******************************************************************************** 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-12.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:13146-13226 1.0000 80 chrM:3909-3989 1.0000 80 chrM:873-953 1.0000 80 chrM:11521-11601 1.0000 80 chrM:7710-7790 1.0000 80 chrM:9619-9699 1.0000 80 chrM:2463-2543 1.0000 80 chrM:3708-3788 1.0000 80 chrIV:1624626-1624706 1.0000 80 chrI:13528261-13528341 1.0000 80 chrM:12339-12419 1.0000 80 chrM:10420-10500 1.0000 80 chrM:6434-6514 1.0000 80 chrI:13475639-13475719 1.0000 80 chrI:7056985-7057065 1.0000 80 chrI:13559875-13559955 1.0000 80 chrM:2187-2267 1.0000 80 chrM:4698-4778 1.0000 80 chrX:15607679-15607759 1.0000 80 chrM:1075-1155 1.0000 80 chrM:6636-6716 1.0000 80 chrM:12540-12620 1.0000 80 chrM:11238-11318 1.0000 80 chrI:11131478-11131558 1.0000 80 chrI:5316145-5316225 1.0000 80 chrX:17216321-17216401 1.0000 80 chrI:13500611-13500691 1.0000 80 chrV:1743651-1743731 1.0000 80 chrI:11120963-11121043 1.0000 80 chrI:13373014-13373094 1.0000 80 chrI:10769944-10770024 1.0000 80 chrII:156039-156119 1.0000 80 chrX:4142214-4142294 1.0000 80 chrII:11974759-11974839 1.0000 80 chrIII:4237883-4237963 1.0000 80 chrI:12995742-12995822 1.0000 80 chrI:4701179-4701259 1.0000 80 chrIII:11689809-11689889 1.0000 80 chrIV:2676450-2676530 1.0000 80 chrI:13812523-13812603 1.0000 80 chrIII:13466366-13466446 1.0000 80 chrX:2364850-2364930 1.0000 80 chrI:13756528-13756608 1.0000 80 chrIII:13256569-13256649 1.0000 80 chrI:13663355-13663435 1.0000 80 chrX:2242927-2243007 1.0000 80 chrX:10435587-10435667 1.0000 80 chrIV:14767878-14767958 1.0000 80 chrIII:1926644-1926724 1.0000 80 chrIII:355122-355202 1.0000 80 chrM:1333-1413 1.0000 80 chrI:9163490-9163570 1.0000 80 chrII:13460870-13460950 1.0000 80 chrV:20005936-20006016 1.0000 80 chrII:9940493-9940573 1.0000 80 chrIII:9631507-9631587 1.0000 80 chrIII:4963094-4963174 1.0000 80 chrI:12966896-12966976 1.0000 80 chrI:7021451-7021531 1.0000 80 chrV:5505153-5505233 1.0000 80 chrX:16056555-16056635 1.0000 80 chrII:8185106-8185186 1.0000 80 chrII:11759438-11759518 1.0000 80 chrI:4699473-4699553 1.0000 80 chrV:11764500-11764580 1.0000 80 chrV:9546869-9546949 1.0000 80 chrI:13514313-13514393 1.0000 80 chrII:2974040-2974120 1.0000 80 chrIII:11946600-11946680 1.0000 80 chrIV:17249879-17249959 1.0000 80 chrX:1345024-1345104 1.0000 80 chrIII:8904246-8904326 1.0000 80 chrX:12363153-12363233 1.0000 80 chrI:12652202-12652282 1.0000 80 chrI:16980-17060 1.0000 80 chrIV:2602116-2602196 1.0000 80 chrV:14685739-14685819 1.0000 80 chrIV:1094317-1094397 1.0000 80 chrIII:3801473-3801553 1.0000 80 chrII:4299421-4299501 1.0000 80 chrII:14795035-14795115 1.0000 80 chrIII:5679053-5679133 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-12/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-12.