******************************************************************************** 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/attf-4.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:13135-13215 1.0000 80 chrM:5249-5329 1.0000 80 chrM:8705-8785 1.0000 80 chrM:1773-1853 1.0000 80 chrM:7664-7744 1.0000 80 chrM:3301-3381 1.0000 80 chrV:12004636-12004716 1.0000 80 chrII:8603637-8603717 1.0000 80 chrX:6520325-6520405 1.0000 80 chrM:13603-13683 1.0000 80 chrM:9601-9681 1.0000 80 chrM:11564-11644 1.0000 80 chrM:10184-10264 1.0000 80 chrM:2863-2943 1.0000 80 chrM:8198-8278 1.0000 80 chrIV:8587273-8587353 1.0000 80 chrM:6367-6447 1.0000 80 chrM:8907-8987 1.0000 80 chrM:3675-3755 1.0000 80 chrM:7440-7520 1.0000 80 chrM:11178-11258 1.0000 80 chrII:6848088-6848168 1.0000 80 chrIII:4560653-4560733 1.0000 80 chrM:7222-7302 1.0000 80 chrM:10978-11058 1.0000 80 chrV:14366679-14366759 1.0000 80 chrV:8039297-8039377 1.0000 80 chrM:210-290 1.0000 80 chrIV:6792495-6792575 1.0000 80 chrM:1053-1133 1.0000 80 chrI:4635529-4635609 1.0000 80 chrIII:4195530-4195610 1.0000 80 chrIII:3980433-3980513 1.0000 80 chrI:9731245-9731325 1.0000 80 chrII:10543106-10543186 1.0000 80 chrX:11465326-11465406 1.0000 80 chrIII:313032-313112 1.0000 80 chrIV:1070625-1070705 1.0000 80 chrM:6156-6236 1.0000 80 chrM:4683-4763 1.0000 80 chrII:7810368-7810448 1.0000 80 chrM:12417-12497 1.0000 80 chrI:852178-852258 1.0000 80 chrM:9169-9249 1.0000 80 chrIII:5943824-5943904 1.0000 80 chrV:13656624-13656704 1.0000 80 chrIV:10935516-10935596 1.0000 80 chrM:12621-12701 1.0000 80 chrX:5686142-5686222 1.0000 80 chrX:7234834-7234914 1.0000 80 chrII:6888448-6888528 1.0000 80 chrV:10681414-10681494 1.0000 80 chrI:10769950-10770030 1.0000 80 chrIII:9717330-9717410 1.0000 80 chrIV:14034323-14034403 1.0000 80 chrIII:8443824-8443904 1.0000 80 chrIII:1419842-1419922 1.0000 80 chrX:5475302-5475382 1.0000 80 chrX:12889848-12889928 1.0000 80 chrX:6286337-6286417 1.0000 80 chrIII:7155555-7155635 1.0000 80 chrV:18723758-18723838 1.0000 80 chrI:7595604-7595684 1.0000 80 chrII:6370329-6370409 1.0000 80 chrX:16930915-16930995 1.0000 80 chrI:9854103-9854183 1.0000 80 chrX:1454519-1454599 1.0000 80 chrX:5319415-5319495 1.0000 80 chrIV:10936184-10936264 1.0000 80 chrX:5165185-5165265 1.0000 80 chrX:14169800-14169880 1.0000 80 chrIII:13464652-13464732 1.0000 80 chrX:14560209-14560289 1.0000 80 chrI:9869322-9869402 1.0000 80 chrI:9097731-9097811 1.0000 80 chrI:5429901-5429981 1.0000 80 chrII:9282919-9282999 1.0000 80 chrIV:9477661-9477741 1.0000 80 chrIV:17281456-17281536 1.0000 80 chrII:6951499-6951579 1.0000 80 chrIV:11593541-11593621 1.0000 80 chrII:6348526-6348606 1.0000 80 chrII:1247104-1247184 1.0000 80 chrX:5429511-5429591 1.0000 80 chrX:5841225-5841305 1.0000 80 chrIII:8802105-8802185 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_attf-4/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/attf-4.