******************************************************************************** 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/sptf-1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:18714561-18714641 1.0000 80 chrV:19634350-19634430 1.0000 80 chrX:14951104-14951184 1.0000 80 chrIII:1427742-1427822 1.0000 80 chrII:10645974-10646054 1.0000 80 chrV:18722669-18722749 1.0000 80 chrV:18165470-18165550 1.0000 80 chrII:10550510-10550590 1.0000 80 chrV:16634967-16635047 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_sptf-1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/sptf-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= 9 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= 720 N= 9 sample: seed= 0 hsfrac= 0 searchsize= 720 norand= no csites= 1000 Letter frequencies in dataset: A 0.369 C 0.178 G 0.16 T 0.293 Background letter frequencies (from file dataset with add-one prior applied): A 0.369 C 0.178 G 0.16 T 0.293 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTTTTVC MEME-1 width = 8 sites = 9 llr = 68 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::2: pos.-specific C 2::1:22a probability G :2:::24: matrix T 88a9a61: bits 2.6 2.4 * 2.1 * 1.8 * * * Relative 1.6 * * * Entropy 1.3 **** * (10.8 bits) 1.1 ***** * 0.8 ****** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTTTTTGC consensus CG CA sequence GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:18165470-18165550 53 2.79e-05 AGTGGTGCTG TTTTTGGC GTTCTGGAAG chrV:16634967-16635047 62 5.96e-05 GACCAATCAG CTTTTTGC AGAGAGGTGG chrV:18722669-18722749 67 8.50e-05 ATATTCCAAT TTTTTTCC AACACG chrII:10645974-10646054 8 9.70e-05 GAGAAAT TGTTTCGC CTAGAATCAG chrIII:1427742-1427822 60 1.27e-04 TAAAATTCGA TTTTTCCC AATTTTTCAG chrX:14951104-14951184 11 1.85e-04 TAGAAAGGAA TTTTTTAC TAAATACAAA chrV:19634350-19634430 47 1.85e-04 gaaaattgag ttttttac tcaaaaattc chrII:10550510-10550590 9 4.72e-04 GGAGCTTC TGTCTGGC TCCATCTGTT chrV:18714561-18714641 12 5.75e-04 AATTCTTCTT CTTTTTTC TTTTTTTAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:18165470-18165550 2.8e-05 52_[+1]_20 chrV:16634967-16635047 6e-05 61_[+1]_11 chrV:18722669-18722749 8.5e-05 66_[+1]_6 chrII:10645974-10646054 9.7e-05 7_[+1]_65 chrIII:1427742-1427822 0.00013 59_[+1]_13 chrX:14951104-14951184 0.00019 10_[+1]_62 chrV:19634350-19634430 0.00019 46_[+1]_26 chrII:10550510-10550590 0.00047 8_[+1]_64 chrV:18714561-18714641 0.00058 11_[+1]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTTTVC width=8 seqs=9 chrV:18165470-18165550 ( 53) TTTTTGGC 1 chrV:16634967-16635047 ( 62) CTTTTTGC 1 chrV:18722669-18722749 ( 67) TTTTTTCC 1 chrII:10645974-10646054 ( 8) TGTTTCGC 1 chrIII:1427742-1427822 ( 60) TTTTTCCC 1 chrX:14951104-14951184 ( 11) TTTTTTAC 1 chrV:19634350-19634430 ( 47) TTTTTTAC 1 chrII:10550510-10550590 ( 9) TGTCTGGC 1 chrV:18714561-18714641 ( 12) CTTTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 657 bayes= 6.30601 E= 1.6e-001 -982 32 -982 141 -982 -982 47 141 -982 -982 -982 177 -982 -68 -982 160 -982 -982 -982 177 -982 32 47 92 -73 32 147 -140 -982 249 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 1.6e-001 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.000000 0.222222 0.222222 0.555556 0.222222 0.222222 0.444444 0.111111 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTVC MEME-1 regular expression -------------------------------------------------------------------------------- [TC][TG]TTT[TCG][GAC]C -------------------------------------------------------------------------------- Time 1.10 secs. ******************************************************************************** ******************************************************************************** MOTIF ATTTSNGG MEME-2 width = 8 sites = 4 llr = 38 E-value = 3.