 E-value = 8.9e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::21: pos.-specific C 2:a1a:35 probability G 3::::132 matrix T 4a:9:733 bits 2.2 * * 1.9 ** * 1.7 ** * 1.5 **** Relative 1.3 **** Entropy 1.1 **** (9.5 bits) 0.9 **** 0.6 ***** 0.4 ****** * 0.2 ****** * 0.0 -------- Multilevel TTCTCTTC consensus G ACT sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:25636-25716 3 3.04e-05 CG TTCTCTTC GTATAAGGCG chrIII:2804635-2804715 71 3.04e-05 TCTCCACTTC TTCTCTTC AC chrX:14557601-14557681 52 3.04e-05 TTCTTCTCCT TTCTCTTC CATCGTGCCC chrI:8426861-8426941 72 5.57e-05 AGGTGCCTGC GTCTCTTC A chrIII:7217321-7217401 50 5.57e-05 CACTGTCTGT GTCTCTTC AATCACTTTG chrII:13195329-13195409 71 5.57e-05 GAAATGCTGC Gtctctcc tg chrV:14366669-14366749 7 5.57e-05 TCTGTC GTCTCTTC ATCCATGCCT chrIV:14033644-14033724 15 5.57e-05 CCGTCTCGCC GTCTCTTC AGTCCTCCAC chrIV:5594045-5594125 69 5.57e-05 GAAGAAAATC GTCTCTTC CTTC chrIV:9538359-9538439 54 5.57e-05 GTGTATGTGT GTCTCTTC GTCAGCTCTT chrIII:8417606-8417686 51 6.94e-05 TTCACTCTTT TTCTCTGC ATCTCTTGTC chrX:5812109-5812189 3 6.94e-05 TT TTCTCTGC CGCACGGCGG chrV:18723770-18723850 5 6.94e-05 TGTT TTCTCTGC CACTCTCTCA chrX:949586-949666 68 1.06e-04 TTGGTGGGTG ctctctcc ctctc chrX:10901192-10901272 36 1.06e-04 TTTTCTTTGA CTCTCTTC CCGCCAAACA chrV:1471207-1471287 59 1.06e-04 aGCTGCCTAT CTCTCTTC TCCTTCCCGC chrII:7838804-7838884 22 1.54e-04 ctctctatgt ttctctct ttctctaaat chrII:7887456-7887536 10 1.54e-04 CTCTTATTC TTCTCTCT CACATTTCGC chrV:18079307-18079387 56 1.84e-04 GTTTTCTCTC GTCTCTCT CAGCTCTCAA chrV:8001044-8001124 45 2.01e-04 AGCTGAGAGC TTCTCTGT TTCTCTCGAT chrX:7823185-7823265 19 2.14e-04 GTAAACAGAC GTCTCTGT CCAATTACGT chrIII:8447129-8447209 52 3.24e-04 CCATGTAAAA TTCTCTAC AGAGCAGACT chrIII:8658559-8658639 15 3.24e-04 CAATTCGGTT TTCTCTCG AACATTCCAT chrI:7492029-7492109 36 3.24e-04 CTGCATGTCT CTCTCTCT CACTTGTTGT chrIII:4552048-4552128 64 3.24e-04 AACAGGCAAT CTCTCTTT CTGTGTCTG chrV:8828-8908 2 3.24e-04 t ctctctct cactTTGCCT chrIV:14032953-14033033 8 3.24e-04 ACActct ctctctct ctttctcGCG chrII:11464650-11464730 47 3.24e-04 CACCCAACAC TTCTCACC TCACGCTGCA chrIV:3161026-3161106 70 3.24e-04 CGtctctggc ctctctct cgg chrI:10539293-10539373 31 3.89e-04 CGATGCCTAC GTCTCTAC TCTACTACAC chrIII:4223848-4223928 49 4.31e-04 CGGGCACGCG CTCTCTGT GCTGTGTTGC chrIV:6879077-6879157 12 4.31e-04 TTTCTTCTCG TTCTCAGC TCGACTGCTC chrI:8409929-8410009 64 4.31e-04 ACACTTCTTC TTCTCAGC TGACCTCTC chrII:8787510-8787590 30 4.31e-04 ACCCTGCCAC TTCTCAGC ATCTCTCATT chrV:14200261-14200341 20 5.20e-04 GTCTCGCACA CTCTCTCG CCCATCCACA chrI:13337228-13337308 40 5.89e-04 AATGTGGTGG GTCTCGTC GCGAAAACGA chrI:7396604-7396684 25 5.89e-04 AGAAGACAGG CTCTCAGC TGTGTACTAG chrI:7321587-7321667 39 6.59e-04 CTTCACTATT TTCTCTAT TTCTTTTCTC chrI:12675370-12675450 53 6.59e-04 AACGCTCCAC TTCTCACT CACTATTTTT chrII:5046404-5046484 3 6.59e-04 TT TTCTCATT CAAACCACCC chrII:13447867-13447947 33 7.55e-04 ACAAACAAGA TTCTCAGT GGGGCGCGTT chrX:9347767-9347847 72 8.93e-04 TTGGGCAGAC TTCTCATG G chrI:14845636-14845716 42 9.78e-04 TCGAGACGAT GTCTCTAG ACCCTCTGCG chrIV:10936963-10937043 37 1.12e-03 AGTAAACAGA CTCTCATG ACTAGTGAAC chrII:410996-411076 16 1.21e-03 AATTCTTAGC TTCTCGCG CTTTTTCAAT chrI:13663321-13663401 61 1.21e-03 AATAAAGAAG TTCCCTCC GTAAATCGTG chrV:6224694-6224774 44 1.32e-03 CGATAAACAA GTCTCGTG ACTAGAGAGA chrII:14018352-14018432 22 1.32e-03 CAGCCAAGGT GTCTCGAC ATATTGGCAT chrIII:8904264-8904344 7 1.32e-03 GTGATG GTCTCGAC GCGATTGCCC chrII:5593655-5593735 23 1.32e-03 CGCAGAGAGT GTCCCTTC CCGATCTCTC chrX:16931500-16931580 46 1.32e-03 CCTTTTACTA TTCTCTCA AATCGAACCG chrIII:13061213-13061293 5 1.32e-03 CTAT TTCTCTTA ATTTTCAATT chrX:14983409-14983489 14 1.32e-03 CACCTCACAC CTCTCAGG CCCATCCGTC chrV:13107873-13107953 9 1.40e-03 GACAGCTA TTCTCAAT TTCAATAAAT chrX:1909551-1909631 34 1.46e-03 CCCACATGCC GTCCCTGC CGCCTAAACA chrX:7234992-7235072 32 1.46e-03 CTTGCCTAGT GTCTCGGG AATTGAGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:25636-25716 3e-05 2_[+1]_70 chrIII:2804635-2804715 3e-05 70_[+1]_2 chrX:14557601-14557681 3e-05 51_[+1]_21 chrI:8426861-8426941 5.6e-05 71_[+1]_1 chrIII:7217321-7217401 5.6e-05 49_[+1]_23 chrII:13195329-13195409 5.6e-05 70_[+1]_2 chrV:14366669-14366749 5.6e-05 6_[+1]_66 chrIV:14033644-14033724 5.6e-05 14_[+1]_58 chrIV:5594045-5594125 