******************************************************************************** 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-10.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIII:1622510-1622590 1.0000 80 chrV:1593910-1593990 1.0000 80 chrIII:10985745-10985825 1.0000 80 chrIV:9676717-9676797 1.0000 80 chrV:12543041-12543121 1.0000 80 chrII:7073348-7073428 1.0000 80 chrIV:8532201-8532281 1.0000 80 chrX:7990526-7990606 1.0000 80 chrX:6792667-6792747 1.0000 80 chrV:6401275-6401355 1.0000 80 chrX:12990897-12990977 1.0000 80 chrIII:6415803-6415883 1.0000 80 chrV:1456783-1456863 1.0000 80 chrIV:7047146-7047226 1.0000 80 chrI:3680136-3680216 1.0000 80 chrX:12425510-12425590 1.0000 80 chrX:10077647-10077727 1.0000 80 chrII:5323943-5324023 1.0000 80 chrX:15374862-15374942 1.0000 80 chrIV:4236797-4236877 1.0000 80 chrIV:8822712-8822792 1.0000 80 chrIV:8154737-8154817 1.0000 80 chrX:8761178-8761258 1.0000 80 chrV:8671732-8671812 1.0000 80 chrIV:6097681-6097761 1.0000 80 chrX:4526476-4526556 1.0000 80 chrX:440588-440668 1.0000 80 chrV:10712618-10712698 1.0000 80 chrV:10087241-10087321 1.0000 80 chrI:7867244-7867324 1.0000 80 chrIV:5388851-5388931 1.0000 80 chrIII:13542594-13542674 1.0000 80 chrII:5572244-5572324 1.0000 80 chrV:3979979-3980059 1.0000 80 chrIII:3804506-3804586 1.0000 80 chrIV:429077-429157 1.0000 80 chrII:11151195-11151275 1.0000 80 chrIII:13344895-13344975 1.0000 80 chrII:11200555-11200635 1.0000 80 chrII:9740732-9740812 1.0000 80 chrII:9275362-9275442 1.0000 80 chrX:11515506-11515586 1.0000 80 chrI:6418862-6418942 1.0000 80 chrX:3115858-3115938 1.0000 80 chrV:9443288-9443368 1.0000 80 chrX:14815982-14816062 1.0000 80 chrII:5281306-5281386 1.0000 80 chrIV:11915047-11915127 1.0000 80 chrV:8655226-8655306 1.0000 80 chrV:18577599-18577679 1.0000 80 chrX:6663949-6664029 1.0000 80 chrX:6059607-6059687 1.0000 80 chrIV:8585241-8585321 1.0000 80 chrIV:13389077-13389157 1.0000 80 chrII:5748551-5748631 1.0000 80 chrX:6057723-6057803 1.0000 80 chrX:13106532-13106612 1.0000 80 chrV:13373776-13373856 1.0000 80 chrII:13298569-13298649 1.0000 80 chrII:6328784-6328864 1.0000 80 chrIII:5506109-5506189 1.0000 80 chrII:5752996-5753076 1.0000 80 chrI:10776042-10776122 1.0000 80 chrV:20712573-20712653 1.0000 80 chrII:9502250-9502330 1.0000 80 chrX:15709676-15709756 1.0000 80 chrIV:3609146-3609226 1.0000 80 chrII:11153928-11154008 1.0000 80 chrX:8243287-8243367 1.0000 80 chrII:15212370-15212450 1.0000 80 chrII:11614724-11614804 1.0000 80 chrV:13198181-13198261 1.0000 80 chrX:10142113-10142193 1.0000 80 chrII:8813759-8813839 1.0000 80 chrII:7631245-7631325 1.0000 80 chrV:10203990-10204070 1.0000 80 chrII:8440967-8441047 1.0000 80 chrV:11822730-11822810 1.0000 80 chrX:8089567-8089647 1.0000 80 chrII:10001145-10001225 1.0000 80 chrX:4564840-4564920 1.0000 80 chrII:5186023-5186103 1.0000 80 chrV:9204897-9204977 1.0000 80 chrIII:13763310-13763390 1.0000 80 chrV:12744427-12744507 1.0000 80 chrII:12996367-12996447 1.0000 80 chrV:10399465-10399545 1.0000 80 chrII:900942-901022 1.0000 80 chrII:10556928-10557008 1.0000 80 chrIV:6083776-6083856 1.0000 80 chrII:8743524-8743604 1.0000 80 chrIV:11901419-11901499 1.0000 80 chrX:3116718-3116798 1.0000 80 chrIV:10243309-10243389 1.0000 80 chrII:5340888-5340968 1.0000 80 chrIV:1837297-1837377 1.0000 80 chrV:17721884-17721964 1.0000 80 chrI:5408453-5408533 1.0000 80 chrX:6240948-6241028 1.0000 80 chrX:12172885-12172965 1.0000 80 chrIV:9716618-9716698 1.0000 80 chrV:4918803-4918883 1.0000 80 chrX:13250251-13250331 1.0000 80 chrIV:9667239-9667319 1.0000 80 chrV:11616908-11616988 1.0000 80 chrIV:5762907-5762987 1.0000 80 chrII:9791325-9791405 1.0000 80 chrIV:6555046-6555126 1.0000 80 chrV:6228793-6228873 1.0000 80 chrIII:3798009-3798089 1.0000 80 chrIV:762268-762348 1.0000 80 chrX:13310860-13310940 1.0000 80 chrV:11976857-11976937 1.0000 80 chrX:9679559-9679639 1.0000 80 chrV:6276242-6276322 1.0000 80 chrV:11543843-11543923 1.0000 80 chrIV:7189006-7189086 1.0000 80 chrII:5280539-5280619 1.0000 80 chrX:5213805-5213885 1.0000 80 chrX:1337106-1337186 1.0000 80 chrX:11661742-11661822 1.0000 80 chrI:4436924-4437004 1.0000 80 chrV:15569872-15569952 1.0000 80 chrX:8473682-8473762 1.0000 80 chrIV:13393409-13393489 1.0000 80 chrV:9074589-9074669 1.0000 80 chrV:12733570-12733650 1.0000 80 chrX:6205072-6205152 1.0000 80 chrX:10340307-10340387 1.0000 80 chrII:6848107-6848187 1.0000 80 chrX:13348562-13348642 1.0000 80 chrI:11577557-11577637 1.0000 80 chrIII:5828834-5828914 1.0000 80 chrX:8475274-8475354 1.0000 80 chrV:15318764-15318844 1.0000 80 chrV:12003636-12003716 1.0000 80 chrI:7079958-7080038 1.0000 80 chrIV:8234055-8234135 1.0000 80 chrX:6818199-6818279 1.0000 80 chrI:5037336-5037416 1.0000 80 chrV:6278045-6278125 1.0000 80 chrV:10480917-10480997 1.0000 80 chrII:8739074-8739154 1.0000 80 chrV:13369908-13369988 1.0000 80 chrV:726988-727068 1.0000 80 chrIV:11899554-11899634 1.0000 80 chrV:13782378-13782458 1.0000 80 chrV:2324426-2324506 1.0000 80 chrV:729346-729426 1.0000 80 chrII:13678650-13678730 1.0000 80 chrI:5372934-5373014 1.0000 80 chrII:11619350-11619430 1.0000 80 chrII:848690-848770 1.0000 80 chrIII:6872713-6872793 1.0000 80 chrV:10891100-10891180 