******************************************************************************** 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/aly-2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrI:8975597-8975677 1.0000 80 chrII:11879753-11879833 1.0000 80 chrI:14856802-14856882 1.0000 80 chrIV:11977402-11977482 1.0000 80 chrIII:10182744-10182824 1.0000 80 chrI:14882898-14882978 1.0000 80 chrII:10933564-10933644 1.0000 80 chrI:14883509-14883589 1.0000 80 chrI:8976946-8977026 1.0000 80 chrI:11764155-11764235 1.0000 80 chrIV:3043001-3043081 1.0000 80 chrII:9888136-9888216 1.0000 80 chrV:12605445-12605525 1.0000 80 chrIII:10182465-10182545 1.0000 80 chrV:4349013-4349093 1.0000 80 chrII:1150352-1150432 1.0000 80 chrIII:8171890-8171970 1.0000 80 chrI:14881328-14881408 1.0000 80 chrIII:4175078-4175158 1.0000 80 chrIII:5198386-5198466 1.0000 80 chrII:9889382-9889462 1.0000 80 chrIII:5229911-5229991 1.0000 80 chrV:10026868-10026948 1.0000 80 chrX:13955382-13955462 1.0000 80 chrIII:7700156-7700236 1.0000 80 chrV:6401737-6401817 1.0000 80 chrV:6401471-6401551 1.0000 80 chrV:19049547-19049627 1.0000 80 chrII:9886673-9886753 1.0000 80 chrIV:3040699-3040779 1.0000 80 chrX:6089140-6089220 1.0000 80 chrIV:11601154-11601234 1.0000 80 chrI:4508613-4508693 1.0000 80 chrIV:5985567-5985647 1.0000 80 chrI:1738065-1738145 1.0000 80 chrIV:1723138-1723218 1.0000 80 chrI:7627064-7627144 1.0000 80 chrI:8677705-8677785 1.0000 80 chrI:14855777-14855857 1.0000 80 chrV:5832024-5832104 1.0000 80 chrIV:17280085-17280165 1.0000 80 chrI:7585391-7585471 1.0000 80 chrX:4526516-4526596 1.0000 80 chrIV:15049694-15049774 1.0000 80 chrIII:6970333-6970413 1.0000 80 chrII:4429215-4429295 1.0000 80 chrIV:5987703-5987783 1.0000 80 chrV:12606469-12606549 1.0000 80 chrII:8141246-8141326 1.0000 80 chrIV:11527795-11527875 1.0000 80 chrIII:9462650-9462730 1.0000 80 chrII:6847972-6848052 1.0000 80 chrV:12004153-12004233 1.0000 80 chrII:7744945-7745025 1.0000 80 chrII:11880562-11880642 1.0000 80 chrII:11691121-11691201 1.0000 80 chrI:12787854-12787934 1.0000 80 chrIII:8805947-8806027 1.0000 80 chrIV:9990740-9990820 1.0000 80 chrIV:6906340-6906420 1.0000 80 chrI:11764737-11764817 1.0000 80 chrIII:4172462-4172542 1.0000 80 chrI:8976437-8976517 1.0000 80 chrIII:2669439-2669519 1.0000 80 chrI:5171260-5171340 1.0000 80 chrV:14688517-14688597 1.0000 80 chrIV:5999204-5999284 1.0000 80 chrII:11125215-11125295 1.0000 80 chrI:2875206-2875286 1.0000 80 chrV:10023071-10023151 1.0000 80 chrX:7825796-7825876 1.0000 80 chrIII:2674034-2674114 1.0000 80 chrV:14354267-14354347 1.0000 80 chrV:4734827-4734907 1.0000 80 chrV:2786865-2786945 1.0000 80 chrIV:10381191-10381271 1.0000 80 chrI:6838097-6838177 1.0000 80 chrI:379139-379219 1.0000 80 chrIII:7637339-7637419 1.0000 80 chrIV:17281304-17281384 1.0000 80 chrIII:1419808-1419888 1.0000 80 chrV:14687982-14688062 1.0000 80 chrIII:5205882-5205962 1.0000 80 chrIII:12599239-12599319 1.0000 80 chrX:4193181-4193261 1.0000 80 chrIV:7623908-7623988 1.0000 80 chrV:5829449-5829529 1.0000 80 chrIII:10209728-10209808 1.0000 80 chrIII:3869452-3869532 1.0000 80 chrIII:13464656-13464736 1.0000 80 chrII:5338800-5338880 1.0000 80 chrIV:8432640-8432720 1.0000 80 chrIV:16483240-16483320 1.0000 80 chrI:7586956-7587036 1.0000 80 chrII:11547263-11547343 1.0000 80 chrI:10553032-10553112 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_aly-2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/aly-2.