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= 86 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= 6880 N= 86 sample: seed= 0 hsfrac= 0 searchsize= 6880 norand= no csites= 1000 Letter frequencies in dataset: A 0.292 C 0.181 G 0.205 T 0.322 Background letter frequencies (from file dataset with add-one prior applied): A 0.292 C 0.181 G 0.205 T 0.322 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YGCGTCTC MEME-1 width = 8 sites = 10 llr = 98 E-value = 5.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::1::: pos.-specific C 4:a21a:a probability G :9:8:::: matrix T 61::8:a: bits 2.5 * * * 2.2 * * * 2.0 * * * 1.7 ** *** Relative 1.5 *** *** Entropy 1.2 *** *** (14.2 bits) 1.0 **** *** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGCGTCTC consensus C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:14366679-14366759 30 4.68e-06 GCGGTTGTCT CGCGTCTC CCGCGCGTCA chrIII:8802105-8802185 4 1.30e-05 CTC TGCGTCTC TTTTGCGCAA chrII:6370329-6370409 57 1.30e-05 TCTAACTGTC TGCGTCTC CACTATTGAA chrV:10681414-10681494 19 1.30e-05 CACATACACA TGCGTCTC AGTCCGTCGT chrIV:10935516-10935596 59 1.30e-05 GTCTGTCCTC TGCGTCTC TGACCTTTTA chrIII:4560653-4560733 55 1.30e-05 GCACGGACTC TGCGTCTC TCTTTCCTTC chrI:10769950-10770030 41 1.71e-05 CTAACTCTCT CGCCTCTC GAACAAAAAG chrIII:3980433-3980513 7 2.71e-05 GGCGCG CGCGCCTC TGTGCCCCCA chrI:9097731-9097811 5 5.09e-05 atct ctcgtctc tGACGACATC chrV:18723758-18723838 22 8.08e-05 ATGTTTTCTC TGCCACTC TCTCACATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:14366679-14366759 4.7e-06 29_[+1]_43 chrIII:8802105-8802185 1.3e-05 3_[+1]_69 chrII:6370329-6370409 1.3e-05 56_[+1]_16 chrV:10681414-10681494 1.3e-05 18_[+1]_54 chrIV:10935516-10935596 1.3e-05 58_[+1]_14 chrIII:4560653-4560733 1.3e-05 54_[+1]_18 chrI:10769950-10770030 1.7e-05 40_[+1]_32 chrIII:3980433-3980513 2.7e-05 6_[+1]_66 chrI:9097731-9097811 5.1e-05 4_[+1]_68 chrV:18723758-18723838 8.1e-05 21_[+1]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YGCGTCTC width=8 seqs=10 chrV:14366679-14366759 ( 30) CGCGTCTC 1 chrIII:8802105-8802185 ( 4) TGCGTCTC 1 chrII:6370329-6370409 ( 57) TGCGTCTC 1 chrV:10681414-10681494 ( 19) TGCGTCTC 1 chrIV:10935516-10935596 ( 59) TGCGTCTC 1 chrIII:4560653-4560733 ( 55) TGCGTCTC 1 chrI:10769950-10770030 ( 41) CGCCTCTC 1 chrIII:3980433-3980513 ( 7) CGCGCCTC 1 chrI:9097731-9097811 ( 5) CTCGTCTC 1 chrV:18723758-18723838 ( 22) TGCCACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6278 bayes= 9.54377 E= 5.7e+000 -997 114 -997 90 -997 -997 213 -169 -997 247 -997 -997 -997 15 196 -997 -154 -85 -997 131 -997 247 -997 -997 -997 -997 -997 163 -997 247 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 5.7e+000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.900000 0.100000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.100000 0.100000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGCGTCTC MEME-1 regular expression -------------------------------------------------------------------------------- [TC]GC[GC]TCTC -------------------------------------------------------------------------------- Time 1.44 secs. ******************************************************************************** ******************************************************************************** MOTIF AMGAGAGA MEME-2 width = 8 sites = 10 llr = 95 E-value = 9.