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= 82 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= 6560 N= 82 sample: seed= 0 hsfrac= 0 searchsize= 6560 norand= no csites= 1000 Letter frequencies in dataset: A 0.28 C 0.198 G 0.193 T 0.329 Background letter frequencies (from file dataset with add-one prior applied): A 0.28 C 0.198 G 0.193 T 0.329 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AARCGCGC MEME-1 width = 8 sites = 12 llr = 121 E-value = 3.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 9a3::::: pos.-specific C :::a:a:8 probability G 1:5:a:92 matrix T ::2:::1: bits 2.4 *** 2.1 *** 1.9 * **** 1.7 * ***** Relative 1.4 ** ***** Entropy 1.2 ** ***** (14.5 bits) 0.9 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AAGCGCGC consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:5679053-5679133 55 4.38e-06 GACAAATGGC AAGCGCGC TCTATAGCAC chrI:12652202-12652282 29 4.38e-06 GAGAGTCAGC AAGCGCGC CCCACTGAGA chrI:5316145-5316225 3 4.38e-06 GG AAGCGCGC AGtctctcca chrV:14685739-14685819 3 1.07e-05 GA AAACGCGC TCTATTGACA chrV:5505153-5505233 67 1.07e-05 GCTGGTCGCG AAACGCGC CAGCAT chrIV:2676450-2676530 27 1.07e-05 CGCGTGCGAG AAACGCGC CAGCACCGTA chrI:4701179-4701259 9 1.07e-05 CACCACAA AAACGCGC ACAATCTCTT chrIII:4963094-4963174 37 1.50e-05 CTTCTTTCAA AAGCGCGG ATTTTCAAAA chrI:13756528-13756608 50 2.24e-05 TGATCACTTG AATCGCGC CAGCAGTTCC chrIV:17249879-17249959 39 2.55e-05 TGCGTCAATG GAGCGCGC TTGCATTTTC chrI:12995742-12995822 26 4.35e-05 AAAACACGCC AAGCGCTC GTGCTGGCGC chrII:8185106-8185186 42 5.08e-05 ATCGGCAATA AATCGCGG GTGGGAACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:5679053-5679133 4.4e-06 54_[+1]_18 chrI:12652202-12652282 4.4e-06 28_[+1]_44 chrI:5316145-5316225 4.4e-06 2_[+1]_70 chrV:14685739-14685819 1.1e-05 2_[+1]_70 chrV:5505153-5505233 1.1e-05 66_[+1]_6 chrIV:2676450-2676530 1.1e-05 26_[+1]_46 chrI:4701179-4701259 1.1e-05 8_[+1]_64 chrIII:4963094-4963174 1.5e-05 36_[+1]_36 chrI:13756528-13756608 2.2e-05 49_[+1]_23 chrIV:17249879-17249959 2.5e-05 38_[+1]_34 chrI:12995742-12995822 4.3e-05 25_[+1]_47 chrII:8185106-8185186 5.1e-05 41_[+1]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AARCGCGC width=8 seqs=12 chrIII:5679053-5679133 ( 55) AAGCGCGC 1 chrI:12652202-12652282 ( 29) AAGCGCGC 1 chrI:5316145-5316225 ( 3) AAGCGCGC 1 chrV:14685739-14685819 ( 3) AAACGCGC 1 chrV:5505153-5505233 ( 67) AAACGCGC 1 chrIV:2676450-2676530 ( 27) AAACGCGC 1 chrI:4701179-4701259 ( 9) AAACGCGC 1 chrIII:4963094-4963174 ( 37) AAGCGCGG 1 chrI:13756528-13756608 ( 50) AATCGCGC 1 chrIV:17249879-17249959 ( 39) GAGCGCGC 1 chrI:12995742-12995822 ( 26) AAGCGCTC 1 chrII:8185106-8185186 ( 42) AATCGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5986 bayes= 8.61771 E= 3.2e-004 171 -1023 -121 -1023 183 -1023 -1023 -1023 25 -1023 137 -98 -1023 233 -1023 -1023 -1023 -1023 237 -1023 -1023 233 -1023 -1023 -1023 -1023 225 -198 -1023 207 -21 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 3.2e-004 0.916667 0.000000 0.083333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.500000 0.166667 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 