5.6e-05 68_[+1]_4 chrIV:9538359-9538439 5.6e-05 53_[+1]_19 chrIII:8417606-8417686 6.9e-05 50_[+1]_22 chrX:5812109-5812189 6.9e-05 2_[+1]_70 chrV:18723770-18723850 6.9e-05 4_[+1]_68 chrX:949586-949666 0.00011 67_[+1]_5 chrX:10901192-10901272 0.00011 35_[+1]_37 chrV:1471207-1471287 0.00011 58_[+1]_14 chrII:7838804-7838884 0.00015 21_[+1]_51 chrII:7887456-7887536 0.00015 9_[+1]_63 chrV:18079307-18079387 0.00018 55_[+1]_17 chrV:8001044-8001124 0.0002 44_[+1]_28 chrX:7823185-7823265 0.00021 18_[+1]_54 chrIII:8447129-8447209 0.00032 51_[+1]_21 chrIII:8658559-8658639 0.00032 14_[+1]_58 chrI:7492029-7492109 0.00032 35_[+1]_37 chrIII:4552048-4552128 0.00032 63_[+1]_9 chrV:8828-8908 0.00032 1_[+1]_71 chrIV:14032953-14033033 0.00032 7_[+1]_65 chrII:11464650-11464730 0.00032 46_[+1]_26 chrIV:3161026-3161106 0.00032 69_[+1]_3 chrI:10539293-10539373 0.00039 30_[+1]_42 chrIII:4223848-4223928 0.00043 48_[+1]_24 chrIV:6879077-6879157 0.00043 11_[+1]_61 chrI:8409929-8410009 0.00043 63_[+1]_9 chrII:8787510-8787590 0.00043 29_[+1]_43 chrV:14200261-14200341 0.00052 19_[+1]_53 chrI:13337228-13337308 0.00059 39_[+1]_33 chrI:7396604-7396684 0.00059 24_[+1]_48 chrI:7321587-7321667 0.00066 38_[+1]_34 chrI:12675370-12675450 0.00066 52_[+1]_20 chrII:5046404-5046484 0.00066 2_[+1]_70 chrII:13447867-13447947 0.00075 32_[+1]_40 chrX:9347767-9347847 0.00089 71_[+1]_1 chrI:14845636-14845716 0.00098 41_[+1]_31 chrIV:10936963-10937043 0.0011 36_[+1]_36 chrII:410996-411076 0.0012 15_[+1]_57 chrI:13663321-13663401 0.0012 60_[+1]_12 chrV:6224694-6224774 0.0013 43_[+1]_29 chrII:14018352-14018432 0.0013 21_[+1]_51 chrIII:8904264-8904344 0.0013 6_[+1]_66 chrII:5593655-5593735 0.0013 22_[+1]_50 chrX:16931500-16931580 0.0013 45_[+1]_27 chrIII:13061213-13061293 0.0013 4_[+1]_68 chrX:14983409-14983489 0.0013 13_[+1]_59 chrV:13107873-13107953 0.0014 8_[+1]_64 chrX:1909551-1909631 0.0015 33_[+1]_39 chrX:7234992-7235072 0.0015 31_[+1]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF BTCTCTBY width=8 seqs=56 chrIII:25636-25716 ( 3) TTCTCTTC 1 chrIII:2804635-2804715 ( 71) TTCTCTTC 1 chrX:14557601-14557681 ( 52) TTCTCTTC 1 chrI:8426861-8426941 ( 72) GTCTCTTC 1 chrIII:7217321-7217401 ( 50) GTCTCTTC 1 chrII:13195329-13195409 ( 71) GTCTCTCC 1 chrV:14366669-14366749 ( 7) GTCTCTTC 1 chrIV:14033644-14033724 ( 15) GTCTCTTC 1 chrIV:5594045-5594125 ( 69) GTCTCTTC 1 chrIV:9538359-9538439 ( 54) GTCTCTTC 1 chrIII:8417606-8417686 ( 51) TTCTCTGC 1 chrX:5812109-5812189 ( 3) TTCTCTGC 1 chrV:18723770-18723850 ( 5) TTCTCTGC 1 chrX:949586-949666 ( 68) CTCTCTCC 1 chrX:10901192-10901272 ( 36) CTCTCTTC 1 chrV:1471207-1471287 ( 59) CTCTCTTC 1 chrII:7838804-7838884 ( 22) TTCTCTCT 1 chrII:7887456-7887536 ( 10) TTCTCTCT 1 chrV:18079307-18079387 ( 56) GTCTCTCT 1 chrV:8001044-8001124 ( 45) TTCTCTGT 1 chrX:7823185-7823265 ( 19) GTCTCTGT 1 chrIII:8447129-8447209 ( 52) TTCTCTAC 1 chrIII:8658559-8658639 ( 15) TTCTCTCG 1 chrI:7492029-7492109 ( 36) CTCTCTCT 1 chrIII:4552048-4552128 ( 64) CTCTCTTT 1 chrV:8828-8908 ( 2) CTCTCTCT 1 chrIV:14032953-14033033 ( 8) CTCTCTCT 1 chrII:11464650-11464730 ( 47) TTCTCACC 1 chrIV:3161026-3161106 ( 70) CTCTCTCT 1 chrI:10539293-10539373 ( 31) GTCTCTAC 1 chrIII:4223848-4223928 ( 49) CTCTCTGT 1 chrIV:6879077-6879157 ( 12) TTCTCAGC 1 chrI:8409929-8410009 ( 64) TTCTCAGC 1 chrII:8787510-8787590 ( 30) TTCTCAGC 1 chrV:14200261-14200341 ( 20) CTCTCTCG 1 chrI:13337228-13337308 ( 40) GTCTCGTC 1 chrI:7396604-7396684 ( 25) CTCTCAGC 1 chrI:7321587-7321667 ( 39) TTCTCTAT 1 chrI:12675370-12675450 ( 53) TTCTCACT 1 chrII:5046404-5046484 ( 3) TTCTCATT 1 chrII:13447867-13447947 ( 33) TTCTCAGT 1 chrX:9347767-9347847 ( 72) TTCTCATG 1 chrI:14845636-14845716 ( 42) GTCTCTAG 1 chrIV:10936963-10937043 ( 37) CTCTCATG 1 chrII:410996-411076 ( 16) TTCTCGCG 1 chrI:13663321-13663401 ( 61) TTCCCTCC 1 chrV:6224694-6224774 ( 44) GTCTCGTG 1 chrII:14018352-14018432 ( 22) GTCTCGAC 1 chrIII:8904264-8904344 ( 7) GTCTCGAC 1 chrII:5593655-5593735 ( 23) GTCCCTTC 1 chrX:16931500-16931580 ( 46) TTCTCTCA 1 chrIII:13061213-13061293 ( 5) TTCTCTTA 1 chrX:14983409-14983489 ( 14) CTCTCAGG 1 chrV:13107873-13107953 ( 9) TTCTCAAT 1 chrX:1909551-1909631 ( 34) GTCCCTGC 1 chrX:7234992-7235072 ( 32) GTCTCGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7373 bayes= 8.25837 E= 8.9e-010 -1245 4 52 72 -1245 -1245 -1245 189 -1245 214 -1245 -1245 -1245 -208 -1245 181 -1245 214 -1245 -1245 -38 -1245 -106 133 -116 34 16 33 -297 119 -48 8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 56 E= 8.9e-010 0.000000 0.232143 0.321429 0.446429 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.053571 0.000000 0.946429 0.000000 1.000000 0.000000 0.000000 0.214286 0.000000 0.107143 0.678571 0.125000 0.285714 0.250000 0.339286 0.035714 0.517857 0.160714 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTCTCTBY MEME-1 regular expression -------------------------------------------------------------------------------- [TGC]TCTC[TA][TCG][CT] -------------------------------------------------------------------------------- Time 2.18 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGAVRVA MEME-2 width = 8 sites = 38 llr = 280 E-value = 1.8e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:a4526 pos.-specific C ::::3:42 probability G a:a:2542 matrix T :::::::: bits 2.2 * * 1.9 **** 1.7 **** 1.5 **** Relative 1.3 **** Entropy 1.1 **** * (10.6 bits) 0.9 **** * 0.6 **** *** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAGAAAGA consensus CGCC sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:6224694-6224774 58 2.80e-05 CGTGACTAGA GAGACGGA GACGCAGACA chrIII:8658559-8658639 41 9.11e-05 ATGACGAGAA GAGACGCA GAACATTCAA chrIII:3677521-3677601 70 9.11e-05 CCagagatga gagacgca gag chrIV:15472525-15472605 58 9.11e-05 TAGAGAGTAC GAGACGCA GAAATCGTTG chrX:1093246-1093326 21 9.11e-05 AGAGGGCATA GAGAAAGA AGTGACAGCT chrII:5593655-5593735 70 9.11e-05 ACTTGGCCCT GAGAAAGA ATA chrIII:13061213-13061293 48 9.11e-05 AAATGATAGA GAGACAGA GAGCGCATTA chrX:1479296-1479376 47 9.11e-05 GGAGAAGCTA GAGACGCA GACTTCGCGG chrX:7234992-7235072 44 9.11e-05 CTCGGGAATT GAGAAAGA GCATGAGGTC chrX:8724061-8724141 22 9.11e-05 TTGAAAGATA GAGAAGCA GCCGACGAGG chrX:535975-536055 55 9.11e-05 AGAGAACTGG GAGACGCA GGAGGGCAGT chrIV:7815901-7815981 59 9.11e-05 GGAATTTTTA GAGACGCA AGAGATACGT chrIV:4033692-4033772 5 9.11e-05 TGAA GAGACGCA AAGATAGTGA chrI:5140475-5140555 21 9.11e-05 GAAAGACGGA GAGAAAGA GATGGAACGT chrX:10901192-10901272 2 1.26e-04 T GAGACACA CAACTCTATT chrX:9347767-9347847 41 1.26e-04 GTCGTCATCT GAGAAACA TCAACAAACA chrX:7823185-7823265 72 1.67e-04 CTCGCACATT GAGAGAGA T chrV:18723770-18723850 70 1.67e-04 ggaggtcaga gagagaga gag chrV:18079307-18079387 19 2.40e-04 ATGAGATGAA GAGACGGC AGACAACGAG chrI:6745493-6745573 5 2.40e-04 CAAC GAGACGAA GAAACAAAGA chrIV:5594045-5594125 57 2.40e-04 ATGTTGACAA GAGAAGAA AATCGTCTCT chrV:10871619-10871699 73 3.57e-04 GGGGAGGCGA GAGAAAAA chrX:949586-949666 27 3.57e-04 ACAAGGGATA GAGAAGGG AGGAAGAGGG chrX:11473523-11473603 41 3.57e-04 gaagaagaag gagaagGG ATAGAAAAAA chrII:14598523-14598603 40 3.57e-04 GTCGGCGCCA GAGACAAA AAGTCATGCT chrI:8409929-8410009 11 4.36e-04 AGTGTTCACA GAGAAACC GACAGGAGGG chrI:12164788-12164868 65 4.36e-04 TTGGAGAAGT GAGAAGCG CAGGCATT chrIII:4223848-4223928 16 4.64e-04 AAGAGTTATG GAGAAACG ATTGGCCCCC chrIII:8447129-8447209 13 4.64e-04 CCGAATATTC GAGAAACG TCTAGTACAT chrX:1909551-1909631 68 5.41e-04 ATTTCACAGG GAGAGGGG AAGAG chrI:8426861-8426941 6 5.41e-04 CAAAC GAGAGAGC ACACATTTTG chrII:9603600-9603680 4 5.41e-04 TTT GAGAGAAA AGACAGTGTA chrIII:86412-86492 64 5.41e-04 ATGCAAAAAC GAGAGAGC GGGAGAGAA chrIV:1105304-1105384 12 5.41e-04 AGCTGTCGTT GAGAGGGG TCACCCCGAG chrV:19897710-19897790 63 5.41e-04 TTGGAGCACA GAGAGAGC ACAACAGGTG chrI:7396604-7396684 14 6.17e-04 TTTTGTGATT GAGAAGAC AGGCTCTCAG chrIV:3161026-3161106 44 6.80e-04 TCGTTCAAAT GAGAAAAC AACACAAGCG chrI:14902827-14902907 31 7.56e-04 AATATTTTTT GAGAGAAC CAATTTATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:6224694-6224774 2.8e-05 57_[+2]_15 chrIII:8658559-8658639 9.1e-05 40_[+2]_32 chrIII:3677521-3677601 9.1e-05 69_[+2]_3 chrIV:15472525-15472605 9.1e-05 57_[+2]_15 chrX:1093246-1093326 9.1e-05 20_[+2]_52 chrII:5593655-5593735 9.1e-05 69_[+2]_3 chrIII:13061213-13061293 9.1e-05 47_[+2]_25 chrX:1479296-1479376 9.1e-05 46_[+2]_26 chrX:7234992-7235072 9.1e-05 43_[+2]_29 chrX:8724061-8724141 9.1e-05 21_[+2]_51 chrX:535975-536055 9.1e-05 54_[+2]_18 chrIV:7815901-7815981 9.1e-05 58_[+2]_14 chrIV:4033692-4033772 9.1e-05 4_[+2]_68 chrI:5140475-5140555 9.1e-05 20_[+2]_52 chrX:10901192-10901272 0.00013 1_[+2]_71 chrX:9347767-9347847 