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A a4:a:a28 pos.-specific C :6:::::: probability G ::a:a:82 matrix T :::::::: bits 2.5 2.2 * * 2.0 * * 1.7 * **** Relative 1.5 * ***** Entropy 1.2 ******** (13.7 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel ACGAGAGA consensus A AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:1247104-1247184 54 1.13e-05 gcggaacggg acgagaga gtgaggagac chrIV:11593541-11593621 31 1.13e-05 CTGTGATGAG ACGAGAGA TGCAGACAGT chrII:9282919-9282999 14 1.13e-05 CAATCAATAG ACGAGAGA AACCAGAGAG chrIII:1419842-1419922 59 1.13e-05 GAACCTGAGA ACGAGAGA AAAAAAATAA chrIII:3980433-3980513 46 1.13e-05 TGTTAGAGGT ACGAGAGA GATGGAGGCA chrII:6348526-6348606 4 2.96e-05 aga aagagaga gagatgagag chrII:6848088-6848168 9 5.37e-05 TCTCTGCG ACGAGAAA AAAGTGGGCA chrX:1454519-1454599 33 6.66e-05 GTGTTGTgag aagagagg aggggacagg chrM:11178-11258 3 6.66e-05 CT AAGAGAGG AGAAGGCTTA chrM:2863-2943 73 9.26e-05 CTTTTATTTC AAGAGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:1247104-1247184 1.1e-05 53_[+2]_19 chrIV:11593541-11593621 1.1e-05 30_[+2]_42 chrII:9282919-9282999 1.1e-05 13_[+2]_59 chrIII:1419842-1419922 1.1e-05 58_[+2]_14 chrIII:3980433-3980513 1.1e-05 45_[+2]_27 chrII:6348526-6348606 3e-05 3_[+2]_69 chrII:6848088-6848168 5.4e-05 8_[+2]_64 chrX:1454519-1454599 6.7e-05 32_[+2]_40 chrM:11178-11258 6.7e-05 2_[+2]_70 chrM:2863-2943 9.3e-05 72_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AMGAGAGA width=8 seqs=10 chrII:1247104-1247184 ( 54) ACGAGAGA 1 chrIV:11593541-11593621 ( 31) ACGAGAGA 1 chrII:9282919-9282999 ( 14) ACGAGAGA 1 chrIII:1419842-1419922 ( 59) ACGAGAGA 1 chrIII:3980433-3980513 ( 46) ACGAGAGA 1 chrII:6348526-6348606 ( 4) AAGAGAGA 1 chrII:6848088-6848168 ( 9) ACGAGAAA 1 chrX:1454519-1454599 ( 33) AAGAGAGG 1 chrM:11178-11258 ( 3) AAGAGAGG 1 chrM:2863-2943 ( 73) AAGAGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6278 bayes= 9.54377 E= 9.2e+001 178 -997 -997 -997 46 173 -997 -997 -997 -997 228 -997 178 -997 -997 -997 -997 -997 228 -997 178 -997 -997 -997 -54 -997 196 -997 145 -997 -4 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 9.2e+001 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 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 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMGAGAGA MEME-2 regular expression -------------------------------------------------------------------------------- A[CA]GAGA[GA][AG] -------------------------------------------------------------------------------- Time 2.31 secs. ******************************************************************************** ******************************************************************************** MOTIF AGACGSAG MEME-3 width = 8 sites = 13 llr = 117 E-value = 2.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:8:228: pos.