******************************************************************************** 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/unc-39.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIII:8392541-8392621 1.0000 80 chrX:7284733-7284813 1.0000 80 chrV:15431455-15431535 1.0000 80 chrX:7234899-7234979 1.0000 80 chrI:4674039-4674119 1.0000 80 chrV:9273803-9273883 1.0000 80 chrX:5729197-5729277 1.0000 80 chrIV:10481797-10481877 1.0000 80 chrIII:4505903-4505983 1.0000 80 chrIV:10500086-10500166 1.0000 80 chrIV:14033098-14033178 1.0000 80 chrV:10174797-10174877 1.0000 80 chrX:13967717-13967797 1.0000 80 chrV:9664819-9664899 1.0000 80 chrV:18490681-18490761 1.0000 80 chrII:10169542-10169622 1.0000 80 chrV:8876-8956 1.0000 80 chrI:4005531-4005611 1.0000 80 chrX:16147999-16148079 1.0000 80 chrI:9373241-9373321 1.0000 80 chrX:7265029-7265109 1.0000 80 chrIV:3135188-3135268 1.0000 80 chrI:5308617-5308697 1.0000 80 chrV:18711209-18711289 1.0000 80 chrX:10568568-10568648 1.0000 80 chrX:4145545-4145625 1.0000 80 chrX:993177-993257 1.0000 80 chrI:10235317-10235397 1.0000 80 chrIV:12771509-12771589 1.0000 80 chrV:18946815-18946895 1.0000 80 chrI:4298060-4298140 1.0000 80 chrX:12200512-12200592 1.0000 80 chrI:1700971-1701051 1.0000 80 chrV:13086076-13086156 1.0000 80 chrX:827713-827793 1.0000 80 chrII:13335391-13335471 1.0000 80 chrII:6491847-6491927 1.0000 80 chrIV:3636756-3636836 1.0000 80 chrI:1068635-1068715 1.0000 80 chrX:10637604-10637684 1.0000 80 chrV:6879730-6879810 1.0000 80 chrI:7518414-7518494 1.0000 80 chrV:13130620-13130700 1.0000 80 chrI:1873903-1873983 1.0000 80 chrI:3824395-3824475 1.0000 80 chrV:13082735-13082815 1.0000 80 chrX:5475074-5475154 1.0000 80 chrI:12039966-12040046 1.0000 80 chrIV:8795116-8795196 1.0000 80 chrII:9985106-9985186 1.0000 80 chrIII:835934-836014 1.0000 80 chrV:10715844-10715924 1.0000 80 chrX:9337860-9337940 1.0000 80 chrX:10146733-10146813 1.0000 80 chrV:13808638-13808718 1.0000 80 chrV:18967778-18967858 1.0000 80 chrV:15071420-15071500 1.0000 80 chrIII:3863022-3863102 1.0000 80 chrV:12814702-12814782 1.0000 80 chrX:13145344-13145424 1.0000 80 chrX:3127844-3127924 1.0000 80 chrII:9060478-9060558 1.0000 80 chrX:949635-949715 1.0000 80 chrII:11759453-11759533 1.0000 80 chrIV:10821859-10821939 1.0000 80 chrIV:16491650-16491730 1.0000 80 chrIV:6839160-6839240 1.0000 80 chrV:14351122-14351202 1.0000 80 chrII:14040452-14040532 1.0000 80 chrX:13969559-13969639 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_unc-39/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/unc-39.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= 70 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= 5600 N= 70 sample: seed= 0 hsfrac= 0 searchsize= 5600 norand= no csites= 1000 Letter frequencies in dataset: A 0.263 C 0.23 G 0.269 T 0.237 Background letter frequencies (from file dataset with add-one prior applied): A 0.263 C 0.23 G 0.269 T 0.237 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTCTCYCT MEME-1 width = 8 sites = 20 llr = 172 E-value = 1.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2::::::1 pos.