0.00013 40_[+2]_32 chrX:7823185-7823265 0.00017 71_[+2]_1 chrV:18723770-18723850 0.00017 69_[+2]_3 chrV:18079307-18079387 0.00024 18_[+2]_54 chrI:6745493-6745573 0.00024 4_[+2]_68 chrIV:5594045-5594125 0.00024 56_[+2]_16 chrV:10871619-10871699 0.00036 72_[+2] chrX:949586-949666 0.00036 26_[+2]_46 chrX:11473523-11473603 0.00036 40_[+2]_32 chrII:14598523-14598603 0.00036 39_[+2]_33 chrI:8409929-8410009 0.00044 10_[+2]_62 chrI:12164788-12164868 0.00044 64_[+2]_8 chrIII:4223848-4223928 0.00046 15_[+2]_57 chrIII:8447129-8447209 0.00046 12_[+2]_60 chrX:1909551-1909631 0.00054 67_[+2]_5 chrI:8426861-8426941 0.00054 5_[+2]_67 chrII:9603600-9603680 0.00054 3_[+2]_69 chrIII:86412-86492 0.00054 63_[+2]_9 chrIV:1105304-1105384 0.00054 11_[+2]_61 chrV:19897710-19897790 0.00054 62_[+2]_10 chrI:7396604-7396684 0.00062 13_[+2]_59 chrIV:3161026-3161106 0.00068 43_[+2]_29 chrI:14902827-14902907 0.00076 30_[+2]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGAVRVA width=8 seqs=38 chrV:6224694-6224774 ( 58) GAGACGGA 1 chrIII:8658559-8658639 ( 41) GAGACGCA 1 chrIII:3677521-3677601 ( 70) GAGACGCA 1 chrIV:15472525-15472605 ( 58) GAGACGCA 1 chrX:1093246-1093326 ( 21) GAGAAAGA 1 chrII:5593655-5593735 ( 70) GAGAAAGA 1 chrIII:13061213-13061293 ( 48) GAGACAGA 1 chrX:1479296-1479376 ( 47) GAGACGCA 1 chrX:7234992-7235072 ( 44) GAGAAAGA 1 chrX:8724061-8724141 ( 22) GAGAAGCA 1 chrX:535975-536055 ( 55) GAGACGCA 1 chrIV:7815901-7815981 ( 59) GAGACGCA 1 chrIV:4033692-4033772 ( 5) GAGACGCA 1 chrI:5140475-5140555 ( 21) GAGAAAGA 1 chrX:10901192-10901272 ( 2) GAGACACA 1 chrX:9347767-9347847 ( 41) GAGAAACA 1 chrX:7823185-7823265 ( 72) GAGAGAGA 1 chrV:18723770-18723850 ( 70) GAGAGAGA 1 chrV:18079307-18079387 ( 19) GAGACGGC 1 chrI:6745493-6745573 ( 5) GAGACGAA 1 chrIV:5594045-5594125 ( 57) GAGAAGAA 1 chrV:10871619-10871699 ( 73) GAGAAAAA 1 chrX:949586-949666 ( 27) GAGAAGGG 1 chrX:11473523-11473603 ( 41) GAGAAGGG 1 chrII:14598523-14598603 ( 40) GAGACAAA 1 chrI:8409929-8410009 ( 11) GAGAAACC 1 chrI:12164788-12164868 ( 65) GAGAAGCG 1 chrIII:4223848-4223928 ( 16) GAGAAACG 1 chrIII:8447129-8447209 ( 13) GAGAAACG 1 chrX:1909551-1909631 ( 68) GAGAGGGG 1 chrI:8426861-8426941 ( 6) GAGAGAGC 1 chrII:9603600-9603680 ( 4) GAGAGAAA 1 chrIII:86412-86492 ( 64) GAGAGAGC 1 chrIV:1105304-1105384 ( 12) GAGAGGGG 1 chrV:19897710-19897790 ( 63) GAGAGAGC 1 chrI:7396604-7396684 ( 14) GAGAAGAC 1 chrIV:3161026-3161106 ( 44) GAGAAAAC 1 chrI:14902827-14902907 ( 31) GAGAGAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7373 bayes= 9.03794 E= 1.8e-005 -1189 -1189 216 -1189 184 -1189 -1189 -1189 -1189 -1189 216 -1189 184 -1189 -1189 -1189 59 60 8 -1189 91 -1189 108 -1189 -41 70 91 -1189 111 -10 -28 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.8e-005 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.421053 0.342105 0.236842 0.000000 0.526316 0.000000 0.473684 0.000000 0.210526 0.368421 0.421053 0.000000 0.605263 0.210526 0.184211 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAVRVA MEME-2 regular expression -------------------------------------------------------------------------------- GAGA[ACG][AG][GCA][AC] -------------------------------------------------------------------------------- Time 3.19 secs. ******************************************************************************** ******************************************************************************** MOTIF TTGTTTWC MEME-3 width = 8 sites = 14 llr = 130 E-value = 2.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 Description -------------------------------------------------------------------------------- Simplified A 2:::::5: pos.-specific C 1::::::a probability G ::a::::: matrix T 6a:aaa5: bits 2.2 * * 1.9 ***** * 1.7 ***** * 1.5 ***** * Relative 1.3 ***** * Entropy 1.1 ***** * (13.3 bits) 0.9 ******* 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTGTTTAC consensus A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:7492029-7492109 50 4.00e-05 CTCTCACTTG TTGTTTTC GTTGAATGTG chrX:5812109-5812189 50 4.00e-05 CGCTGCCTCG TTGTTTAC CGGGTTTATC chrV:8828-8908 19 4.00e-05 tcactTTGCC TTGTTTTC CCTGCCCATC chrII:11464650-11464730 17 4.00e-05 tgtctgcgtC TTGTTTTC CCTCACATCT chrII:13195329-13195409 24 4.00e-05 CTTTTGTCTC TTGTTTAC ACGTCTGTTG chrX:14983409-14983489 45 4.00e-05 