-specific C :::8:52: probability G :a2284:a matrix T :::::::: bits 2.5 2.2 * * 2.0 * * 1.7 ** * * Relative 1.5 ** ** * Entropy 1.2 ***** ** (13.0 bits) 1.0 ***** ** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AGACGCAG consensus GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:1247104-1247184 68 7.03e-06 gagagtgagg agacgcag agcgg chrX:1454519-1454599 51 7.03e-06 aggggacagg agacgcag agCTTGCGAT chrIV:10936184-10936264 15 1.50e-05 CATGACCGCG AGACGGAG AGACGATGAG chrM:6156-6236 70 1.50e-05 TTTCTATTGC AGACGGAG TAT chrIII:3980433-3980513 70 1.50e-05 GGCAAATTAG AGACGGAG ACG chrII:6370329-6370409 26 2.43e-05 GGCGTGCACG AGACGGCG GGTCGATTCA chrX:11465326-11465406 25 2.92e-05 ATTCACAAGG AGGCGCAG GCATGGGTGG chrIII:8802105-8802185 25 4.05e-05 TGCGCAATCG AGACGAAG AAACCTTGGA chrI:7595604-7595684 68 6.72e-05 TGTTTTCTAT AGACACAG AGATC chrX:14169800-14169880 8 7.62e-05 AGGGACT AGAGGGAG AAAAGGGAAT chrII:6348526-6348606 30 8.32e-05 agagGGGCGG AGACGACG AGACACCACG chrII:9282919-9282999 39 1.09e-04 GAGATGCATC AGACACCG TATACTTGAT chrX:5686142-5686222 19 1.35e-04 TGGTCAGCGA AGGGGCAG GCGGACGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:1247104-1247184 7e-06 67_[+3]_5 chrX:1454519-1454599 7e-06 50_[+3]_22 chrIV:10936184-10936264 1.5e-05 14_[+3]_58 chrM:6156-6236 1.5e-05 69_[+3]_3 chrIII:3980433-3980513 1.5e-05 69_[+3]_3 chrII:6370329-6370409 2.4e-05 25_[+3]_47 chrX:11465326-11465406 2.9e-05 24_[+3]_48 chrIII:8802105-8802185 4.1e-05 24_[+3]_48 chrI:7595604-7595684 6.7e-05 67_[+3]_5 chrX:14169800-14169880 7.6e-05 7_[+3]_65 chrII:6348526-6348606 8.3e-05 29_[+3]_43 chrII:9282919-9282999 0.00011 38_[+3]_34 chrX:5686142-5686222 0.00014 18_[+3]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGACGSAG width=8 seqs=13 chrII:1247104-1247184 ( 68) AGACGCAG 1 chrX:1454519-1454599 ( 51) AGACGCAG 1 chrIV:10936184-10936264 ( 15) AGACGGAG 1 chrM:6156-6236 ( 70) AGACGGAG 1 chrIII:3980433-3980513 ( 70) AGACGGAG 1 chrII:6370329-6370409 ( 26) AGACGGCG 1 chrX:11465326-11465406 ( 25) AGGCGCAG 1 chrIII:8802105-8802185 ( 25) AGACGAAG 1 chrI:7595604-7595684 ( 68) AGACACAG 1 chrX:14169800-14169880 ( 8) AGAGGGAG 1 chrII:6348526-6348606 ( 30) AGACGACG 1 chrII:9282919-9282999 ( 39) AGACACCG 1 chrX:5686142-5686222 ( 19) AGGGGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6278 bayes= 9.44409 E= 2.4e+001 178 -1035 -1035 -1035 -1035 -1035 228 -1035 154 -1035 -41 -1035 -1035 223 -41 -1035 -92 -1035 204 -1035 -92 135 91 -1035 140 35 -1035 -1035 -1035 -1035 228 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 2.4e+001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.846154 0.000000 0.153846 0.000000 0.000000 0.846154 0.153846 0.000000 0.153846 0.000000 0.846154 0.000000 0.153846 0.461538 0.384615 0.000000 0.769231 0.230769 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACGSAG MEME-3 regular expression -------------------------------------------------------------------------------- AGACG[CG][AC]G -------------------------------------------------------------------------------- Time 3.18 secs. ******************************************************************************** ******************************************************************************** MOTIF GCMCCCAC MEME-4 width = 8 sites = 6 llr = 62 E-value = 4.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::5:::8: pos.