0.916667 0.083333 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARCGCGC MEME-1 regular expression -------------------------------------------------------------------------------- AA[GA]CGCGC -------------------------------------------------------------------------------- Time 1.03 secs. ******************************************************************************** ******************************************************************************** MOTIF CYGCGTCW MEME-2 width = 8 sites = 19 llr = 160 E-value = 3.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2:1::::4 pos.-specific C 84:9::a: probability G ::8191:: matrix T :61:19:6 bits 2.4 * 2.1 * 1.9 ** * 1.7 * ** * Relative 1.4 * ***** Entropy 1.2 * ***** (12.1 bits) 0.9 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTGCGTCT consensus C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:2602116-2602196 61 1.65e-05 CTTTGCCTGT CTGCGTCT CCTCCGTAGT chrI:16980-17060 25 1.65e-05 TAGCCGCTCT CTGCGTCT CTCACCCTTC chrI:13514313-13514393 62 1.65e-05 CGTCAACTCT CTGCGTCT CTACTCTCTA chrIV:14767878-14767958 9 1.65e-05 TGCATACT CTGCGTCT CGTCTTTTTG chrI:13373014-13373094 65 1.65e-05 ACAGTGTACT CTGCGTCT CTTCAATT chrV:1743651-1743731 73 1.65e-05 CGTTTTGTGT CTGCGTCT chrI:13528261-13528341 1 1.65e-05 . CTGCGTCT CTTACTCTCT chrV:9546869-9546949 64 2.18e-05 ACAACCTTTC CCGCGTCA TCGAATCCG chrIV:17249879-17249959 28 3.05e-05 CAGCAGCTGT CTGCGTCA ATGGAGCGCG chrIII:3801473-3801553 43 4.53e-05 ACTCTCTCAG CCGGGTCT AACCAGTCTC chrIV:2676450-2676530 8 8.10e-05 ACTGAAT ACGCGTCA GCGCGTGCGA chrIII:1926644-1926724 6 1.15e-04 CCTCT CCTCGTCT TTCGCCCATT chrIII:13466366-13466446 21 1.15e-04 CAAAATCAAT ATGCGTCA AGGAGTGGTT chrIII:4963094-4963174 24 1.34e-04 GCGCAAGCAG CCGCTTCT TTCAAAAGCG chrIII:8904246-8904326 42 1.87e-04 CGCGATTGCC CTGCGGCA GTGTAGCGAG chrI:10769944-10770024 17 1.87e-04 CTGCCCACTG CCTCGTCA GCTTCAGACT chrII:11974759-11974839 43 1.96e-04 TTTTGAATTC CCGCTTCA CCGAATAATT chrX:17216321-17216401 54 2.20e-04 tctctcATTT CCACGTCT AGCGGTACAA chrI:7021451-7021531 51 2.92e-04 ACTCCGCCCA ATGGGTCT CGCACGGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:2602116-2602196 1.6e-05 60_[+2]_12 chrI:16980-17060 1.6e-05 24_[+2]_48 chrI:13514313-13514393 1.6e-05 61_[+2]_11 chrIV:14767878-14767958 1.6e-05 8_[+2]_64 chrI:13373014-13373094 1.6e-05 64_[+2]_8 chrV:1743651-1743731 1.6e-05 72_[+2] chrI:13528261-13528341 1.6e-05 [+2]_72 chrV:9546869-9546949 2.2e-05 63_[+2]_9 chrIV:17249879-17249959 3.1e-05 27_[+2]_45 chrIII:3801473-3801553 4.5e-05 42_[+2]_30 chrIV:2676450-2676530 8.1e-05 7_[+2]_65 chrIII:1926644-1926724 0.00012 5_[+2]_67 chrIII:13466366-13466446 0.00012 20_[+2]_52 chrIII:4963094-4963174 0.00013 23_[+2]_49 chrIII:8904246-8904326 0.00019 41_[+2]_31 chrI:10769944-10770024 0.00019 16_[+2]_56 chrII:11974759-11974839 0.0002 42_[+2]_30 chrX:17216321-17216401 0.00022 53_[+2]_19 chrI:7021451-7021531 0.00029 50_[+2]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CYGCGTCW width=8 