******************************************************************************** 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/mbf-1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:584-664 1.0000 80 chrM:13143-13223 1.0000 80 chrM:6730-6810 1.0000 80 chrM:7666-7746 1.0000 80 chrM:3908-3988 1.0000 80 chrM:11701-11781 1.0000 80 chrM:164-244 1.0000 80 chrM:5559-5639 1.0000 80 chrM:9608-9688 1.0000 80 chrM:11470-11550 1.0000 80 chrM:3706-3786 1.0000 80 chrM:9392-9472 1.0000 80 chrM:2457-2537 1.0000 80 chrIII:13779016-13779096 1.0000 80 chrX:16664501-16664581 1.0000 80 chrM:12344-12424 1.0000 80 chrM:13611-13691 1.0000 80 chrM:11238-11318 1.0000 80 chrIII:5506649-5506729 1.0000 80 chrX:4208659-4208739 1.0000 80 chrM:12633-12713 1.0000 80 chrM:1309-1389 1.0000 80 chrM:4719-4799 1.0000 80 chrM:2234-2314 1.0000 80 chrV:18708720-18708800 1.0000 80 chrX:11603355-11603435 1.0000 80 chrIV:8431113-8431193 1.0000 80 chrM:1087-1167 1.0000 80 chrI:6441575-6441655 1.0000 80 chrX:15983404-15983484 1.0000 80 chrV:20790706-20790786 1.0000 80 chrX:13514529-13514609 1.0000 80 chrX:16675175-16675255 1.0000 80 chrIII:12369745-12369825 1.0000 80 chrIV:2711077-2711157 1.0000 80 chrX:7181683-7181763 1.0000 80 chrX:11603636-11603716 1.0000 80 chrX:2364859-2364939 1.0000 80 chrI:5372660-5372740 1.0000 80 chrX:4395589-4395669 1.0000 80 chrIV:8432072-8432152 1.0000 80 chrI:12532371-12532451 1.0000 80 chrX:1389571-1389651 1.0000 80 chrX:1909500-1909580 1.0000 80 chrI:6493959-6494039 1.0000 80 chrIV:17281554-17281634 1.0000 80 chrI:1273704-1273784 1.0000 80 chrIV:6376746-6376826 1.0000 80 chrV:11764540-11764620 1.0000 80 chrX:12363153-12363233 1.0000 80 chrIII:1419849-1419929 1.0000 80 chrX:16056523-16056603 1.0000 80 chrII:8185129-8185209 1.0000 80 chrX:8036333-8036413 1.0000 80 chrIII:4963071-4963151 1.0000 80 chrX:1344982-1345062 1.0000 80 chrIII:3456400-3456480 1.0000 80 chrIV:15472524-15472604 1.0000 80 chrX:16682102-16682182 1.0000 80 chrII:10542239-10542319 1.0000 80 chrV:12343684-12343764 1.0000 80 chrI:7079545-7079625 1.0000 80 chrIII:4378822-4378902 1.0000 80 chrI:12995772-12995852 1.0000 80 chrI:12966919-12966999 1.0000 80 chrIII:8767990-8768070 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_mbf-1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/mbf-1.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= 66 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= 5280 N= 66 sample: seed= 0 hsfrac= 0 searchsize= 5280 norand= no csites= 1000 Letter frequencies in dataset: A 0.338 C 0.144 G 0.158 T 0.36 Background letter frequencies (from file dataset with add-one prior applied): A 0.338 C 0.144 G 0.158 T 0.36 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF SCYKGCGC MEME-1 width = 8 sites = 13 llr = 123 E-value = 7.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::21:::1 pos.-specific C 48511a18 probability G 61:39:91 matrix T :245:::: bits 2.8 * 2.5 * 2.2 *** 2.0 **** Relative 1.7 ** **** Entropy 1.4 ** **** (13.6 bits) 1.1 ** **** 0.8 ** **** 0.6 *** **** 0.3 ******** 0.0 -------- Multilevel GCCTGCGC consensus C TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:16682102-16682182 70 1.68e-06 ATTTGATGTT CCCTGCGC GAT chrX:8036333-8036413 68 1.68e-06 CGACATACGT CCCTGCGC GATAA chrX:2364859-2364939 40 1.68e-06 TACTATATAT CCCTGCGC TTAATTATTT chrI:12995772-12995852 37 2.35e-06 TTCCAAAAAG GCTGGCGC ACTTCTCGTG chrV:12343684-12343764 71 4.12e-06 CAGCAAACAT GCTTGCGC AC chrX:16056523-16056603 10 2.42e-05 