******************************************************************************** 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/hlh-17.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIV:16237733-16237813 1.0000 80 chrI:1326327-1326407 1.0000 80 chrIV:8595087-8595167 1.0000 80 chrII:13282932-13283012 1.0000 80 chrV:13786421-13786501 1.0000 80 chrX:767820-767900 1.0000 80 chrIV:3621994-3622074 1.0000 80 chrV:17587214-17587294 1.0000 80 chrX:1503877-1503957 1.0000 80 chrII:11977387-11977467 1.0000 80 chrIV:10426697-10426777 1.0000 80 chrIV:14403136-14403216 1.0000 80 chrII:11974811-11974891 1.0000 80 chrI:11221424-11221504 1.0000 80 chrIII:13635149-13635229 1.0000 80 chrIII:5829419-5829499 1.0000 80 chrIV:10177605-10177685 1.0000 80 chrIV:2107630-2107710 1.0000 80 chrIV:16415754-16415834 1.0000 80 chrV:12510128-12510208 1.0000 80 chrIV:11644919-11644999 1.0000 80 chrX:14614472-14614552 1.0000 80 chrI:5992297-5992377 1.0000 80 chrIV:8431735-8431815 1.0000 80 chrIII:12660471-12660551 1.0000 80 chrX:936025-936105 1.0000 80 chrIII:5169556-5169636 1.0000 80 chrII:10935020-10935100 1.0000 80 chrI:933436-933516 1.0000 80 chrIII:9868276-9868356 1.0000 80 chrI:13421154-13421234 1.0000 80 chrIII:5349400-5349480 1.0000 80 chrX:3631679-3631759 1.0000 80 chrIII:4143981-4144061 1.0000 80 chrV:3715704-3715784 1.0000 80 chrI:7872274-7872354 1.0000 80 chrV:6223265-6223345 1.0000 80 chrV:727743-727823 1.0000 80 chrII:9934755-9934835 1.0000 80 chrX:15650537-15650617 1.0000 80 chrI:11630101-11630181 1.0000 80 chrIII:11921817-11921897 1.0000 80 chrIV:468206-468286 1.0000 80 chrIV:12862005-12862085 1.0000 80 chrIII:11946494-11946574 1.0000 80 chrIII:6133443-6133523 1.0000 80 chrIV:9444935-9445015 1.0000 80 chrIV:2602954-2603034 1.0000 80 chrV:12870076-12870156 1.0000 80 chrII:6913451-6913531 1.0000 80 chrX:1504681-1504761 1.0000 80 chrX:6253960-6254040 1.0000 80 chrI:1878905-1878985 1.0000 80 chrX:2871194-2871274 1.0000 80 chrIV:14903534-14903614 1.0000 80 chrV:5917870-5917950 1.0000 80 chrII:9285394-9285474 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_hlh-17/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/hlh-17.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= 57 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= 4560 N= 57 sample: seed= 0 hsfrac= 0 searchsize= 4560 norand= no csites= 1000 Letter frequencies in dataset: A 0.262 C 0.222 G 0.242 T 0.273 Background letter frequencies (from file dataset with add-one prior applied): A 0.262 C 0.222 G 0.242 T 0.273 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCCGAGAG MEME-1 width = 8 sites = 8 llr = 82 E-value = 5.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::8:a: pos.-specific C :a9::::: probability G :::a3a:a matrix T a:1::::: bits 2.2 * 2.0 ** * *** 1.7 ** * *** 1.5 **** *** Relative 1.3 **** *** Entropy 1.1 ******** (14.8 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCCGAGAG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:6913451-6913531 17 1.31e-05 AAATTTATTG TCCGAGAG GAGTACACGA chrIII:5349400-5349480 24 1.31e-05 AAAAATGCTG TCCGAGAG GAGTCCGCGG chrIII:9868276-9868356 11 1.31e-05 GAAATTATTT TCCGAGAG GACTCCGCCA chrII:10935020-10935100 27 1.31e-05 ttgctgctgc tccgagag tggtgtggtt chrIV:16415754-16415834 14 1.31e-05 TTCTCGTTTG TCCGAGAG GAGTACACGG chrII:9934755-9934835 62 2.52e-05 TCACACGGGC TCCGGGAG