seqs=19 chrIV:2602116-2602196 ( 61) CTGCGTCT 1 chrI:16980-17060 ( 25) CTGCGTCT 1 chrI:13514313-13514393 ( 62) CTGCGTCT 1 chrIV:14767878-14767958 ( 9) CTGCGTCT 1 chrI:13373014-13373094 ( 65) CTGCGTCT 1 chrV:1743651-1743731 ( 73) CTGCGTCT 1 chrI:13528261-13528341 ( 1) CTGCGTCT 1 chrV:9546869-9546949 ( 64) CCGCGTCA 1 chrIV:17249879-17249959 ( 28) CTGCGTCA 1 chrIII:3801473-3801553 ( 43) CCGGGTCT 1 chrIV:2676450-2676530 ( 8) ACGCGTCA 1 chrIII:1926644-1926724 ( 6) CCTCGTCT 1 chrIII:13466366-13466446 ( 21) ATGCGTCA 1 chrIII:4963094-4963174 ( 24) CCGCTTCT 1 chrIII:8904246-8904326 ( 42) CTGCGGCA 1 chrI:10769944-10770024 ( 17) CCTCGTCA 1 chrII:11974759-11974839 ( 43) CCGCTTCA 1 chrX:17216321-17216401 ( 54) CCACGTCT 1 chrI:7021451-7021531 ( 51) ATGGGTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5986 bayes= 9.19442 E= 3.3e-002 -83 209 -1089 -1089 -1089 109 -1089 82 -241 -1089 212 -164 -1089 217 -87 -1089 -1089 -1089 221 -164 -1089 -1089 -187 153 -1089 233 -1089 -1089 39 -1089 -1089 94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.3e-002 0.157895 0.842105 0.000000 0.000000 0.000000 0.421053 0.000000 0.578947 0.052632 0.000000 0.842105 0.105263 0.000000 0.894737 0.105263 0.000000 0.000000 0.000000 0.894737 0.105263 0.000000 0.000000 0.052632 0.947368 0.000000 1.000000 0.000000 0.000000 0.368421 0.000000 0.000000 0.631579 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYGCGTCW MEME-2 regular expression -------------------------------------------------------------------------------- C[TC]GCGTC[TA] -------------------------------------------------------------------------------- Time 1.91 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCTGGCG MEME-3 width = 8 sites = 4 llr = 48 E-value = 6.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a:::a: probability G :a::aa:a matrix T a::a:::: bits 2.4 ** **** 2.1 ** **** 1.9 ** **** 1.7 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.4 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGCTGGCG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:1094317-1094397 3 5.89e-06 AT TGCTGGCG GGTCCCGCCG chrI:13756528-13756608 25 5.89e-06 CACAGAGACT TGCTGGCG CAACACGTGA chrIII:13466366-13466446 38 5.89e-06 AAGGAGTGGT TGCTGGCG TACTTTGCGA chrI:12995742-12995822 35 5.89e-06 CAAGCGCTCG TGCTGGCG CATTTGCCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:1094317-1094397 5.9e-06 2_[+3]_70 chrI:13756528-13756608 5.9e-06 24_[+3]_48 chrIII:13466366-13466446 5.9e-06 37_[+3]_35 chrI:12995742-12995822 5.9e-06 34_[+3]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCTGGCG width=8 seqs=4 chrIV:1094317-1094397 ( 3) TGCTGGCG 1 chrI:13756528-13756608 ( 25) TGCTGGCG 1 chrIII:13466366-13466446 ( 38) TGCTGGCG 1 chrI:12995742-12995822 ( 35) TGCTGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5986 bayes= 10.5464 E= 6.6e+001 -865 -865 -865 160 -865 -865 237 -865 -865 233 -865 -865 -865 -865 -865 160 -865 -865 237 -865 -865 -865 237 -865 -865 233 -865 -865 -865 -865 237 