-specific C 8:81a591 probability G 1::::12: matrix T :a2a:5:9 bits 2.1 * * 1.9 * * 1.7 * ** 1.5 **** ** Relative 1.3 ***** ** Entropy 1.1 ***** ** (12.4 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTCTCCCT consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:949635-949715 21 8.57e-06 GGTGGGTGct ctctccct ctcttcatct chrV:15071420-15071500 13 1.74e-05 ctaattctct ctctctct cattcactct chrII:9985106-9985186 23 1.74e-05 TTATTCAACA CTCTCTCT TCCCACGGGC chrV:6879730-6879810 22 1.74e-05 CTCTCTGCCG CTCTCTCT GACTCTCCGA chrIV:14033098-14033178 68 1.74e-05 AATGGTGACT CTCTCTCT CTCCA chrI:1873903-1873983 48 2.62e-05 GTGCCTCCTT CTTTCCCT TTTTAAGCAC chrV:18967778-18967858 69 3.53e-05 TTTTGCGTCA CTTTCTCT GCGT chrV:13086076-13086156 37 3.53e-05 TGCTCCCTTT CTTTCTCT ATATCTCTTA chrI:4674039-4674119 65 3.53e-05 CCTCCCCCAT CTTTCTCT CCCGTGCT chrX:12200512-12200592 14 4.51e-05 CCAAAGTCTC ATCTCCCT TGTTTCCCTG chrX:993177-993257 14 4.51e-05 GCTAACTGAA ATCTCCCT GAATGACATG chrI:3824395-3824475 4 6.52e-05 ttc atctctct TGTTATAGAC chrIV:12771509-12771589 56 6.52e-05 GCTTCTGCGC CTCTCCGT TTTTCTGTCT chrV:15431455-15431535 55 6.52e-05 TCGAAGTCTC CTCTCCGT ATGTGAGGAC chrX:7265029-7265109 24 7.56e-05 TTCTTTCTCC CTCTCTGT GAGTAAATGT chrV:13130620-13130700 51 8.56e-05 TGCTTGCACA CTCTCGCT TCTTCATAGC chrI:12039966-12040046 36 9.39e-05 GCGTCTCTTA CTCTCCCC TCACTATGTG chrI:1068635-1068715 73 1.20e-04 CCCAACCACC CTCTCCCA chrV:18490681-18490761 60 1.20e-04 CTCTTCTTTT CTCCCCCT TCCTCCATAT chrIV:3636756-3636836 73 1.49e-04 TACTCGTCTC GTCTCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:949635-949715 8.6e-06 20_[+1]_52 chrV:15071420-15071500 1.7e-05 12_[+1]_60 chrII:9985106-9985186 1.7e-05 22_[+1]_50 chrV:6879730-6879810 1.7e-05 21_[+1]_51 chrIV:14033098-14033178 1.7e-05 67_[+1]_5 chrI:1873903-1873983 2.6e-05 47_[+1]_25 chrV:18967778-18967858 3.5e-05 68_[+1]_4 chrV:13086076-13086156 3.5e-05 36_[+1]_36 chrI:4674039-4674119 3.5e-05 64_[+1]_8 chrX:12200512-12200592 4.5e-05 13_[+1]_59 chrX:993177-993257 4.5e-05 13_[+1]_59 chrI:3824395-3824475 6.5e-05 3_[+1]_69 chrIV:12771509-12771589 6.5e-05 55_[+1]_17 chrV:15431455-15431535 6.5e-05 54_[+1]_18 chrX:7265029-7265109 7.6e-05 23_[+1]_49 chrV:13130620-13130700 8.6e-05 50_[+1]_22 chrI:12039966-12040046 9.4e-05 35_[+1]_37 chrI:1068635-1068715 0.00012 72_[+1] chrV:18490681-18490761 0.00012 59_[+1]_13 chrIV:3636756-3636836 0.00015 72_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCTCYCT width=8 seqs=20 chrX:949635-949715 ( 21) CTCTCCCT 1 chrV:15071420-15071500 ( 13) CTCTCTCT 1 chrII:9985106-9985186 ( 23) CTCTCTCT 1 chrV:6879730-6879810 ( 22) CTCTCTCT 1 chrIV:14033098-14033178 ( 68) CTCTCTCT 1 chrI:1873903-1873983 ( 48) CTTTCCCT 1 chrV:18967778-18967858 ( 69) CTTTCTCT 1 chrV:13086076-13086156 ( 37) CTTTCTCT 1 chrI:4674039-4674119 ( 65) CTTTCTCT 1 chrX:12200512-12200592 ( 14) ATCTCCCT 1 chrX:993177-993257 ( 14) ATCTCCCT 1 chrI:3824395-3824475 ( 4) ATCTCTCT 1 chrIV:12771509-12771589 ( 56) CTCTCCGT 1 chrV:15431455-15431535 ( 55) CTCTCCGT 1 chrX:7265029-7265109 ( 24) CTCTCTGT 1 chrV:13130620-13130700 ( 51) CTCTCGCT 1 chrI:12039966-12040046 ( 36) CTCTCCCC 1 chrI:1068635-1068715 ( 73) CTCTCCCA 1 chrV:18490681-18490761 ( 60) CTCCCCCT 1 chrIV:3636756-3636836 ( 73) GTCTCCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5110 bayes= 9.46908 E= 1.4e-006 -81 180 -242 -1097 -1097 -1097 -1097 208 -1097 180 -1097 -25 -1097 -220 -1097 200 -1097 212 -1097 -1097 -1097 112 -242 92 -1097 188 -84 -1097 -239 -220 -1097 192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.4e-006 0.150000 0.800000 0.050000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.050000 0.000000 0.950000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.050000 0.450000 0.000000 0.850000 0.150000 0.000000 0.050000 0.050000 0.000000 0.900000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCTCYCT MEME-1 regular expression -------------------------------------------------------------------------------- CT[CT]TC[CT]CT -------------------------------------------------------------------------------- Time 0.99 secs. ******************************************************************************** ******************************************************************************** MOTIF AARAAGAR MEME-2 width = 8 sites = 27 llr = 208 E-value = 2.