TGTGCAACT CCCTGCGG CAAATTTGAA chrI:12966919-12966999 35 2.61e-05 ACATCTAACT CTCTGCGC GGCAATTCAA chrIV:6376746-6376826 44 2.95e-05 AACCAAATTT GGTGGCGC CATGGCCAAA chrIV:15472524-15472604 73 3.45e-05 CGCAGAAATC GTTGGCGC chrX:1909500-1909580 31 3.45e-05 GAGCAGAAGA GCCCGCCC CTGCATTCTT chrIII:3456400-3456480 27 5.31e-05 TTTGCGCGAT GCAAGCGC GCTCCACCGC chrIII:4963071-4963151 43 6.64e-05 AATAGCGCAA GCAGCCGC TTCTTTCAAA chrII:10542239-10542319 44 7.64e-05 ATGAGGCGTA GCTTGCGA TTCCACAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:16682102-16682182 1.7e-06 69_[+1]_3 chrX:8036333-8036413 1.7e-06 67_[+1]_5 chrX:2364859-2364939 1.7e-06 39_[+1]_33 chrI:12995772-12995852 2.3e-06 36_[+1]_36 chrV:12343684-12343764 4.1e-06 70_[+1]_2 chrX:16056523-16056603 2.4e-05 9_[+1]_63 chrI:12966919-12966999 2.6e-05 34_[+1]_38 chrIV:6376746-6376826 3e-05 43_[+1]_29 chrIV:15472524-15472604 3.5e-05 72_[+1] chrX:1909500-1909580 3.5e-05 30_[+1]_42 chrIII:3456400-3456480 5.3e-05 26_[+1]_46 chrIII:4963071-4963151 6.6e-05 42_[+1]_30 chrII:10542239-10542319 7.6e-05 43_[+1]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SCYKGCGC width=8 seqs=13 chrX:16682102-16682182 ( 70) CCCTGCGC 1 chrX:8036333-8036413 ( 68) CCCTGCGC 1 chrX:2364859-2364939 ( 40) CCCTGCGC 1 chrI:12995772-12995852 ( 37) GCTGGCGC 1 chrV:12343684-12343764 ( 71) GCTTGCGC 1 chrX:16056523-16056603 ( 10) CCCTGCGG 1 chrI:12966919-12966999 ( 35) CTCTGCGC 1 chrIV:6376746-6376826 ( 44) GGTGGCGC 1 chrIV:15472524-15472604 ( 73) GTTGGCGC 1 chrX:1909500-1909580 ( 31) GCCCGCCC 1 chrIII:3456400-3456480 ( 27) GCAAGCGC 1 chrIII:4963071-4963151 ( 43) GCAGCCGC 1 chrII:10542239-10542319 ( 44) GCTTGCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4818 bayes= 9.69643 E= 7.6e-004 -1035 141 196 -1035 -1035 241 -104 -122 -114 168 -1035 10 -213 -91 96 58 -1035 -91 255 -1035 -1035 279 -1035 -1035 -1035 -91 255 -1035 -213 255 -104 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 7.6e-004 0.000000 0.384615 0.615385 0.000000 0.000000 0.769231 0.076923 0.153846 0.153846 0.461538 0.000000 0.384615 0.076923 0.076923 0.307692 0.538462 0.000000 0.076923 0.923077 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.076923 0.923077 0.000000 0.076923 0.846154 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCYKGCGC MEME-1 regular expression -------------------------------------------------------------------------------- [GC]C[CT][TG]GCGC -------------------------------------------------------------------------------- Time 0.83 secs. ******************************************************************************** ******************************************************************************** MOTIF CGMGCAGR MEME-2 width = 8 sites = 9 llr = 90 E-value = 5.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2:3::6:4 pos.-specific C 8:6:9::: probability G :a:a12a6 matrix T ::1::2:: bits 2.8 * * * 2.5 * * * 2.2 * ** * 2.0 * ** * Relative 1.7 ** ** * Entropy 1.4 ** ** * (14.4 bits) 1.1 ** ** ** 0.8 ***** ** 0.6 ***** ** 0.3 ******** 0.0 -------- Multilevel CGCGCAGG consensus A A G A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:1344982-1345062 73 6.29e-07 CAATGTCATT CGCGCAGG chrX:13514529-13514609 28 6.29e-07 ATACCTTTAT CGCGCAGG GATATTGAAA chrI:12532371-12532451 45 3.57e-06 ATTTTTGTTT CGCGCGGA TTTGCCGCAA chrX:4395589-4395669 25 8.64e-06 AAAGGAGACA AGCGCAGG GAGAACTGGT chrX:1909500-1909580 20 1.51e-05 AATTGAAGCT CGAGCAGA AGAGCCCGCC chrIII:4963071-4963151 61 2.73e-05 TTCTTTCAAA AGCGCGGA TTTTCAAAAT