CCCCCTTCTT TTGTTTAC GTGCTGACGT chrX:9347767-9347847 15 4.00e-05 TACTGCATCG TTGTTTAC TGGACTCTGT chrII:5092562-5092642 21 4.00e-05 TCTGAGGCGC TTGTTTAC ATGAGCCAGA chrX:16391227-16391307 36 4.00e-05 atgaGCCAAT TTGTTTAC AGGCATCTGA chrV:18079307-18079387 44 8.14e-05 GAGAGGTTCC ATGTTTTC TCTCGTCTCT chrIV:10936963-10937043 61 8.14e-05 GAACTCAATT ATGTTTAC GTCTCAAAAT chrI:14845636-14845716 26 8.14e-05 CAGGTTGTTG ATGTTTTC GAGACGATGT chrII:14018352-14018432 66 1.15e-04 GAAACCTGTC CTGTTTTC ATCCTCA chrIII:7217321-7217401 18 1.15e-04 AAAAAGCCAA CTGTTTTC TGTTTCTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:7492029-7492109 4e-05 49_[+3]_23 chrX:5812109-5812189 4e-05 49_[+3]_23 chrV:8828-8908 4e-05 18_[+3]_54 chrII:11464650-11464730 4e-05 16_[+3]_56 chrII:13195329-13195409 4e-05 23_[+3]_49 chrX:14983409-14983489 4e-05 44_[+3]_28 chrX:9347767-9347847 4e-05 14_[+3]_58 chrII:5092562-5092642 4e-05 20_[+3]_52 chrX:16391227-16391307 4e-05 35_[+3]_37 chrV:18079307-18079387 8.1e-05 43_[+3]_29 chrIV:10936963-10937043 8.1e-05 60_[+3]_12 chrI:14845636-14845716 8.1e-05 25_[+3]_47 chrII:14018352-14018432 0.00011 65_[+3]_7 chrIII:7217321-7217401 0.00011 17_[+3]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTGTTTWC width=8 seqs=14 chrI:7492029-7492109 ( 50) TTGTTTTC 1 chrX:5812109-5812189 ( 50) TTGTTTAC 1 chrV:8828-8908 ( 19) TTGTTTTC 1 chrII:11464650-11464730 ( 17) TTGTTTTC 1 chrII:13195329-13195409 ( 24) TTGTTTAC 1 chrX:14983409-14983489 ( 45) TTGTTTAC 1 chrX:9347767-9347847 ( 15) TTGTTTAC 1 chrII:5092562-5092642 ( 21) TTGTTTAC 1 chrX:16391227-16391307 ( 36) TTGTTTAC 1 chrV:18079307-18079387 ( 44) ATGTTTTC 1 chrIV:10936963-10937043 ( 61) ATGTTTAC 1 chrI:14845636-14845716 ( 26) ATGTTTTC 1 chrII:14018352-14018432 ( 66) CTGTTTTC 1 chrIII:7217321-7217401 ( 18) CTGTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7373 bayes= 9.6446 E= 2.3e-001 -38 -66 -1045 125 -1045 -1045 -1045 189 -1045 -1045 216 -1045 -1045 -1045 -1045 189 -1045 -1045 -1045 189 -1045 -1045 -1045 189 84 -1045 -1045 89 -1045 214 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 2.3e-001 0.214286 0.142857 0.000000 0.642857 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTTTWC MEME-3 regular expression -------------------------------------------------------------------------------- [TA]TGTTT[AT]C -------------------------------------------------------------------------------- Time 4.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GAAGARGA MEME-4 width = 8 sites = 19 llr = 155 E-value = 4.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 Description -------------------------------------------------------------------------------- Simplified A :86:95:9 pos.-specific C ::1:11:: probability G a22a:4a1 matrix T ::1::::: bits 2.2 * * * 1.9 * * * 1.7 * * * 1.5 * ** * Relative 1.3 * ** ** Entropy 1.1 ** ** ** (11.7 bits) 0.9 ** ** ** 0.6 ** ***** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAGAAGA consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:6224694-6224774 6 3.48e-05 AATTA GAAGAGGA GAGAGAATAG chrX:11473523-11473603 7 3.48e-05 aaagaa gaagaaga agaaggagcc chrX:10901192-10901272 71 3.48e-05 TGTTGAGTAT GAAGAAGA AA chrX:8724061-8724141 42 3.48e-05 CGACGAGGAA GAAGAAGA CAACAAACAA chrI:5140475-5140555 73 3.48e-05 GCAAGAAGGA GAAGAAGA chrX:16391227-16391307 1 3.48e-05 . gaagaaga atccgaagat chrIII:3677521-3677601 2 9.05e-05 A GAGGAAGA GACGGGGGCT chrV:18723770-18723850 55 9.05e-05 CTTACTCGTT Ggagagga ggtcagagag chrII:12102575-12102655 19 9.05e-05 TTGCAACGGG GAGGAGGA GGAGGGACAC chrIV:7815901-7815981 4 9.05e-05 GGC GGAGAAGA CCCCGTGCAA chrV:5917874-5917954 19 1.19e-04 CGGTCGTGTG GACGAGGA AGCAAATGAG chrV:10871619-10871699 54 1.52e-04 AAAGGATATC GATGAGGA GGGGGAGGCG chrIII:12583574-12583654 28 1.52e-04 ACATTGGAGA GATGAAGA GATTTAGACA chrX:949586-949666 37 1.80e-04 GAGAAGGGAG GAAGAGGG GTTTATGGGT chrI:8426861-8426941 23 1.80e-04 CACACATTTT GAAGAGGG TGGAAACAAC chrIII:86412-86492 40 1.96e-04 ATTCGAAAGC GAAGACGA GAGAGCATGC chrX:535975-536055 25 2.18e-04 TGGTGAAACG GGGGAAGA CATTGATGAC chrI:8409929-8410009 34 2.40e-04 GAGGGCATTG GGCGAGGA GCTGTGTGCG chrIV:6879077-6879157 51 2.69e-04 CAATTCACGT GAAGCAGA GCATGGGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:6224694-6224774 3.5e-05 5_[+4]_67 chrX:11473523-11473603 3.5e-05 6_[+4]_66 