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= 96 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= 7680 N= 96 sample: seed= 0 hsfrac= 0 searchsize= 7680 norand= no csites= 1000 Letter frequencies in dataset: A 0.288 C 0.208 G 0.201 T 0.303 Background letter frequencies (from file dataset with add-one prior applied): A 0.288 C 0.208 G 0.201 T 0.303 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTCMAYCT MEME-1 width = 8 sites = 19 llr = 153 E-value = 2.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::5a12: pos.-specific C 9:a5:571 probability G 1::::11: matrix T :a:::4:9 bits 2.3 * 2.1 * * 1.8 * * * 1.6 *** * Relative 1.4 *** * * Entropy 1.2 ***** ** (11.6 bits) 0.9 ***** ** 0.7 ***** ** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTCCACCT consensus A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:7637339-7637419 71 1.03e-05 ACGACTCCAG CTCCACCT CC chrIII:4175078-4175158 64 1.03e-05 CTTCCACCGC CTCCACCT TTCATTTCG chrII:1150352-1150432 5 1.03e-05 CCGC CTCCACCT ACTCCCGTGA chrIII:6970333-6970413 34 2.45e-05 TTGGGAAGTC CTCAACCT TCTTACCGGT chrIII:8805947-8806027 11 3.95e-05 CGTCACTTTT CTCCATCT CATCCTTCCC chrX:7825796-7825876 13 6.03e-05 TAGATTGTCT CTCAATCT GCTTACTCCC chrII:9889382-9889462 3 6.03e-05 TT CTCAATCT TTGTGACAAT chrIV:11977402-11977482 14 6.03e-05 TGCTGTTGTT CTCAATCT TCTCTCCATC chrIV:7623908-7623988 1 1.15e-04 . CTCAAGCT TTGAGGTAAA chrV:14687982-14688062 33 1.15e-04 ATCATGAAAG CTCAAGCT CTTCGTGATT chrIV:9990740-9990820 51 1.15e-04 ATGCTAGAAG CTCCACGT TCATTCTGTT chrI:8677705-8677785 13 1.15e-04 TCTGGTACTT CTCCACGT GTCACAGCAG chrII:7744945-7745025 11 1.59e-04 CGATGACATT CTCAACAT CACATGCATC chrIV:3040699-3040779 47 1.59e-04 CTGGATTCTG CTCAACAT GTCGAAcatc chrIV:5999204-5999284 58 1.69e-04 CGTCCCGAAT CTCCATCC GGATCCCCGC chrII:5338800-5338880 58 2.18e-04 GAAAAACTTT CTCCATAT TTTCCAATGG chrV:4349013-4349093 16 2.18e-04 AAGACGTATA CTCCAACT GTCGATCCAG chrI:12787854-12787934 40 2.28e-04 TCCTACCGTA GTCCACCT TTAAAAAATT chrIII:10182744-10182824 55 2.43e-04 GCATATCAAT CTCAATCC CAACAGCAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:7637339-7637419 1e-05 70_[+1]_2 chrIII:4175078-4175158 1e-05 63_[+1]_9 chrII:1150352-1150432 1e-05 4_[+1]_68 chrIII:6970333-6970413 2.5e-05 33_[+1]_39 chrIII:8805947-8806027 4e-05 10_[+1]_62 chrX:7825796-7825876 6e-05 12_[+1]_60 chrII:9889382-9889462 6e-05 2_[+1]_70 chrIV:11977402-11977482 6e-05 13_[+1]_59 chrIV:7623908-7623988 0.00012 [+1]_72 chrV:14687982-14688062 0.00012 32_[+1]_40 chrIV:9990740-9990820 0.00012 50_[+1]_22 chrI:8677705-8677785 0.00012 12_[+1]_60 chrII:7744945-7745025 0.00016 10_[+1]_62 chrIV:3040699-3040779 0.00016 46_[+1]_26 chrIV:5999204-5999284 0.00017 57_[+1]_15 chrII:5338800-5338880 0.00022 57_[+1]_15 chrV:4349013-4349093 0.00022 15_[+1]_57 chrI:12787854-12787934 0.00023 39_[+1]_33 chrIII:10182744-10182824 0.00024 54_[+1]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCMAYCT width=8 seqs=19 chrIII:7637339-7637419 ( 71) CTCCACCT 1 chrIII:4175078-4175158 ( 64) CTCCACCT 1 chrII:1150352-1150432 ( 5) CTCCACCT 1 chrIII:6970333-6970413 ( 34) CTCAACCT 1 chrIII:8805947-8806027 ( 11) CTCCATCT 1 chrX:7825796-7825876 ( 13) CTCAATCT 1 chrII:9889382-9889462 ( 3) CTCAATCT 1 chrIV:11977402-11977482 ( 14) CTCAATCT 1 chrIV:7623908-7623988 ( 1) CTCAAGCT 1 chrV:14687982-14688062 ( 33) CTCAAGCT 1 chrIV:9990740-9990820 ( 51) CTCCACGT 1 chrI:8677705-8677785 ( 13) CTCCACGT 1 chrII:7744945-7745025 ( 11) CTCAACAT 1 chrIV:3040699-3040779 ( 47) CTCAACAT 1 chrIV:5999204-5999284 ( 58) CTCCATCC 1 chrII:5338800-5338880 ( 58) CTCCATAT 1 chrV:4349013-4349093 ( 16) CTCCAACT 1 chrI:12787854-12787934 ( 40) GTCCACCT 1 chrIII:10182744-10182824 ( 55) CTCAATCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7008 bayes= 9.42219 E= 2.1e+003 -1089 218 -193 -1089 -1089 -1089 -1089 172 -1089 226 -1089 -1089 72 134 -1089 -1089 180 -1089 -1089 -1089 -245 118 -94 28 -86 182 -94 -1089 -1089 -98 -1089 156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 2.1e+003 0.000000 0.947368 0.052632 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.473684 0.526316 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.052632 0.473684 0.105263 0.368421 0.157895 0.736842 0.105263 0.000000 0.000000 0.105263 0.000000 0.894737 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCMAYCT MEME-1 regular expression -------------------------------------------------------------------------------- CTC[CA]A[CT]CT -------------------------------------------------------------------------------- Time 1.19 secs. ******************************************************************************** ******************************************************************************** MOTIF GRGGGAGC MEME-2 width = 8 sites = 2 llr = 23 E-value = 1.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :5:::a:: pos.-specific C :::::::a probability G a5aaa:a: matrix T :::::::: bits 2.3 * *** ** 2.1 * *** ** 1.8 * ****** 1.6 * ****** Relative 1.4 * ****** Entropy 1.2 ******** (16.7 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAGGGAGC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:379139-379219 65 3.95e-06 GGGAGAGGGA GGGGGAGC AAAGTCGC chrI:8677705-8677785 70 9.61e-06 TTGTATCCTG GAGGGAGC ATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:379139-379219 4e-06 64_[+2]_8 chrI:8677705-8677785 9.6e-06 69_[+2]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GRGGGAGC width=8 seqs=2 chrI:379139-379219 ( 65) GGGGGAGC 1 chrI:8677705-8677785 ( 70) GAGGGAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7008 bayes= 10.926 E= 1.1e+004 -765 -765 231 -765 79 -765 131 -765 -765 -765 231 -765 -765 -765 231 -765 -765 -765 231 -765 179 -765 -765 -765 -765 -765 231 -765 -765 226 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.1e+004 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRGGGAGC MEME-2 regular expression -------------------------------------------------------------------------------- G[AG]GGGAGC -------------------------------------------------------------------------------- Time 2.15 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGGAGAG MEME-3 width = 8 sites = 2 llr = 24 E-value = 3.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::a:a: pos.-specific C :::::::: probability G aaaa:a:a matrix T :::::::: bits 2.3 **** * * 2.1 **** * * 1.8 ******** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGGAGAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:379139-379219 54 5.47e-06 ATTATTTAGA GGGGAGAG GGAGGGGGAG chrI:8975597-8975677 2 5.47e-06 G GGGGAGAG AGAGAGACCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:379139-379219 5.5e-06 53_[+3]_19 chrI:8975597-8975677 5.5e-06 1_[+3]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGGAGAG width=8 seqs=2 chrI:379139-379219 ( 54) GGGGAGAG 1 chrI:8975597-8975677 ( 2) GGGGAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7008 bayes= 11.7744 E= 3.4e+003 -765 -765 231 -765 -765 -765 231 -765 -765 -765 231 -765 -765 -765 231 -765 179 -765 -765 -765 -765 -765 231 -765 179 -765 -765 -765 -765 -765 231 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.4e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGAGAG MEME-3 regular expression -------------------------------------------------------------------------------- GGGGAGAG -------------------------------------------------------------------------------- Time 3.24 secs. ******************************************************************************** ******************************************************************************** MOTIF GATGACGG MEME-4 width = 8 sites = 2 llr = 23 E-value = 1.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :a::a::: pos.-specific C :::::a:: probability G a::a::aa matrix T ::a::::: bits 2.3 * * *** 2.1 * * *** 1.8 ** ***** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (16.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GATGACGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:4734827-4734907 40 8.53e-06 TTTTTTCAGG GATGACGG CGATGATATG chrII:11879753-11879833 24 8.53e-06 CGATTCGGAC GATGACGG TGTGGAGCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:4734827-4734907 8.5e-06 39_[+4]_33 chrII:11879753-11879833 8.5e-06 23_[+4]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GATGACGG width=8 seqs=2 chrV:4734827-4734907 ( 40) GATGACGG 1 chrII:11879753-11879833 ( 24) GATGACGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7008 bayes= 11.7744 E= 1.8e+004 -765 -765 231 -765 179 -765 -765 -765 -765 -765 -765 172 -765 -765 231 -765 179 -765 -765 -765 -765 226 -765 -765 -765 -765 231 -765 -765 -765 231 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.8e+004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATGACGG MEME-4 regular expression -------------------------------------------------------------------------------- GATGACGG -------------------------------------------------------------------------------- Time 4.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGGACGG MEME-5 width = 8 sites = 2 llr = 24 E-value = 7.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C :::::a:: probability G a:aa::aa matrix T :a:::::: bits 2.3 * ** *** 2.1 * ** *** 1.8 * ****** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GTGGACGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:1723138-1723218 9 5.95e-06 CGCAAGTT GTGGACGG AAAACCTTTA chrV:19049547-19049627 27 5.95e-06 ACAATCCCTT GTGGACGG CGGTGGCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:1723138-1723218 6e-06 8_[+5]_64 chrV:19049547-19049627 6e-06 26_[+5]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGGACGG width=8 seqs=2 chrIV:1723138-1723218 ( 9) GTGGACGG 1 chrV:19049547-19049627 ( 27) GTGGACGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7008 bayes= 11.7744 E= 7.2e+003 -765 -765 231 -765 -765 -765 -765 172 -765 -765 231 -765 -765 -765 231 -765 179 -765 -765 -765 -765 226 -765 -765 -765 -765 231 -765 -765 -765 231 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.2e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGACGG MEME-5 regular expression -------------------------------------------------------------------------------- GTGGACGG -------------------------------------------------------------------------------- Time 6.74 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:8975597-8975677 3.43e-05 1_[+3(5.47e-06)]_71 chrII:11879753-11879833 8.65e-05 23_[+4(8.53e-06)]_49 chrI:14856802-14856882 4.06e-03 80 chrIV:11977402-11977482 2.41e-01 13_[+1(6.03e-05)]_59 