chrX:16664501-16664581 68 3.13e-05 AAAAATCTCT CGAGCTGA AGAGA chrI:12995772-12995852 3 4.31e-05 CT CGTGCTGG CGCATTTGCC chrIII:12369745-12369825 49 4.31e-05 TTCTTGGGAT CGAGGAGG ATTTTTTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1344982-1345062 6.3e-07 72_[+2] chrX:13514529-13514609 6.3e-07 27_[+2]_45 chrI:12532371-12532451 3.6e-06 44_[+2]_28 chrX:4395589-4395669 8.6e-06 24_[+2]_48 chrX:1909500-1909580 1.5e-05 19_[+2]_53 chrIII:4963071-4963151 2.7e-05 60_[+2]_12 chrX:16664501-16664581 3.1e-05 67_[+2]_5 chrI:12995772-12995852 4.3e-05 2_[+2]_70 chrIII:12369745-12369825 4.3e-05 48_[+2]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGMGCAGR width=8 seqs=9 chrX:1344982-1345062 ( 73) CGCGCAGG 1 chrX:13514529-13514609 ( 28) CGCGCAGG 1 chrI:12532371-12532451 ( 45) CGCGCGGA 1 chrX:4395589-4395669 ( 25) AGCGCAGG 1 chrX:1909500-1909580 ( 20) CGAGCAGA 1 chrIII:4963071-4963151 ( 61) AGCGCGGA 1 chrX:16664501-16664581 ( 68) CGAGCTGA 1 chrI:12995772-12995852 ( 3) CGTGCTGG 1 chrIII:12369745-12369825 ( 49) CGAGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4818 bayes= 9.91079 E= 5.9e-001 -60 243 -982 -982 -982 -982 266 -982 -2 194 -982 -169 -982 -982 266 -982 -982 262 -51 -982 72 -982 49 -69 -982 -982 266 -982 39 -982 181 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 5.9e-001 0.222222 0.777778 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.555556 0.000000 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.555556 0.000000 0.222222 0.222222 0.000000 0.000000 1.000000 0.000000 0.444444 0.000000 0.555556 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGMGCAGR MEME-2 regular expression -------------------------------------------------------------------------------- [CA]G[CA]GC[AGT]G[GA] -------------------------------------------------------------------------------- Time 1.59 secs. ******************************************************************************** ******************************************************************************** MOTIF STCCACCK MEME-3 width = 8 sites = 3 llr = 36 E-value = 6.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C 7:aa:aa: probability G 3::::::7 matrix T :a:::::3 bits 2.8 ** ** 2.5 ** ** 2.2 ** ** 2.0 * ** ** Relative 1.7 * ***** Entropy 1.4 ******** (17.4 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTCCACCG consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:3456400-3456480 36 1.19e-06 TGCAAGCGCG CTCCACCG CACGTGTGTA chrX:7181683-7181763 58 2.50e-06 ATACGACACT GTCCACCG ATTTACCCAG chrX:11603355-11603435 47 5.21e-06 TAATCCAGGA CTCCACCT TTTCTTATTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:3456400-3456480 1.2e-06 35_[+3]_37 chrX:7181683-7181763 2.5e-06 57_[+3]_15 chrX:11603355-11603435 5.2e-06 46_[+3]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STCCACCK width=8 seqs=3 chrIII:3456400-3456480 ( 36) CTCCACCG 1 chrX:7181683-7181763 ( 58) GTCCACCG 1 chrX:11603355-11603435 ( 47) CTCCACCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4818 bayes= 11.0961 E= 6.0e+002 -823 220 108 -823 -823 -823 -823 147 -823 279 -823 -823 -823 279 -823 -823 156 -823 -823 -823 -823 279 -823 -823 -823 279 -823 -823 -823 -823 207 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 6.0e+002 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STCCACCK MEME-3 regular expression -------------------------------------------------------------------------------- [CG]TCCACC[GT] -------------------------------------------------------------------------------- Time 2.28 secs. ******************************************************************************** ******************************************************************************** MOTIF CSACACRY MEME-4 width = 8 sites = 7 llr = 69 E-value = 2.