******************************************************************************** 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-67.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:13119-13199 1.0000 80 chrM:11994-12074 1.0000 80 chrM:460-540 1.0000 80 chrM:13601-13681 1.0000 80 chrM:9767-9847 1.0000 80 chrM:2707-2787 1.0000 80 chrM:11394-11474 1.0000 80 chrM:3860-3940 1.0000 80 chrM:6659-6739 1.0000 80 chrM:7525-7605 1.0000 80 chrM:7743-7823 1.0000 80 chrM:10335-10415 1.0000 80 chrM:5466-5546 1.0000 80 chrM:6458-6538 1.0000 80 chrM:5747-5827 1.0000 80 chrM:3653-3733 1.0000 80 chrM:9436-9516 1.0000 80 chrM:3200-3280 1.0000 80 chrM:6968-7048 1.0000 80 chrX:13349736-13349816 1.0000 80 chrX:16931701-16931781 1.0000 80 chrM:1361-1441 1.0000 80 chrIV:3864936-3865016 1.0000 80 chrII:8577518-8577598 1.0000 80 chrII:2570822-2570902 1.0000 80 chrM:1021-1101 1.0000 80 chrM:8254-8334 1.0000 80 chrM:9041-9121 1.0000 80 chrM:4676-4756 1.0000 80 chrM:10916-10996 1.0000 80 chrM:8643-8723 1.0000 80 chrIV:4555761-4555841 1.0000 80 chrM:12389-12469 1.0000 80 chrM:2207-2287 1.0000 80 chrIII:9881430-9881510 1.0000 80 chrI:1175836-1175916 1.0000 80 chrM:6137-6217 1.0000 80 chrI:3547012-3547092 1.0000 80 chrII:1226472-1226552 1.0000 80 chrX:2364843-2364923 1.0000 80 chrI:9381922-9382002 1.0000 80 chrIII:8307487-8307567 1.0000 80 chrV:265204-265284 1.0000 80 chrII:11637562-11637642 1.0000 80 chrV:6785254-6785334 1.0000 80 chrI:1958506-1958586 1.0000 80 chrV:13176473-13176553 1.0000 80 chrIII:8768068-8768148 1.0000 80 chrIV:14464186-14464266 1.0000 80 chrII:7708734-7708814 1.0000 80 chrI:9343979-9344059 1.0000 80 chrII:4999305-4999385 1.0000 80 chrI:8411375-8411455 1.0000 80 chrV:724098-724178 1.0000 80 chrIII:5555088-5555168 1.0000 80 chrX:4388971-4389051 1.0000 80 chrV:10965637-10965717 1.0000 80 chrII:14349691-14349771 1.0000 80 chrI:1444169-1444249 1.0000 80 chrIV:15471535-15471615 1.0000 80 chrX:16056568-16056648 1.0000 80 chrIII:2768795-2768875 1.0000 80 chrI:4633636-4633716 1.0000 80 chrIII:9629921-9630001 1.0000 80 chrI:535378-535458 1.0000 80 chrI:14737445-14737525 1.0000 80 chrX:12363128-12363208 1.0000 80 chrX:10568980-10569060 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-67/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-67.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= 68 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= 5440 N= 68 sample: seed= 0 hsfrac= 0 searchsize= 5440 norand= no csites= 1000 Letter frequencies in dataset: A 0.306 C 0.157 G 0.181 T 0.356 Background letter frequencies (from file dataset with add-one prior applied): A 0.306 C 0.157 G 0.181 T 0.355 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GYGCGCRC MEME-1 width = 8 sites = 19 llr = 166 E-value = 1.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::11::3: pos.