******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-23.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIV:9614227-9614307 1.0000 80 chrIV:9613350-9613430 1.0000 80 chrIV:1915054-1915134 1.0000 80 chrI:14948647-14948727 1.0000 80 chrIV:9617539-9617619 1.0000 80 chrII:1149309-1149389 1.0000 80 chrII:1605552-1605632 1.0000 80 chrI:2842146-2842226 1.0000 80 chrIV:5475040-5475120 1.0000 80 chrV:13333521-13333601 1.0000 80 chrI:10793646-10793726 1.0000 80 chrII:1523807-1523887 1.0000 80 chrV:5426494-5426574 1.0000 80 chrIV:9618083-9618163 1.0000 80 chrX:16073538-16073618 1.0000 80 chrI:14908063-14908143 1.0000 80 chrIV:10950514-10950594 1.0000 80 chrII:9064587-9064667 1.0000 80 chrII:11076673-11076753 1.0000 80 chrX:12511544-12511624 1.0000 80 chrIV:4338349-4338429 1.0000 80 chrIV:3438147-3438227 1.0000 80 chrI:32750-32830 1.0000 80 chrV:19429746-19429826 1.0000 80 chrV:9218343-9218423 1.0000 80 chrIII:9991492-9991572 1.0000 80 chrX:10769525-10769605 1.0000 80 chrX:12671771-12671851 1.0000 80 chrV:13866532-13866612 1.0000 80 chrII:1670748-1670828 1.0000 80 chrIV:9615698-9615778 1.0000 80 chrX:12515992-12516072 1.0000 80 chrIII:5229551-5229631 1.0000 80 chrIV:1911519-1911599 1.0000 80 chrV:14506868-14506948 1.0000 80 chrV:9274393-9274473 1.0000 80 chrII:1594293-1594373 1.0000 80 chrV:1536361-1536441 1.0000 80 chrV:4499748-4499828 1.0000 80 chrII:1676251-1676331 1.0000 80 chrV:5523398-5523478 1.0000 80 chrI:6996074-6996154 1.0000 80 chrV:18719569-18719649 1.0000 80 chrIII:13780342-13780422 1.0000 80 chrV:15661098-15661178 1.0000 80 chrI:8986060-8986140 1.0000 80 chrX:13248417-13248497 1.0000 80 chrV:19429046-19429126 1.0000 80 chrV:539223-539303 1.0000 80 chrV:8661327-8661407 1.0000 80 chrX:4522324-4522404 1.0000 80 chrIII:3797281-3797361 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/worm/inference_raw/MEME/RankLinear2.0_40_nhr-23/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-23.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= 52 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= 4160 N= 52 sample: seed= 0 hsfrac= 0 searchsize= 4160 norand= no csites= 1000 Letter frequencies in dataset: A 0.298 C 0.213 G 0.213 T 0.276 Background letter frequencies (from file dataset with add-one prior applied): A 0.298 C 0.213 G 0.213 T 0.276 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TBTBATCT MEME-1 width = 8 sites = 12 llr = 105 E-value = 6.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C :3:3::a: probability G :5:3:::: matrix T a3a5:a:a bits 2.2 * 2.0 * 1.8 * * **** 1.6 * * **** Relative 1.3 * * **** Entropy 1.1 * * **** (12.6 bits) 0.9 * * **** 0.7 *** **** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGTTATCT consensus C C sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:14506868-14506948 48 2.17e-05 ATCAAAAGAT TGTTATCT GATTTTTGAA chrI:8986060-8986140 23 5.51e-05 TCAGTTACTG TGTGATCT AATCTCGGGG chrII:1594293-1594373 27 5.51e-05 TAAGATTCTT TGTCATCT TCGCTAAAAA chrI:32750-32830 10 5.51e-05 TTGCATCTT TGTGATCT AAAAGATTAA chrII:11076673-11076753 73 5.51e-05 ACCACGAGAT TGTCATCT chrIV:9614227-9614307 30 5.51e-05 GATCCCAATC TGTGATCT GATAATGTCC chrX:10769525-10769605 7 7.67e-05 AAACCA TCTTATCT AGTCTAAATC chrII:9064587-9064667 40 7.67e-05 TGCCATGAGA TCTTATCT ACACGACATC chrI:14948647-14948727 43 7.67e-05 CAGATGGCAA TCTTATCT GCGCCAGCAT chrIV:9615698-9615778 61 1.05e-04 GCTGATAATC TTTTATCT TCAAGCCGCA chrV:19429746-19429826 42 1.05e-04 GGGGATTCAA TTTTATCT TGATTGCGAA