chrIII:10182744-10182824 5.11e-02 80 chrI:14882898-14882978 7.09e-02 80 chrII:10933564-10933644 1.46e-01 80 chrI:14883509-14883589 1.91e-01 80 chrI:8976946-8977026 5.81e-01 80 chrI:11764155-11764235 9.99e-01 80 chrIV:3043001-3043081 3.44e-03 80 chrII:9888136-9888216 2.98e-01 80 chrV:12605445-12605525 7.50e-02 80 chrIII:10182465-10182545 8.79e-01 80 chrV:4349013-4349093 1.14e-01 80 chrII:1150352-1150432 3.32e-02 4_[+1(1.03e-05)]_68 chrIII:8171890-8171970 4.94e-01 80 chrI:14881328-14881408 3.64e-03 80 chrIII:4175078-4175158 1.18e-01 63_[+1(1.03e-05)]_9 chrIII:5198386-5198466 6.37e-01 80 chrII:9889382-9889462 2.54e-01 2_[+1(6.03e-05)]_70 chrIII:5229911-5229991 3.12e-01 80 chrV:10026868-10026948 9.97e-01 80 chrX:13955382-13955462 6.59e-01 80 chrIII:7700156-7700236 2.31e-01 80 chrV:6401737-6401817 9.34e-01 80 chrV:6401471-6401551 7.67e-01 80 chrV:19049547-19049627 2.34e-03 26_[+5(5.95e-06)]_46 chrII:9886673-9886753 5.15e-01 80 chrIV:3040699-3040779 3.02e-01 80 chrX:6089140-6089220 1.97e-01 80 chrIV:11601154-11601234 1.00e+00 80 chrI:4508613-4508693 9.86e-01 80 chrIV:5985567-5985647 5.66e-01 80 chrI:1738065-1738145 5.61e-02 80 chrIV:1723138-1723218 4.85e-03 8_[+5(5.95e-06)]_64 chrI:7627064-7627144 9.60e-01 80 chrI:8677705-8677785 1.39e-04 69_[+2(9.61e-06)]_3 chrI:14855777-14855857 9.66e-01 80 chrV:5832024-5832104 7.49e-01 80 chrIV:17280085-17280165 9.02e-01 80 chrI:7585391-7585471 6.58e-01 80 chrX:4526516-4526596 9.96e-01 80 chrIV:15049694-15049774 3.21e-01 80 chrIII:6970333-6970413 1.36e-02 33_[+1(2.45e-05)]_39 chrII:4429215-4429295 3.06e-01 80 chrIV:5987703-5987783 5.26e-01 80 chrV:12606469-12606549 5.56e-01 80 chrII:8141246-8141326 3.80e-02 80 chrIV:11527795-11527875 9.82e-01 80 chrIII:9462650-9462730 8.81e-01 80 chrII:6847972-6848052 8.51e-01 80 chrV:12004153-12004233 2.64e-01 80 chrII:7744945-7745025 2.62e-01 80 chrII:11880562-11880642 9.83e-01 80 chrII:11691121-11691201 3.00e-01 80 chrI:12787854-12787934 6.01e-01 80 chrIII:8805947-8806027 2.60e-01 10_[+1(3.95e-05)]_62 chrIV:9990740-9990820 7.59e-02 80 chrIV:6906340-6906420 9.94e-01 80 chrI:11764737-11764817 2.82e-01 80 chrIII:4172462-4172542 2.38e-01 80 chrI:8976437-8976517 2.92e-01 80 chrIII:2669439-2669519 8.20e-02 80 chrI:5171260-5171340 9.37e-01 80 chrV:14688517-14688597 6.64e-01 80 chrIV:5999204-5999284 4.10e-01 80 chrII:11125215-11125295 9.63e-01 80 chrI:2875206-2875286 1.94e-01 80 chrV:10023071-10023151 9.23e-01 80 chrX:7825796-7825876 1.97e-01 12_[+1(6.03e-05)]_60 chrIII:2674034-2674114 5.78e-01 80 chrV:14354267-14354347 1.00e+00 80 chrV:4734827-4734907 8.71e-03 39_[+4(8.53e-06)]_33 chrV:2786865-2786945 2.26e-01 80 chrIV:10381191-10381271 6.21e-01 80 chrI:6838097-6838177 9.49e-01 80 chrI:379139-379219 2.25e-05 53_[+3(5.47e-06)]_3_[+2(3.95e-06)]_\ 8 chrIII:7637339-7637419 5.56e-02 70_[+1(1.03e-05)]_2 chrIV:17281304-17281384 7.61e-01 80 chrIII:1419808-1419888 9.98e-01 80 chrV:14687982-14688062 9.59e-02 80 chrIII:5205882-5205962 8.42e-01 80 chrIII:12599239-12599319 2.17e-01 80 chrX:4193181-4193261 5.10e-01 80 chrIV:7623908-7623988 5.56e-02 80 chrV:5829449-5829529 9.89e-01 80 chrIII:10209728-10209808 9.96e-01 80 chrIII:3869452-3869532 1.00e+00 80 chrIII:13464656-13464736 9.48e-01 80 chrII:5338800-5338880 5.52e-01 80 chrIV:8432640-8432720 5.65e-01 80 chrIV:16483240-16483320 4.93e-01 80 chrI:7586956-7587036 4.32e-01 80 chrII:11547263-11547343 9.19e-01 80 chrI:10553032-10553112 9.10e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************