-specific C 26:73a:8 probability G 8:8:7:62 matrix T 1412::1: bits 2.7 * 2.4 * 2.1 * * 1.9 * * Relative 1.6 * ** * Entropy 1.3 ****** * (12.6 bits) 1.1 ****** * 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCGCGCGC consensus T C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:1444169-1444249 23 6.52e-07 TTTGCAACCA GCGCGCGC ACTTTTCGCA chrIII:5555088-5555168 49 6.52e-07 TGCGCAAAAA GCGCGCGC ACATTGCGTT chrII:7708734-7708814 20 6.52e-07 ACAATGCAAT GCGCGCGC ACGGTTTTTG chrI:1175836-1175916 44 6.07e-06 CAAAAACCGT GCGCCCAC CTTGCAATGA chrI:4633636-4633716 31 9.31e-06 AGCATCAATT GCGTGCGC CGTTTTTGCA chrI:14737445-14737525 46 1.31e-05 TGCAAAATGT GTGCGCAC CACTTGCGGT chrI:3547012-3547092 53 1.31e-05 TTTGCAAGTG GTGCGCAC ATTTTCAAGG chrIII:8768068-8768148 71 3.45e-05 CGATTCAACT CCGCCCAC AA chrV:6785254-6785334 59 3.45e-05 TTTGCAAGGA GCGTGCAC GCAGTTGCCT chrIV:15471535-15471615 47 4.80e-05 AATAATGCAA GTGCGCTC TATCTGCACG chrIII:9629921-9630001 55 5.40e-05 TTTTTGCAAC GCTCGCAC GCAGTTTTTG chrX:10568980-10569060 38 7.54e-05 ACTTGCGTAC TCGCCCGC TTTTTTTATT chrII:14349691-14349771 42 7.54e-05 TAACTGTCTT CCTCGCGC CAATTTTGTT chrI:9381922-9382002 41 8.14e-05 GAAGAGTTGA GCGAGCGG CGGCGACAGC chrV:13176473-13176553 56 9.53e-05 GTGATGAAAA CTGCGCGG TGGTTGCAAG chrX:4388971-4389051 71 1.03e-04 GAGGCAAGAG GTACCCGC CG chrX:16056568-16056648 41 1.17e-04 TCCCATATCT GTGACCGC CTAAAAGCGA chrI:535378-535458 35 1.34e-04 TTTTGTGCAA GCACGCTC CATCGCACAG chrI:1958506-1958586 38 1.95e-04 AACGGGAATT GTGTGCGG CGGTGTTGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:1444169-1444249 6.5e-07 22_[+1]_50 chrIII:5555088-5555168 6.5e-07 48_[+1]_24 chrII:7708734-7708814 6.5e-07 19_[+1]_53 chrI:1175836-1175916 6.1e-06 43_[+1]_29 chrI:4633636-4633716 9.3e-06 30_[+1]_42 chrI:14737445-14737525 1.3e-05 45_[+1]_27 chrI:3547012-3547092 1.3e-05 52_[+1]_20 chrIII:8768068-8768148 3.4e-05 70_[+1]_2 chrV:6785254-6785334 3.4e-05 58_[+1]_14 chrIV:15471535-15471615 4.8e-05 46_[+1]_26 chrIII:9629921-9630001 5.4e-05 54_[+1]_18 chrX:10568980-10569060 7.5e-05 37_[+1]_35 chrII:14349691-14349771 7.5e-05 41_[+1]_31 chrI:9381922-9382002 8.1e-05 40_[+1]_32 chrV:13176473-13176553 9.5e-05 55_[+1]_17 chrX:4388971-4389051 0.0001 70_[+1]_2 chrX:16056568-16056648 0.00012 40_[+1]_32 chrI:535378-535458 0.00013 34_[+1]_38 chrI:1958506-1958586 0.00019 37_[+1]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GYGCGCRC width=8 seqs=19 chrI:1444169-1444249 ( 23) GCGCGCGC 1 chrIII:5555088-5555168 ( 49) GCGCGCGC 1 chrII:7708734-7708814 ( 20) GCGCGCGC 1 chrI:1175836-1175916 ( 44) GCGCCCAC 1 chrI:4633636-4633716 ( 31) GCGTGCGC 1 chrI:14737445-14737525 ( 46) GTGCGCAC 1 chrI:3547012-3547092 ( 53) GTGCGCAC 1 chrIII:8768068-8768148 ( 71) CCGCCCAC 1 chrV:6785254-6785334 ( 59) GCGTGCAC 1 chrIV:15471535-15471615 ( 47) GTGCGCTC 1 chrIII:9629921-9630001 ( 55) GCTCGCAC 1 chrX:10568980-10569060 ( 38) TCGCCCGC 1 chrII:14349691-14349771 ( 42) CCTCGCGC 1 chrI:9381922-9382002 ( 41) GCGAGCGG 1 chrV:13176473-13176553 ( 56) CTGCGCGG 1 chrX:4388971-4389051 ( 71) GTACCCGC 1 chrX:16056568-16056648 ( 41) GTGACCGC 1 chrI:535378-535458 ( 35) GCACGCTC 1 chrI:1958506-1958586 ( 38) GTGTGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 9.4679 E= 1.4e-006 -1089 