chrV:5523398-5523478 29 1.82e-04 ATCGCATCTG TTTCATCT TTTATTGCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:14506868-14506948 2.2e-05 47_[+1]_25 chrI:8986060-8986140 5.5e-05 22_[+1]_50 chrII:1594293-1594373 5.5e-05 26_[+1]_46 chrI:32750-32830 5.5e-05 9_[+1]_63 chrII:11076673-11076753 5.5e-05 72_[+1] chrIV:9614227-9614307 5.5e-05 29_[+1]_43 chrX:10769525-10769605 7.7e-05 6_[+1]_66 chrII:9064587-9064667 7.7e-05 39_[+1]_33 chrI:14948647-14948727 7.7e-05 42_[+1]_30 chrIV:9615698-9615778 0.0001 60_[+1]_12 chrV:19429746-19429826 0.0001 41_[+1]_31 chrV:5523398-5523478 0.00018 28_[+1]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TBTBATCT width=8 seqs=12 chrV:14506868-14506948 ( 48) TGTTATCT 1 chrI:8986060-8986140 ( 23) TGTGATCT 1 chrII:1594293-1594373 ( 27) TGTCATCT 1 chrI:32750-32830 ( 10) TGTGATCT 1 chrII:11076673-11076753 ( 73) TGTCATCT 1 chrIV:9614227-9614307 ( 30) TGTGATCT 1 chrX:10769525-10769605 ( 7) TCTTATCT 1 chrII:9064587-9064667 ( 40) TCTTATCT 1 chrI:14948647-14948727 ( 43) TCTTATCT 1 chrIV:9615698-9615778 ( 61) TTTTATCT 1 chrV:19429746-19429826 ( 42) TTTTATCT 1 chrV:5523398-5523478 ( 29) TTTCATCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3796 bayes= 8.74941 E= 6.4e+000 -1023 -1023 -1023 186 -1023 23 123 -14 -1023 -1023 -1023 186 -1023 23 23 86 175 -1023 -1023 -1023 -1023 -1023 -1023 186 -1023 223 -1023 -1023 -1023 -1023 -1023 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 6.4e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBTBATCT MEME-1 regular expression -------------------------------------------------------------------------------- T[GCT]T[TCG]ATCT -------------------------------------------------------------------------------- Time 1.90 secs. ******************************************************************************** ******************************************************************************** MOTIF GATAAGAT MEME-2 width = 8 sites = 10 llr = 89 E-value = 7.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :9:7a:a2 pos.-specific C :::::::1 probability G a::3:a:: matrix T :1a::::7 bits 2.2 * * 2.0 * * 1.8 * * *** 1.6 * * *** Relative 1.3 *** *** Entropy 1.1 ******* (12.8 bits) 0.9 ******* 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GATAAGAT consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:1594293-1594373 15 2.73e-05 GATCGGAACA GATAAGAT TCTTTGTCAT chrIII:9991492-9991572 69 2.73e-05 AAAAAACTGA GATAAGAT TTTT chrV:5426494-5426574 9 2.73e-05 AAAACATC GATAAGAT CAGAGTAAAA chrIV:9614227-9614307 15 2.73e-05 TTTATATTGT GATAAGAT CCCAATCTGT chrV:13866532-13866612 6 4.67e-05 GCGGA GATGAGAT CAGTGCAGAT chrI:2842146-2842226 57 4.67e-05 TCAACAGATT GATGAGAT TAATTTTGGG chrIV:1911519-1911599 64 7.62e-05 CAATCGAATC GATAAGAA TGTTTGAAG chrIV:10950514-10950594 39 9.72e-05 CAAGGCTCTT GATAAGAC TCTTGATACT chrI:10793646-10793726 56 1.18e-04 GTGGAAAAAT GATGAGAA GTAATGAAAA chrIV:1915054-1915134 6 1.43e-04 ACCTA GTTAAGAT AGCGGCAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:1594293-1594373 2.7e-05 14_[+2]_58 chrIII:9991492-9991572 2.7e-05 68_[+2]_4 chrV:5426494-5426574 2.7e-05 8_[+2]_64 chrIV:9614227-9614307 2.7e-05 14_[+2]_58 chrV:13866532-13866612 4.7e-05 5_[+2]_67 chrI:2842146-2842226 4.7e-05 56_[+2]_16 chrIV:1911519-1911599 7.6e-05 63_[+2]_9 chrIV:10950514-10950594 9.7e-05 38_[+2]_34 chrI:10793646-10793726 0.00012 55_[+2]_17 chrIV:1915054-1915134 0.00014 5_[+2]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GATAAGAT width=8 seqs=10 chrII:1594293-1594373 ( 15) GATAAGAT 1 chrIII:9991492-9991572 ( 69) GATAAGAT 1 chrV:5426494-5426574 ( 9) GATAAGAT 1 chrIV:9614227-9614307 ( 15) GATAAGAT 1 chrV:13866532-13866612 ( 6) GATGAGAT 1 chrI:2842146-2842226 ( 57) GATGAGAT 1 chrIV:1911519-1911599 ( 64) GATAAGAA 1 chrIV:10950514-10950594 ( 39) GATAAGAC 1 chrI:10793646-10793726 ( 56) GATGAGAA 1 chrIV:1915054-1915134 ( 6) GTTAAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3796 bayes= 8.81668 E= 7.7e+002 -997 -997 223 -997 159 -997 -997 -146 -997 -997 -997 186 123 -997 50 -997 175 -997 -997 -997 -997 -997 223 -997 175 -997 -997 -997 -57 -109 -997 134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 7.7e+002 0.000000 0.000000 1.000000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 1.000000 0.700000 0.000000 0.300000 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 0.100000 0.000000 0.700000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAT MEME-2 regular expression -------------------------------------------------------------------------------- GAT[AG]AGA[TA] -------------------------------------------------------------------------------- Time 2.50 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTWYCTC MEME-3 width = 8 sites = 11 llr = 92 E-value = 1.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTWYCTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::24:::: pos.-specific C :6::5a:a probability G :::1:::: matrix T a4855:a: bits 2.2 * * 2.0 * * 1.8 * *** 1.6 * *** Relative 1.3 * *** Entropy 1.1 *** **** (12.1 bits) 0.9 *** **** 0.7 *** **** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCTTCCTC consensus T AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTWYCTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:13866532-13866612 39 1.19e-05 TCTAAGCCCA TCTTCCTC ACGTCCGTTC chrIV:9618083-9618163 40 1.19e-05 ATGAATTCTC TCTTCCTC TTTTCGTCAC chrI:14948647-14948727 72 2.74e-05 ACGTCGCTCT TCTTTCTC G chrII:1670748-1670828 47 5.58e-05 GCCGCCTACT TTTTCCTC ACTTATAATA chrV:8661327-8661407 1 7.25e-05 . TCTATCTC GTTTAACCGC chrX:10769525-10769605 52 9.26e-05 TTCTCTCGTA TTTTTCTC GGTTAGGGGT chrII:1149309-1149389 63 1.18e-04 AATACCGTGC TCTGCCTC AACGATCGAC chrV:9218343-9218423 60 1.31e-04 AACGCATCAA TCATCCTC CACGCGAAAG chrI:6996074-6996154 33 1.53e-04 CAATAGGGAA TTTATCTC GTGGGCCGGG chrX:12511544-12511624 55 1.53e-04 AGGGAGATAG TTTATCTC AGAAGGTAAT chrII:11076673-11076753 35 1.96e-04 AGCGGCGCCC TCAACCTC AAAATCAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTWYCTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:13866532-13866612 1.2e-05 38_[+3]_34 chrIV:9618083-9618163 1.2e-05 39_[+3]_33 chrI:14948647-14948727 2.7e-05 71_[+3]_1 chrII:1670748-1670828 5.6e-05 46_[+3]_26 chrV:8661327-8661407 7.3e-05 [+3]_72 chrX:10769525-10769605 9.3e-05 51_[+3]_21 chrII:1149309-1149389 0.00012 62_[+3]_10 chrV:9218343-9218423 0.00013 59_[+3]_13 chrI:6996074-6996154 0.00015 32_[+3]_40 chrX:12511544-12511624 0.00015 54_[+3]_18 chrII:11076673-11076753 0.0002 34_[+3]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTWYCTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TYTWYCTC width=8 seqs=11 chrV:13866532-13866612 ( 39) TCTTCCTC 1 chrIV:9618083-9618163 ( 40) TCTTCCTC 1 chrI:14948647-14948727 ( 72) TCTTTCTC 1 chrII:1670748-1670828 ( 47) TTTTCCTC 1 chrV:8661327-8661407 ( 1) TCTATCTC 1 chrX:10769525-10769605 ( 52) TTTTTCTC 1 chrII:1149309-1149389 ( 63) TCTGCCTC 1 chrV:9218343-9218423 ( 60) TCATCCTC 1 chrI:6996074-6996154 ( 33) TTTATCTC 1 