-specific C :83aa82a probability G a22::::: matrix T :::::2:: bits 2.5 ** * 2.2 * ** * 2.0 * ** * 1.7 ** *** * Relative 1.5 ** *** * Entropy 1.2 ** ***** (15.0 bits) 1.0 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCACCCAC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:16930915-16930995 14 5.50e-06 GGATCATCAA GCACCCAC GACGCGCTAT chrIII:3980433-3980513 18 5.50e-06 GCGCCTCTGT GCCCCCAC GCCACTGAGT chrIV:8587273-8587353 58 5.50e-06 AGTGCGTAGT GCACCCAC ACCAGGCATC chrX:5686142-5686222 50 1.75e-05 CGGAAAACGA GGACCCAC ACATTTCTCT chrIV:1070625-1070705 48 1.90e-05 TCTCGGTGTT GCGCCCCC CGTGCTTGTC chrIII:4195530-4195610 53 2.88e-05 ACACCACGTG GCCCCTAC TTTCGTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:16930915-16930995 5.5e-06 13_[+4]_59 chrIII:3980433-3980513 5.5e-06 17_[+4]_55 chrIV:8587273-8587353 5.5e-06 57_[+4]_15 chrX:5686142-5686222 1.8e-05 49_[+4]_23 chrIV:1070625-1070705 1.9e-05 47_[+4]_25 chrIII:4195530-4195610 2.9e-05 52_[+4]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCMCCCAC width=8 seqs=6 chrX:16930915-16930995 ( 14) GCACCCAC 1 chrIII:3980433-3980513 ( 18) GCCCCCAC 1 chrIV:8587273-8587353 ( 58) GCACCCAC 1 chrX:5686142-5686222 ( 50) GGACCCAC 1 chrIV:1070625-1070705 ( 48) GCGCCCCC 1 chrIII:4195530-4195610 ( 53) GCCCCTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6278 bayes= 11.13 E= 4.5e+002 -923 -923 228 -923 -923 220 -30 -923 78 88 -30 -923 -923 247 -923 -923 -923 247 -923 -923 -923 220 -923 -95 151 -12 -923 -923 -923 247 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 4.5e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.500000 0.333333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCMCCCAC MEME-4 regular expression -------------------------------------------------------------------------------- GC[AC]CCCAC -------------------------------------------------------------------------------- Time 4.17 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTCWCTC MEME-5 width = 8 sites = 17 llr = 140 E-value = 7.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A 2:::3::: pos.-specific C :52a:a:a probability G ::1:1:1: matrix T 857:6:9: bits 2.5 * * * 2.2 * * * 2.0 * * * 1.7 * * * Relative 1.5 * * * Entropy 1.2 * *** (11.9 bits) 1.0 ** * *** 0.7 **** *** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTCTCTC consensus C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:9854103-9854183 58 1.15e-05 TCCTtcgctc tctctctc tcttgcactc chrX:5686142-5686222 63 1.15e-05 CCCACACATT TCTCTCTC CTATAATACT chrX:5841225-5841305 6 3.21e-05 ctctc tttctctc ggttctctgc chrX:12889848-12889928 29 3.21e-05 CATCACATTT TTTCTCTC TGTCTCGGCT chrII:6888448-6888528 57 4.25e-05 AAGTTGTTTG TCTCACTC ACAGCTCGAA chrI:4635529-4635609 6 4.25e-05 TGACT TCTCACTC TTTTTAACAT chrX:7234834-7234914 40 6.76e-05 TCTTCTCCCA TTTCACTC GGTTTCTCGG chrX:5165185-5165265 24 8.65e-05 CTTTCCTCTC TTCCTCTC CGCTGGTGCC chrV:18723758-18723838 44 1.10e-04 ACATTTCTGC ACTCTCTC GCCTACTTAC chrIII:4560653-4560733 71 1.10e-04 TCTCTTTCCT TCCCACTC TC chrV:10681414-10681494 41 1.23e-04 CGTCGTCACT TTTCGCTC CTCTTTTTAT chrI:9731245-9731325 33 1.23e-04 AGTGAGTCAT TTTCGCTC CTTGCGAACT chrIV:1070625-1070705 34 1.36e-04 TCCTGCTGTG TTGCTCTC GGTGTTGCGC chrX:5429511-5429591 9 1.65e-04 AGTACCCC TTCCACTC