1.0000 80 chrIII:9462729-9462809 1.0000 80 chrIV:3653485-3653565 1.0000 80 chrV:6994237-6994317 1.0000 80 chrIII:9851043-9851123 1.0000 80 chrX:1272691-1272771 1.0000 80 chrV:13878308-13878388 1.0000 80 chrII:5605554-5605634 1.0000 80 chrII:6049680-6049760 1.0000 80 chrI:9862838-9862918 1.0000 80 chrX:13165851-13165931 1.0000 80 chrI:7661065-7661145 1.0000 80 chrII:4745430-4745510 1.0000 80 chrIII:13606295-13606375 1.0000 80 chrX:6743028-6743108 1.0000 80 chrV:11888132-11888212 1.0000 80 chrIV:5778459-5778539 1.0000 80 chrX:8750416-8750496 1.0000 80 chrX:4794249-4794329 1.0000 80 chrII:11617865-11617945 1.0000 80 chrII:11150187-11150267 1.0000 80 chrII:8383068-8383148 1.0000 80 chrII:13465480-13465560 1.0000 80 chrIV:2281553-2281633 1.0000 80 chrIV:10469650-10469730 1.0000 80 chrV:7809933-7810013 1.0000 80 chrX:7233756-7233836 1.0000 80 chrV:19050933-19051013 1.0000 80 chrV:3579873-3579953 1.0000 80 chrIV:8026497-8026577 1.0000 80 chrII:5282179-5282259 1.0000 80 chrV:8267489-8267569 1.0000 80 chrV:20163234-20163314 1.0000 80 chrIV:16181007-16181087 1.0000 80 chrIV:9801598-9801678 1.0000 80 chrIII:13605288-13605368 1.0000 80 chrX:14558101-14558181 1.0000 80 chrI:7056993-7057073 1.0000 80 chrIV:16169793-16169873 1.0000 80 chrI:6728100-6728180 1.0000 80 chrX:11791853-11791933 1.0000 80 chrIII:10717632-10717712 1.0000 80 chrV:13892646-13892726 1.0000 80 chrX:10480683-10480763 1.0000 80 chrV:16045940-16046020 1.0000 80 chrV:5512737-5512817 1.0000 80 chrX:6338666-6338746 1.0000 80 chrIII:6857625-6857705 1.0000 80 chrI:7054677-7054757 1.0000 80 chrX:7244928-7245008 1.0000 80 chrIV:13318873-13318953 1.0000 80 chrIV:9674270-9674350 1.0000 80 chrIV:12601082-12601162 1.0000 80 chrIV:12306129-12306209 1.0000 80 chrI:8344640-8344720 1.0000 80 chrX:15382926-15383006 1.0000 80 chrIII:7736722-7736802 1.0000 80 chrV:10565084-10565164 1.0000 80 chrX:15610604-15610684 1.0000 80 chrV:10936861-10936941 1.0000 80 chrX:11603786-11603866 1.0000 80 chrII:13469300-13469380 1.0000 80 chrII:6892028-6892108 1.0000 80 chrV:6239984-6240064 1.0000 80 chrV:1176516-1176596 1.0000 80 chrX:12627900-12627980 1.0000 80 chrX:11727978-11728058 1.0000 80 chrI:14855798-14855878 1.0000 80 chrIV:11284235-11284315 1.0000 80 chrX:7316960-7317040 1.0000 80 chrIV:13919356-13919436 1.0000 80 chrIV:8032261-8032341 1.0000 80 chrX:6250374-6250454 1.0000 80 chrII:14825526-14825606 1.0000 80 chrII:9935194-9935274 1.0000 80 chrX:12501039-12501119 1.0000 80 chrII:5019528-5019608 1.0000 80 chrIII:5953554-5953634 1.0000 80 chrII:4089435-4089515 1.0000 80 chrIV:11488229-11488309 1.0000 80 chrIV:9651380-9651460 1.0000 80 chrX:7200527-7200607 1.0000 80 chrV:333856-333936 1.0000 80 chrX:2541405-2541485 1.0000 80 chrIV:14594393-14594473 1.0000 80 chrI:7081179-7081259 1.0000 80 chrV:8651473-8651553 1.0000 80 chrX:16192712-16192792 1.0000 80 chrX:6271922-6272002 1.0000 80 chrIV:11955740-11955820 1.0000 80 chrIII:833095-833175 1.0000 80 chrIV:8530717-8530797 1.0000 80 chrI:12937733-12937813 1.0000 80 chrX:1504059-1504139 1.0000 80 chrV:2327347-2327427 1.0000 80 chrII:5202194-5202274 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-10/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-10.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= 250 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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.306 C 0.192 G 0.199 T 0.303 Background letter frequencies (from file dataset with add-one prior applied): A 0.306 C 0.192 G 0.199 T 0.303 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCTCTCTC MEME-1 width = 8 sites = 34 llr = 288 E-value = 7.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 16:8:8:a probability G :1:::::: matrix T 82a2a1a: bits 2.4 * 2.1 * 1.9 * 1.7 * * ** Relative 1.4 ****** Entropy 1.2 ****** (12.2 bits) 1.0 * ****** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCTCTCTC consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:5019528-5019608 53 1.15e-05 TTTTTCTCTA TCTCTCTC AACTGTCTAC chrIV:16181007-16181087 50 1.15e-05 AATTTTCCAC TCTCTCTC CTGTTCTTTC chrV:3579873-3579953 48 1.15e-05 CGCCTGCTTC TCTCTCTC TCTGTTTCCC chrIV:11899554-11899634 2 1.15e-05 c tctctctc tctTCATTTC chrV:9074589-9074669 71 1.15e-05 tccctctctc tctctctc tc chrII:7631245-7631325 28 1.15e-05 TGTCTCTTTT TCTCTCTC ACTTTGCCCC chrIII:5506109-5506189 73 1.15e-05 CCACACACCA TCTCTCTC chrX:6057723-6057803 45 1.15e-05 gttctctctc tctctctc tgtcGAGTAC chrII:11200555-11200635 17 1.15e-05 TCTCTTTTTC TCTCTCTC GAAGCTTCGG chrX:6743028-6743108 8 2.95e-05 TCTCTCA TTTCTCTC ACTATTTACC chrX:8475274-8475354 5 2.95e-05 GGCA TTTCTCTC ATCTCTTATT chrV:12543041-12543121 43 2.95e-05 TCACGTCATT TTTCTCTC ATTTCCAGTT chrIII:13606295-13606375 8 3.68e-05 ATAACTC CCTCTCTC ACTTCGTTCT chrI:9862838-9862918 7 3.68e-05 CTCCAC CCTCTCTC TTTTTACATC chrIV:8026497-8026577 46 4.87e-05 TATGGGGCGG TGTCTCTC TATGATAATA chrX:10340307-10340387 14 4.87e-05 ATAACATTTT TGTCTCTC CAGTCGAAAA chrIV:9716618-9716698 44 4.87e-05 CATATCTATG TGTCTCTC TACATCGTGT chrV:2324426-2324506 9 6.67e-05 TTTTATGA TCTTTCTC CTTCTCATTC chrX:6240948-6241028 39 6.67e-05 ATTCAGGTAA TCTTTCTC CAATCAACAA chrIV:429077-429157 2 6.67e-05 C TCTTTCTC CCTTATCAGT