******************************************************************************** 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-84.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:4844763-4844843 1.0000 80 chrV:14686342-14686422 1.0000 80 chrV:15887230-15887310 1.0000 80 chrX:6735616-6735696 1.0000 80 chrV:727023-727103 1.0000 80 chrII:7345824-7345904 1.0000 80 chrIV:5656969-5657049 1.0000 80 chrII:12239513-12239593 1.0000 80 chrIV:4468873-4468953 1.0000 80 chrIII:8658544-8658624 1.0000 80 chrIII:11915918-11915998 1.0000 80 chrII:4999216-4999296 1.0000 80 chrIV:8431765-8431845 1.0000 80 chrII:5544259-5544339 1.0000 80 chrI:881553-881633 1.0000 80 chrII:11729079-11729159 1.0000 80 chrIV:3694313-3694393 1.0000 80 chrIII:13464870-13464950 1.0000 80 chrV:724079-724159 1.0000 80 chrIII:3954742-3954822 1.0000 80 chrIII:12549891-12549971 1.0000 80 chrI:110224-110304 1.0000 80 chrV:1195627-1195707 1.0000 80 chrIII:3456377-3456457 1.0000 80 chrIII:7729926-7730006 1.0000 80 chrX:15616425-15616505 1.0000 80 chrV:5592483-5592563 1.0000 80 chrII:9937737-9937817 1.0000 80 chrX:7823279-7823359 1.0000 80 chrV:6224713-6224793 1.0000 80 chrX:12363181-12363261 1.0000 80 chrI:535458-535538 1.0000 80 chrI:17012-17092 1.0000 80 chrIII:5706385-5706465 1.0000 80 chrI:7872315-7872395 1.0000 80 chrI:7492997-7493077 1.0000 80 chrX:16931387-16931467 1.0000 80 chrII:2974025-2974105 1.0000 80 chrII:10785234-10785314 1.0000 80 chrX:2591750-2591830 1.0000 80 chrX:4145445-4145525 1.0000 80 chrX:1345058-1345138 1.0000 80 chrX:15354234-15354314 1.0000 80 chrIV:6585726-6585806 1.0000 80 chrI:13663285-13663365 1.0000 80 chrII:12042243-12042323 1.0000 80 chrIII:6972031-6972111 1.0000 80 chrI:8133880-8133960 1.0000 80 chrI:3824298-3824378 1.0000 80 chrII:1320593-1320673 1.0000 80 chrV:9546950-9547030 1.0000 80 chrX:4142184-4142264 1.0000 80 chrX:806629-806709 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-84/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-84.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= 53 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= 4240 N= 53 sample: seed= 0 hsfrac= 0 searchsize= 4240 norand= no csites= 1000 Letter frequencies in dataset: A 0.283 C 0.217 G 0.213 T 0.287 Background letter frequencies (from file dataset with add-one prior applied): A 0.283 C 0.217 G 0.213 T 0.287 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GMGAGCGC MEME-1 width = 8 sites = 14 llr = 114 E-value = 4.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :629:1:3 pos.-specific C :3:1:617 probability G a:8:a:9: matrix T :1:::2:: bits 2.2 * * 2.0 * * 1.8 * * * 1.6 * ** * Relative 1.3 * *** ** Entropy 1.1 * *** ** (11.8 bits) 0.9 * *** ** 0.7 * ****** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAGAGCGC consensus CA T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:2974025-2974105 58 7.76e-06 GGAAGAGTGA GAGAGCGC GAGAGAACAC chrV:4844763-4844843 64 7.76e-06 TGCAGTTTGA GAGAGCGC AGTCACATG chrIII:7729926-7730006 23 1.37e-05 TCGCGCGCGC GCGAGCGC CCTCCTCCGC chrI:13663285-13663365 34 2.38e-05 GAGAGACGAC GAGAGCGA CTTGCTTGCG chrX:7823279-7823359 8 4.20e-05 AAACTCG GAGAGTGC GAGACGGTTA