CAGAGACAAG chrII:13282932-13283012 5 2.52e-05 AGAC TCCGGGAG ATGTTGAGCA chrIII:11946494-11946574 16 4.13e-05 ATAAAGTTTG TCTGAGAG GACTACACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:6913451-6913531 1.3e-05 16_[+1]_56 chrIII:5349400-5349480 1.3e-05 23_[+1]_49 chrIII:9868276-9868356 1.3e-05 10_[+1]_62 chrII:10935020-10935100 1.3e-05 26_[+1]_46 chrIV:16415754-16415834 1.3e-05 13_[+1]_59 chrII:9934755-9934835 2.5e-05 61_[+1]_11 chrII:13282932-13283012 2.5e-05 4_[+1]_68 chrIII:11946494-11946574 4.1e-05 15_[+1]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCCGAGAG width=8 seqs=8 chrII:6913451-6913531 ( 17) TCCGAGAG 1 chrIII:5349400-5349480 ( 24) TCCGAGAG 1 chrIII:9868276-9868356 ( 11) TCCGAGAG 1 chrII:10935020-10935100 ( 27) TCCGAGAG 1 chrIV:16415754-16415834 ( 14) TCCGAGAG 1 chrII:9934755-9934835 ( 62) TCCGGGAG 1 chrII:13282932-13283012 ( 5) TCCGGGAG 1 chrIII:11946494-11946574 ( 16) TCTGAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4161 bayes= 9.01994 E= 5.8e-001 -965 -965 -965 187 -965 217 -965 -965 -965 198 -965 -113 -965 -965 204 -965 151 -965 4 -965 -965 -965 204 -965 193 -965 -965 -965 -965 -965 204 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 5.8e-001 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGAGAG MEME-1 regular expression -------------------------------------------------------------------------------- TCCG[AG]GAG -------------------------------------------------------------------------------- Time 0.79 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCCACCG MEME-2 width = 8 sites = 2 llr = 23 E-value = 5.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C ::aa:aa: probability G aa:::::a matrix T :::::::: bits 2.2 ** ** 2.0 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.7 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GGCCACCG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:5349400-5349480 65 9.02e-06 AAGAAAGCTA GGCCACCG ATGCGGAA chrIII:9868276-9868356 58 9.02e-06 TCTAGTCCGC GGCCACCG GAAAAGCGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:5349400-5349480 9e-06 64_[+2]_8 chrIII:9868276-9868356 9e-06 57_[+2]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCCACCG width=8 seqs=2 chrIII:5349400-5349480 ( 65) GGCCACCG 1 chrIII:9868276-9868356 ( 58) GGCCACCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4161 bayes= 11.022 E= 5.2e+003 -765 -765 204 -765 -765 -765 204 -765 -765 216 -765 -765 -765 216 -765 -765 193 -765 -765 -765 -765 216 -765 -765 -765 216 -765 -765 -765 -765 204 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.2e+003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCCACCG MEME-2 regular expression -------------------------------------------------------------------------------- GGCCACCG -------------------------------------------------------------------------------- Time 1.39 secs. ******************************************************************************** ******************************************************************************** MOTIF GASTACAC MEME-3 width = 8 sites = 5 llr = 53 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a::a:a: pos.