1 212 -275 -1089 201 -1089 5 -154 -1089 212 -175 -154 223 -1089 -117 -1089 74 202 -1089 -1089 267 -1089 -1089 4 -1089 167 -175 -1089 242 -20 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 1.4e-006 0.000000 0.157895 0.789474 0.052632 0.000000 0.631579 0.000000 0.368421 0.105263 0.000000 0.789474 0.105263 0.105263 0.736842 0.000000 0.157895 0.000000 0.263158 0.736842 0.000000 0.000000 1.000000 0.000000 0.000000 0.315789 0.000000 0.578947 0.105263 0.000000 0.842105 0.157895 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGCGCRC MEME-1 regular expression -------------------------------------------------------------------------------- G[CT]GC[GC]C[GA]C -------------------------------------------------------------------------------- Time 2.02 secs. ******************************************************************************** ******************************************************************************** MOTIF RCYCCGCC MEME-2 width = 8 sites = 5 llr = 60 E-value = 9.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4::::::: pos.-specific C :86aa:aa probability G 6::::a:: matrix T :24::::: bits 2.7 ** ** 2.4 ***** 2.1 ***** 1.9 ***** Relative 1.6 * ***** Entropy 1.3 ******* (17.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCCCCGCC consensus ATT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:9629921-9630001 35 4.91e-07 TCCAAATGAA GCCCCGCC TCTTTTTGCA chrV:6785254-6785334 19 4.91e-07 TCATTCATAA GCCCCGCC TTCGCAATCC chrI:1444169-1444249 2 1.32e-06 G ACCCCGCC CCCTTTGCAA chrIII:8307487-8307567 16 5.41e-06 ATCGTAAAAA ACTCCGCC ATTTTTCTCA chrX:2364843-2364923 28 9.80e-06 AATGGATAAC GTTCCGCC ATATAACAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:9629921-9630001 4.9e-07 34_[+2]_38 chrV:6785254-6785334 4.9e-07 18_[+2]_54 chrI:1444169-1444249 1.3e-06 1_[+2]_71 chrIII:8307487-8307567 5.4e-06 15_[+2]_57 chrX:2364843-2364923 9.8e-06 27_[+2]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCYCCGCC width=8 seqs=5 chrIII:9629921-9630001 ( 35) GCCCCGCC 1 chrV:6785254-6785334 ( 19) GCCCCGCC 1 chrI:1444169-1444249 ( 2) ACCCCGCC 1 chrIII:8307487-8307567 ( 16) ACTCCGCC 1 chrX:2364843-2364923 ( 28) GTTCCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 10.898 E= 9.4e-001 38 -897 172 -897 -897 235 -897 -83 -897 193 -897 17 -897 267 -897 -897 -897 267 -897 -897 -897 -897 246 -897 -897 267 -897 -897 -897 267 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 9.4e-001 0.400000 0.000000 0.600000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.600000 0.000000 0.400000 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 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYCCGCC MEME-2 regular expression -------------------------------------------------------------------------------- [GA][CT][CT]CCGCC -------------------------------------------------------------------------------- Time 2.74 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTGGCAC MEME-3 width = 8 sites = 5 llr = 58 E-value = 1.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::2::a: pos.