chrX:12511544-12511624 ( 55) TTTATCTC 1 chrII:11076673-11076753 ( 35) TCAACCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTWYCTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3796 bayes= 8.78266 E= 1.3e+004 -1010 -1010 -1010 186 -1010 157 -1010 40 -71 -1010 -1010 157 29 -1010 -123 98 -1010 135 -1010 72 -1010 223 -1010 -1010 -1010 -1010 -1010 186 -1010 223 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTWYCTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 1.3e+004 0.000000 0.000000 0.000000 1.000000 0.000000 0.636364 0.000000 0.363636 0.181818 0.000000 0.000000 0.818182 0.363636 0.000000 0.090909 0.545455 0.000000 0.545455 0.000000 0.454545 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 TYTWYCTC MEME-3 regular expression -------------------------------------------------------------------------------- T[CT]T[TA][CT]CTC -------------------------------------------------------------------------------- Time 3.04 secs. ******************************************************************************** ******************************************************************************** MOTIF CAAGGCYC MEME-4 width = 8 sites = 4 llr = 43 E-value = 1.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :aa::::: pos.-specific C a::::a5a probability G :::aa::: matrix T ::::::5: bits 2.2 * *** * 2.0 * *** * 1.8 ****** * 1.6 ****** * Relative 1.3 ****** * Entropy 1.1 ******** (15.7 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CAAGGCCC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:4499748-4499828 22 8.29e-06 TCTTATTCAG CAAGGCCC CGTGTGTCGG chrI:14948647-14948727 7 8.29e-06 TCCCTG CAAGGCCC ATAGTTGACG chrIV:10950514-10950594 29 1.90e-05 GTCAACTTGT CAAGGCTC TTGATAAGAC chrII:1523807-1523887 22 1.90e-05 CAGAGCACCG CAAGGCTC AGTGGCATAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:4499748-4499828 8.3e-06 21_[+4]_51 chrI:14948647-14948727 8.3e-06 6_[+4]_66 chrIV:10950514-10950594 1.9e-05 28_[+4]_44 chrII:1523807-1523887 1.9e-05 21_[+4]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAAGGCYC width=8 seqs=4 chrV:4499748-4499828 ( 22) CAAGGCCC 1 chrI:14948647-14948727 ( 7) CAAGGCCC 1 chrIV:10950514-10950594 ( 29) CAAGGCTC 1 chrII:1523807-1523887 ( 22) CAAGGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3796 bayes= 9.88874 E= 1.4e+004 -865 222 -865 -865 174 -865 -865 -865 174 -865 -865 -865 -865 -865 223 -865 -865 -865 223 -865 -865 222 -865 -865 -865 123 -865 86 -865 222 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.4e+004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGGCYC MEME-4 regular expression -------------------------------------------------------------------------------- CAAGGC[CT]C -------------------------------------------------------------------------------- Time 3.58 secs. ******************************************************************************** ******************************************************************************** MOTIF GGKKTCCT MEME-5 width = 8 sites = 3 llr = 31 E-value = 8.