chrI:7081179-7081259 1 8.48e-05 . TCTCTTTC GCGCCAATAT chrI:10776042-10776122 66 8.48e-05 GTCTAGCGAT TCTCTTTC TTTTTTT chrII:7073348-7073428 51 8.48e-05 TTGCTCTCAC TCTCTTTC TTTACTGTCT chrX:440588-440668 45 1.04e-04 GACTATATTA GCTCTCTC CGAAGCAAAG chrV:13782378-13782458 31 1.11e-04 ACCACTTCTG CGTCTCTC CATCTCTTTA chrII:4089435-4089515 70 1.40e-04 ATTTTCTATC TTTTTCTC TGT chrX:12627900-12627980 11 1.40e-04 ATGATTTTGA TTTTTCTC ATTATTTCAT chrV:6994237-6994317 38 1.40e-04 GATTGTACTT TTTTTCTC TGAATGCCTA chrIII:10985745-10985825 13 1.40e-04 TTTCAATTTT TTTTTCTC AAATAGTCAT chrIV:11284235-11284315 67 1.75e-04 GGTTATTTGC TCTCTGTC CGGGGA chrIV:9667239-9667319 60 1.75e-04 ACGGGGGAAT ACTCTCTC CTCCAGACGG chrX:7200527-7200607 15 2.40e-04 GGTCTTATAC TTTCTTTC AGGTCAACAC chrIV:4236797-4236877 24 2.40e-04 GTTTCGACCT TATCTCTC AGTAGTCGCA chrX:13165851-13165931 9 2.52e-04 TTACGTCT CCTCTTTC CTTTTCACCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:5019528-5019608 1.1e-05 52_[+1]_20 chrIV:16181007-16181087 1.1e-05 49_[+1]_23 chrV:3579873-3579953 1.1e-05 47_[+1]_25 chrIV:11899554-11899634 1.1e-05 1_[+1]_71 chrV:9074589-9074669 1.1e-05 70_[+1]_2 chrII:7631245-7631325 1.1e-05 27_[+1]_45 chrIII:5506109-5506189 1.1e-05 72_[+1] chrX:6057723-6057803 1.1e-05 44_[+1]_28 chrII:11200555-11200635 1.1e-05 16_[+1]_56 chrX:6743028-6743108 3e-05 7_[+1]_65 chrX:8475274-8475354 3e-05 4_[+1]_68 chrV:12543041-12543121 3e-05 42_[+1]_30 chrIII:13606295-13606375 3.7e-05 7_[+1]_65 chrI:9862838-9862918 3.7e-05 6_[+1]_66 chrIV:8026497-8026577 4.9e-05 45_[+1]_27 chrX:10340307-10340387 4.9e-05 13_[+1]_59 chrIV:9716618-9716698 4.9e-05 43_[+1]_29 chrV:2324426-2324506 6.7e-05 8_[+1]_64 chrX:6240948-6241028 6.7e-05 38_[+1]_34 chrIV:429077-429157 6.7e-05 1_[+1]_71 chrI:7081179-7081259 8.5e-05 [+1]_72 chrI:10776042-10776122 8.5e-05 65_[+1]_7 chrII:7073348-7073428 8.5e-05 50_[+1]_22 chrX:440588-440668 0.0001 44_[+1]_28 chrV:13782378-13782458 0.00011 30_[+1]_42 chrII:4089435-4089515 0.00014 69_[+1]_3 chrX:12627900-12627980 0.00014 10_[+1]_62 chrV:6994237-6994317 0.00014 37_[+1]_35 chrIII:10985745-10985825 0.00014 12_[+1]_60 chrIV:11284235-11284315 0.00017 66_[+1]_6 chrIV:9667239-9667319 0.00017 59_[+1]_13 chrX:7200527-7200607 0.00024 14_[+1]_58 chrIV:4236797-4236877 0.00024 23_[+1]_49 chrX:13165851-13165931 0.00025 8_[+1]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTCTCTC width=8 seqs=34 chrII:5019528-5019608 ( 53) TCTCTCTC 1 chrIV:16181007-16181087 ( 50) TCTCTCTC 1 chrV:3579873-3579953 ( 48) TCTCTCTC 1 chrIV:11899554-11899634 ( 2) TCTCTCTC 1 chrV:9074589-9074669 ( 71) TCTCTCTC 1 chrII:7631245-7631325 ( 28) TCTCTCTC 1 chrIII:5506109-5506189 ( 73) TCTCTCTC 1 chrX:6057723-6057803 ( 45) TCTCTCTC 1 chrII:11200555-11200635 ( 17) TCTCTCTC 1 chrX:6743028-6743108 ( 8) TTTCTCTC 1 chrX:8475274-8475354 ( 5) TTTCTCTC 1 chrV:12543041-12543121 ( 43) TTTCTCTC 1 chrIII:13606295-13606375 ( 8) CCTCTCTC 1 chrI:9862838-9862918 ( 7) CCTCTCTC 1 chrIV:8026497-8026577 ( 46) TGTCTCTC 1 chrX:10340307-10340387 ( 14) TGTCTCTC 1 chrIV:9716618-9716698 ( 44) TGTCTCTC 1 chrV:2324426-2324506 ( 9) TCTTTCTC 1 chrX:6240948-6241028 ( 39) TCTTTCTC 1 chrIV:429077-429157 ( 2) TCTTTCTC 1 chrI:7081179-7081259 ( 1) TCTCTTTC 1 chrI:10776042-10776122 ( 66) TCTCTTTC 1 chrII:7073348-7073428 ( 51) TCTCTTTC 1 chrX:440588-440668 ( 45) GCTCTCTC 1 chrV:13782378-13782458 ( 31) CGTCTCTC 1 chrII:4089435-4089515 ( 70) TTTTTCTC 1 chrX:12627900-12627980 ( 11) TTTTTCTC 1 chrV:6994237-6994317 ( 38) TTTTTCTC 1 chrIII:10985745-10985825 ( 13) TTTTTCTC 1 chrIV:11284235-11284315 ( 67) TCTCTGTC 1 chrIV:9667239-9667319 ( 60) ACTCTCTC 1 chrX:7200527-7200607 ( 15) TTTCTTTC 1 chrIV:4236797-4236877 ( 24) TATCTCTC 1 chrX:13165851-13165931 ( 9) CCTCTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.4321 E= 7.8e-004 -337 -71 -276 144 -337 168 -76 -36 -1173 -1173 -1173 172 -1173 204 -1173 -56 -1173 -1173 -1173 172 -1173 210 -276 -104 -1173 -1173 -1173 172 -1173 238 -1173 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 7.8e-004 0.029412 0.117647 0.029412 0.823529 0.029412 0.617647 0.117647 0.235294 0.000000 0.000000 0.000000 1.000000 0.000000 0.794118 0.000000 0.205882 0.000000 0.000000 0.000000 1.000000 0.000000 0.823529 0.029412 0.147059 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTCTC MEME-1 regular expression -------------------------------------------------------------------------------- T[CT]T[CT]TCTC -------------------------------------------------------------------------------- Time 5.50 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTTATCA MEME-2 width = 8 sites = 49 llr = 384 E-value = 9.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::9::a pos.