chrV:727023-727103 65 4.20e-05 TGACCGAGAA GTGAGCGC TGCGATGA chrI:17012-17092 19 7.81e-05 TCAGCACGCG GAGAGAGC CACGAGAAAT chrIII:3456377-3456457 50 8.60e-05 TTTGCGCGAT GCAAGCGC GCTCCACCGC chrX:2591750-2591830 44 1.36e-04 GCCCTCTTTT GCGCGCGc acacacacac chrI:881553-881633 64 1.60e-04 ctgtgagtct gtgagtgC AGTGTACAA chrII:10785234-10785314 50 2.13e-04 CACGGTACGT GAAAGTGC GTCACGGTGT chrIII:12549891-12549971 43 2.13e-04 ACTTGCGAGA GAGAGAGA GATAGTACAT chrII:5544259-5544339 72 2.34e-04 ATTTTTCGAG GCAAGCGA T chrI:7492997-7493077 62 3.10e-04 CGTATTGCTT GAGAGCCA ACTTGTTACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:2974025-2974105 7.8e-06 57_[+1]_15 chrV:4844763-4844843 7.8e-06 63_[+1]_9 chrIII:7729926-7730006 1.4e-05 22_[+1]_50 chrI:13663285-13663365 2.4e-05 33_[+1]_39 chrX:7823279-7823359 4.2e-05 7_[+1]_65 chrV:727023-727103 4.2e-05 64_[+1]_8 chrI:17012-17092 7.8e-05 18_[+1]_54 chrIII:3456377-3456457 8.6e-05 49_[+1]_23 chrX:2591750-2591830 0.00014 43_[+1]_29 chrI:881553-881633 0.00016 63_[+1]_9 chrII:10785234-10785314 0.00021 49_[+1]_23 chrIII:12549891-12549971 0.00021 42_[+1]_30 chrII:5544259-5544339 0.00023 71_[+1]_1 chrI:7492997-7493077 0.00031 61_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GMGAGCGC width=8 seqs=14 chrII:2974025-2974105 ( 58) GAGAGCGC 1 chrV:4844763-4844843 ( 64) GAGAGCGC 1 chrIII:7729926-7730006 ( 23) GCGAGCGC 1 chrI:13663285-13663365 ( 34) GAGAGCGA 1 chrX:7823279-7823359 ( 8) GAGAGTGC 1 chrV:727023-727103 ( 65) GTGAGCGC 1 chrI:17012-17092 ( 19) GAGAGAGC 1 chrIII:3456377-3456457 ( 50) GCAAGCGC 1 chrX:2591750-2591830 ( 44) GCGCGCGC 1 chrI:881553-881633 ( 64) GTGAGTGC 1 chrII:10785234-10785314 ( 50) GAAAGTGC 1 chrIII:12549891-12549971 ( 43) GAGAGAGA 1 chrII:5544259-5544339 ( 72) GCAAGCGA 1 chrI:7492997-7493077 ( 62) GAGAGCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3869 bayes= 9.33054 E= 4.7e+001 -1045 -1045 223 -1045 101 40 -1045 -101 -40 -1045 188 -1045 171 -160 -1045 -1045 -1045 -1045 223 -1045 -99 157 -1045 -42 -1045 -160 212 -1045 1 172 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 4.7e+001 0.000000 0.000000 1.000000 0.000000 0.571429 0.285714 0.000000 0.142857 0.214286 0.000000 0.785714 0.000000 0.928571 0.071429 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.642857 0.000000 0.214286 0.000000 0.071429 0.928571 0.000000 0.285714 0.714286 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMGAGCGC MEME-1 regular expression -------------------------------------------------------------------------------- G[AC][GA]AG[CT]G[CA] -------------------------------------------------------------------------------- Time 1.15 secs. ******************************************************************************** ******************************************************************************** MOTIF ATTTTTCA MEME-2 width = 8 sites = 22 llr = 161 E-value = 3.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 71:::::9 pos.