-specific C a8:::a:a probability G :228a::: matrix T ::8::::: bits 2.7 * * * 2.4 * ** * 2.1 * ** * 1.9 ** ** * Relative 1.6 ** ***** Entropy 1.3 ** ***** (16.6 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CCTGGCAC consensus GGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:2768795-2768875 34 2.16e-06 GTTTGGCAAG CCTGGCAC GTGGTTTTTG chrV:6785254-6785334 35 2.16e-06 CCTTCGCAAT CCTGGCAC GCAGTTTTTG chrI:3547012-3547092 29 2.16e-06 TAATTGCAAC CCTGGCAC GGCATTTTTG chrIV:4555761-4555841 2 9.41e-06 G CCTAGCAC CTTCCTCTCC chrIII:5555088-5555168 30 1.07e-05 AAACTGTGCG CGGGGCAC TTGCGCAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:2768795-2768875 2.2e-06 33_[+3]_39 chrV:6785254-6785334 2.2e-06 34_[+3]_38 chrI:3547012-3547092 2.2e-06 28_[+3]_44 chrIV:4555761-4555841 9.4e-06 1_[+3]_71 chrIII:5555088-5555168 1.1e-05 29_[+3]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCTGGCAC width=8 seqs=5 chrIII:2768795-2768875 ( 34) CCTGGCAC 1 chrV:6785254-6785334 ( 35) CCTGGCAC 1 chrI:3547012-3547092 ( 29) CCTGGCAC 1 chrIV:4555761-4555841 ( 2) CCTAGCAC 1 chrIII:5555088-5555168 ( 30) CGGGGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 10.2057 E= 1.0e+001 -897 267 -897 -897 -897 235 14 -897 -897 -897 14 117 -61 -897 214 -897 -897 -897 246 -897 -897 267 -897 -897 171 -897 -897 -897 -897 267 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.0e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.000000 0.800000 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 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGGCAC MEME-3 regular expression -------------------------------------------------------------------------------- C[CG][TG][GA]GCAC -------------------------------------------------------------------------------- Time 3.45 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGCGGMR MEME-4 width = 8 sites = 10 llr = 95 E-value = 8.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::64 pos.-specific C ::1a1:4: probability G 729:9a:6 matrix T 38:::::: bits 2.7 * 2.4 * * 2.1 **** 1.9 **** Relative 1.6 **** Entropy 1.3 * **** (13.7 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GTGCGGAG consensus TG CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:8768068-8768148 15 1.70e-06 TGAGTAAACT GTGCGGCG TGTTTGCGGA chrI:1958506-1958586 63 1.70e-06 GCGCAACGGT GTGCGGCG GCCTTGCAGT chrI:4633636-4633716 15 1.04e-05 aataacaaGT GGGCGGAG CATCAATTGC chrI:3547012-3547092 7 1.04e-05 AATAGT GGGCGGAG TCGATAATTG chrI:1175836-1175916 20 1.04e-05 CATAAACTCC GTGCGGCA CACTTGCAAA chrIV:14464186-14464266 65 2.73e-05 CACTCTGTAA TTGCGGAG TGTCGTTG chrX:13349736-13349816 55 4.06e-05 ACCCATGTAT GTCCGGAG AAACCGAATG chrII:4999305-4999385 63 6.20e-05 GTGACGGTGT TTGCGGAA GAGAGAGGCA chrI:9343979-9344059 10 6.20e-05 CTTTTTTTT TTGCGGAA AAAAGGGGAA chrIII:2768795-2768875 57 6.99e-05 TTTTGCAAGA GTGCCGCA CGTGGTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:8768068-8768148 1.7e-06 14_[+4]_58 chrI:1958506-1958586 1.7e-06 62_[+4]_10 chrI:4633636-4633716 1e-05 14_[+4]_58 