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::aa: probability G aa73:::: matrix T ::37a::a bits 2.2 ** ** 2.0 ** ** 1.8 ** **** 1.6 ** **** Relative 1.3 ** **** Entropy 1.1 ******** (14.9 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GGGTTCCT consensus TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:9617539-9617619 63 9.22e-06 TTTGGGAAGA GGGTTCCT CCTTTTTTCG chrIV:9613350-9613430 66 9.22e-06 TGGGGTGTCA GGGTTCCT GAGGAAT chrX:12671771-12671851 66 3.75e-05 AGTAGGGTTA GGTGTCCT TCTATAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:9617539-9617619 9.2e-06 62_[+5]_10 chrIV:9613350-9613430 9.2e-06 65_[+5]_7 chrX:12671771-12671851 3.7e-05 65_[+5]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGKKTCCT width=8 seqs=3 chrIV:9617539-9617619 ( 63) GGGTTCCT 1 chrIV:9613350-9613430 ( 66) GGGTTCCT 1 chrX:12671771-12671851 ( 66) GGTGTCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3796 bayes= 9.96282 E= 8.6e+004 -823 -823 223 -823 -823 -823 223 -823 -823 -823 164 27 -823 -823 65 127 -823 -823 -823 186 -823 222 -823 -823 -823 222 -823 -823 -823 -823 -823 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 8.6e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKKTCCT MEME-5 regular expression -------------------------------------------------------------------------------- GG[GT][TG]TCCT -------------------------------------------------------------------------------- Time 4.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:9614227-9614307 5.25e-03 14_[+2(2.73e-05)]_7_[+1(5.51e-05)]_\ 43 chrIV:9613350-9613430 2.22e-02 65_[+5(9.22e-06)]_7 chrIV:1915054-1915134 2.80e-01 80 chrI:14948647-14948727 3.36e-05 6_[+4(8.29e-06)]_28_[+1(7.67e-05)]_\ 21_[+3(2.74e-05)]_1 chrIV:9617539-9617619 4.51e-02 62_[+5(9.22e-06)]_10 chrII:1149309-1149389 5.94e-02 80 chrII:1605552-1605632 1.20e-01 80 chrI:2842146-2842226 1.14e-01 56_[+2(4.67e-05)]_16 chrIV:5475040-5475120 9.90e-01 80 chrV:13333521-13333601 3.50e-02 80 chrI:10793646-10793726 1.93e-02 80 chrII:1523807-1523887 2.34e-02 21_[+4(1.90e-05)]_51 chrV:5426494-5426574 7.18e-02 8_[+2(2.73e-05)]_64 chrIV:9618083-9618163 9.73e-02 39_[+3(1.19e-05)]_33 chrX:16073538-16073618 6.53e-01 80 chrI:14908063-14908143 4.12e-01 80 chrIV:10950514-10950594 3.57e-03 28_[+4(1.90e-05)]_2_[+2(9.72e-05)]_\ 34 chrII:9064587-9064667 2.36e-02 39_[+1(7.67e-05)]_33 chrII:11076673-11076753 6.60e-04 72_[+1(5.51e-05)] chrX:12511544-12511624 1.39e-01 80 chrIV:4338349-4338429 2.35e-01 80 chrIV:3438147-3438227 2.61e-01 80 chrI:32750-32830 1.02e-01 9_[+1(5.51e-05)]_63 chrV:19429746-19429826 1.04e-01 80 chrV:9218343-9218423 9.61e-02 80 chrIII:9991492-9991572 8.48e-02 68_[+2(2.73e-05)]_4 chrX:10769525-10769605 9.44e-04 6_[+1(7.67e-05)]_37_[+3(9.26e-05)]_\ 21 chrX:12671771-12671851 1.20e-01 65_[+5(3.75e-05)]_7 chrV:13866532-13866612 2.36e-04 5_[+2(4.67e-05)]_25_[+3(1.19e-05)]_\ 34 chrII:1670748-1670828 7.83e-02 46_[+3(5.58e-05)]_26 chrIV:9615698-9615778 2.52e-03 80 chrX:12515992-12516072 8.02e-01 80 chrIII:5229551-5229631 9.37e-01 80 chrIV:1911519-1911599 1.31e-01 63_[+2(7.62e-05)]_9 chrV:14506868-14506948 3.46e-03 47_[+1(2.17e-05)]_25 chrV:9274393-9274473 3.66e-02 80 chrII:1594293-1594373 7.43e-04 14_[+2(2.73e-05)]_4_[+1(5.51e-05)]_\ 46 chrV:1536361-1536441 8.36e-01 80 chrV:4499748-4499828 2.22e-03 21_[+4(8.29e-06)]_51 chrII:1676251-1676331 3.35e-01 80 chrV:5523398-5523478 3.61e-02 80 chrI:6996074-6996154 5.53e-02 80 chrV:18719569-18719649 6.23e-02 80 chrIII:13780342-13780422 5.78e-01 80 chrV:15661098-15661178 2.55e-01 80 chrI:8986060-8986140 3.38e-02 22_[+1(5.51e-05)]_50 chrX:13248417-13248497 8.10e-01 80 chrV:19429046-19429126 9.60e-01 80 chrV:539223-539303 5.92e-01 80 chrV:8661327-8661407 9.71e-02 [+3(7.25e-05)]_72 chrX:4522324-4522404 9.34e-01 80 chrIII:3797281-3797361 6.68e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n10.farnam.hpc.yale.internal ********************************************************************************