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 6.6e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGCG MEME-3 regular expression -------------------------------------------------------------------------------- TGCTGGCG -------------------------------------------------------------------------------- Time 2.85 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGGTASA MEME-4 width = 8 sites = 7 llr = 72 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::a:a pos.-specific C :3::::6: probability G a7aa1:4: matrix T ::::9::: bits 2.4 * ** 2.1 * ** 1.9 * ** * * 1.7 * ** * * Relative 1.4 **** *** Entropy 1.2 ******** (14.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGGTACA consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:12363153-12363233 38 7.09e-06 CAATTCAAGA GGGGTACA ATCTTTTCCC chrI:11131478-11131558 34 7.09e-06 ATTGAAAACG GGGGTACA CCCCTCATAA chrM:13146-13226 20 7.09e-06 TTAATTCTAA GGGGTACA CCTTATTTTT chrIII:355122-355202 18 1.40e-05 TGGGGGACCA GGGGTAGA AAGTGCTTCT chrX:17216321-17216401 63 2.13e-05 TCCACGTCTA GCGGTACA AAGTCCAAGT chrII:156039-156119 56 2.83e-05 CGCGTGTGTT GCGGTAGA GCGTGTTTCC chrII:4299421-4299501 50 3.66e-05 GAGACGACGC GGGGGAGA TTTACGATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:12363153-12363233 7.1e-06 37_[+4]_35 chrI:11131478-11131558 7.1e-06 33_[+4]_39 chrM:13146-13226 7.1e-06 19_[+4]_53 chrIII:355122-355202 1.4e-05 17_[+4]_55 chrX:17216321-17216401 2.1e-05 62_[+4]_10 chrII:156039-156119 2.8e-05 55_[+4]_17 chrII:4299421-4299501 3.7e-05 49_[+4]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGGTASA width=8 seqs=7 chrX:12363153-12363233 ( 38) GGGGTACA 1 chrI:11131478-11131558 ( 34) GGGGTACA 1 chrM:13146-13226 ( 20) GGGGTACA 1 chrIII:355122-355202 ( 18) GGGGTAGA 1 chrX:17216321-17216401 ( 63) GCGGTACA 1 chrII:156039-156119 ( 56) GCGGTAGA 1 chrII:4299421-4299501 ( 50) GGGGGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5986 bayes= 10.3446 E= 1.0e+002 -945 -945 237 -945 -945 53 189 -945 -945 -945 237 -945 -945 -945 237 -945 -945 -945 -43 138 183 -945 -945 -945 -945 153 115 -945 183 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.0e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 1.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTASA MEME-4 regular expression -------------------------------------------------------------------------------- G[GC]GGTA[CG]A -------------------------------------------------------------------------------- Time 3.79 secs. ******************************************************************************** ******************************************************************************** MOTIF SRAGAGAC MEME-5 width = 8 sites = 9 llr = 86 E-value = 6.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :4a:a:8: pos.-specific C 3::::::8 probability G 76:a:a22 matrix T :::::::: bits 2.4 * * 2.1 * * 1.9 **** 1.7 **** * Relative 1.4 * **** * Entropy 1.2 ******** (13.