-specific C 3611::a: probability G :1:1:::: matrix T 73981a:: bits 2.4 * 2.1 * 1.9 * 1.7 *** Relative 1.4 *** Entropy 1.2 * **** (11.3 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCTTATCA consensus CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:833095-833175 54 2.91e-05 AATCTTCAAT TCTTATCA AATGACGTTA chrII:9935194-9935274 51 2.91e-05 ATCATATTTA TCTTATCA CTCGGTCGAT chrIV:13919356-13919436 23 2.91e-05 CAGCTTCTTA TCTTATCA ACAACTGCAC chrX:12627900-12627980 62 2.91e-05 TGCCGGCCAG TCTTATCA AATTTGTCTC chrIV:16181007-16181087 66 2.91e-05 TCCTGTTCTT TCTTATCA GTTAATG chrX:13165851-13165931 37 2.91e-05 CTTATTATTA TCTTATCA CTTTCATCCG chrV:2324426-2324506 28 2.91e-05 TTCTCATTCT TCTTATCA GTACTTTGTG chrI:5037336-5037416 73 2.91e-05 ACAACCACAA TCTTATCA chrIV:6555046-6555126 60 2.91e-05 CCGCATGTTC TCTTATCA CACATTCTCT chrII:9791325-9791405 65 2.91e-05 ATGTGATCAG TCTTATCA TTTCACCT chrV:18577599-18577679 13 2.91e-05 ATGTGCATTT TCTTATCA GTTAATGATC chrII:5323943-5324023 61 2.91e-05 CCATAGTGTC TCTTATCA GCTGCGTGTT chrX:16192712-16192792 13 4.75e-05 TTATCAGCTT CCTTATCA CTCAATGAGC chrV:15318764-15318844 6 4.75e-05 AATTT CCTTATCA GTGCATTTGT chrV:17721884-17721964 52 4.75e-05 AAAACTTGCG CCTTATCA CTTGGGGTCA chrIV:429077-429157 10 4.75e-05 CTCTTTCTC CCTTATCA GTTGTCCAAC chrIV:4236797-4236877 5 4.75e-05 GCAT CCTTATCA AGTTTCGACC chrIV:14594393-14594473 12 9.34e-05 TTCTTCACTG TTTTATCA CACAATGGAG chrIV:12601082-12601162 60 9.34e-05 CTTTGAACAT TTTTATCA TTATGGGTGA chrIV:10469650-10469730 17 9.34e-05 TCAATAGATA TTTTATCA ATGACGTTAT chrIII:6872713-6872793 62 9.34e-05 TCCATTGATC TTTTATCA AGTGAGATAA chrX:8473682-8473762 54 9.34e-05 TAAAAAAATA TTTTATCA TCAAGATACT chrII:5748551-5748631 62 9.34e-05 GAGTACGCTG TTTTATCA GTTCCAACCA chrII:11151195-11151275 46 9.34e-05 ACCGATTGAT TTTTATCA AATATTTATC chrX:12425510-12425590 41 1.12e-04 GACAACTTCC TCCTATCA TTCATTCTCT chrX:15610604-15610684 51 1.41e-04 GAGATAAGAA CTTTATCA TTGAAAAGTG chrX:6338666-6338746 14 1.59e-04 TTTTGTGTCC TCTCATCA CAAATTGCTA chrII:13678650-13678730 40 1.59e-04 TCGGGGGGCA TCTCATCA GAGAATTGAA chrII:5572244-5572324 21 1.59e-04 TTCCTTGTTT TCTCATCA TTTCCTCCCG chrV:3579873-3579953 63 1.71e-04 CTCTCTGTTT CCCTATCA GTGTCCGTCG chrII:7631245-7631325 44 1.71e-04 TCACTTTGCC CCCTATCA TTATAAAGTA chrIV:13393409-13393489 58 1.90e-04 TCTAGTGTTC TCTGATCA CGTGATGATC chrX:3116718-3116798 68 1.90e-04 TTCAAATGTA TCTGATCA GTTGA chrII:5281306-5281386 11 1.90e-04 ATCATCTCAA TCTGATCA TTTTATTTTT chrV:20712573-20712653 8 2.20e-04 TTTCGGT TGTTATCA AAAAGTTTTT chrII:6328784-6328864 62 2.20e-04 CAAAGAGCAC TGTTATCA CCTACACCAC chrII:4089435-4089515 47 3.02e-04 TTTTAATTTG TCTTTTCA AAGACATTTT chrI:8344640-8344720 60 3.02e-04 TCTGACTTCT TCTTTTCA TTTGGAAAAC chrIII:9462729-9462809 53 3.02e-04 CATCATATGC TTCTATCA GCCTCAAACA chrIV:9716618-9716698 12 3.02e-04 ccttttcatt tcttttca tttttccttt chrV:10087241-10087321 62 3.02e-04 ACACGTGCTG TTCTATCA TCTTTAGTGT chrIV:8822712-8822792 5 3.02e-04 TCGC TTCTATCA CTTATCTGGC chrIV:13318873-13318953 31 3.21e-04 TGATTATGAA CGTTATCA TACCATTTTC chrX:6818199-6818279 29 3.21e-04 TCGAGTGTAC CGTTATCA TACGCAACGC chrV:11543843-11543923 17 3.50e-04 ACTTTAAACT TTTCATCA ATTGATTTGA chrI:6728100-6728180 70 3.87e-04 CGCCTCCACC CCTTTTCA ATA chrV:1593910-1593990 4 3.87e-04 CTA CTCTATCA ATCTATCAAC chrIII:1622510-1622590 29 4.29e-04 GCGAGCATTT TTTGATCA GTGATGTTTG chrIII:3798009-3798089 30 4.78e-04 AAACTAGCAA CTTCATCA AAAAAAATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:833095-833175 2.9e-05 53_[+2]_19 chrII:9935194-9935274 2.9e-05 50_[+2]_22 chrIV:13919356-13919436 2.9e-05 22_[+2]_50 chrX:12627900-12627980 2.9e-05 61_[+2]_11 chrIV:16181007-16181087 2.9e-05 65_[+2]_7 chrX:13165851-13165931 2.9e-05 36_[+2]_36 chrV:2324426-2324506 2.9e-05 27_[+2]_45 chrI:5037336-5037416 2.9e-05 72_[+2] chrIV:6555046-6555126 2.9e-05 59_[+2]_13 chrII:9791325-9791405 2.9e-05 64_[+2]_8 chrV:18577599-18577679 2.9e-05 12_[+2]_60 chrII:5323943-5324023 2.9e-05 60_[+2]_12 chrX:16192712-16192792 4.8e-05 12_[+2]_60 chrV:15318764-15318844 4.8e-05 5_[+2]_67 chrV:17721884-17721964 4.8e-05 51_[+2]_21 chrIV:429077-429157 4.8e-05 9_[+2]_63 chrIV:4236797-4236877 4.8e-05 4_[+2]_68 chrIV:14594393-14594473 9.3e-05 11_[+2]_61 chrIV:12601082-12601162 9.3e-05 59_[+2]_13 chrIV:10469650-10469730 9.3e-05 16_[+2]_56 chrIII:6872713-6872793 9.3e-05 61_[+2]_11 chrX:8473682-8473762 9.3e-05 53_[+2]_19 chrII:5748551-5748631 9.3e-05 61_[+2]_11 chrII:11151195-11151275 9.3e-05 45_[+2]_27 chrX:12425510-12425590 0.00011 40_[+2]_32 chrX:15610604-15610684 0.00014 50_[+2]_22 chrX:6338666-6338746 0.00016 13_[+2]_59 chrII:13678650-13678730 0.00016 39_[+2]_33 chrII:5572244-5572324 0.00016 20_[+2]_52 chrV:3579873-3579953 0.00017 62_[+2]_10 chrII:7631245-7631325 0.00017 43_[+2]_29 chrIV:13393409-13393489 0.00019 57_[+2]_15 chrX:3116718-3116798 0.00019 67_[+2]_5 chrII:5281306-5281386 0.00019 10_[+2]_62 chrV:20712573-20712653 0.00022 7_[+2]_65 chrII:6328784-6328864 0.00022 61_[+2]_11 chrII:4089435-4089515 0.0003 46_[+2]_26 chrI:8344640-8344720 0.0003 59_[+2]_13 chrIII:9462729-9462809 0.0003 52_[+2]_20 chrIV:9716618-9716698 0.0003 11_[+2]_61 chrV:10087241-10087321 0.0003 61_[+2]_11 chrIV:8822712-8822792 0.0003 4_[+2]_68 chrIV:13318873-13318953 0.00032 30_[+2]_42 chrX:6818199-6818279 0.00032 28_[+2]_44 chrV:11543843-11543923 0.00035 16_[+2]_56 chrI:6728100-6728180 0.00039 69_[+2]_3 chrV:1593910-1593990 0.00039 3_[+2]_69 chrIII:1622510-1622590 0.00043 28_[+2]_44 chrIII:3798009-3798089 0.00048 29_[+2]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TYTTATCA width=8 seqs=49 chrIII:833095-833175 ( 54) TCTTATCA 1 chrII:9935194-9935274 ( 51) TCTTATCA 1 chrIV:13919356-13919436 ( 23) TCTTATCA 1 chrX:12627900-12627980 ( 62) TCTTATCA 1 