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 8779a:a5 pos.-specific C :::::::1 probability G 2331:a:4 matrix T :::::::: bits 2.1 1.9 *** 1.7 *** 1.5 **** Relative 1.3 **** Entropy 1.1 ******* (11.1 bits) 0.8 ******* 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAAAGAA consensus GGG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:6839160-6839240 10 2.34e-05 TTTTCATTC AAAAAGAA AAGCGACATG chrV:13808638-13808718 50 2.34e-05 AGCAAAATGA AAAAAGAA GAAACGAAAA chrV:10715844-10715924 36 2.34e-05 aatgccggag aaaaagaa ggaagagaat chrI:7518414-7518494 39 2.34e-05 AGAGCTTCGC AAAAAGAA ATCGTGTGCA chrX:827713-827793 57 2.34e-05 GCTGGCAGAA AAAAAGAA GATGGCAGTA chrI:4005531-4005611 45 2.34e-05 gaaaaagaag aaaaagaa gaaaaagaag chrX:7284733-7284813 73 2.34e-05 Cgaaaagaag aaaaagaa chrIV:16491650-16491730 17 4.74e-05 TCGCGTAGAG AAAAAGAG GGGACACACt chrI:10235317-10235397 61 4.74e-05 GAGAGAGAAG AAAAAGAG AAGAAAGTGT chrIII:4505903-4505983 51 4.74e-05 ATGGAGAGGA AAAAAGAG ACGCTGTGAG chrIV:10481797-10481877 51 4.74e-05 TCTGTGTCTG AAAAAGAG CACGCCTTCG chrX:9337860-9337940 51 7.13e-05 TACATCGAGA AAGAAGAA TAAGGGACCC chrI:4674039-4674119 10 7.13e-05 aagaagacg aagaagaa gatgaGGGGG chrII:11759453-11759533 10 1.44e-04 CATTATAAG AGAAAGAG ACGGCCGACA chrX:5729197-5729277 61 1.44e-04 TCTGAAAGGC AGAAAGAG GGACGTGGAG chrIV:8795116-8795196 55 1.68e-04 AGGAGTTAGA GAAAAGAA AGGAGCGAAC chrI:4298060-4298140 65 1.93e-04 CATATACATC GAAAAGAG AGTAGGAA chrV:9273803-9273883 41 1.93e-04 GCGGGAGGTG GAAAAGAG GAGAGAGAGA chrV:12814702-12814782 3 2.17e-04 AC AGGAAGAA AGTGCAGAGA chrV:13130620-13130700 11 2.17e-04 CCGTCAGCAT AGGAAGAA GATGCTTTCC chrV:13082735-13082815 48 2.42e-04 AGCACACCGG AGGAAGAG GTGGGATTCA chrIV:3135188-3135268 18 3.37e-04 ctgcATCGAC GAGAAGAG TGAGcacata chrV:18490681-18490761 16 3.37e-04 GGAGGGGGAT GAGAAGAG AGGAGGGGGG chrV:15071420-15071500 50 4.52e-04 AGTCGGTCAG AGAAAGAC AACCGGAGGG chrI:12039966-12040046 2 6.44e-04 G AGAGAGAG GGAGAGACAA chrII:13335391-13335471 52 6.90e-04 AAGGTCGGGT GAGAAGAC ATGCATTGTT chrX:993177-993257 72 7.62e-04 GCGGCGGGTG AGGGAGAA G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:6839160-6839240 2.3e-05 9_[+2]_63 chrV:13808638-13808718 2.3e-05 49_[+2]_23 chrV:10715844-10715924 2.3e-05 35_[+2]_37 chrI:7518414-7518494 2.3e-05 38_[+2]_34 chrX:827713-827793 2.3e-05 56_[+2]_16 chrI:4005531-4005611 2.3e-05 44_[+2]_28 chrX:7284733-7284813 2.3e-05 72_[+2] chrIV:16491650-16491730 4.7e-05 16_[+2]_56 chrI:10235317-10235397 4.7e-05 60_[+2]_12 chrIII:4505903-4505983 4.7e-05 50_[+2]_22 chrIV:10481797-10481877 4.7e-05 50_[+2]_22 chrX:9337860-9337940 7.1e-05 50_[+2]_22 chrI:4674039-4674119 7.1e-05 9_[+2]_63 chrII:11759453-11759533 0.00014 9_[+2]_63 chrX:5729197-5729277 0.00014 60_[+2]_12 chrIV:8795116-8795196 0.00017 54_[+2]_18 chrI:4298060-4298140 0.00019 64_[+2]_8 chrV:9273803-9273883 0.00019 40_[+2]_32 chrV:12814702-12814782 0.00022 2_[+2]_70 chrV:13130620-13130700 0.00022 10_[+2]_62 