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGAGAGAC consensus CA GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:4299421-4299501 37 1.48e-05 GTCTCGCAGG GAAGAGAC GACGCGGGGG chrII:11759438-11759518 43 1.48e-05 ACGGCCGACA GAAGAGAC AACACAGCTG chrX:10435587-10435667 33 1.48e-05 acgggaggag gaagagac ggagaagaaa chrI:13756528-13756608 8 2.10e-05 TAGAGAG CGAGAGAC ACAGAGACTT chrI:13475639-13475719 8 2.10e-05 agagata cgagagaC ATAAGTCTAT chrI:16980-17060 50 4.00e-05 TTCAGCACGC GGAGAGAG CCACGAGAAA chrV:20005936-20006016 5 4.00e-05 TATG GGAGAGAG ACCCAGACAT chrI:7021451-7021531 65 4.60e-05 GTCTCGCACG GAAGAGGC GACCATCA chrX:2242927-2243007 17 5.03e-05 CTGCAGAATA CGAGAGGC AAAATGACTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:4299421-4299501 1.5e-05 36_[+5]_36 chrII:11759438-11759518 1.5e-05 42_[+5]_30 chrX:10435587-10435667 1.5e-05 32_[+5]_40 chrI:13756528-13756608 2.1e-05 7_[+5]_65 chrI:13475639-13475719 2.1e-05 7_[+5]_65 chrI:16980-17060 4e-05 49_[+5]_23 chrV:20005936-20006016 4e-05 4_[+5]_68 chrI:7021451-7021531 4.6e-05 64_[+5]_8 chrX:2242927-2243007 5e-05 16_[+5]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SRAGAGAC width=8 seqs=9 chrII:4299421-4299501 ( 37) GAAGAGAC 1 chrII:11759438-11759518 ( 43) GAAGAGAC 1 chrX:10435587-10435667 ( 33) GAAGAGAC 1 chrI:13756528-13756608 ( 8) CGAGAGAC 1 chrI:13475639-13475719 ( 8) CGAGAGAC 1 chrI:16980-17060 ( 50) GGAGAGAG 1 chrV:20005936-20006016 ( 5) GGAGAGAG 1 chrI:7021451-7021531 ( 65) GAAGAGGC 1 chrX:2242927-2243007 ( 17) CGAGAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5986 bayes= 9.50978 E= 6.4e+002 -982 75 179 -982 67 -982 152 -982 183 -982 -982 -982 -982 -982 237 -982 183 -982 -982 -982 -982 -982 237 -982 147 -982 20 -982 -982 197 20 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 6.4e+002 0.000000 0.333333 0.666667 0.000000 0.444444 0.000000 0.555556 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 0.000000 0.000000 1.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.777778 0.222222 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SRAGAGAC MEME-5 regular expression -------------------------------------------------------------------------------- [GC][GA]AGAG[AG][CG] -------------------------------------------------------------------------------- Time 5.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:13146-13226 9.07e-02 19_[+4(7.09e-06)]_53 chrM:3909-3989 1.00e+00 80 chrM:873-953 9.99e-01 80 chrM:11521-11601 1.00e+00 80 chrM:7710-7790 9.11e-01 80 chrM:9619-9699 9.96e-01 80 chrM:2463-2543 9.97e-01 80 chrM:3708-3788 9.99e-01 80 chrIV:1624626-1624706 8.63e-01 80 chrI:13528261-13528341 3.28e-02 [+2(1.65e-05)]_72 chrM:12339-12419 9.96e-01 80 chrM:10420-10500 5.05e-01 80 chrM:6434-6514 1.00e+00 80 chrI:13475639-13475719 1.36e-02 7_[+5(2.10e-05)]_65 chrI:7056985-7057065 3.74e-01 80 chrI:13559875-13559955 1.00e+00 80 chrM:2187-2267 9.98e-01 80 chrM:4698-4778 6.05e-01 80 chrX:15607679-15607759 1.25e-01 80 chrM:1075-1155 9.79e-01 80 chrM:6636-6716 1.00e+00 80 chrM:12540-12620 3.93e-01 80 chrM:11238-11318 