chrIV:16181007-16181087 ( 66) TCTTATCA 1 chrX:13165851-13165931 ( 37) TCTTATCA 1 chrV:2324426-2324506 ( 28) TCTTATCA 1 chrI:5037336-5037416 ( 73) TCTTATCA 1 chrIV:6555046-6555126 ( 60) TCTTATCA 1 chrII:9791325-9791405 ( 65) TCTTATCA 1 chrV:18577599-18577679 ( 13) TCTTATCA 1 chrII:5323943-5324023 ( 61) TCTTATCA 1 chrX:16192712-16192792 ( 13) CCTTATCA 1 chrV:15318764-15318844 ( 6) CCTTATCA 1 chrV:17721884-17721964 ( 52) CCTTATCA 1 chrIV:429077-429157 ( 10) CCTTATCA 1 chrIV:4236797-4236877 ( 5) CCTTATCA 1 chrIV:14594393-14594473 ( 12) TTTTATCA 1 chrIV:12601082-12601162 ( 60) TTTTATCA 1 chrIV:10469650-10469730 ( 17) TTTTATCA 1 chrIII:6872713-6872793 ( 62) TTTTATCA 1 chrX:8473682-8473762 ( 54) TTTTATCA 1 chrII:5748551-5748631 ( 62) TTTTATCA 1 chrII:11151195-11151275 ( 46) TTTTATCA 1 chrX:12425510-12425590 ( 41) TCCTATCA 1 chrX:15610604-15610684 ( 51) CTTTATCA 1 chrX:6338666-6338746 ( 14) TCTCATCA 1 chrII:13678650-13678730 ( 40) TCTCATCA 1 chrII:5572244-5572324 ( 21) TCTCATCA 1 chrV:3579873-3579953 ( 63) CCCTATCA 1 chrII:7631245-7631325 ( 44) CCCTATCA 1 chrIV:13393409-13393489 ( 58) TCTGATCA 1 chrX:3116718-3116798 ( 68) TCTGATCA 1 chrII:5281306-5281386 ( 11) TCTGATCA 1 chrV:20712573-20712653 ( 8) TGTTATCA 1 chrII:6328784-6328864 ( 62) TGTTATCA 1 chrII:4089435-4089515 ( 47) TCTTTTCA 1 chrI:8344640-8344720 ( 60) TCTTTTCA 1 chrIII:9462729-9462809 ( 53) TTCTATCA 1 chrIV:9716618-9716698 ( 12) TCTTTTCA 1 chrV:10087241-10087321 ( 62) TTCTATCA 1 chrIV:8822712-8822792 ( 5) TTCTATCA 1 chrIV:13318873-13318953 ( 31) CGTTATCA 1 chrX:6818199-6818279 ( 29) CGTTATCA 1 chrV:11543843-11543923 ( 17) TTTCATCA 1 chrI:6728100-6728180 ( 70) CCTTTTCA 1 chrV:1593910-1593990 ( 4) CTCTATCA 1 chrIII:1622510-1622590 ( 29) TTTGATCA 1 chrIII:3798009-3798089 ( 30) CTTCATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.65557 E= 9.1e-005 -1226 46 -1226 128 -1226 167 -129 2 -1226 -43 -1226 150 -1226 -92 -129 143 159 -1226 -1226 -189 -1226 -1226 -1226 172 -1226 238 -1226 -1226 171 -1226 -1226 -1226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 9.1e-005 0.000000 0.265306 0.000000 0.734694 0.000000 0.612245 0.081633 0.306122 0.000000 0.142857 0.000000 0.857143 0.000000 0.102041 0.081633 0.816327 0.918367 0.000000 0.000000 0.081633 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTATCA MEME-2 regular expression -------------------------------------------------------------------------------- [TC][CT]TTATCA -------------------------------------------------------------------------------- Time 9.32 secs. ******************************************************************************** ******************************************************************************** MOTIF GATAAGAA MEME-3 width = 8 sites = 21 llr = 197 E-value = 2.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:aa:a9 pos.-specific C :::::::: probability G a:2::a:1 matrix T ::7::::: bits 2.4 * * 2.1 * * 1.9 * * 1.7 ** **** Relative 1.4 ** **** Entropy 1.2 ** ***** (13.5 bits) 1.0 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GATAAGAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:8651473-8651553 7 3.22e-05 AAAACT GATAAGAA AAGCCTAATA chrIV:8032261-8032341 69 3.22e-05 GACGTAAACT GATAAGAA CGAC chrX:15610604-15610684 43 3.22e-05 TTGCATTCGA GATAAGAA CTTTATCATT chrX:10480683-10480763 34 3.22e-05 GGCTGAAACT GATAAGAA TAGTCGACAC chrIII:13605288-13605368 25 3.22e-05 TTGTGGATCA GATAAGAA GATCAGAAGC chrX:8750416-8750496 23 3.22e-05 GATAACAAGC GATAAGAA CTAATTGTAC chrI:11577557-11577637 32 3.22e-05 ACACAAAAAA GATAAGAA ATAGGTGAGA chrV:4918803-4918883 7 3.22e-05 AGCAGA GATAAGAA GTCACTTTCA chrI:5408453-5408533 41 3.22e-05 CGGAGGGATT GATAAGAA AATGGGAGAA chrX:6059607-6059687 70 3.22e-05 ATCACAACGA GATAAGAA ATA chrV:9443288-9443368 32 3.22e-05 ATATACATGT GATAAGAA TTGGGCGTTA chrIII:13542594-13542674 58 3.22e-05 TCATTGATAA GATAAGAA GACAAAGTTC chrII:13678650-13678730 13 5.33e-05 CGATGAAAGA GAGAAGAA CTGAGAGCAT chrV:726988-727068 72 5.33e-05 GAGAAAAATA GAGAAGAA A chrII:12996367-12996447 26 5.33e-05 TGGAGAAATA GAGAAGAA AACAAGTGGA chrV:11822730-11822810 28 5.33e-05 GATATTTGTA GAGAAGAA TAACAACAGT chrV:3979979-3980059 56 5.33e-05 GTGAGAGAGG GAGAAGAA GGAAAATGGT chrX:11661742-11661822 62 7.43e-05 GATGTAATAT GATAAGAG TGTTTCGTGC chrII:10556928-10557008 57 7.43e-05 TATTCGGAGC GATAAGAG CGACGCGCTC chrII:10001145-10001225 41 7.43e-05 TCAATGGACT GATAAGAG GCCTAAAACA chrX:1337106-1337186 68 1.21e-04 GATAAGACCC GAAAAGAA CTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:8651473-8651553 3.2e-05 6_[+3]_66 chrIV:8032261-8032341 3.2e-05 68_[+3]_4 chrX:15610604-15610684 3.2e-05 42_[+3]_30 chrX:10480683-10480763 3.2e-05 33_[+3]_39 chrIII:13605288-13605368 3.2e-05 24_[+3]_48 chrX:8750416-8750496 3.2e-05 22_[+3]_50 chrI:11577557-11577637 3.2e-05 31_[+3]_41 chrV:4918803-4918883 3.2e-05 6_[+3]_66 chrI:5408453-5408533 3.2e-05 40_[+3]_32 chrX:6059607-6059687 3.2e-05 69_[+3]_3 chrV:9443288-9443368 3.2e-05 31_[+3]_41 chrIII:13542594-13542674 3.2e-05 57_[+3]_15 chrII:13678650-13678730 5.3e-05 12_[+3]_60 chrV:726988-727068 5.3e-05 71_[+3]_1 chrII:12996367-12996447 5.3e-05 25_[+3]_47 chrV:11822730-11822810 5.3e-05 27_[+3]_45 chrV:3979979-3980059 5.3e-05 55_[+3]_17 chrX:11661742-11661822 