chrV:13082735-13082815 0.00024 47_[+2]_25 chrIV:3135188-3135268 0.00034 17_[+2]_55 chrV:18490681-18490761 0.00034 15_[+2]_57 chrV:15071420-15071500 0.00045 49_[+2]_23 chrI:12039966-12040046 0.00064 1_[+2]_71 chrII:13335391-13335471 0.00069 51_[+2]_21 chrX:993177-993257 0.00076 71_[+2]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AARAAGAR width=8 seqs=27 chrIV:6839160-6839240 ( 10) AAAAAGAA 1 chrV:13808638-13808718 ( 50) AAAAAGAA 1 chrV:10715844-10715924 ( 36) AAAAAGAA 1 chrI:7518414-7518494 ( 39) AAAAAGAA 1 chrX:827713-827793 ( 57) AAAAAGAA 1 chrI:4005531-4005611 ( 45) AAAAAGAA 1 chrX:7284733-7284813 ( 73) AAAAAGAA 1 chrIV:16491650-16491730 ( 17) AAAAAGAG 1 chrI:10235317-10235397 ( 61) AAAAAGAG 1 chrIII:4505903-4505983 ( 51) AAAAAGAG 1 chrIV:10481797-10481877 ( 51) AAAAAGAG 1 chrX:9337860-9337940 ( 51) AAGAAGAA 1 chrI:4674039-4674119 ( 10) AAGAAGAA 1 chrII:11759453-11759533 ( 10) AGAAAGAG 1 chrX:5729197-5729277 ( 61) AGAAAGAG 1 chrIV:8795116-8795196 ( 55) GAAAAGAA 1 chrI:4298060-4298140 ( 65) GAAAAGAG 1 chrV:9273803-9273883 ( 41) GAAAAGAG 1 chrV:12814702-12814782 ( 3) AGGAAGAA 1 chrV:13130620-13130700 ( 11) AGGAAGAA 1 chrV:13082735-13082815 ( 48) AGGAAGAG 1 chrIV:3135188-3135268 ( 18) GAGAAGAG 1 chrV:18490681-18490761 ( 16) GAGAAGAG 1 chrV:15071420-15071500 ( 50) AGAAAGAC 1 chrI:12039966-12040046 ( 2) AGAGAGAG 1 chrII:13335391-13335471 ( 52) GAGAAGAC 1 chrX:993177-993257 ( 72) AGGGAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5110 bayes= 8.75506 E= 2.6e-005 156 -1140 -28 -1140 142 -1140 14 -1140 134 -1140 31 -1140 181 -1140 -186 -1140 192 -1140 -1140 -1140 -1140 -1140 189 -1140 192 -1140 -1140 -1140 87 -164 72 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.6e-005 0.777778 0.000000 0.222222 0.000000 0.703704 0.000000 0.296296 0.000000 0.666667 0.000000 0.333333 0.000000 0.925926 0.000000 0.074074 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 0.481481 0.074074 0.444444 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAAGAR MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG][AG]AAGA[AG] -------------------------------------------------------------------------------- Time 1.76 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTGTGHG MEME-3 width = 8 sites = 25 llr = 188 E-value = 4.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 2:::314: pos.-specific C :::2::2: probability G :a:8:9:a matrix T 8:a:7:4: bits 2.1 1.9 * * 1.7 ** * 1.5 ** * * Relative 1.3 *** * * Entropy 1.1 ****** * (10.9 bits) 0.8 ****** * 0.6 ****** * 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGTGTGTG consensus A A A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:16491650-16491730 40 1.65e-05 ACACtgtgtg tgtgtgtg tgtAAGAGAA chrIV:10821859-10821939 45 1.65e-05 agtgtatgtg tgtgtgtg cgtatgtgtg chrI:1873903-1873983 31 1.65e-05 GCCACCAGTG TGTGTGTG TGCCTCCTTC chrV:13808638-13808718 9 3.49e-05 tgagtgcg tgtgtgag tgagtgagag chrX:10568568-10568648 42 3.49e-05 tccacgtgag tgtgtgag tgagtagatg chrX:7265029-7265109 59 3.49e-05 AACGTCGGCT TGTGTGAG TGAATGGTGA chrV:9273803-9273883 9 3.49e-05 CTCGATGT TGTGTGAG AAAACGTTCT chrV:13130620-13130700 69 5.09e-05 TCTTCATAGC TGTGTGCG TCTC chrI:7518414-7518494 19 5.09e-05 ACATGATGGC TGTGTGCG CGAGAGCTTC chrI:10235317-10235397 46 8.96e-05 ACAACTATTT TGTGAGAG AGAGAAGAAA chrIII:4505903-4505983 63 8.96e-05 AAAGAGACGC TGTGAGAG AATGAGTGTT chrIII:8392541-8392621 42 8.96e-05 ACATTTTTCT TGTGAGAG GAGACGAAGA chrV:13082735-13082815 67 