TAACCTTATC chrI:9869322-9869402 27 1.65e-04 TGTCAACTCC ATTCTCTC TAGTTTTTCA chrIV:10935516-10935596 21 1.99e-04 TTCCTCATGC TCTCTCGC TGAAACGCAT chrX:5319415-5319495 16 2.77e-04 CTTCAGTCGT ACGCTCTC CCAACTGAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:9854103-9854183 1.2e-05 57_[+5]_15 chrX:5686142-5686222 1.2e-05 62_[+5]_10 chrX:5841225-5841305 3.2e-05 5_[+5]_67 chrX:12889848-12889928 3.2e-05 28_[+5]_44 chrII:6888448-6888528 4.3e-05 56_[+5]_16 chrI:4635529-4635609 4.3e-05 5_[+5]_67 chrX:7234834-7234914 6.8e-05 39_[+5]_33 chrX:5165185-5165265 8.7e-05 23_[+5]_49 chrV:18723758-18723838 0.00011 43_[+5]_29 chrIII:4560653-4560733 0.00011 70_[+5]_2 chrV:10681414-10681494 0.00012 40_[+5]_32 chrI:9731245-9731325 0.00012 32_[+5]_40 chrIV:1070625-1070705 0.00014 33_[+5]_39 chrX:5429511-5429591 0.00017 8_[+5]_64 chrI:9869322-9869402 0.00017 26_[+5]_46 chrIV:10935516-10935596 0.0002 20_[+5]_52 chrX:5319415-5319495 0.00028 15_[+5]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TYTCWCTC width=8 seqs=17 chrI:9854103-9854183 ( 58) TCTCTCTC 1 chrX:5686142-5686222 ( 63) TCTCTCTC 1 chrX:5841225-5841305 ( 6) TTTCTCTC 1 chrX:12889848-12889928 ( 29) TTTCTCTC 1 chrII:6888448-6888528 ( 57) TCTCACTC 1 chrI:4635529-4635609 ( 6) TCTCACTC 1 chrX:7234834-7234914 ( 40) TTTCACTC 1 chrX:5165185-5165265 ( 24) TTCCTCTC 1 chrV:18723758-18723838 ( 44) ACTCTCTC 1 chrIII:4560653-4560733 ( 71) TCCCACTC 1 chrV:10681414-10681494 ( 41) TTTCGCTC 1 chrI:9731245-9731325 ( 33) TTTCGCTC 1 chrIV:1070625-1070705 ( 34) TTGCTCTC 1 chrX:5429511-5429591 ( 9) TTCCACTC 1 chrI:9869322-9869402 ( 27) ATTCTCTC 1 chrIV:10935516-10935596 ( 21) TCTCTCGC 1 chrX:5319415-5319495 ( 16) ACGCTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6278 bayes= 9.32105 E= 7.1e+002 -72 -1073 -1073 135 -1073 138 -1073 72 -1073 -4 -80 113 -1073 247 -1073 -1073 1 -1073 -80 87 -1073 247 -1073 -1073 -1073 -1073 -180 155 -1073 247 -1073 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 17 E= 7.1e+002 0.176471 0.000000 0.000000 0.823529 0.000000 0.470588 0.000000 0.529412 0.000000 0.176471 0.117647 0.705882 0.000000 1.000000 0.000000 0.000000 0.294118 0.000000 0.117647 0.588235 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.058824 0.941176 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCWCTC MEME-5 regular expression -------------------------------------------------------------------------------- T[TC]TC[TA]CTC -------------------------------------------------------------------------------- Time 5.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:13135-13215 9.96e-01 80 chrM:5249-5329 8.81e-01 80 chrM:8705-8785 8.88e-01 80 chrM:1773-1853 9.86e-01 80 chrM:7664-7744 9.97e-01 80 chrM:3301-3381 9.83e-01 80 chrV:12004636-12004716 8.98e-01 80 chrII:8603637-8603717 4.81e-01 80 chrX:6520325-6520405 8.62e-01 80 chrM:13603-13683 1.00e+00 80 chrM:9601-9681 7.31e-01 80 chrM:11564-11644 9.99e-01 80 chrM:10184-10264 8.49e-01 80 chrM:2863-2943 3.69e-01 72_[+2(9.26e-05)] chrM:8198-8278 7.78e-01 80 chrIV:8587273-8587353 1.85e-03 57_[+4(5.50e-06)]_15 chrM:6367-6447 1.00e+00 80 chrM:8907-8987 9.99e-01 80 chrM:3675-3755 1.00e+00 