chrX:10901192-10901272 3.5e-05 70_[+4]_2 chrX:8724061-8724141 3.5e-05 41_[+4]_31 chrI:5140475-5140555 3.5e-05 72_[+4] chrX:16391227-16391307 3.5e-05 [+4]_72 chrIII:3677521-3677601 9.1e-05 1_[+4]_71 chrV:18723770-18723850 9.1e-05 54_[+4]_18 chrII:12102575-12102655 9.1e-05 18_[+4]_54 chrIV:7815901-7815981 9.1e-05 3_[+4]_69 chrV:5917874-5917954 0.00012 18_[+4]_54 chrV:10871619-10871699 0.00015 53_[+4]_19 chrIII:12583574-12583654 0.00015 27_[+4]_45 chrX:949586-949666 0.00018 36_[+4]_36 chrI:8426861-8426941 0.00018 22_[+4]_50 chrIII:86412-86492 0.0002 39_[+4]_33 chrX:535975-536055 0.00022 24_[+4]_48 chrI:8409929-8410009 0.00024 33_[+4]_39 chrIV:6879077-6879157 0.00027 50_[+4]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAAGARGA width=8 seqs=19 chrV:6224694-6224774 ( 6) GAAGAGGA 1 chrX:11473523-11473603 ( 7) GAAGAAGA 1 chrX:10901192-10901272 ( 71) GAAGAAGA 1 chrX:8724061-8724141 ( 42) GAAGAAGA 1 chrI:5140475-5140555 ( 73) GAAGAAGA 1 chrX:16391227-16391307 ( 1) GAAGAAGA 1 chrIII:3677521-3677601 ( 2) GAGGAAGA 1 chrV:18723770-18723850 ( 55) GGAGAGGA 1 chrII:12102575-12102655 ( 19) GAGGAGGA 1 chrIV:7815901-7815981 ( 4) GGAGAAGA 1 chrV:5917874-5917954 ( 19) GACGAGGA 1 chrV:10871619-10871699 ( 54) GATGAGGA 1 chrIII:12583574-12583654 ( 28) GATGAAGA 1 chrX:949586-949666 ( 37) GAAGAGGG 1 chrI:8426861-8426941 ( 23) GAAGAGGG 1 chrIII:86412-86492 ( 40) GAAGACGA 1 chrX:535975-536055 ( 25) GGGGAAGA 1 chrI:8409929-8410009 ( 34) GGCGAGGA 1 chrIV:6879077-6879157 ( 51) GAAGCAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7373 bayes= 10.414 E= 4.4e+002 -1089 -1089 216 -1089 150 -1089 -9 -1089 118 -110 -50 -136 -1089 -1089 216 -1089 176 -210 -1089 -1089 91 -210 91 -1089 -1089 -1089 216 -1089 168 -1089 -109 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.4e+002 0.000000 0.000000 1.000000 0.000000 0.789474 0.000000 0.210526 0.000000 0.631579 0.105263 0.157895 0.105263 0.000000 0.000000 1.000000 0.000000 0.947368 0.052632 0.000000 0.000000 0.526316 0.052632 0.421053 0.000000 0.000000 0.000000 1.000000 0.000000 0.894737 0.000000 0.105263 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGARGA MEME-4 regular expression -------------------------------------------------------------------------------- G[AG]AGA[AG]GA -------------------------------------------------------------------------------- Time 5.17 secs. ******************************************************************************** ******************************************************************************** MOTIF CDCAMACA MEME-5 width = 8 sites = 29 llr = 211 E-value = 9.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :2:73a1a pos.-specific C a1a16:9: probability G :2::1::: matrix T :4:2:::: bits 2.2 * 1.9 * * * 1.7 * * * * 1.5 * * *** Relative 1.3 * * *** Entropy 1.1 * * *** (10.5 bits) 0.9 * * *** 0.6 * ****** 0.4 * ****** 0.2 * ****** 0.0 -------- Multilevel CTCACACA consensus A A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:3677521-3677601 18 1.55e-05 GAGACGGGGG CTCACACA CACACACACG chrII:7887456-7887536 52 1.55e-05 CGTCTCATCG CTCACACA ATTTCTCGGG chrIII:8417606-8417686 27 2.83e-05 TTCAAGAAAG CGCACACA CCCTCGTTCA chrIV:5607480-5607560 17 4.43e-05 AAGGGGTACA CACACACA CACATTCATA chrV:1471207-1471287 22 4.43e-05 ATTCTCTGca cacacaca cacacacaaa chrII:13447867-13447947 18 4.43e-05 CATACACGAA CACACACA AACAAGATTC chrX:7823185-7823265 46 6.35e-05 TATCTGCTCG CTCAAACA CACGCGCTCT chrIV:8431889-8431969 41 6.35e-05 AAATCTGGAA CTCAAACA AACCGTCTTT chrIV:1105304-1105384 46 6.35e-05 CATCGGGGAG CTCAAACA TCTAAACAAT chrII:5593655-5593735 40 7.64e-05 CCCGATCTCT CCCACACA GAATGATGAT chrI:5140475-5140555 50 7.64e-05 AAGCAAGGGA CCCACACA ACTATGCAAG chrX:9441644-9441724 37 9.23e-05 AGTCGTCGTA CGCAAACA CAACGACGCA chrI:12164788-12164868 7 9.23e-05 CGCCCT CGCAAACA TAGTAAACAA chrIV:6879077-6879157 31 1.27e-04 CGACTGCTCC CTCTCACA GGCAATTCAC chrV:18723770-18723850 17 1.27e-04 CTCTGCCACT CTCTCACA TTTCTGCACT chrII:14018352-14018432 6 1.58e-04 ACGTC CTCAGACA GCCAAGGTGT chrX:8206051-8206131 37 1.86e-04 TTGAGTCACA CACTCACA GAGAGATGTG chrV:6224694-6224774 68 2.49e-04 GAGACGGAGA CGCAGACA CCAAC chrI:14845636-14845716 1 2.49e-04 . CGCAGACA CATTGAGCAG chrI:7492029-7492109 12 2.77e-04 AGATCGTCGT CCCTCACA TCAATTCTGC chrX:1909551-1909631 22 3.58e-04 GCAAGCGACA CGCCCACA TGCCGTCCCT