7.4e-05 61_[+3]_11 chrII:10556928-10557008 7.4e-05 56_[+3]_16 chrII:10001145-10001225 7.4e-05 40_[+3]_32 chrX:1337106-1337186 0.00012 67_[+3]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GATAAGAA width=8 seqs=21 chrV:8651473-8651553 ( 7) GATAAGAA 1 chrIV:8032261-8032341 ( 69) GATAAGAA 1 chrX:15610604-15610684 ( 43) GATAAGAA 1 chrX:10480683-10480763 ( 34) GATAAGAA 1 chrIII:13605288-13605368 ( 25) GATAAGAA 1 chrX:8750416-8750496 ( 23) GATAAGAA 1 chrI:11577557-11577637 ( 32) GATAAGAA 1 chrV:4918803-4918883 ( 7) GATAAGAA 1 chrI:5408453-5408533 ( 41) GATAAGAA 1 chrX:6059607-6059687 ( 70) GATAAGAA 1 chrV:9443288-9443368 ( 32) GATAAGAA 1 chrIII:13542594-13542674 ( 58) GATAAGAA 1 chrII:13678650-13678730 ( 13) GAGAAGAA 1 chrV:726988-727068 ( 72) GAGAAGAA 1 chrII:12996367-12996447 ( 26) GAGAAGAA 1 chrV:11822730-11822810 ( 28) GAGAAGAA 1 chrV:3979979-3980059 ( 56) GAGAAGAA 1 chrX:11661742-11661822 ( 62) GATAAGAG 1 chrII:10556928-10557008 ( 57) GATAAGAG 1 chrII:10001145-10001225 ( 41) GATAAGAG 1 chrX:1337106-1337186 ( 68) GAAAAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.0668 E= 2.1e-001 -1104 -1104 233 -1104 171 -1104 -1104 -1104 -268 -1104 26 124 171 -1104 -1104 -1104 171 -1104 -1104 -1104 -1104 -1104 233 -1104 171 -1104 -1104 -1104 149 -1104 -48 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 2.1e-001 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.238095 0.714286 1.000000 0.000000 0.000000 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 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATAAGAA MEME-3 regular expression -------------------------------------------------------------------------------- GA[TG]AAGAA -------------------------------------------------------------------------------- Time 13.17 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGCCTKC MEME-4 width = 8 sites = 3 llr = 36 E-value = 4.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C aa:aa::a probability G ::a:::7: matrix T :::::a3: bits 2.4 ***** * 2.1 ***** * 1.9 ***** * 1.7 ****** * Relative 1.4 ****** * Entropy 1.2 ******** (17.1 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCGCCTGC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:3579873-3579953 37 3.13e-06 ATTTGAATCT CCGCCTGC TTCTCTCTCT chrV:6276242-6276322 10 3.13e-06 GCCTCTTAG CCGCCTGC GCTCTTTTCT chrV:11888132-11888212 57 7.90e-06 GCGGGAAGCC CCGCCTTC CAGCGTTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:3579873-3579953 3.1e-06 36_[+4]_36 chrV:6276242-6276322 3.1e-06 9_[+4]_63 chrV:11888132-11888212 7.9e-06 56_[+4]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGCCTKC width=8 seqs=3 chrV:3579873-3579953 ( 37) CCGCCTGC 1 chrV:6276242-6276322 ( 10) CCGCCTGC 1 chrV:11888132-11888212 ( 57) CCGCCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.0179 E= 4.0e+004 -823 237 -823 -823 -823 237 -823 -823 -823 -823 232 -823 -823 237 -823 -823 -823 237 -823 -823 -823 -823 -823 172 -823 -823 174 14 -823 237 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 4.0e+004 0.000000 1.000000 0.000000 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCTKC MEME-4 regular expression -------------------------------------------------------------------------------- CCGCCT[GT]C -------------------------------------------------------------------------------- Time 16.85 secs. ******************************************************************************** ******************************************************************************** MOTIF CBCTTCCC MEME-5 width = 8 sites = 5 llr = 55 E-value = 2.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a4a::aaa probability G :2:::::: matrix T :4:aa::: bits 2.4 * * *** 2.1 * * *** 1.9 * * *** 1.7 * ****** Relative 1.4 * ****** Entropy 1.2 * ****** (15.9 bits) 1.0 * ****** 0.7 * ****** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCTTCCC consensus T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:12937733-12937813 34 4.60e-06 TTCCAATTCC CCCTTCCC ATGCAATTTT chrV:13373776-13373856 35 4.60e-06 TGGAGAAAAA CCCTTCCC AACAACTGAT chrV:6994237-6994317 60 1.19e-05 TGCCTACTTC CTCTTCCC TATTTGCACA chrX:12172885-12172965 57 1.19e-05 TGATAACTAT CTCTTCCC ACTACCTAAT chrIII:13542594-13542674 38 1.66e-05 CACCGCCAAC CGCTTCCC CGTCATTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:12937733-12937813 4.6e-06 33_[+5]_39 chrV:13373776-13373856 4.6e-06 34_[+5]_38 chrV:6994237-6994317 1.2e-05 59_[+5]_13 chrX:12172885-12172965 1.2e-05 56_[+5]_16 chrIII:13542594-13542674 1.7e-05 37_[+5]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CBCTTCCC width=8 seqs=5 chrI:12937733-12937813 ( 34) CCCTTCCC 1 chrV:13373776-13373856 ( 35) CCCTTCCC 1 chrV:6994237-6994317 ( 60) CTCTTCCC 1 chrX:12172885-12172965 ( 57) CTCTTCCC 1 chrIII:13542594-13542674 ( 38) CGCTTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.7769 E= 2.2e+004 -897 238 -897 -897 -897 105 1 40 -897 238 -897 -897 -897 -897 -897 172 -897 -897 -897 172 -897 238 -897 -897 -897 238 -897 -897 -897 238 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 2.2e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.400000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CBCTTCCC MEME-5 regular expression -------------------------------------------------------------------------------- C[CTG]CTTCCC -------------------------------------------------------------------------------- Time 20.