9.14e-01 80 chrI:11131478-11131558 1.13e-02 33_[+4(7.09e-06)]_39 chrI:5316145-5316225 1.03e-02 2_[+1(4.38e-06)]_70 chrX:17216321-17216401 1.18e-02 62_[+4(2.13e-05)]_10 chrI:13500611-13500691 1.00e+00 80 chrV:1743651-1743731 5.76e-02 72_[+2(1.65e-05)] chrI:11120963-11121043 9.31e-01 80 chrI:13373014-13373094 8.62e-02 64_[+2(1.65e-05)]_8 chrI:10769944-10770024 7.10e-02 80 chrII:156039-156119 9.13e-03 55_[+4(2.83e-05)]_17 chrX:4142214-4142294 7.44e-01 80 chrII:11974759-11974839 3.72e-01 80 chrIII:4237883-4237963 6.93e-02 80 chrI:12995742-12995822 7.07e-04 25_[+1(4.35e-05)]_1_[+3(5.89e-06)]_\ 23_[+3(2.99e-05)]_7 chrI:4701179-4701259 5.10e-02 8_[+1(1.07e-05)]_64 chrIII:11689809-11689889 9.88e-01 80 chrIV:2676450-2676530 8.34e-05 7_[+2(8.10e-05)]_11_[+1(1.07e-05)]_\ 46 chrI:13812523-13812603 5.30e-01 80 chrIII:13466366-13466446 6.66e-04 37_[+3(5.89e-06)]_35 chrX:2364850-2364930 9.62e-01 80 chrI:13756528-13756608 6.71e-07 7_[+5(2.10e-05)]_9_[+3(5.89e-06)]_\ 17_[+1(2.24e-05)]_23 chrIII:13256569-13256649 9.67e-01 80 chrI:13663355-13663435 5.49e-01 80 chrX:2242927-2243007 4.45e-02 16_[+5(5.03e-05)]_56 chrX:10435587-10435667 1.57e-02 32_[+5(1.48e-05)]_40 chrIV:14767878-14767958 1.05e-02 8_[+2(1.65e-05)]_64 chrIII:1926644-1926724 1.96e-01 80 chrIII:355122-355202 2.09e-02 17_[+4(1.40e-05)]_55 chrM:1333-1413 8.69e-01 80 chrI:9163490-9163570 1.18e-01 80 chrII:13460870-13460950 9.68e-01 80 chrV:20005936-20006016 2.35e-02 4_[+5(4.00e-05)]_68 chrII:9940493-9940573 9.84e-01 80 chrIII:9631507-9631587 8.88e-01 80 chrIII:4963094-4963174 1.22e-03 36_[+1(1.50e-05)]_36 chrI:12966896-12966976 3.61e-01 80 chrI:7021451-7021531 9.92e-03 64_[+5(4.60e-05)]_8 chrV:5505153-5505233 5.25e-03 66_[+1(1.07e-05)]_6 chrX:16056555-16056635 8.03e-01 80 chrII:8185106-8185186 2.87e-02 41_[+1(5.08e-05)]_31 chrII:11759438-11759518 1.09e-02 42_[+5(1.48e-05)]_30 chrI:4699473-4699553 3.16e-01 80 chrV:11764500-11764580 8.04e-02 80 chrV:9546869-9546949 5.77e-02 63_[+2(2.18e-05)]_9 chrI:13514313-13514393 1.45e-02 61_[+2(1.65e-05)]_11 chrII:2974040-2974120 7.09e-03 80 chrIII:11946600-11946680 9.18e-01 80 chrIV:17249879-17249959 1.53e-03 27_[+2(3.05e-05)]_3_[+1(2.55e-05)]_\ 34 chrX:1345024-1345104 4.11e-01 80 chrIII:8904246-8904326 4.39e-03 80 chrX:12363153-12363233 1.99e-03 37_[+4(7.09e-06)]_35 chrI:12652202-12652282 1.86e-03 28_[+1(4.38e-06)]_44 chrI:16980-17060 4.68e-05 5_[+2(8.10e-05)]_11_[+2(1.65e-05)]_\ 17_[+5(4.00e-05)]_23 chrIV:2602116-2602196 9.48e-02 31_[+2(1.65e-05)]_21_[+2(1.65e-05)]_\ 12 chrV:14685739-14685819 2.52e-02 2_[+1(1.07e-05)]_70 chrIV:1094317-1094397 1.23e-03 2_[+3(5.89e-06)]_70 chrIII:3801473-3801553 3.55e-02 42_[+2(4.53e-05)]_30 chrII:4299421-4299501 4.66e-04 36_[+5(1.48e-05)]_5_[+4(3.66e-05)]_\ 23 chrII:14795035-14795115 4.91e-01 80 chrIII:5679053-5679133 2.07e-02 54_[+1(4.38e-06)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n08.farnam.hpc.yale.internal ********************************************************************************