-specific C ::3:::7: probability G 3:11:::1 matrix T :969aa3: bits 2.2 2.0 1.8 ** 1.6 ** Relative 1.3 * ***** Entropy 1.1 ** ***** (10.5 bits) 0.9 ** ***** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ATTTTTCA consensus G C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:17012-17092 67 3.38e-05 GCGGAAAATC ATTTTTCA AAATAA chrI:535458-535538 67 3.38e-05 ATTTTGCGCG ATTTTTCA ACTATT chrII:12042243-12042323 29 5.93e-05 GTCTCGTCTA GTTTTTCA GCGGGTTTCT chrI:7872315-7872395 43 5.93e-05 CTTGTTTGTT GTTTTTCA GCCAAAATCC chrIV:3694313-3694393 72 5.93e-05 GCCGGATCCT GTTTTTCA A chrX:6735616-6735696 26 5.93e-05 AGTTATTTCT GTTTTTCA ATTGGAAAAC chrV:5592483-5592563 70 8.49e-05 AGCGAACCTG ATCTTTCA TTA chrI:8133880-8133960 38 1.04e-04 GGTTGGTGGT GTCTTTCA CTTTCACTAC chrIV:4468873-4468953 48 1.04e-04 CTCTTATTCA GTCTTTCA TGTAGTTGCT chrII:11729079-11729159 48 1.49e-04 TTTTTATAAT ATTTTTTA ACAAAAAATC chrX:4142184-4142264 3 1.99e-04 AA ATGTTTCA ACACCTTATT chrV:9546950-9547030 26 1.99e-04 TTTTTGACGT ATTTTTCG TTTCTGTGAC chrII:5544259-5544339 62 1.99e-04 GTGTTCAGAC ATTTTTCG AGGCAAGCGA chrIV:6585726-6585806 25 3.00e-04 GTTGCTGAAA ATCTTTTA TGAACAACTG chrX:12363181-12363261 29 3.00e-04 TCTTTTCCCT ATCTTTTA TCGGTAGGGC chrV:724079-724159 46 3.00e-04 CTGCAGCTTC AATTTTCA CGCTTCATAG chrV:14686342-14686422 57 3.26e-04 CTGGAAAGGA ATTGTTCA TCAAAATTAC chrII:4999216-4999296 18 4.59e-04 GAGTTATTTT AACTTTCA TTTCTTATAA chrV:1195627-1195707 15 4.78e-04 CGGCACTATG GTTGTTCA CGAGGAGGAG chrII:9937737-9937817 5 5.97e-04 TCGC ATTTTTTG TCTACTTTTT chrX:15616425-15616505 63 5.97e-04 ATGCATCGAA ATGTTTTA ATGACCAAAG chrIII:13464870-13464950 64 6.55e-04 GAGTAAGTAT AATTTTTA TTGGAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:17012-17092 3.4e-05 66_[+2]_6 chrI:535458-535538 3.4e-05 66_[+2]_6 chrII:12042243-12042323 5.9e-05 28_[+2]_44 chrI:7872315-7872395 5.9e-05 42_[+2]_30 chrIV:3694313-3694393 5.9e-05 71_[+2]_1 chrX:6735616-6735696 5.9e-05 25_[+2]_47 chrV:5592483-5592563 8.5e-05 69_[+2]_3 chrI:8133880-8133960 0.0001 37_[+2]_35 chrIV:4468873-4468953 0.0001 47_[+2]_25 chrII:11729079-11729159 0.00015 47_[+2]_25 chrX:4142184-4142264 0.0002 2_[+2]_70 chrV:9546950-9547030 0.0002 25_[+2]_47 chrII:5544259-5544339 0.0002 61_[+2]_11 chrIV:6585726-6585806 0.0003 24_[+2]_48 chrX:12363181-12363261 0.0003 28_[+2]_44 chrV:724079-724159 0.0003 45_[+2]_27 chrV:14686342-14686422 0.00033 56_[+2]_16 chrII:4999216-4999296 0.00046 17_[+2]_55 chrV:1195627-1195707 0.00048 14_[+2]_58 chrII:9937737-9937817 0.0006 4_[+2]_68 chrX:15616425-15616505 0.0006 62_[+2]_10 chrIII:13464870-13464950 0.00066 63_[+2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATTTTTCA width=8 seqs=22 chrI:17012-17092 ( 67) ATTTTTCA 1 chrI:535458-535538 ( 67) ATTTTTCA 1 chrII:12042243-12042323 ( 29) GTTTTTCA 1 chrI:7872315-7872395 ( 43) GTTTTTCA 1 chrIV:3694313-3694393 ( 72) GTTTTTCA 1 chrX:6735616-6735696 ( 26) GTTTTTCA 1 chrV:5592483-5592563 ( 70) ATCTTTCA 1 chrI:8133880-8133960 ( 38) GTCTTTCA 1 chrIV:4468873-4468953 ( 48) GTCTTTCA 1 chrII:11729079-11729159 ( 48) ATTTTTTA 1 chrX:4142184-4142264 ( 3) ATGTTTCA 1 chrV:9546950-9547030 ( 26) ATTTTTCG 1 chrII:5544259-5544339 ( 62) ATTTTTCG 1 chrIV:6585726-6585806 ( 25) ATCTTTTA 1 chrX:12363181-12363261 ( 29) ATCTTTTA 1 chrV:724079-724159 ( 46) AATTTTCA 1 chrV:14686342-14686422 ( 57) ATTGTTCA 1 chrII:4999216-4999296 ( 18) AACTTTCA 1 chrV:1195627-1195707 ( 15) GTTGTTCA 1 chrII:9937737-9937817 ( 5) ATTTTTTG 1 chrX:15616425-15616505 ( 63) ATGTTTTA 1 chrIII:13464870-13464950 ( 64) AATTTTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3869 bayes= 7.80698 E= 3.0e+001 127 -1110 58 -1110 -105 -1110 -1110 159 -1110 33 -123 115 -1110 -1110 -123 166 -1110 -1110 -1110 180 -1110 -1110 -1110 180 -1110 174 -1110 -7 161 -1110 -64 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 3.0e+001 0.681818 0.000000 0.318182 0.000000 0.136364 0.000000 0.000000 0.863636 0.000000 0.272727 0.090909 0.636364 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.727273 0.000000 0.272727 0.863636 0.000000 0.136364 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTTTCA MEME-2 regular expression -------------------------------------------------------------------------------- [AG]T[TC]TTT[CT]A -------------------------------------------------------------------------------- Time 1.73 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGACGCA MEME-3 width = 8 sites = 5 llr = 52 E-value = 7.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:a:::a pos.-specific C ::::a2a: probability G a:8::8:: matrix T ::2::::: bits 2.2 * * * 2.0 * * * 1.8 ** ** ** 1.6 ** ***** Relative 1.3 ******** Entropy 1.1 ******** (15.0 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAGACGCA consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:6224713-6224793 45 1.03e-05 TAGAGAGACG GAGACGCA GACACCAACT chrII:9937737-9937817 26 1.03e-05 ACTTTTTATA GAGACGCA GACAGAAAAT chrIII:8658544-8658624 56 1.03e-05 ATGACGAGAA GAGACGCA GAACATTCAA chrIII:5706385-5706465 55 2.08e-05 TCTTCTGTGT GAGACCCA TAGGGGTCAC chrII:1320593-1320673 60 3.47e-05 ACACTATTGT GATACGCA GCCAAACCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:6224713-6224793 1e-05 44_[+3]_28 chrII:9937737-9937817 1e-05 25_[+3]_47 chrIII:8658544-8658624 1e-05 55_[+3]_17 chrIII:5706385-5706465 2.1e-05 54_[+3]_18 chrII:1320593-1320673 3.5e-05 59_[+3]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGACGCA width=8 seqs=5 chrV:6224713-6224793 ( 45) GAGACGCA 1 chrII:9937737-9937817 ( 26) GAGACGCA 1 chrIII:8658544-8658624 ( 56) GAGACGCA 1 chrIII:5706385-5706465 ( 55) GAGACCCA 1 chrII:1320593-1320673 ( 60) GATACGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3869 bayes= 9.02746 E= 7.7e+002 -897 -897 223 -897 182 -897 -897 -897 -897 -897 191 -52 182 -897 -897 -897 -897 220 -897 -897 -897 -12 191 -897 -897 220 -897 -897 182 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 7.7e+002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGACGCA MEME-3 regular expression -------------------------------------------------------------------------------- GA[GT]AC[GC]CA -------------------------------------------------------------------------------- Time 2.33 secs. ******************************************************************************** ******************************************************************************** MOTIF YGGCGCGG MEME-4 width = 8 sites = 4 llr = 44 E-value = 8.