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A a::::3:: pos.-specific C ::::53:: probability G ::::53aa matrix T :aaa:3:: bits 2.6 ** 2.4 ** 2.1 ** 1.8 *** ** Relative 1.6 **** ** Entropy 1.3 ***** ** (13.7 bits) 1.1 ***** ** 0.8 ***** ** 0.5 ***** ** 0.3 ***** ** 0.0 -------- Multilevel ATTTCAGG consensus GC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:19634350-19634430 69 6.08e-06 aaattccagc atttgggg gaaa chrV:18722669-18722749 4 2.71e-05 ACA ATTTCCGG TCGCTTAATC chrV:18714561-18714641 62 3.83e-05 CTATGTACCG ATTTGTGG TAATAATTAT chrV:18165470-18165550 29 8.03e-05 GTCATCTTCA ATTTCAGG CTCAGAAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:19634350-19634430 6.1e-06 68_[+2]_4 chrV:18722669-18722749 2.7e-05 3_[+2]_69 chrV:18714561-18714641 3.8e-05 61_[+2]_11 chrV:18165470-18165550 8e-05 28_[+2]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATTTSNGG width=8 seqs=4 chrV:19634350-19634430 ( 69) ATTTGGGG 1 chrV:18722669-18722749 ( 4) ATTTCCGG 1 chrV:18714561-18714641 ( 62) ATTTGTGG 1 chrV:18165470-18165550 ( 29) ATTTCAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 657 bayes= 7.35094 E= 3.6e+001 144 -865 -865 -865 -865 -865 -865 177 -865 -865 -865 177 -865 -865 -865 177 -865 149 164 -865 -56 49 64 -23 -865 -865 264 -865 -865 -865 264 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 3.6e+001 1.000000 0.000000 0.000000 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 0.000000 0.500000 0.500000 0.000000 0.250000 0.250000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTSNGG MEME-2 regular expression -------------------------------------------------------------------------------- ATTT[CG][ACGT]GG -------------------------------------------------------------------------------- Time 1.43 secs. ******************************************************************************** ******************************************************************************** MOTIF AGWGGTGS MEME-3 width = 8 sites = 2 llr = 22 E-value = 2.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:5::::: pos.-specific C :::::::5 probability G :a:aa:a5 matrix T ::5::a:: bits 2.6 * ** * 2.4 * ** * 2.1 * ** * 1.8 * **** Relative 1.6 * ***** Entropy 1.3 ** ***** (15.9 bits) 1.1 ** ***** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGAGGTGC consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:18165470-18165550 43 7.02e-06 CAGGCTCAGA AGTGGTGC TGTTTTTGGC chrV:16634967-16635047 72 1.12e-05 CTTTTTGCAG AGAGGTGG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:18165470-18165550 7e-06 42_[+3]_30 chrV:16634967-16635047 1.1e-05 71_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGWGGTGS width=8 seqs=2 chrV:18165470-18165550 ( 43) AGTGGTGC 1 chrV:16634967-16635047 ( 72) AGAGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 657 bayes= 8.35535 E= 2.5e+002 143 -765 -765 -765 -765 -765 264 -765 44 -765 -765 77 -765 -765 264 -765 -765 -765 264 -765 -765 -765 -765 177 -765 -765 264 -765 -765 148 164 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.5e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 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 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGGTGS MEME-3 regular expression -------------------------------------------------------------------------------- AG[AT]GGTG[CG] -------------------------------------------------------------------------------- Time 1.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CGAGACGS MEME-4 width = 8 sites = 4 llr = 37 E-value = 6.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a383:: pos.