-specific C ::4::a:a probability G a:6::::: matrix T :::a:::: bits 2.2 * * 2.0 ** ***** 1.7 ** ***** 1.5 ** ***** Relative 1.3 ** ***** Entropy 1.1 ******** (15.2 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAGTACAC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:5917870-5917950 6 1.42e-05 TAGAG GAGTACAC GGTCGTGTGG chrII:6913451-6913531 25 1.42e-05 TGTCCGAGAG GAGTACAC GACTGATGGC chrIV:16415754-16415834 22 1.42e-05 TGTCCGAGAG GAGTACAC GGCCGAGTGG chrV:12870076-12870156 31 2.72e-05 CGTCCTGGAG GACTACAC GGCGGGATGG chrIII:11946494-11946574 24 2.72e-05 TGTCTGAGAG GACTACAC TGCGCGGGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:5917870-5917950 1.4e-05 5_[+3]_67 chrII:6913451-6913531 1.4e-05 24_[+3]_48 chrIV:16415754-16415834 1.4e-05 21_[+3]_51 chrV:12870076-12870156 2.7e-05 30_[+3]_42 chrIII:11946494-11946574 2.7e-05 23_[+3]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GASTACAC width=8 seqs=5 chrV:5917870-5917950 ( 6) GAGTACAC 1 chrII:6913451-6913531 ( 25) GAGTACAC 1 chrIV:16415754-16415834 ( 22) GAGTACAC 1 chrV:12870076-12870156 ( 31) GACTACAC 1 chrIII:11946494-11946574 ( 24) GACTACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4161 bayes= 9.95087 E= 2.3e+003 -897 -897 204 -897 193 -897 -897 -897 -897 85 131 -897 -897 -897 -897 187 193 -897 -897 -897 -897 217 -897 -897 193 -897 -897 -897 -897 217 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 2.3e+003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GASTACAC MEME-3 regular expression -------------------------------------------------------------------------------- GA[GC]TACAC -------------------------------------------------------------------------------- Time 1.97 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAATKTT MEME-4 width = 8 sites = 14 llr = 111 E-value = 1.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A 99aa11:: pos.-specific C ::::::2: probability G 11:::4:: matrix T 1:::968a bits 2.2 2.0 ** * 1.7 ** * 1.5 ** * Relative 1.3 ***** * Entropy 1.1 ***** ** (11.4 bits) 0.9 ***** ** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAATTTT consensus GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:1503877-1503957 65 2.62e-05 cagtaaatag aaaatttt caaaaata chrII:9285394-9285474 23 4.94e-05 CATGCTTCGG AAAATGTT CAGGTCTCGT chrIII:11921817-11921897 27 4.94e-05 TCAAAAATGG AAAATGTT CAGAATGACA chrI:11221424-11221504 3 4.94e-05 GG AAAATGTT GTGGTGGGCC chrI:11630101-11630181 11 7.07e-05 TCCGATTAAA AAAATTCT GAATATCCAA chrX:14614472-14614552 31 7.07e-05 CTATAGTGAC AAAATTCT TCGCACTCCA chrIII:5349400-5349480 15 8.95e-05 AAGTACAACA AAAATGCT GTCCGAGAGG chrII:9934755-9934835 6 1.14e-04 GCTCT AGAATTTT TGGCTCTCCG chrIV:16415754-16415834 71 1.14e-04 TATTTGAATC AGAATTTT GT chrV:12870076-12870156 2 1.39e-04 A AAAAATTT GGTTCCCACT chrI:13421154-13421234 19 1.85e-04 ACTTCGCTGT AAAATATT TCAATTATAA chrIV:11644919-11644999 22 2.08e-04 ATATTGCTTT AAAAAGTT AGAAGTTCAG chrIII:5829419-5829499 7 2.32e-04 aAAATG GAAATTTT GAACCGTATT chrII:11974811-11974891 43 2.59e-04 gatttttagg taaatttt cgaatttcag -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1503877-1503957 2.6e-05 64_[+4]_8 chrII:9285394-9285474 4.9e-05 22_[+4]_50 chrIII:11921817-11921897 4.9e-05 26_[+4]_46 chrI:11221424-11221504 4.9e-05 2_[+4]_70 chrI:11630101-11630181 7.1e-05 10_[+4]_62 chrX:14614472-14614552 7.1e-05 30_[+4]_42 chrIII:5349400-5349480 9e-05 14_[+4]_58 chrII:9934755-9934835 0.00011 5_[+4]_67 chrIV:16415754-16415834 0.00011 70_[+4]_2 chrV:12870076-12870156 0.00014 1_[+4]_71 chrI:13421154-13421234 0.00019 18_[+4]_54 chrIV:11644919-11644999 0.00021 21_[+4]_51 