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 5::a:a:3 probability G :aa:a:a8 matrix T 5::::::: bits 2.2 ****** 2.0 ****** 1.8 ****** 1.6 ****** Relative 1.3 ******* Entropy 1.1 ******* (15.8 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGGCGCGG consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:15354234-15354314 31 4.48e-06 GCATTCATTG CGGCGCGG TTGCGTCGCG chrI:17012-17092 53 4.48e-06 AGGCTAAATT CGGCGCGG AAAATCATTT chrV:15887230-15887310 39 1.04e-05 CGAGCCTTTC TGGCGCGG AACCTGAAAG chrIV:3694313-3694393 40 2.10e-05 GAGTGGGCCG TGGCGCGC TGACTTTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:15354234-15354314 4.5e-06 30_[+4]_42 chrI:17012-17092 4.5e-06 52_[+4]_20 chrV:15887230-15887310 1e-05 38_[+4]_34 chrIV:3694313-3694393 2.1e-05 39_[+4]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YGGCGCGG width=8 seqs=4 chrX:15354234-15354314 ( 31) CGGCGCGG 1 chrI:17012-17092 ( 53) CGGCGCGG 1 chrV:15887230-15887310 ( 39) TGGCGCGG 1 chrIV:3694313-3694393 ( 40) TGGCGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3869 bayes= 10.6538 E= 8.9e+002 -865 120 -865 80 -865 -865 223 -865 -865 -865 223 -865 -865 220 -865 -865 -865 -865 223 -865 -865 220 -865 -865 -865 -865 223 -865 -865 20 182 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 8.9e+002 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGCGG MEME-4 regular expression -------------------------------------------------------------------------------- [CT]GGCGCG[GC] -------------------------------------------------------------------------------- Time 2.86 secs. ******************************************************************************** ******************************************************************************** MOTIF GYGGTCDC MEME-5 width = 8 sites = 7 llr = 65 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :1::::3: pos.-specific C :3:::a:a probability G a1aa::4: matrix T :4::a:3: bits 2.2 * ** * * 2.0 * ** * * 1.8 * **** * 1.6 * **** * Relative 1.3 * **** * Entropy 1.1 * **** * (13.5 bits) 0.9 * **** * 0.7 * **** * 0.4 * ****** 0.2 ******** 0.0 -------- Multilevel GTGGTCGC consensus C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6735616-6735696 58 7.98e-06 ACAAAAACGC GTGGTCGC AAAGAATTTC chrII:1320593-1320673 8 1.40e-05 CATTTCG GCGGTCGC ATTTGGCTGC chrIII:7729926-7730006 39 1.40e-05 GCCCTCCTCC GCGGTCGC CGACCGCTCG chrII:12042243-12042323 16 3.54e-05 TTTTGGAGAA GTGGTCTC GTCTAGTTTT chrIV:6585726-6585806 42 3.54e-05 ATGAACAACT GTGGTCAC GCGATTTAAA chrIII:5706385-5706465 65 8.12e-05 GAGACCCATA GGGGTCAC ATCGATTT chrI:881553-881633 29 1.02e-04 AAAAATGTAT GAGGTCTC CTGAtgtgtg -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6735616-6735696 8e-06 57_[+5]_15 chrII:1320593-1320673 1.4e-05 7_[+5]_65 chrIII:7729926-7730006 1.4e-05 38_[+5]_34 chrII:12042243-12042323 3.5e-05 15_[+5]_57 chrIV:6585726-6585806 3.5e-05 41_[+5]_31 chrIII:5706385-5706465 8.1e-05 64_[+5]_8 chrI:881553-881633 0.0001 28_[+5]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GYGGTCDC width=8 seqs=7 chrX:6735616-6735696 ( 58) GTGGTCGC 1 chrII:1320593-1320673 ( 8) GCGGTCGC 1 chrIII:7729926-7730006 ( 39) GCGGTCGC 1 chrII:12042243-12042323 ( 16) GTGGTCTC 1 chrIV:6585726-6585806 ( 42) GTGGTCAC 1 chrIII:5706385-5706465 ( 65) GGGGTCAC 1 chrI:881553-881633 ( 29) GAGGTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3869 bayes= 