chrI:3547012-3547092 1e-05 6_[+4]_66 chrI:1175836-1175916 1e-05 19_[+4]_53 chrIV:14464186-14464266 2.7e-05 64_[+4]_8 chrX:13349736-13349816 4.1e-05 54_[+4]_18 chrII:4999305-4999385 6.2e-05 62_[+4]_10 chrI:9343979-9344059 6.2e-05 9_[+4]_63 chrIII:2768795-2768875 7e-05 56_[+4]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGCGGMR width=8 seqs=10 chrIII:8768068-8768148 ( 15) GTGCGGCG 1 chrI:1958506-1958586 ( 63) GTGCGGCG 1 chrI:4633636-4633716 ( 15) GGGCGGAG 1 chrI:3547012-3547092 ( 7) GGGCGGAG 1 chrI:1175836-1175916 ( 20) GTGCGGCA 1 chrIV:14464186-14464266 ( 65) TTGCGGAG 1 chrX:13349736-13349816 ( 55) GTCCGGAG 1 chrII:4999305-4999385 ( 63) TTGCGGAA 1 chrI:9343979-9344059 ( 10) TTGCGGAA 1 chrIII:2768795-2768875 ( 57) GTGCCGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 9.20445 E= 8.4e+000 -997 -997 195 -24 -997 -997 14 117 -997 -65 231 -997 -997 267 -997 -997 -997 -65 231 -997 -997 -997 246 -997 97 135 -997 -997 39 -997 173 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 8.4e+000 0.000000 0.000000 0.700000 0.300000 0.000000 0.000000 0.200000 0.800000 0.000000 0.100000 0.900000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCGGMR MEME-4 regular expression -------------------------------------------------------------------------------- [GT][TG]GCGG[AC][GA] -------------------------------------------------------------------------------- Time 4.14 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGCCAGG MEME-5 width = 8 sites = 4 llr = 47 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C 33:aa::: probability G 8:a:::aa matrix T :8:::::: bits 2.7 ** 2.4 *** ** 2.1 *** ** 1.9 *** ** Relative 1.6 * ****** Entropy 1.3 * ****** (17.1 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GTGCCAGG consensus CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:4633636-4633716 57 2.87e-06 CATAAAGTGT GTGCCAGG GTTGCAAAAA chrIII:8768068-8768148 39 2.87e-06 CGGAAATCGC GTGCCAGG CTTGCAACAG chrI:8411375-8411455 53 4.14e-06 GAAGGGTCAG GCGCCAGG ACAAAAAGTG chrV:10965637-10965717 69 6.64e-06 TACTGGCATT CTGCCAGG GGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:4633636-4633716 2.9e-06 56_[+5]_16 chrIII:8768068-8768148 2.9e-06 38_[+5]_34 chrI:8411375-8411455 4.1e-06 52_[+5]_20 chrV:10965637-10965717 6.6e-06 68_[+5]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGCCAGG width=8 seqs=4 chrI:4633636-4633716 ( 57) GTGCCAGG 1 chrIII:8768068-8768148 ( 39) GTGCCAGG 1 chrI:8411375-8411455 ( 53) GCGCCAGG 1 chrV:10965637-10965717 ( 69) CTGCCAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4964 bayes= 10.2761 E= 1.7e+002 -865 67 205 -865 -865 67 -865 108 -865 -865 246 -865 -865 267 -865 -865 -865 267 -865 -865 170 -865 -865 -865 -865 -865 246 -865 -865 -865 246 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.7e+002 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCAGG MEME-5 regular expression -------------------------------------------------------------------------------- [GC][TC]GCCAGG -------------------------------------------------------------------------------- Time 4.