******************************************************************************** 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/lin-13.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIII:11372695-11372775 1.0000 80 chrII:2221668-2221748 1.0000 80 chrIII:2482346-2482426 1.0000 80 chrIII:1520041-1520121 1.0000 80 chrII:732592-732672 1.0000 80 chrV:14687357-14687437 1.0000 80 chrII:456541-456621 1.0000 80 chrIII:1231340-1231420 1.0000 80 chrIII:1938180-1938260 1.0000 80 chrI:12893117-12893197 1.0000 80 chrIV:1624599-1624679 1.0000 80 chrI:12536134-12536214 1.0000 80 chrIII:1574796-1574876 1.0000 80 chrII:1358183-1358263 1.0000 80 chrIII:2150821-2150901 1.0000 80 chrX:343965-344045 1.0000 80 chrIII:1612725-1612805 1.0000 80 chrI:13651954-13652034 1.0000 80 chrIII:2393827-2393907 1.0000 80 chrI:13642774-13642854 1.0000 80 chrIII:4236434-4236514 1.0000 80 chrIII:3887717-3887797 1.0000 80 chrIV:15107414-15107494 1.0000 80 chrIII:1877319-1877399 1.0000 80 chrI:1050817-1050897 1.0000 80 chrIII:7712064-7712144 1.0000 80 chrIV:2711443-2711523 1.0000 80 chrII:9656352-9656432 1.0000 80 chrII:14010939-14011019 1.0000 80 chrII:2456315-2456395 1.0000 80 chrIII:2879865-2879945 1.0000 80 chrIII:1599047-1599127 1.0000 80 chrI:13637295-13637375 1.0000 80 chrIII:1898930-1899010 1.0000 80 chrII:12344964-12345044 1.0000 80 chrM:13156-13236 1.0000 80 chrV:18573300-18573380 1.0000 80 chrIII:1616415-1616495 1.0000 80 chrI:12571053-12571133 1.0000 80 chrIV:15059341-15059421 1.0000 80 chrIII:1587235-1587315 1.0000 80 chrII:13298104-13298184 1.0000 80 chrIV:13893304-13893384 1.0000 80 chrII:10174531-10174611 1.0000 80 chrIV:1459554-1459634 1.0000 80 chrIII:1938737-1938817 1.0000 80 chrIII:1988603-1988683 1.0000 80 chrII:11846030-11846110 1.0000 80 chrIII:2031367-2031447 1.0000 80 chrIII:12847781-12847861 1.0000 80 chrI:1227877-1227957 1.0000 80 chrI:13367720-13367800 1.0000 80 chrII:1334082-1334162 1.0000 80 chrIV:11479272-11479352 1.0000 80 chrV:13043346-13043426 1.0000 80 chrIII:6340183-6340263 1.0000 80 chrIII:1563785-1563865 1.0000 80 chrV:18780798-18780878 1.0000 80 chrII:463164-463244 1.0000 80 chrV:19550400-19550480 1.0000 80 chrIII:1603892-1603972 1.0000 80 chrI:11803293-11803373 1.0000 80 chrIII:1611639-1611719 1.0000 80 chrI:13600644-13600724 1.0000 80 chrV:3579898-3579978 1.0000 80 chrIII:1141603-1141683 1.0000 80 chrV:20423276-20423356 1.0000 80 chrII:10545460-10545540 1.0000 80 chrIII:5506042-5506122 1.0000 80 chrX:14978866-14978946 1.0000 80 chrIII:1879604-1879684 1.0000 80 chrIII:70083-70163 1.0000 80 chrIV:4212846-4212926 1.0000 80 chrIV:14985314-14985394 1.0000 80 chrIV:2710308-2710388 1.0000 80 chrV:8179011-8179091 1.0000 80 chrIII:72686-72766 1.0000 80 chrIII:1939974-1940054 1.0000 80 chrI:316179-316259 1.0000 80 chrI:12904112-12904192 1.0000 80 chrII:12346808-12346888 1.0000 80 chrII:7791169-7791249 1.0000 80 chrIII:7711042-7711122 1.0000 80 chrII:2186937-2187017 1.0000 80 chrI:15040268-15040348 1.0000 80 chrIII:1516749-1516829 1.0000 80 chrII:12778503-12778583 1.0000 80 chrIII:1602877-1602957 1.0000 80 chrIV:16181253-16181333 1.0000 80 chrI:13310826-13310906 1.0000 80 chrII:2735778-2735858 1.0000 80 chrI:716714-716794 1.0000 80 chrI:545542-545622 1.0000 80 chrIII:1931768-1931848 1.0000 80 chrI:8027988-8028068 1.0000 80 chrV:18622694-18622774 1.0000 80 chrIII:984801-984881 1.0000 80 chrI:11965947-11966027 1.0000 80 chrIII:2169647-2169727 1.0000 80 chrII:11978039-11978119 1.0000 80 chrM:5266-5346 1.0000 80 chrI:12491172-12491252 1.0000 80 chrIV:15984339-15984419 1.0000 80 chrX:11791516-11791596 1.0000 80 chrIV:11913782-11913862 1.0000 80 chrIII:10533438-10533518 1.0000 80 chrIII:9443078-9443158 1.0000 80 chrII:1329764-1329844 1.0000 80 