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:1622510-1622590 1.11e-01 80 chrV:1593910-1593990 3.94e-02 80 chrIII:10985745-10985825 1.25e-01 80 chrIV:9676717-9676797 8.45e-01 80 chrV:12543041-12543121 7.20e-02 42_[+1(2.95e-05)]_30 chrII:7073348-7073428 1.25e-02 50_[+1(8.48e-05)]_22 chrIV:8532201-8532281 4.48e-01 80 chrX:7990526-7990606 6.19e-01 80 chrX:6792667-6792747 3.20e-01 80 chrV:6401275-6401355 9.22e-01 80 chrX:12990897-12990977 6.32e-01 80 chrIII:6415803-6415883 9.02e-01 80 chrV:1456783-1456863 2.98e-01 80 chrIV:7047146-7047226 8.68e-02 36_[+5(7.85e-05)]_36 chrI:3680136-3680216 3.87e-01 80 chrX:12425510-12425590 6.35e-02 80 chrX:10077647-10077727 2.46e-03 20_[+5(7.85e-05)]_52 chrII:5323943-5324023 8.91e-03 60_[+2(2.91e-05)]_12 chrX:15374862-15374942 8.31e-01 80 chrIV:4236797-4236877 6.73e-03 4_[+2(4.75e-05)]_68 chrIV:8822712-8822792 5.46e-02 80 chrIV:8154737-8154817 5.96e-01 80 chrX:8761178-8761258 7.27e-02 80 chrV:8671732-8671812 1.30e-01 80 chrIV:6097681-6097761 8.56e-01 80 chrX:4526476-4526556 8.79e-01 80 chrX:440588-440668 6.09e-02 80 chrV:10712618-10712698 7.81e-01 80 chrV:10087241-10087321 1.31e-01 80 chrI:7867244-7867324 9.18e-01 80 chrIV:5388851-5388931 6.43e-01 80 chrIII:13542594-13542674 1.50e-06 37_[+5(1.66e-05)]_12_[+3(3.22e-05)]_\ 15 chrII:5572244-5572324 2.74e-03 80 chrV:3979979-3980059 6.12e-02 55_[+3(5.33e-05)]_17 chrIII:3804506-3804586 8.25e-01 80 chrIV:429077-429157 2.00e-03 1_[+1(6.67e-05)]_[+2(4.75e-05)]_63 chrII:11151195-11151275 9.10e-02 45_[+2(9.34e-05)]_27 chrIII:13344895-13344975 6.76e-01 80 chrII:11200555-11200635 1.68e-03 14_[+1(1.15e-05)]_58 chrII:9740732-9740812 4.15e-03 14_[+5(4.51e-05)]_58 chrII:9275362-9275442 2.62e-01 80 chrX:11515506-11515586 7.13e-01 80 chrI:6418862-6418942 7.99e-01 80 chrX:3115858-3115938 9.49e-01 80 chrV:9443288-9443368 2.27e-02 31_[+3(3.22e-05)]_41 chrX:14815982-14816062 8.26e-02 80 chrII:5281306-5281386 1.48e-01 80 chrIV:11915047-11915127 9.72e-01 80 chrV:8655226-8655306 2.63e-01 80 chrV:18577599-18577679 3.58e-03 12_[+2(2.91e-05)]_60 chrX:6663949-6664029 1.40e-01 80 chrX:6059607-6059687 1.72e-01 69_[+3(3.22e-05)]_3 chrIV:8585241-8585321 8.77e-01 80 chrIV:13389077-13389157 5.58e-01 80 chrII:5748551-5748631 3.56e-02 61_[+2(9.34e-05)]_11 chrX:6057723-6057803 4.27e-02 36_[+1(1.15e-05)]_[+1(1.15e-05)]_28 chrX:13106532-13106612 8.95e-02 80 chrV:13373776-13373856 3.36e-03 34_[+5(4.60e-06)]_38 chrII:13298569-13298649 1.16e-01 80 chrII:6328784-6328864 6.08e-02 80 chrIII:5506109-5506189 1.41e-04 72_[+1(1.15e-05)] chrII:5752996-5753076 8.44e-01 80 chrI:10776042-10776122 4.00e-02 65_[+1(8.48e-05)]_7 chrV:20712573-20712653 1.46e-01 80 chrII:9502250-9502330 8.24e-01 80 chrX:15709676-15709756 2.81e-01 80 chrIV:3609146-3609226 3.06e-01 80 chrII:11153928-11154008 7.42e-01 80 chrX:8243287-8243367 4.10e-01 80 chrII:15212370-15212450 5.74e-01 80 chrII:11614724-11614804 1.00e+00 80 chrV:13198181-13198261 8.89e-01 80 chrX:10142113-10142193 9.19e-01 80 chrII:8813759-8813839 2.79e-01 80 chrII:7631245-7631325 7.67e-04 27_[+1(1.15e-05)]_45 chrV:10203990-10204070 9.69e-03 64_[+5(7.85e-05)]_8 chrII:8440967-8441047 7.95e-01 80 chrV:11822730-11822810 1.96e-01 27_[+3(5.33e-05)]_45 chrX:8089567-8089647 1.16e-01 80 chrII:10001145-10001225 3.31e-01 40_[+3(7.43e-05)]_32 chrX:4564840-4564920 4.17e-01 80 chrII:5186023-5186103 9.71e-01 80 chrV:9204897-9204977 7.12e-01 80 chrIII:13763310-13763390 9.61e-01 80 chrV:12744427-12744507 1.62e-01 80 chrII:12996367-12996447 3.26e-01 25_[+3(5.33e-05)]_47 chrV:10399465-10399545 7.66e-01 80 chrII:900942-901022 9.94e-01 80 chrII:10556928-10557008 3.23e-01 56_[+3(7.43e-05)]_16 chrIV:6083776-6083856 2.49e-01 80 chrII:8743524-8743604 6.42e-01 80 chrIV:11901419-11901499 4.96e-01 80 chrX:3116718-3116798 3.67e-01 80 chrIV:10243309-10243389 2.34e-01 80 chrII:5340888-5340968 9.57e-01 80 chrIV:1837297-1837377 1.67e-01 80 chrV:17721884-17721964 1.01e-03 51_[+2(4.75e-05)]_21 chrI:5408453-5408533 1.85e-01 40_[+3(3.22e-05)]_32 chrX:6240948-6241028 7.89e-02 38_[+1(6.67e-05)]_34 chrX:12172885-12172965 7.46e-03 56_[+5(1.19e-05)]_16 chrIV:9716618-9716698 1.14e-02 43_[+1(4.87e-05)]_29 chrV:4918803-4918883 3.20e-03 6_[+3(3.22e-05)]_66 chrX:13250251-13250331 6.89e-01 80 chrIV:9667239-9667319 1.10e-01 80 chrV:11616908-11616988 4.78e-01 80 chrIV:5762907-5762987 8.26e-01 80 chrII:9791325-9791405 1.50e-02 33_[+2(4.75e-05)]_23_[+2(2.91e-05)]_\ 8 chrIV:6555046-6555126 3.47e-04 59_[+2(2.91e-05)]_13 chrV:6228793-6228873 9.03e-01 80 chrIII:3798009-3798089 6.51e-01 80 chrIV:762268-762348 9.22e-01 80 chrX:13310860-13310940 9.00e-01 80 chrV:11976857-11976937 5.40e-01 80 chrX:9679559-9679639 8.00e-01 80 chrV:6276242-6276322 1.21e-03 9_[+4(3.13e-06)]_63 chrV:11543843-11543923 2.41e-01 80 chrIV:7189006-7189086 5.16e-01 80 chrII:5280539-5280619 4.47e-01 80 chrX:5213805-5213885 5.91e-01 80 chrX:1337106-1337186 9.94e-04 80 chrX:11661742-11661822 8.02e-02 61_[+3(7.43e-05)]_11 chrI:4436924-4437004 3.92e-01 80 chrV:15569872-15569952 5.21e-01 80 chrX:8473682-8473762 2.46e-01 