chrIII:5829419-5829499 0.00023 6_[+4]_66 chrII:11974811-11974891 0.00026 42_[+4]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAATKTT width=8 seqs=14 chrX:1503877-1503957 ( 65) AAAATTTT 1 chrII:9285394-9285474 ( 23) AAAATGTT 1 chrIII:11921817-11921897 ( 27) AAAATGTT 1 chrI:11221424-11221504 ( 3) AAAATGTT 1 chrI:11630101-11630181 ( 11) AAAATTCT 1 chrX:14614472-14614552 ( 31) AAAATTCT 1 chrIII:5349400-5349480 ( 15) AAAATGCT 1 chrII:9934755-9934835 ( 6) AGAATTTT 1 chrIV:16415754-16415834 ( 71) AGAATTTT 1 chrV:12870076-12870156 ( 2) AAAAATTT 1 chrI:13421154-13421234 ( 19) AAAATATT 1 chrIV:11644919-11644999 ( 22) AAAAAGTT 1 chrIII:5829419-5829499 ( 7) GAAATTTT 1 chrII:11974811-11974891 ( 43) TAAATTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4161 bayes= 8.05382 E= 1.4e+004 171 -1045 -176 -193 171 -1045 -76 -1045 193 -1045 -1045 -1045 193 -1045 -1045 -1045 -88 -1045 -1045 165 -187 -1045 56 106 -1045 -5 -1045 152 -1045 -1045 -1045 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 1.4e+004 0.857143 0.000000 0.071429 0.071429 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.071429 0.000000 0.357143 0.571429 0.000000 0.214286 0.000000 0.785714 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATKTT MEME-4 regular expression -------------------------------------------------------------------------------- AAAAT[TG][TC]T -------------------------------------------------------------------------------- Time 2.59 secs. ******************************************************************************** ******************************************************************************** MOTIF CGCAAAAA MEME-5 width = 8 sites = 9 llr = 79 E-value = 5.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a9a9a pos.-specific C 9:7:::1: probability G 191::::: matrix T :12:1::: bits 2.2 2.0 * * * 1.7 * * * * 1.5 ** ***** Relative 1.3 ** ***** Entropy 1.1 ** ***** (12.7 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGCAAAAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:11921817-11921897 65 1.47e-05 AGCAAAAACT CGCAAAAA CGGCGAAA chrX:15650537-15650617 56 1.47e-05 actatgcagt cgcaaaaa cgtccaccgc chrV:6223265-6223345 44 3.28e-05 TAAGGGACCA CGTAAAAA TAACCGAGAT chrIII:9868276-9868356 38 3.28e-05 AGAATACGGC CGTAAAAA CCTCTAGTCC chrII:9285394-9285474 62 4.89e-05 GTCACCATGA CGGAAAAA TGCAGATTGT chrII:11974811-11974891 21 6.14e-05 GACATTTTTC CGCAAACa ttgcgatttt chrI:7872274-7872354 46 9.28e-05 ACATTGAGCA CGCATAAA TGATTGTTGC chrX:1503877-1503957 25 9.28e-05 aattatgagt ggcaaaaa ctgagcaatt chrIII:13635149-13635229 48 1.09e-04 AAAAAAGCGT CTCAAAAA AGGCATCTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:11921817-11921897 1.5e-05 64_[+5]_8 chrX:15650537-15650617 1.5e-05 55_[+5]_17 chrV:6223265-6223345 3.3e-05 43_[+5]_29 chrIII:9868276-9868356 3.3e-05 37_[+5]_35 chrII:9285394-9285474 4.9e-05 61_[+5]_11 chrII:11974811-11974891 6.1e-05 20_[+5]_52 chrI:7872274-7872354 9.3e-05 45_[+5]_27 chrX:1503877-1503957 9.3e-05 24_[+5]_48 chrIII:13635149-13635229 0.00011 47_[+5]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGCAAAAA width=8 seqs=9 chrIII:11921817-11921897 ( 65) CGCAAAAA 1 chrX:15650537-15650617 ( 56) CGCAAAAA 1 chrV:6223265-6223345 ( 44) CGTAAAAA 1 chrIII:9868276-9868356 ( 38) CGTAAAAA 1 chrII:9285394-9285474 ( 62) CGGAAAAA 1 chrII:11974811-11974891 ( 21) CGCAAACA 1 chrI:7872274-7872354 ( 46) CGCATAAA 1 chrX:1503877-1503957 ( 25) GGCAAAAA 1 chrIII:13635149-13635229 ( 48) CTCAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4161 bayes= 8.98424 E= 5.9e+003 -982 200 -112 -982 -982 -982 187 -130 -982 158 -112 -30 193 -982 -982 -982 176 -982 -982 -130 193 -982 -982 -982 176 -100 -982 -982 193 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 5.9e+003 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.666667 0.111111 0.222222 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAAAAA MEME-5 regular expression -------------------------------------------------------------------------------- CG[CT]AAAAA -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:16237733-16237813 7.66e-01 80 chrI:1326327-1326407 6.42e-01 80 chrIV:8595087-8595167 4.16e-01 80 chrII:13282932-13283012 7.06e-02 4_[+1(2.52e-05)]_68 chrV:13786421-13786501 2.48e-01 80 chrX:767820-767900 8.64e-01 80 chrIV:3621994-3622074 7.10e-01 80 chrV:17587214-17587294 9.95e-01 80 chrX:1503877-1503957 6.50e-03 24_[+5(9.28e-05)]_32_[+4(2.62e-05)]_\ 8 chrII:11977387-11977467 8.85e-01 80 chrIV:10426697-10426777 5.04e-01 80 chrIV:14403136-14403216 9.89e-01 80 chrII:11974811-11974891 3.19e-02 20_[+5(6.14e-05)]_52 chrI:11221424-11221504 1.32e-01 2_[+4(4.94e-05)]_70 chrIII:13635149-13635229 1.56e-01 80 chrIII:5829419-5829499 4.72e-01 80 chrIV:10177605-10177685 3.79e-01 80 chrIV:2107630-2107710 2.84e-01 80 chrIV:16415754-16415834 3.20e-05 13_[+1(1.31e-05)]_[+3(1.42e-05)]_51 chrV:12510128-12510208 9.98e-01 80 chrIV:11644919-11644999 2.24e-01 80 chrX:14614472-14614552 7.52e-02 30_[+4(7.07e-05)]_42 chrI:5992297-5992377 1.17e-01 80 chrIV:8431735-8431815 3.47e-01 80 chrIII:12660471-12660551 6.33e-01 80 chrX:936025-936105 1.53e-01 80 chrIII:5169556-5169636 3.52e-01 80 chrII:10935020-10935100 1.30e-02 26_[+1(1.31e-05)]_46 chrI:933436-933516 4.28e-01 80 chrIII:9868276-9868356 7.15e-07 10_[+1(1.31e-05)]_19_[+5(3.28e-05)]_\ 12_[+2(9.02e-06)]_15 chrI:13421154-13421234 3.11e-01 80 chrIII:5349400-5349480 3.57e-06 14_[+4(8.95e-05)]_1_[+1(1.31e-05)]_\ 33_[+2(9.02e-06)]_8 chrX:3631679-3631759 9.96e-01 80 chrIII:4143981-4144061 9.91e-01 80 chrV:3715704-3715784 2.92e-01 80 chrI:7872274-7872354 6.30e-02 45_[+5(9.28e-05)]_27 chrV:6223265-6223345 7.93e-03 43_[+5(3.28e-05)]_29 chrV:727743-727823 7.53e-01 80 chrII:9934755-9934835 2.12e-04 61_[+1(2.52e-05)]_11 chrX:15650537-15650617 2.49e-03 55_[+5(1.47e-05)]_17 chrI:11630101-11630181 4.24e-02 10_[+4(7.07e-05)]_62 chrIII:11921817-11921897 2.66e-03 26_[+4(4.94e-05)]_30_[+5(1.47e-05)]_\ 8 chrIV:468206-468286 6.57e-01 80 chrIV:12862005-12862085 7.19e-01 80 chrIII:11946494-11946574 9.15e-04 15_[+1(4.13e-05)]_[+3(2.72e-05)]_49 chrIII:6133443-6133523 9.60e-01 80 chrIV:9444935-9445015 9.25e-01 80 chrIV:2602954-2603034 9.61e-01 80 chrV:12870076-12870156 1.54e-03 30_[+3(2.72e-05)]_42 chrII:6913451-6913531 8.66e-05 16_[+1(1.31e-05)]_[+3(1.42e-05)]_48 chrX:1504681-1504761 8.85e-01 80 chrX:6253960-6254040 7.75e-02 80 chrI:1878905-1878985 3.44e-01 80 chrX:2871194-2871274 2.75e-01 80 chrIV:14903534-14903614 7.50e-01 80 chrV:5917870-5917950 1.37e-02 5_[+3(1.42e-05)]_67 chrII:9285394-9285474 6.34e-03 22_[+4(4.94e-05)]_31_[+5(4.89e-05)]_\ 11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c26n03.farnam.hpc.yale.internal ********************************************************************************