1.26e-04 TGGGATTCAG AGTGTGTG CAGCGG chrV:18711209-18711289 37 1.26e-04 GTTGACGAAT AGTGTGTG TTTTACGATA chrII:10169542-10169622 72 1.40e-04 agagagtgtc tgtctgtg t chrIV:10481797-10481877 39 1.40e-04 ACTCTCTAGT TGTCTGTG TCTGAAAAAG chrIV:12771509-12771589 69 2.07e-04 TCCGTTTTTC TGTCTGCG TGTG chrIV:14033098-14033178 6 2.07e-04 CTAGT TGTCTGCG TCTCTCATCA chrII:9985106-9985186 68 2.28e-04 TTGCAAAACT AGTGAGTG AAAAG chrIV:6839160-6839240 42 2.82e-04 TTAGAGAGAT AGTGAGAG GAATAGAGAA chrV:15431455-15431535 5 4.83e-04 CGCG TGTGAATG TTGGGTCCGA chrX:5729197-5729277 4 5.32e-04 TGG CGTGTGCG GCAAATACTG chrX:949635-949715 44 5.86e-04 catctcactc tctGTGCG GTGTCTCAAT chrV:15071420-15071500 34 9.32e-04 tcactctcAT TGAGAGAG TCGGTCAGAG chrIV:8795116-8795196 26 1.03e-03 AAGAGACACA AGTGAATG ATATGAGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:16491650-16491730 1.7e-05 39_[+3]_33 chrIV:10821859-10821939 1.7e-05 44_[+3]_28 chrI:1873903-1873983 1.7e-05 30_[+3]_42 chrV:13808638-13808718 3.5e-05 8_[+3]_64 chrX:10568568-10568648 3.5e-05 41_[+3]_31 chrX:7265029-7265109 3.5e-05 58_[+3]_14 chrV:9273803-9273883 3.5e-05 8_[+3]_64 chrV:13130620-13130700 5.1e-05 68_[+3]_4 chrI:7518414-7518494 5.1e-05 18_[+3]_54 chrI:10235317-10235397 9e-05 45_[+3]_27 chrIII:4505903-4505983 9e-05 62_[+3]_10 chrIII:8392541-8392621 9e-05 41_[+3]_31 chrV:13082735-13082815 0.00013 66_[+3]_6 chrV:18711209-18711289 0.00013 36_[+3]_36 chrII:10169542-10169622 0.00014 71_[+3]_1 chrIV:10481797-10481877 0.00014 38_[+3]_34 chrIV:12771509-12771589 0.00021 68_[+3]_4 chrIV:14033098-14033178 0.00021 5_[+3]_67 chrII:9985106-9985186 0.00023 67_[+3]_5 chrIV:6839160-6839240 0.00028 41_[+3]_31 chrV:15431455-15431535 0.00048 4_[+3]_68 chrX:5729197-5729277 0.00053 3_[+3]_69 chrX:949635-949715 0.00059 43_[+3]_29 chrV:15071420-15071500 0.00093 33_[+3]_39 chrIV:8795116-8795196 0.001 25_[+3]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTGTGHG width=8 seqs=25 chrIV:16491650-16491730 ( 40) TGTGTGTG 1 chrIV:10821859-10821939 ( 45) TGTGTGTG 1 chrI:1873903-1873983 ( 31) TGTGTGTG 1 chrV:13808638-13808718 ( 9) TGTGTGAG 1 chrX:10568568-10568648 ( 42) TGTGTGAG 1 chrX:7265029-7265109 ( 59) TGTGTGAG 1 chrV:9273803-9273883 ( 9) TGTGTGAG 1 chrV:13130620-13130700 ( 69) TGTGTGCG 1 chrI:7518414-7518494 ( 19) TGTGTGCG 1 chrI:10235317-10235397 ( 46) TGTGAGAG 1 chrIII:4505903-4505983 ( 63) TGTGAGAG 1 chrIII:8392541-8392621 ( 42) TGTGAGAG 1 chrV:13082735-13082815 ( 67) AGTGTGTG 1 chrV:18711209-18711289 ( 37) AGTGTGTG 1 chrII:10169542-10169622 ( 72) TGTCTGTG 1 chrIV:10481797-10481877 ( 39) TGTCTGTG 1 chrIV:12771509-12771589 ( 69) TGTCTGCG 1 chrIV:14033098-14033178 ( 6) TGTCTGCG 1 chrII:9985106-9985186 ( 68) AGTGAGTG 1 chrIV:6839160-6839240 ( 42) AGTGAGAG 1 chrV:15431455-15431535 ( 5) TGTGAATG 1 chrX:5729197-5729277 ( 4) CGTGTGCG 1 chrX:949635-949715 ( 44) TCTGTGCG 1 chrV:15071420-15071500 ( 34) TGAGAGAG 1 chrIV:8795116-8795196 ( 26) AGTGAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5110 bayes= 8.16027 E= 4.0e-001 -40 -252 -1129 168 -1129 -252 183 -1129 -272 -1129 -1129 202 -1129 -53 164 -1129 28 -1129 -1129 152 -172 -1129 177 -1129 45 6 -1129 75 -1129 -1129 189 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 4.0e-001 0.200000 0.040000 0.000000 0.760000 0.000000 0.040000 0.960000 0.000000 0.040000 0.000000 0.000000 0.960000 0.000000 0.160000 0.840000 0.000000 0.320000 0.000000 0.000000 0.680000 0.080000 0.000000 0.920000 0.000000 0.360000 0.240000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTGTGHG MEME-3 regular expression -------------------------------------------------------------------------------- [TA]GTG[TA]G[TAC]G -------------------------------------------------------------------------------- Time 2.48 secs. ******************************************************************************** ******************************************************************************** MOTIF CTTCTCTT MEME-4 width = 8 sites = 7 llr = 68 E-value = 7.