53_[+2(9.34e-05)]_19 chrIV:13393409-13393489 2.15e-02 80 chrV:9074589-9074669 2.18e-02 54_[+1(6.67e-05)]_2_[+1(1.15e-05)]_\ [+1(1.15e-05)] chrV:12733570-12733650 1.10e-01 80 chrX:6205072-6205152 9.56e-01 80 chrX:10340307-10340387 1.61e-02 13_[+1(4.87e-05)]_59 chrII:6848107-6848187 3.85e-01 80 chrX:13348562-13348642 4.75e-01 80 chrI:11577557-11577637 2.56e-01 31_[+3(3.22e-05)]_41 chrIII:5828834-5828914 8.33e-01 80 chrX:8475274-8475354 2.66e-02 4_[+1(2.95e-05)]_68 chrV:15318764-15318844 4.64e-03 5_[+2(4.75e-05)]_67 chrV:12003636-12003716 4.31e-02 80 chrI:7079958-7080038 9.99e-01 80 chrIV:8234055-8234135 7.91e-01 80 chrX:6818199-6818279 1.71e-01 80 chrI:5037336-5037416 1.80e-03 72_[+2(2.91e-05)] chrV:6278045-6278125 2.14e-01 80 chrV:10480917-10480997 2.12e-01 80 chrII:8739074-8739154 4.61e-01 80 chrV:13369908-13369988 3.78e-01 80 chrV:726988-727068 7.64e-02 71_[+3(5.33e-05)]_1 chrIV:11899554-11899634 9.99e-04 1_[+1(1.15e-05)]_71 chrV:13782378-13782458 1.23e-01 80 chrV:2324426-2324506 3.64e-04 8_[+1(6.67e-05)]_11_[+2(2.91e-05)]_\ 45 chrV:729346-729426 6.96e-01 80 chrII:13678650-13678730 2.33e-02 12_[+3(5.33e-05)]_60 chrI:5372934-5373014 9.85e-01 80 chrII:11619350-11619430 6.79e-01 80 chrII:848690-848770 9.98e-01 80 chrIII:6872713-6872793 1.33e-02 61_[+2(9.34e-05)]_11 chrV:10891100-10891180 9.99e-01 80 chrIII:9462729-9462809 1.11e-02 29_[+5(7.85e-05)]_43 chrIV:3653485-3653565 8.15e-01 80 chrV:6994237-6994317 1.31e-03 59_[+5(1.19e-05)]_13 chrIII:9851043-9851123 6.81e-01 80 chrX:1272691-1272771 9.09e-01 80 chrV:13878308-13878388 1.89e-01 80 chrII:5605554-5605634 1.55e-02 80 chrII:6049680-6049760 3.04e-01 80 chrI:9862838-9862918 5.06e-03 6_[+1(3.68e-05)]_66 chrX:13165851-13165931 4.88e-04 36_[+2(2.91e-05)]_36 chrI:7661065-7661145 1.53e-01 80 chrII:4745430-4745510 8.02e-01 80 chrIII:13606295-13606375 5.44e-02 7_[+1(3.68e-05)]_65 chrX:6743028-6743108 8.71e-03 7_[+1(2.95e-05)]_65 chrV:11888132-11888212 9.00e-03 56_[+4(7.90e-06)]_16 chrIV:5778459-5778539 7.03e-01 80 chrX:8750416-8750496 2.19e-01 22_[+3(3.22e-05)]_50 chrX:4794249-4794329 5.76e-02 80 chrII:11617865-11617945 9.06e-01 80 chrII:11150187-11150267 8.93e-01 80 chrII:8383068-8383148 7.22e-01 80 chrII:13465480-13465560 5.49e-01 80 chrIV:2281553-2281633 2.28e-01 80 chrIV:10469650-10469730 2.36e-01 16_[+2(9.34e-05)]_56 chrV:7809933-7810013 8.13e-01 80 chrX:7233756-7233836 4.49e-01 80 chrV:19050933-19051013 7.42e-01 80 chrV:3579873-3579953 2.37e-06 36_[+4(3.13e-06)]_1_[+1(1.15e-05)]_\ 27 chrIV:8026497-8026577 8.87e-02 45_[+1(4.87e-05)]_27 chrII:5282179-5282259 9.57e-01 80 chrV:8267489-8267569 9.22e-01 80 chrV:20163234-20163314 3.55e-01 80 chrIV:16181007-16181087 2.78e-05 49_[+1(1.15e-05)]_8_[+2(2.91e-05)]_\ 7 chrIV:9801598-9801678 4.65e-01 80 chrIII:13605288-13605368 2.15e-01 24_[+3(3.22e-05)]_48 chrX:14558101-14558181 5.60e-01 80 chrI:7056993-7057073 5.55e-01 80 chrIV:16169793-16169873 7.95e-01 80 chrI:6728100-6728180 2.23e-02 80 chrX:11791853-11791933 7.93e-01 80 chrIII:10717632-10717712 2.72e-01 80 chrV:13892646-13892726 9.50e-01 80 chrX:10480683-10480763 2.37e-02 33_[+3(3.22e-05)]_39 chrV:16045940-16046020 3.46e-01 80 chrV:5512737-5512817 3.91e-01 80 chrX:6338666-6338746 4.44e-02 80 chrIII:6857625-6857705 6.77e-01 80 chrI:7054677-7054757 9.78e-01 80 chrX:7244928-7245008 9.45e-01 80 chrIV:13318873-13318953 2.51e-02 80 chrIV:9674270-9674350 2.27e-01 80 chrIV:12601082-12601162 1.00e-01 59_[+2(9.34e-05)]_13 chrIV:12306129-12306209 8.38e-01 80 chrI:8344640-8344720 5.04e-02 80 chrX:15382926-15383006 9.66e-01 80 chrIII:7736722-7736802 2.65e-01 80 chrV:10565084-10565164 9.55e-01 80 chrX:15610604-15610684 1.04e-02 42_[+3(3.22e-05)]_30 chrV:10936861-10936941 2.94e-01 80 chrX:11603786-11603866 9.37e-01 80 chrII:13469300-13469380 5.16e-02 80 chrII:6892028-6892108 3.07e-01 80 chrV:6239984-6240064 8.55e-01 80 chrV:1176516-1176596 1.07e-01 80 chrX:12627900-12627980 7.74e-04 61_[+2(2.91e-05)]_11 chrX:11727978-11728058 9.81e-01 80 chrI:14855798-14855878 7.53e-01 80 chrIV:11284235-11284315 5.02e-02 80 chrX:7316960-7317040 7.99e-01 80 chrIV:13919356-13919436 3.34e-02 22_[+2(2.91e-05)]_50 chrIV:8032261-8032341 3.46e-02 68_[+3(3.22e-05)]_4 chrX:6250374-6250454 2.02e-01 80 chrII:14825526-14825606 3.17e-02 80 chrII:9935194-9935274 6.94e-02 50_[+2(2.91e-05)]_22 chrX:12501039-12501119 6.24e-01 80 chrII:5019528-5019608 1.55e-02 52_[+1(1.15e-05)]_20 chrIII:5953554-5953634 8.14e-01 80 chrII:4089435-4089515 2.63e-02 80 chrIV:11488229-11488309 7.43e-01 80 chrIV:9651380-9651460 9.76e-01 80 chrX:7200527-7200607 6.26e-02 80 chrV:333856-333936 2.07e-01 80 chrX:2541405-2541485 2.20e-01 80 chrIV:14594393-14594473 1.51e-01 11_[+2(9.34e-05)]_61 chrI:7081179-7081259 8.80e-02 [+1(8.48e-05)]_72 chrV:8651473-8651553 1.67e-01 6_[+3(3.22e-05)]_66 chrX:16192712-16192792 3.22e-02 [+2(4.75e-05)]_4_[+2(4.75e-05)]_60 chrX:6271922-6272002 1.27e-01 80 chrIV:11955740-11955820 2.71e-01 80 chrIII:833095-833175 2.60e-02 53_[+2(2.91e-05)]_19 chrIV:8530717-8530797 4.48e-01 80 chrI:12937733-12937813 2.66e-03 33_[+5(4.60e-06)]_39 chrX:1504059-1504139 8.30e-01 80 chrV:2327347-2327427 2.45e-02 80 chrII:5202194-5202274 4.12e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************