chrIII:4552048-4552128 3 4.08e-04 CA CTCAAAAA CTCAAACTAG chrV:14200261-14200341 12 4.35e-04 GCATCTTCGT CTCGCACA CTCTCTCGCC chrII:11464650-11464730 35 5.24e-04 CCTCACATCT CTCACCCA ACACTTCTCA chrIV:6881315-6881395 28 5.72e-04 GAGACTTCAA CACAAAAA GCGCCCAAAA chrI:14902827-14902907 63 6.35e-04 ACAAATGTCC CACCAACA GGTCCATGTA chrIII:7217321-7217401 5 7.08e-04 AAAT CCCAAAAA GCCAACTGTT chrI:12675370-12675450 24 8.67e-04 AAGTCGAGAA CACTCAAA TCCCTTTCCA chrIII:3560472-3560552 22 9.37e-04 CAGGAAGTGG GTCAAACA GGTCAACCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:3677521-3677601 1.5e-05 17_[+5]_55 chrII:7887456-7887536 1.5e-05 51_[+5]_21 chrIII:8417606-8417686 2.8e-05 26_[+5]_46 chrIV:5607480-5607560 4.4e-05 16_[+5]_56 chrV:1471207-1471287 4.4e-05 21_[+5]_51 chrII:13447867-13447947 4.4e-05 17_[+5]_55 chrX:7823185-7823265 6.3e-05 45_[+5]_27 chrIV:8431889-8431969 6.3e-05 40_[+5]_32 chrIV:1105304-1105384 6.3e-05 45_[+5]_27 chrII:5593655-5593735 7.6e-05 39_[+5]_33 chrI:5140475-5140555 7.6e-05 49_[+5]_23 chrX:9441644-9441724 9.2e-05 36_[+5]_36 chrI:12164788-12164868 9.2e-05 6_[+5]_66 chrIV:6879077-6879157 0.00013 30_[+5]_42 chrV:18723770-18723850 0.00013 16_[+5]_56 chrII:14018352-14018432 0.00016 5_[+5]_67 chrX:8206051-8206131 0.00019 36_[+5]_36 chrV:6224694-6224774 0.00025 67_[+5]_5 chrI:14845636-14845716 0.00025 [+5]_72 chrI:7492029-7492109 0.00028 11_[+5]_61 chrX:1909551-1909631 0.00036 21_[+5]_51 chrIII:4552048-4552128 0.00041 2_[+5]_70 chrV:14200261-14200341 0.00044 11_[+5]_61 chrII:11464650-11464730 0.00052 34_[+5]_38 chrIV:6881315-6881395 0.00057 27_[+5]_45 chrI:14902827-14902907 0.00063 62_[+5]_10 chrIII:7217321-7217401 0.00071 4_[+5]_68 chrI:12675370-12675450 0.00087 23_[+5]_49 chrIII:3560472-3560552 0.00094 21_[+5]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CDCAMACA width=8 seqs=29 chrIII:3677521-3677601 ( 18) CTCACACA 1 chrII:7887456-7887536 ( 52) CTCACACA 1 chrIII:8417606-8417686 ( 27) CGCACACA 1 chrIV:5607480-5607560 ( 17) CACACACA 1 chrV:1471207-1471287 ( 22) CACACACA 1 chrII:13447867-13447947 ( 18) CACACACA 1 chrX:7823185-7823265 ( 46) CTCAAACA 1 chrIV:8431889-8431969 ( 41) CTCAAACA 1 chrIV:1105304-1105384 ( 46) CTCAAACA 1 chrII:5593655-5593735 ( 40) CCCACACA 1 chrI:5140475-5140555 ( 50) CCCACACA 1 chrX:9441644-9441724 ( 37) CGCAAACA 1 chrI:12164788-12164868 ( 7) CGCAAACA 1 chrIV:6879077-6879157 ( 31) CTCTCACA 1 chrV:18723770-18723850 ( 17) CTCTCACA 1 chrII:14018352-14018432 ( 6) CTCAGACA 1 chrX:8206051-8206131 ( 37) CACTCACA 1 chrV:6224694-6224774 ( 68) CGCAGACA 1 chrI:14845636-14845716 ( 1) CGCAGACA 1 chrI:7492029-7492109 ( 12) CCCTCACA 1 chrX:1909551-1909631 ( 22) CGCCCACA 1 chrIII:4552048-4552128 ( 3) CTCAAAAA 1 chrV:14200261-14200341 ( 12) CTCGCACA 1 chrII:11464650-11464730 ( 35) CTCACCCA 1 chrIV:6881315-6881395 ( 28) CACAAAAA 1 chrI:14902827-14902907 ( 63) CACCAACA 1 chrIII:7217321-7217401 ( 5) CCCAAAAA 1 chrI:12675370-12675450 ( 24) CACTCAAA 1 chrIII:3560472-3560552 ( 22) GTCAAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7373 bayes= 8.62716 E= 9.5e+002 -1150 209 -270 -1150 -21 -71 -11 61 -1150 214 -1150 -1150 137 -171 -270 -65 30 128 -111 -1150 179 -271 -1150 -1150 -102 193 -1150 -1150 184 -1150 -1150 -1150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 9.5e+002 0.000000 0.965517 0.034483 0.000000 0.241379 0.137931 0.206897 0.413793 0.000000 1.000000 0.000000 0.000000 0.724138 0.068966 0.034483 0.172414 0.344828 0.551724 0.103448 0.000000 0.965517 0.034483 0.000000 0.000000 0.137931 0.862069 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDCAMACA MEME-5 regular expression -------------------------------------------------------------------------------- C[TAG]CA[CA]ACA -------------------------------------------------------------------------------- Time 8.