80 chrM:7440-7520 9.20e-01 80 chrM:11178-11258 1.22e-01 2_[+2(6.66e-05)]_70 chrII:6848088-6848168 1.14e-01 8_[+2(5.37e-05)]_64 chrIII:4560653-4560733 3.89e-04 54_[+1(1.30e-05)]_18 chrM:7222-7302 6.95e-01 80 chrM:10978-11058 7.43e-01 80 chrV:14366679-14366759 7.66e-04 29_[+1(4.68e-06)]_43 chrV:8039297-8039377 4.64e-01 80 chrM:210-290 9.90e-01 80 chrIV:6792495-6792575 6.75e-01 80 chrM:1053-1133 1.00e+00 80 chrI:4635529-4635609 1.60e-01 5_[+5(4.25e-05)]_67 chrIII:4195530-4195610 1.52e-02 52_[+4(2.88e-05)]_20 chrIII:3980433-3980513 8.74e-09 6_[+1(2.71e-05)]_3_[+4(5.50e-06)]_\ 20_[+2(1.13e-05)]_16_[+3(1.50e-05)]_3 chrI:9731245-9731325 1.35e-01 80 chrII:10543106-10543186 5.38e-01 80 chrX:11465326-11465406 1.50e-01 24_[+3(2.92e-05)]_48 chrIII:313032-313112 6.40e-01 80 chrIV:1070625-1070705 1.29e-03 47_[+4(1.90e-05)]_25 chrM:6156-6236 9.08e-02 69_[+3(1.50e-05)]_3 chrM:4683-4763 9.84e-01 80 chrII:7810368-7810448 1.60e-01 80 chrM:12417-12497 9.88e-01 80 chrI:852178-852258 2.16e-01 80 chrM:9169-9249 2.82e-01 80 chrIII:5943824-5943904 9.69e-01 80 chrV:13656624-13656704 7.39e-01 80 chrIV:10935516-10935596 2.39e-03 58_[+1(1.30e-05)]_14 chrM:12621-12701 1.00e+00 80 chrX:5686142-5686222 7.57e-06 49_[+4(1.75e-05)]_5_[+5(1.15e-05)]_\ 10 chrX:7234834-7234914 3.09e-02 39_[+5(6.76e-05)]_33 chrII:6888448-6888528 2.85e-02 56_[+5(4.25e-05)]_16 chrV:10681414-10681494 3.16e-04 18_[+1(1.30e-05)]_54 chrI:10769950-10770030 9.14e-04 40_[+1(1.71e-05)]_32 chrIII:9717330-9717410 7.21e-01 80 chrIV:14034323-14034403 9.00e-01 80 chrIII:8443824-8443904 8.10e-01 80 chrIII:1419842-1419922 6.98e-02 58_[+2(1.13e-05)]_14 chrX:5475302-5475382 9.03e-01 80 chrX:12889848-12889928 1.13e-02 28_[+5(3.21e-05)]_44 chrX:6286337-6286417 2.19e-01 80 chrIII:7155555-7155635 9.95e-01 80 chrV:18723758-18723838 5.96e-04 21_[+1(8.08e-05)]_51 chrI:7595604-7595684 1.21e-02 67_[+3(6.72e-05)]_5 chrII:6370329-6370409 2.88e-05 25_[+3(2.43e-05)]_23_[+1(1.30e-05)]_\ 16 chrX:16930915-16930995 1.62e-02 13_[+4(5.50e-06)]_59 chrI:9854103-9854183 1.23e-03 55_[+5(1.15e-05)]_17 chrX:1454519-1454599 1.28e-03 32_[+2(6.66e-05)]_10_[+3(7.03e-06)]_\ 22 chrX:5319415-5319495 7.80e-02 80 chrIV:10936184-10936264 6.07e-03 14_[+3(1.50e-05)]_58 chrX:5165185-5165265 3.93e-03 15_[+5(8.65e-05)]_[+5(8.65e-05)]_49 chrX:14169800-14169880 1.41e-03 7_[+3(7.62e-05)]_65 chrIII:13464652-13464732 6.81e-01 80 chrX:14560209-14560289 3.93e-01 80 chrI:9869322-9869402 1.18e-01 80 chrI:9097731-9097811 7.31e-04 4_[+1(5.09e-05)]_59_[+2(6.66e-05)]_\ 1 chrI:5429901-5429981 7.23e-01 80 chrII:9282919-9282999 1.36e-03 13_[+2(1.13e-05)]_59 chrIV:9477661-9477741 5.73e-01 80 chrIV:17281456-17281536 9.68e-01 80 chrII:6951499-6951579 3.67e-01 80 chrIV:11593541-11593621 8.61e-03 30_[+2(1.13e-05)]_42 chrII:6348526-6348606 4.94e-04 3_[+2(2.96e-05)]_18_[+3(8.32e-05)]_\ 43 chrII:1247104-1247184 1.67e-04 53_[+2(1.13e-05)]_6_[+3(7.03e-06)]_\ 5 chrX:5429511-5429591 6.38e-03 80 chrX:5841225-5841305 3.81e-02 5_[+5(3.21e-05)]_67 chrIII:8802105-8802185 4.00e-04 3_[+1(1.30e-05)]_13_[+3(4.05e-05)]_\ 15_[+3(8.32e-05)]_25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************