10.3317 E= 1.7e+003 -945 -945 223 -945 -98 40 -57 58 -945 -945 223 -945 -945 -945 223 -945 -945 -945 -945 180 -945 220 -945 -945 1 -945 101 -1 -945 220 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.7e+003 0.000000 0.000000 1.000000 0.000000 0.142857 0.285714 0.142857 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.428571 0.285714 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGTCDC MEME-5 regular expression -------------------------------------------------------------------------------- G[TC]GGTC[GAT]C -------------------------------------------------------------------------------- Time 3.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:4844763-4844843 6.88e-03 63_[+1(7.76e-06)]_9 chrV:14686342-14686422 3.18e-01 80 chrV:15887230-15887310 1.77e-02 38_[+4(1.04e-05)]_34 chrX:6735616-6735696 1.46e-03 25_[+2(5.93e-05)]_24_[+5(7.98e-06)]_\ 15 chrV:727023-727103 9.59e-03 64_[+1(4.20e-05)]_8 chrII:7345824-7345904 6.33e-01 80 chrIV:5656969-5657049 7.70e-01 80 chrII:12239513-12239593 9.88e-01 80 chrIV:4468873-4468953 7.60e-02 80 chrIII:8658544-8658624 4.17e-02 55_[+3(1.03e-05)]_17 chrIII:11915918-11915998 7.42e-01 80 chrII:4999216-4999296 7.30e-01 80 chrIV:8431765-8431845 7.59e-01 80 chrII:5544259-5544339 9.39e-03 80 chrI:881553-881633 3.18e-02 80 chrII:11729079-11729159 1.21e-01 80 chrIV:3694313-3694393 1.79e-03 39_[+4(2.10e-05)]_24_[+2(5.93e-05)]_\ 1 chrIII:13464870-13464950 7.32e-01 80 chrV:724079-724159 2.90e-01 80 chrIII:3954742-3954822 9.90e-01 80 chrIII:12549891-12549971 1.08e-01 80 chrI:110224-110304 6.32e-01 80 chrV:1195627-1195707 2.11e-01 80 chrIII:3456377-3456457 2.39e-02 49_[+1(8.60e-05)]_23 chrIII:7729926-7730006 5.42e-05 22_[+1(1.37e-05)]_8_[+5(1.40e-05)]_\ 34 chrX:15616425-15616505 1.64e-01 80 chrV:5592483-5592563 1.05e-01 69_[+2(8.49e-05)]_3 chrII:9937737-9937817 6.90e-03 25_[+3(1.03e-05)]_47 chrX:7823279-7823359 2.08e-02 7_[+1(4.20e-05)]_65 chrV:6224713-6224793 4.53e-03 44_[+3(1.03e-05)]_28 chrX:12363181-12363261 3.67e-01 80 chrI:535458-535538 2.26e-02 66_[+2(3.38e-05)]_6 chrI:17012-17092 2.22e-06 18_[+1(7.81e-05)]_26_[+4(4.48e-06)]_\ 6_[+2(3.38e-05)]_6 chrIII:5706385-5706465 1.78e-04 54_[+3(2.08e-05)]_2_[+5(8.12e-05)]_\ 8 chrI:7872315-7872395 2.97e-01 42_[+2(5.93e-05)]_30 chrI:7492997-7493077 1.19e-01 80 chrX:16931387-16931467 9.67e-01 80 chrII:2974025-2974105 3.11e-02 57_[+1(7.76e-06)]_15 chrII:10785234-10785314 2.17e-01 80 chrX:2591750-2591830 1.90e-02 80 chrX:4145445-4145525 9.98e-01 80 chrX:1345058-1345138 8.08e-01 80 chrX:15354234-15354314 1.86e-03 30_[+4(4.48e-06)]_42 chrIV:6585726-6585806 1.32e-02 41_[+5(3.54e-05)]_31 chrI:13663285-13663365 3.01e-02 33_[+1(2.38e-05)]_39 chrII:12042243-12042323 3.86e-04 15_[+5(3.54e-05)]_5_[+2(5.93e-05)]_\ 44 chrIII:6972031-6972111 9.57e-01 80 chrI:8133880-8133960 1.11e-01 80 chrI:3824298-3824378 5.40e-01 80 chrII:1320593-1320673 4.22e-05 7_[+5(1.40e-05)]_44_[+3(3.47e-05)]_\ 13 chrV:9546950-9547030 1.33e-01 80 chrX:4142184-4142264 8.77e-02 80 chrX:806629-806709 8.91e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n11.farnam.hpc.yale.internal ********************************************************************************