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 9::a:91: probability G :3:::::: matrix T 17a:a19a bits 2.1 *** * 1.9 *** * 1.7 *** * 1.5 * ****** Relative 1.3 * ****** Entropy 1.1 ******** (14.0 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTTCTCTT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:13082735-13082815 13 9.10e-06 CTCGAATTTC CTTCTCTT CAAAAACTAT chrIV:12771509-12771589 30 9.10e-06 agcagaagcT CTTCTCTT CTGCTTCAGC chrV:10174797-10174877 70 9.10e-06 CTCTATGAGT CTTCTCTT CGA chrI:12039966-12040046 27 1.94e-05 CAAGTGCCTG CGTCTCTT ACTCTCCCCT chrI:4674039-4674119 50 2.83e-05 TGCACAACGG CTTCTCCT CCCCCATCTT chrV:18490681-18490761 52 4.70e-05 TAGTGTAACT CTTCTTTT CTCCCCCTTC chrX:10146733-10146813 59 7.83e-05 GGGGCCCCTA TGTCTCTT CTGACGAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:13082735-13082815 9.1e-06 12_[+4]_60 chrIV:12771509-12771589 9.1e-06 29_[+4]_43 chrV:10174797-10174877 9.1e-06 69_[+4]_3 chrI:12039966-12040046 1.9e-05 26_[+4]_46 chrI:4674039-4674119 2.8e-05 49_[+4]_23 chrV:18490681-18490761 4.7e-05 51_[+4]_21 chrX:10146733-10146813 7.8e-05 58_[+4]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTTCTCTT width=8 seqs=7 chrV:13082735-13082815 ( 13) CTTCTCTT 1 chrIV:12771509-12771589 ( 30) CTTCTCTT 1 chrV:10174797-10174877 ( 70) CTTCTCTT 1 chrI:12039966-12040046 ( 27) CGTCTCTT 1 chrI:4674039-4674119 ( 50) CTTCTCCT 1 chrV:18490681-18490761 ( 52) CTTCTTTT 1 chrX:10146733-10146813 ( 59) TGTCTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5110 bayes= 8.48727 E= 7.9e+002 -945 189 -945 -73 -945 -945 9 159 -945 -945 -945 207 -945 212 -945 -945 -945 -945 -945 207 -945 189 -945 -73 -945 -69 -945 185 -945 -945 -945 207 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 7.9e+002 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.285714 0.714286 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 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCTCTT MEME-4 regular expression -------------------------------------------------------------------------------- C[TG]TCTCTT -------------------------------------------------------------------------------- Time 3.19 secs. ******************************************************************************** ******************************************************************************** MOTIF ACRCACAC MEME-5 width = 8 sites = 13 llr = 111 E-value = 5.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACRCACAC MEME-5 Description -------------------------------------------------------------------------------- Simplified A 836:8:a: pos.