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:a:4: pos.-specific C a3:9:a:4 probability G :6:1::6: matrix T :1:::::6 bits 2.8 * * 2.5 * * 2.2 * * * 2.0 * * * Relative 1.7 * **** Entropy 1.4 * **** (14.3 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CGACACGT consensus C AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:1909500-1909580 68 1.23e-06 GGGTAGCAAG CGACACGC CCACA chrI:7079545-7079625 5 5.41e-06 AAGT CGACACGT TGGTTTTATA chrX:1389571-1389651 53 1.08e-05 TTTTATATAT CCACACGT TTCAAAAATA chrIV:6376746-6376826 3 1.98e-05 GA CGACACAT TGCGGACTTG chrIV:15472524-15472604 58 2.11e-05 GTAGAGAGTA CGAGACGC AGAAATCGTT chrI:6441575-6441655 67 2.99e-05 CACGAAAGAA CCACACAT TCATTT chrX:4208659-4208739 3 5.34e-05 TT CTACACAC TTTCCATTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1909500-1909580 1.2e-06 67_[+4]_5 chrI:7079545-7079625 5.4e-06 4_[+4]_68 chrX:1389571-1389651 1.1e-05 52_[+4]_20 chrIV:6376746-6376826 2e-05 2_[+4]_70 chrIV:15472524-15472604 2.1e-05 57_[+4]_15 chrI:6441575-6441655 3e-05 66_[+4]_6 chrX:4208659-4208739 5.3e-05 2_[+4]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CSACACRY width=8 seqs=7 chrX:1909500-1909580 ( 68) CGACACGC 1 chrI:7079545-7079625 ( 5) CGACACGT 1 chrX:1389571-1389651 ( 53) CCACACGT 1 chrIV:6376746-6376826 ( 3) CGACACAT 1 chrIV:15472524-15472604 ( 58) CGAGACGC 1 chrI:6441575-6441655 ( 67) CCACACAT 1 chrX:4208659-4208739 ( 3) CTACACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4818 bayes= 10.6484 E= 2.5e+002 -945 279 -945 -945 -945 98 185 -133 156 -945 -945 -945 -945 257 -14 -945 156 -945 -945 -945 -945 279 -945 -945 34 -945 185 -945 -945 157 -945 67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.5e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.571429 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 0.571429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSACACRY MEME-4 regular expression -------------------------------------------------------------------------------- C[GC]ACAC[GA][TC] -------------------------------------------------------------------------------- Time 2.97 secs. ******************************************************************************** ******************************************************************************** MOTIF GSGYCAGS MEME-5 width = 8 sites = 3 llr = 36 E-value = 6.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C :7:7a::7 probability G a3a:::a3 matrix T :::3:::: bits 2.8 * * * * 2.5 * * * * 2.2 * * * * 2.0 *** * ** Relative 1.7 *** **** Entropy 1.4 ******** (17.4 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCGCCAGC consensus G T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:4963071-4963151 20 5.73e-07 ATCGCGAAGT GCGCCAGC ACGAGAATAG chrV:12343684-12343764 57 3.26e-06 TTGTACAATC GCGTCAGC AAACATGCTT chrM:4719-4799 32 3.95e-06 CATTTTAATG GGGCCAGG TTATTTTTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:4963071-4963151 5.7e-07 19_[+5]_53 chrV:12343684-12343764 3.3e-06 56_[+5]_16 chrM:4719-4799 4e-06 31_[+5]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GSGYCAGS width=8 seqs=3 chrIII:4963071-4963151 ( 20) GCGCCAGC 1 chrV:12343684-12343764 ( 57) GCGTCAGC 1 chrM:4719-4799 ( 32) GGGCCAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4818 