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:5046404-5046484 4.12e-01 80 chrIV:9538359-9538439 6.07e-02 53_[+1(5.57e-05)]_19 chrI:12164788-12164868 1.66e-02 6_[+5(9.23e-05)]_66 chrII:7887456-7887536 1.81e-03 51_[+5(1.55e-05)]_21 chrX:16391227-16391307 2.19e-03 [+4(3.48e-05)]_27_[+3(4.00e-05)]_37 chrV:5330077-5330157 7.78e-01 80 chrII:5092562-5092642 4.33e-02 20_[+3(4.00e-05)]_52 chrIV:5594045-5594125 1.65e-03 68_[+1(5.57e-05)]_4 chrI:5140475-5140555 3.37e-04 8_[+2(9.11e-05)]_4_[+2(9.11e-05)]_\ 21_[+5(7.64e-05)]_15_[+4(3.48e-05)] chrI:12548183-12548263 9.14e-01 80 chrI:7396604-7396684 2.48e-02 80 chrIII:3560472-3560552 2.39e-01 80 chrIV:4033692-4033772 9.44e-03 4_[+2(9.11e-05)]_68 chrX:3257994-3258074 5.12e-01 80 chrV:19897710-19897790 2.40e-01 80 chrII:7838804-7838884 9.34e-02 80 chrIV:1105304-1105384 1.88e-02 45_[+5(6.35e-05)]_27 chrX:9347767-9347847 9.59e-04 14_[+3(4.00e-05)]_58 chrII:14598523-14598603 7.63e-03 80 chrIV:7815901-7815981 1.99e-02 3_[+4(9.05e-05)]_47_[+2(9.11e-05)]_\ 14 chrI:9375291-9375371 2.10e-01 80 chrX:14557601-14557681 3.79e-02 51_[+1(3.04e-05)]_21 chrI:14902827-14902907 1.24e-02 80 chrX:14983409-14983489 3.92e-02 44_[+3(4.00e-05)]_28 chrI:14845636-14845716 1.48e-03 25_[+3(8.14e-05)]_47 chrIII:2804635-2804715 3.72e-02 54_[+1(5.57e-05)]_8_[+1(3.04e-05)]_\ 2 chrX:8206051-8206131 4.22e-02 80 chrIV:14033644-14033724 4.67e-02 14_[+1(5.57e-05)]_58 chrV:20646387-20646467 8.19e-01 80 chrV:14366669-14366749 1.72e-01 6_[+1(5.57e-05)]_66 chrV:14393229-14393309 7.43e-01 80 chrII:13195329-13195409 9.74e-03 23_[+3(4.00e-05)]_39_[+1(5.57e-05)]_\ 2 chrIII:12583574-12583654 6.15e-02 80 chrII:13447867-13447947 8.95e-04 17_[+5(4.43e-05)]_55 chrX:535975-536055 2.15e-02 54_[+2(9.11e-05)]_18 chrIII:7217321-7217401 8.24e-04 49_[+1(5.57e-05)]_23 chrV:8001044-8001124 2.71e-01 80 chrX:8724061-8724141 1.38e-03 21_[+2(9.11e-05)]_9_[+4(3.48e-05)]_\ 34 chrI:6745493-6745573 2.34e-02 80 chrI:10539293-10539373 3.71e-01 80 chrI:12675370-12675450 8.11e-03 80 chrIV:3161026-3161106 4.38e-02 80 chrII:11464650-11464730 2.37e-03 16_[+3(4.00e-05)]_56 chrIV:5530667-5530747 4.05e-01 80 chrV:13107873-13107953 2.98e-01 80 chrIII:86412-86492 1.68e-02 80 chrI:7321587-7321667 2.83e-01 80 chrV:14200261-14200341 9.42e-02 80 chrX:7234992-7235072 4.80e-02 43_[+2(9.11e-05)]_29 chrI:7867730-7867810 6.21e-01 80 chrIV:11744507-11744587 4.42e-01 80 chrII:9603600-9603680 1.98e-01 80 chrII:8787510-8787590 2.63e-01 80 chrII:12102575-12102655 5.93e-02 18_[+4(9.05e-05)]_54 chrIV:6881315-6881395 2.37e-01 80 chrV:1471207-1471287 1.16e-02 19_[+5(4.43e-05)]_[+5(4.43e-05)]_45 chrX:1479296-1479376 4.58e-02 46_[+2(9.11e-05)]_26 chrV:18712415-18712495 6.68e-01 80 chrIV:14032953-14033033 3.26e-01 80 chrX:10901192-10901272 1.44e-05 70_[+4(3.48e-05)]_2 chrI:8409929-8410009 2.97e-03 80 chrIV:5209569-5209649 1.23e-01 80 chrIII:13061213-13061293 8.58e-03 47_[+2(9.11e-05)]_25 chrIV:8431889-8431969 9.00e-02 40_[+5(6.35e-05)]_32 chrI:8426861-8426941 1.36e-03 71_[+1(5.57e-05)]_1 chrV:18723770-18723850 2.18e-05 4_[+1(6.94e-05)]_42_[+4(9.05e-05)]_\ 18 chrIV:6879077-6879157 6.78e-04 80 chrV:9212748-9212828 5.48e-01 80 chrX:16931500-16931580 1.96e-01 80 chrV:5917874-5917954 3.72e-02 80 chrII:5593655-5593735 1.37e-03 39_[+5(7.64e-05)]_22_[+2(9.11e-05)]_\ 3 chrX:11473523-11473603 2.74e-02 3_[+4(3.48e-05)]_19_[+4(3.48e-05)]_\ 42 chrIII:25636-25716 7.49e-02 2_[+1(3.04e-05)]_44_[+1(6.94e-05)]_\ 18 chrII:9062033-9062113 8.66e-01 80 chrIII:8904264-8904344 6.85e-01 80 chrV:8828-8908 7.99e-03 18_[+3(4.00e-05)]_54 chrX:5812109-5812189 4.95e-04 2_[+1(6.94e-05)]_39_[+3(4.00e-05)]_\ 23 chrX:1909551-1909631 1.62e-03 80 chrX:1093246-1093326 1.10e-01 20_[+2(9.11e-05)]_52 chrV:12814546-12814626 4.40e-01 80 chrIV:10936963-10937043 1.67e-02 60_[+3(8.14e-05)]_12 chrIV:5607480-5607560 1.69e-02 14_[+5(4.43e-05)]_58 chrII:14018352-14018432 4.76e-03 80 chrIII:4552048-4552128 3.77e-02 80 chrIV:15472525-15472605 6.64e-03 57_[+2(9.11e-05)]_15 chrI:7492029-7492109 1.70e-03 49_[+3(4.00e-05)]_23 chrX:13969454-13969534 5.32e-01 80 chrV:18079307-18079387 1.52e-05 43_[+3(8.14e-05)]_29 chrX:9441644-9441724 2.52e-01 36_[+5(9.23e-05)]_36 chrI:13337228-13337308 7.82e-02 80 chrIII:3677521-3677601 5.89e-05 1_[+4(9.05e-05)]_8_[+5(1.55e-05)]_\ [+5(4.43e-05)]_36_[+2(9.11e-05)]_3 chrI:13663321-13663401 3.36e-01 80 chrIII:8658559-8658639 1.77e-04 40_[+2(9.11e-05)]_32 chrIII:8447129-8447209 6.10e-02 80 chrII:410996-411076 1.23e-01 80 chrX:949586-949666 1.80e-03 33_[+4(9.05e-05)]_39 chrX:7823185-7823265 1.07e-03 45_[+5(6.35e-05)]_27 chrIII:8417606-8417686 2.45e-03 26_[+5(2.83e-05)]_16_[+1(6.94e-05)]_\ 22 chrV:6224694-6224774 5.32e-05 5_[+4(3.48e-05)]_44_[+2(2.80e-05)]_\ 15 chrIII:4223848-4223928 5.22e-02 80 chrV:10871619-10871699 8.37e-02 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************