-specific C a::::8:5 probability G :8:8::a5 matrix T :3::3::: bits 2.6 * 2.4 * * 2.1 * * 1.8 * * Relative 1.6 ** * ** Entropy 1.3 **** *** (13.4 bits) 1.1 **** *** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGAGACGC consensus T ATA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:18165470-18165550 10 8.22e-06 TCCACGTTC CGAGTCGG TGTCATCTTC chrV:16634967-16635047 43 2.17e-05 TTTTTTTAAA CTAGACGC CGACCAATCA chrII:10550510-10550590 57 4.06e-05 GTAGGAATAA CGAAACGG GAAAAATAAC chrII:10645974-10646054 30 4.06e-05 AATCAGTTAC CGAGAAGC TGAACTTGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:18165470-18165550 8.2e-06 9_[+4]_63 chrV:16634967-16635047 2.2e-05 42_[+4]_30 chrII:10550510-10550590 4.1e-05 56_[+4]_16 chrII:10645974-10646054 4.1e-05 29_[+4]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGAGACGS width=8 seqs=4 chrV:18165470-18165550 ( 10) CGAGTCGG 1 chrV:16634967-16635047 ( 43) CTAGACGC 1 chrII:10550510-10550590 ( 57) CGAAACGG 1 chrII:10645974-10646054 ( 30) CGAGAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 657 bayes= 8.09144 E= 6.8e+002 -865 249 -865 -865 -865 -865 222 -23 144 -865 -865 -865 -56 -865 222 -865 102 -865 -865 -23 -56 207 -865 -865 -865 -865 264 -865 -865 149 164 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 6.8e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGACGS MEME-4 regular expression -------------------------------------------------------------------------------- C[GT]A[GA][AT][CA]G[CG] -------------------------------------------------------------------------------- Time 2.08 secs. ******************************************************************************** ******************************************************************************** MOTIF GTTCTGKA MEME-5 width = 8 sites = 2 llr = 22 E-value = 5.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::a pos.-specific C :::a:::: probability G a::::a5: matrix T :aa:a:5: bits 2.6 * * 2.4 * * * 2.1 * * * 1.8 ****** Relative 1.6 ****** Entropy 1.3 ******** (15.7 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GTTCTGGA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:18165470-18165550 61 6.77e-06 TGTTTTTGGC GTTCTGGA AGAATTTACA chrII:10550510-10550590 24 1.92e-05 GGCTCCATCT GTTCTGTA AGGCAAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:18165470-18165550 6.8e-06 60_[+5]_12 chrII:10550510-10550590 1.9e-05 23_[+5]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTTCTGKA width=8 seqs=2 chrV:18165470-18165550 ( 61) GTTCTGGA 1 chrII:10550510-10550590 ( 24) GTTCTGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 657 bayes= 8.35535 E= 5.7e+002 -765 -765 264 -765 -765 -765 -765 177 -765 -765 -765 177 -765 248 -765 -765 -765 -765 -765 177 -765 -765 264 -765 -765 -765 164 77 143 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.7e+002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTCTGKA MEME-5 regular expression -------------------------------------------------------------------------------- GTTCTG[GT]A -------------------------------------------------------------------------------- Time 2.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:18714561-18714641 1.40e-02 61_[+2(3.83e-05)]_11 chrV:19634350-19634430 1.59e-03 68_[+2(6.08e-06)]_4 chrX:14951104-14951184 4.90e-01 80 chrIII:1427742-1427822 1.25e-01 80 chrII:10645974-10646054 3.22e-03 7_[+1(9.70e-05)]_14_[+4(4.06e-05)]_\ 43 chrV:18722669-18722749 3.86e-03 3_[+2(2.71e-05)]_55_[+1(8.50e-05)]_\ 6 chrV:18165470-18165550 1.13e-10 9_[+4(8.22e-06)]_11_[+2(8.03e-05)]_\ 6_[+3(7.02e-06)]_2_[+1(2.79e-05)]_[+5(6.77e-06)]_12 chrII:10550510-10550590 1.24e-04 23_[+5(1.92e-05)]_25_[+4(4.06e-05)]_\ 16 chrV:16634967-16635047 8.43e-06 42_[+4(2.17e-05)]_11_[+1(5.96e-05)]_\ 2_[+3(1.12e-05)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n06.farnam.hpc.yale.internal ********************************************************************************