-specific C 27:8:a:a probability G ::4::::: matrix T :::22::: bits 2.1 * * 1.9 *** 1.7 *** 1.5 * *** Relative 1.3 ** ***** Entropy 1.1 ** ***** (12.3 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACACACAC consensus AG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRCACAC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:9060478-9060558 56 1.34e-05 acacggagac acacacac acaacaACCA chrIV:3135188-3135268 45 1.34e-05 acacacacac acacacac acacacacac chrV:10174797-10174877 30 1.34e-05 AGGCATTcac acacacac atacacactc chrX:7234899-7234979 51 2.71e-05 ACTGCCACAT ACGCACAC AAAACACATT chrI:4298060-4298140 44 4.24e-05 TGCCAACAGC AAACACAC CAACATATAC chrV:9664819-9664899 13 4.24e-05 TGGAGCACAC AAACACAC CATGCACATG chrI:3824395-3824475 59 5.45e-05 CGCTCACGAG ACACTCAC CACGCGCTCA chrI:7518414-7518494 60 5.45e-05 GTGTGCATGT ACACTCAC GCTCACTGAA chrV:13082735-13082815 37 7.01e-05 CTATTTGTAA AAGCACAC CGGAGGAAGA chrX:5729197-5729277 29 1.08e-04 CTGAAGACAT ACATACAC GACGATGATG chrIV:3636756-3636836 53 1.34e-04 CCGCCCTCCT CCGCACAC GTTACTCGTC chrX:3127844-3127924 49 2.28e-04 TTCCTCTCAA CAGCACAC AGTCCCTCAC chrIII:835934-836014 20 2.80e-04 GAGCCAATCC ACGTTCAC GGATTCCGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRCACAC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:9060478-9060558 1.3e-05 55_[+5]_17 chrIV:3135188-3135268 1.3e-05 44_[+5]_28 chrV:10174797-10174877 1.3e-05 29_[+5]_43 chrX:7234899-7234979 2.7e-05 50_[+5]_22 chrI:4298060-4298140 4.2e-05 43_[+5]_29 chrV:9664819-9664899 4.2e-05 12_[+5]_60 chrI:3824395-3824475 5.4e-05 58_[+5]_14 chrI:7518414-7518494 5.4e-05 59_[+5]_13 chrV:13082735-13082815 7e-05 36_[+5]_36 chrX:5729197-5729277 0.00011 28_[+5]_44 chrIV:3636756-3636836 0.00013 52_[+5]_20 chrX:3127844-3127924 0.00023 48_[+5]_24 chrIII:835934-836014 0.00028 19_[+5]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRCACAC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACRCACAC width=8 seqs=13 chrII:9060478-9060558 ( 56) ACACACAC 1 chrIV:3135188-3135268 ( 45) ACACACAC 1 chrV:10174797-10174877 ( 30) ACACACAC 1 chrX:7234899-7234979 ( 51) ACGCACAC 1 chrI:4298060-4298140 ( 44) AAACACAC 1 chrV:9664819-9664899 ( 13) AAACACAC 1 chrI:3824395-3824475 ( 59) ACACTCAC 1 chrI:7518414-7518494 ( 60) ACACTCAC 1 chrV:13082735-13082815 ( 37) AAGCACAC 1 chrX:5729197-5729277 ( 29) ACATACAC 1 chrIV:3636756-3636836 ( 53) CCGCACAC 1 chrX:3127844-3127924 ( 49) CAGCACAC 1 chrIII:835934-836014 ( 20) ACGTTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRCACAC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5110 bayes= 9.78142 E= 5.4e+002 168 -58 -1035 -1035 22 159 -1035 -1035 122 -1035 51 -1035 -1035 188 -1035 -62 155 -1035 -1035 -4 -1035 212 -1035 -1035 192 -1035 -1035 -1035 -1035 212 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACRCACAC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 5.4e+002 0.846154 0.153846 0.000000 0.000000 0.307692 0.692308 0.000000 0.000000 0.615385 0.000000 0.384615 0.000000 0.000000 0.846154 0.000000 0.153846 0.769231 0.000000 0.000000 0.230769 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 ACRCACAC MEME-5 regular expression -------------------------------------------------------------------------------- A[CA][AG]C[AT]CAC -------------------------------------------------------------------------------- Time 4.