bayes= 11.0961 E= 6.4e+002 -823 -823 266 -823 -823 220 108 -823 -823 -823 266 -823 -823 220 -823 -11 -823 279 -823 -823 156 -823 -823 -823 -823 -823 266 -823 -823 220 108 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 6.4e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSGYCAGS MEME-5 regular expression -------------------------------------------------------------------------------- G[CG]G[CT]CAG[CG] -------------------------------------------------------------------------------- Time 3.66 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:584-664 1.00e+00 80 chrM:13143-13223 1.37e-01 80 chrM:6730-6810 1.00e+00 80 chrM:7666-7746 8.40e-01 80 chrM:3908-3988 1.00e+00 80 chrM:11701-11781 7.19e-01 80 chrM:164-244 9.84e-01 80 chrM:5559-5639 9.48e-01 80 chrM:9608-9688 9.98e-01 80 chrM:11470-11550 9.36e-01 80 chrM:3706-3786 9.96e-01 80 chrM:9392-9472 1.00e+00 80 chrM:2457-2537 1.00e+00 80 chrIII:13779016-13779096 9.16e-01 80 chrX:16664501-16664581 2.20e-03 67_[+2(3.13e-05)]_5 chrM:12344-12424 9.87e-01 80 chrM:13611-13691 1.00e+00 80 chrM:11238-11318 9.72e-01 80 chrIII:5506649-5506729 9.95e-01 80 chrX:4208659-4208739 9.13e-04 2_[+4(5.34e-05)]_70 chrM:12633-12713 9.25e-01 80 chrM:1309-1389 9.05e-01 80 chrM:4719-4799 5.88e-02 31_[+5(3.95e-06)]_41 chrM:2234-2314 9.94e-01 80 chrV:18708720-18708800 6.88e-01 80 chrX:11603355-11603435 4.62e-03 46_[+3(5.21e-06)]_26 chrIV:8431113-8431193 1.49e-01 80 chrM:1087-1167 1.00e+00 80 chrI:6441575-6441655 1.60e-01 66_[+4(2.99e-05)]_6 chrX:15983404-15983484 7.53e-01 80 chrV:20790706-20790786 9.83e-01 80 chrX:13514529-13514609 1.38e-04 27_[+2(6.29e-07)]_45 chrX:16675175-16675255 5.87e-01 80 chrIII:12369745-12369825 1.55e-01 48_[+2(4.31e-05)]_24 chrIV:2711077-2711157 4.55e-01 80 chrX:7181683-7181763 6.36e-03 57_[+3(2.50e-06)]_15 chrX:11603636-11603716 2.69e-01 80 chrX:2364859-2364939 2.68e-03 39_[+1(1.68e-06)]_33 chrI:5372660-5372740 4.82e-01 80 chrX:4395589-4395669 1.36e-03 24_[+2(8.64e-06)]_48 chrIV:8432072-8432152 8.11e-01 80 chrI:12532371-12532451 6.20e-03 44_[+2(3.57e-06)]_28 chrX:1389571-1389651 5.82e-03 52_[+4(1.08e-05)]_20 chrX:1909500-1909580 3.31e-08 19_[+2(1.51e-05)]_3_[+1(3.45e-05)]_\ 29_[+4(1.23e-06)]_5 chrI:6493959-6494039 3.81e-01 80 chrIV:17281554-17281634 3.57e-01 80 chrI:1273704-1273784 4.10e-02 80 chrIV:6376746-6376826 9.58e-06 2_[+4(1.98e-05)]_33_[+1(2.95e-05)]_\ 29 chrV:11764540-11764620 7.01e-01 80 chrX:12363153-12363233 2.48e-01 80 chrIII:1419849-1419929 9.59e-01 80 chrX:16056523-16056603 3.72e-03 9_[+1(2.42e-05)]_63 chrII:8185129-8185209 6.50e-02 80 chrX:8036333-8036413 4.08e-05 67_[+1(1.68e-06)]_5 chrIII:4963071-4963151 7.88e-07 19_[+5(5.73e-07)]_9_[+5(3.25e-05)]_\ 16_[+2(2.73e-05)]_12 chrX:1344982-1345062 5.63e-05 72_[+2(6.29e-07)] chrIII:3456400-3456480 1.03e-06 26_[+1(5.31e-05)]_1_[+3(1.19e-06)]_\ 37 chrIV:15472524-15472604 2.55e-04 57_[+4(2.11e-05)]_7_[+1(3.45e-05)] chrX:16682102-16682182 3.86e-04 69_[+1(1.68e-06)]_3 chrII:10542239-10542319 3.54e-02 43_[+1(7.64e-05)]_29 chrV:12343684-12343764 2.79e-05 36_[+5(8.86e-05)]_12_[+5(3.26e-06)]_\ 6_[+1(4.12e-06)]_2 chrI:7079545-7079625 6.22e-03 4_[+4(5.41e-06)]_68 chrIII:4378822-4378902 8.99e-02 80 chrI:12995772-12995852 3.86e-05 5_[+1(2.35e-06)]_23_[+1(2.35e-06)]_\ 36 chrI:12966919-12966999 4.22e-03 34_[+1(2.61e-05)]_38 chrIII:8767990-8768070 7.07e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n11.farnam.hpc.yale.internal ********************************************************************************