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:13119-13199 7.68e-01 80 chrM:11994-12074 9.85e-01 80 chrM:460-540 9.95e-01 80 chrM:13601-13681 1.00e+00 80 chrM:9767-9847 9.84e-01 80 chrM:2707-2787 1.00e+00 80 chrM:11394-11474 1.00e+00 80 chrM:3860-3940 8.48e-01 80 chrM:6659-6739 1.00e+00 80 chrM:7525-7605 1.00e+00 80 chrM:7743-7823 5.54e-01 80 chrM:10335-10415 9.86e-01 80 chrM:5466-5546 9.59e-01 80 chrM:6458-6538 1.00e+00 80 chrM:5747-5827 1.00e+00 80 chrM:3653-3733 9.58e-02 80 chrM:9436-9516 9.44e-01 80 chrM:3200-3280 4.63e-01 80 chrM:6968-7048 1.00e+00 80 chrX:13349736-13349816 2.00e-02 54_[+4(4.06e-05)]_18 chrX:16931701-16931781 9.74e-01 80 chrM:1361-1441 7.43e-01 80 chrIV:3864936-3865016 3.65e-01 80 chrII:8577518-8577598 5.92e-01 80 chrII:2570822-2570902 8.95e-01 80 chrM:1021-1101 3.09e-01 80 chrM:8254-8334 2.59e-02 80 chrM:9041-9121 9.91e-01 80 chrM:4676-4756 8.48e-01 80 chrM:10916-10996 1.00e+00 80 chrM:8643-8723 9.94e-01 80 chrIV:4555761-4555841 8.31e-03 1_[+3(9.41e-06)]_71 chrM:12389-12469 6.09e-01 80 chrM:2207-2287 1.00e+00 80 chrIII:9881430-9881510 8.72e-01 80 chrI:1175836-1175916 1.49e-05 19_[+4(1.04e-05)]_16_[+1(6.07e-06)]_\ 29 chrM:6137-6217 9.60e-01 80 chrI:3547012-3547092 4.68e-08 6_[+4(1.04e-05)]_14_[+3(2.16e-06)]_\ 16_[+1(1.31e-05)]_20 chrII:1226472-1226552 6.34e-02 80 chrX:2364843-2364923 3.93e-03 27_[+2(9.80e-06)]_45 chrI:9381922-9382002 4.78e-03 40_[+1(8.14e-05)]_32 chrIII:8307487-8307567 4.34e-03 15_[+2(5.41e-06)]_57 chrV:265204-265284 6.44e-01 80 chrII:11637562-11637642 9.95e-01 80 chrV:6785254-6785334 7.24e-09 18_[+2(4.91e-07)]_8_[+3(2.16e-06)]_\ 16_[+1(3.45e-05)]_14 chrI:1958506-1958586 3.08e-05 39_[+4(1.70e-06)]_15_[+4(1.70e-06)]_\ 10 chrV:13176473-13176553 7.45e-03 55_[+1(9.53e-05)]_17 chrIII:8768068-8768148 1.65e-10 14_[+4(1.70e-06)]_3_[+4(6.20e-05)]_\ 5_[+5(2.87e-06)]_21_[+2(5.41e-06)]_5 chrIV:14464186-14464266 3.19e-03 64_[+4(2.73e-05)]_8 chrII:7708734-7708814 4.77e-05 19_[+1(6.52e-07)]_53 chrI:9343979-9344059 2.80e-02 9_[+4(6.20e-05)]_63 chrII:4999305-4999385 3.33e-02 62_[+4(6.20e-05)]_10 chrI:8411375-8411455 1.32e-03 52_[+5(4.14e-06)]_20 chrV:724098-724178 8.16e-01 80 chrIII:5555088-5555168 1.96e-07 29_[+3(1.07e-05)]_11_[+1(6.52e-07)]_\ 24 chrX:4388971-4389051 8.74e-04 80 chrV:10965637-10965717 2.48e-04 68_[+5(6.64e-06)]_4 chrII:14349691-14349771 3.03e-03 41_[+1(7.54e-05)]_31 chrI:1444169-1444249 8.59e-07 1_[+2(1.32e-06)]_13_[+1(6.52e-07)]_\ 50 chrIV:15471535-15471615 6.65e-02 46_[+1(4.80e-05)]_26 chrX:16056568-16056648 1.20e-02 80 chrIII:2768795-2768875 3.62e-05 33_[+3(2.16e-06)]_15_[+4(6.99e-05)]_\ 16 chrI:4633636-4633716 4.09e-08 14_[+4(1.04e-05)]_8_[+1(9.31e-06)]_\ 18_[+5(2.87e-06)]_16 chrIII:9629921-9630001 1.90e-05 34_[+2(4.91e-07)]_12_[+1(5.40e-05)]_\ 18 chrI:535378-535458 1.16e-03 80 chrI:14737445-14737525 1.10e-03 45_[+1(1.31e-05)]_27 chrX:12363128-12363208 8.90e-01 80 chrX:10568980-10569060 3.39e-02 37_[+1(7.54e-05)]_35 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************