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:8392541-8392621 7.84e-03 41_[+3(8.96e-05)]_31 chrX:7284733-7284813 7.80e-02 21_[+2(2.34e-05)]_43_[+2(2.34e-05)] chrV:15431455-15431535 9.82e-03 54_[+1(6.52e-05)]_18 chrX:7234899-7234979 3.68e-02 50_[+5(2.71e-05)]_22 chrI:4674039-4674119 3.80e-05 9_[+2(7.13e-05)]_15_[+1(6.52e-05)]_\ 9_[+4(2.83e-05)]_7_[+1(3.53e-05)]_8 chrV:9273803-9273883 4.78e-03 8_[+3(3.49e-05)]_64 chrX:5729197-5729277 4.70e-03 80 chrIV:10481797-10481877 5.77e-03 7_[+2(7.13e-05)]_35_[+2(4.74e-05)]_\ 22 chrIII:4505903-4505983 8.39e-03 50_[+2(4.74e-05)]_4_[+3(8.96e-05)]_\ 10 chrIV:10500086-10500166 7.38e-01 80 chrIV:14033098-14033178 1.07e-03 65_[+1(1.74e-05)]_7 chrV:10174797-10174877 9.85e-05 27_[+5(1.34e-05)]_12_[+5(2.71e-05)]_\ 14_[+4(9.10e-06)]_3 chrX:13967717-13967797 7.90e-01 80 chrV:9664819-9664899 6.27e-02 12_[+5(4.24e-05)]_60 chrV:18490681-18490761 1.11e-03 51_[+4(4.70e-05)]_21 chrII:10169542-10169622 9.54e-03 80 chrV:8876-8956 7.60e-01 80 chrI:4005531-4005611 4.70e-02 35_[+2(2.34e-05)]_1_[+2(2.34e-05)]_\ 1_[+2(2.34e-05)]_19 chrX:16147999-16148079 4.69e-01 80 chrI:9373241-9373321 1.41e-01 80 chrX:7265029-7265109 2.96e-03 23_[+1(7.56e-05)]_27_[+3(3.49e-05)]_\ 14 chrIV:3135188-3135268 1.89e-03 34_[+5(1.34e-05)]_[+5(1.34e-05)]_\ [+5(1.34e-05)]_[+5(1.34e-05)]_14 chrI:5308617-5308697 5.47e-01 80 chrV:18711209-18711289 2.17e-02 80 chrX:10568568-10568648 1.14e-01 11_[+3(6.92e-05)]_22_[+3(3.49e-05)]_\ 31 chrX:4145545-4145625 3.65e-01 80 chrX:993177-993257 1.32e-03 13_[+1(4.51e-05)]_59 chrI:10235317-10235397 2.20e-03 45_[+3(8.96e-05)]_7_[+2(4.74e-05)]_\ 12 chrIV:12771509-12771589 1.56e-04 29_[+4(9.10e-06)]_18_[+1(6.52e-05)]_\ 17 chrV:18946815-18946895 5.78e-01 80 chrI:4298060-4298140 2.43e-02 43_[+5(4.24e-05)]_29 chrX:12200512-12200592 1.18e-01 13_[+1(4.51e-05)]_59 chrI:1700971-1701051 4.59e-01 80 chrV:13086076-13086156 3.49e-02 36_[+1(3.53e-05)]_36 chrX:827713-827793 1.53e-02 56_[+2(2.34e-05)]_16 chrII:13335391-13335471 3.25e-01 80 chrII:6491847-6491927 3.64e-01 80 chrIV:3636756-3636836 4.62e-03 80 chrI:1068635-1068715 1.63e-01 80 chrX:10637604-10637684 5.16e-01 80 chrV:6879730-6879810 1.48e-02 21_[+1(1.74e-05)]_51 chrI:7518414-7518494 3.47e-05 18_[+3(5.09e-05)]_12_[+2(2.34e-05)]_\ 13_[+5(5.45e-05)]_13 chrV:13130620-13130700 3.04e-05 50_[+1(8.56e-05)]_10_[+3(5.09e-05)]_\ 4 chrI:1873903-1873983 1.09e-04 28_[+3(1.65e-05)]_11_[+1(2.62e-05)]_\ 25 chrI:3824395-3824475 9.85e-04 3_[+1(6.52e-05)]_36_[+5(9.42e-05)]_\ 3_[+5(5.45e-05)]_14 chrV:13082735-13082815 1.33e-06 12_[+4(9.10e-06)]_16_[+5(7.01e-05)]_\ 36 chrX:5475074-5475154 4.52e-01 80 chrI:12039966-12040046 5.56e-05 26_[+4(1.94e-05)]_1_[+1(9.39e-05)]_\ 37 chrIV:8795116-8795196 6.39e-02 80 chrII:9985106-9985186 2.53e-04 22_[+1(1.74e-05)]_50 chrIII:835934-836014 5.19e-01 80 chrV:10715844-10715924 7.35e-02 35_[+2(2.34e-05)]_37 chrX:9337860-9337940 7.80e-02 50_[+2(7.13e-05)]_22 chrX:10146733-10146813 8.44e-02 58_[+4(7.83e-05)]_14 chrV:13808638-13808718 5.86e-04 8_[+3(3.49e-05)]_33_[+2(2.34e-05)]_\ 23 chrV:18967778-18967858 7.77e-03 68_[+1(3.53e-05)]_4 chrV:15071420-15071500 5.20e-04 8_[+1(1.74e-05)]_64 chrIII:3863022-3863102 5.23e-01 80 chrV:12814702-12814782 2.01e-01 80 chrX:13145344-13145424 3.20e-01 80 chrX:3127844-3127924 1.23e-02 80 chrII:9060478-9060558 1.25e-02 41_[+5(1.34e-05)]_4_[+5(1.34e-05)]_\ 19 chrX:949635-949715 3.39e-04 20_[+1(8.57e-06)]_12_[+1(7.56e-05)]_\ 32 chrII:11759453-11759533 1.23e-01 80 chrIV:10821859-10821939 2.88e-03 40_[+3(1.65e-05)]_8_[+3(3.49e-05)]_\ 16 chrIV:16491650-16491730 1.04e-03 16_[+2(4.74e-05)]_9_[+3(1.65e-05)]_\ [+3(1.65e-05)]_31 chrIV:6839160-6839240 6.87e-03 9_[+2(2.34e-05)]_40_[+2(4.74e-05)]_\ 15 chrV:14351122-14351202 9.63e-01 80 chrII:14040452-14040532 6.40e-02 80 chrX:13969559-13969639 9.79e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c26n06.farnam.hpc.yale.internal ********************************************************************************