chrI:1229407-1229487 1.0000 80 chrIII:8867553-8867633 1.0000 80 chrII:10197260-10197340 1.0000 80 chrIV:6117908-6117988 1.0000 80 chrII:11542520-11542600 1.0000 80 chrII:2986118-2986198 1.0000 80 chrV:13411732-13411812 1.0000 80 chrV:7857954-7858034 1.0000 80 chrV:20413606-20413686 1.0000 80 chrIV:6330935-6331015 1.0000 80 chrV:10960747-10960827 1.0000 80 chrII:2861528-2861608 1.0000 80 chrIV:5656131-5656211 1.0000 80 chrI:9383902-9383982 1.0000 80 chrX:13108649-13108729 1.0000 80 chrII:14043363-14043443 1.0000 80 chrIV:1276065-1276145 1.0000 80 chrX:3541033-3541113 1.0000 80 chrIII:1608227-1608307 1.0000 80 chrV:3588317-3588397 1.0000 80 chrII:14238078-14238158 1.0000 80 chrIV:2316948-2317028 1.0000 80 chrIII:1496070-1496150 1.0000 80 chrIV:11145812-11145892 1.0000 80 chrII:1301127-1301207 1.0000 80 chrV:19050756-19050836 1.0000 80 chrV:7198514-7198594 1.0000 80 chrI:12893319-12893399 1.0000 80 chrV:19158817-19158897 1.0000 80 chrV:2664672-2664752 1.0000 80 chrIV:2603644-2603724 1.0000 80 chrX:16721966-16722046 1.0000 80 chrIII:11463932-11464012 1.0000 80 chrIII:1531912-1531992 1.0000 80 chrII:7056187-7056267 1.0000 80 chrII:1141850-1141930 1.0000 80 chrII:12666177-12666257 1.0000 80 chrIII:12317615-12317695 1.0000 80 chrIII:2032423-2032503 1.0000 80 chrIII:2030882-2030962 1.0000 80 chrIV:2704166-2704246 1.0000 80 chrX:11482892-11482972 1.0000 80 chrIV:3012593-3012673 1.0000 80 chrI:2875223-2875303 1.0000 80 chrIII:11084179-11084259 1.0000 80 chrIII:8242981-8243061 1.0000 80 chrI:10103255-10103335 1.0000 80 chrIII:1533737-1533817 1.0000 80 chrI:3152682-3152762 1.0000 80 chrV:14350511-14350591 1.0000 80 chrIII:5917568-5917648 1.0000 80 chrII:3087792-3087872 1.0000 80 chrIII:13542680-13542760 1.0000 80 chrIII:1208017-1208097 1.0000 80 chrV:2277425-2277505 1.0000 80 chrI:6163487-6163567 1.0000 80 chrII:8603738-8603818 1.0000 80 chrX:5213709-5213789 1.0000 80 chrX:10576615-10576695 1.0000 80 chrIII:7358752-7358832 1.0000 80 chrV:6228529-6228609 1.0000 80 chrIII:3307322-3307402 1.0000 80 chrII:9934187-9934267 1.0000 80 chrIII:1820969-1821049 1.0000 80 chrII:12542774-12542854 1.0000 80 chrIII:3503618-3503698 1.0000 80 chrX:17056734-17056814 1.0000 80 chrIV:1416328-1416408 1.0000 80 chrIV:2801145-2801225 1.0000 80 chrIII:1214843-1214923 1.0000 80 chrI:14662980-14663060 1.0000 80 chrIII:1600840-1600920 1.0000 80 chrX:4997850-4997930 1.0000 80 chrV:5835625-5835705 1.0000 80 chrI:4653966-4654046 1.0000 80 chrIII:11981747-11981827 1.0000 80 chrIII:5196598-5196678 1.0000 80 chrIII:2760827-2760907 1.0000 80 chrII:13298815-13298895 1.0000 80 chrIII:9240126-9240206 1.0000 80 chrII:8484603-8484683 1.0000 80 chrII:13678436-13678516 1.0000 80 chrII:1335679-1335759 1.0000 80 chrIV:5665504-5665584 1.0000 80 chrIII:13767088-13767168 1.0000 80 chrV:18354397-18354477 1.0000 80 chrII:13575688-13575768 1.0000 80 chrI:10565943-10566023 1.0000 80 chrII:2970607-2970687 1.0000 80 chrII:873542-873622 1.0000 80 chrIV:3741272-3741352 1.0000 80 chrIII:11834901-11834981 1.0000 80 chrI:11977966-11978046 1.0000 80 chrV:18346238-18346318 1.0000 80 chrV:19207081-19207161 1.0000 80 chrX:15610594-15610674 1.0000 80 chrII:10543768-10543848 1.0000 80 chrII:7669572-7669652 1.0000 80 chrV:15982919-15982999 1.0000 80 chrIV:16490174-16490254 1.0000 80 chrIV:9993879-9993959 1.0000 80 chrII:2250340-2250420 1.0000 80 chrM:1786-1866 1.0000 80 chrIV:11820723-11820803 1.0000 80 chrIII:1533266-1533346 1.0000 80 chrIV:2655183-2655263 1.0000 80 chrI:9168581-9168661 1.0000 80 chrV:10169060-10169140 1.0000 80 chrII:7350465-7350545 1.0000 80 chrI:11930631-11930711 1.0000 80 chrII:13079102-13079182 1.0000 80 chrIII:3104704-3104784 1.0000 80 chrIII:1744646-1744726 1.0000 80 chrII:13836057-13836137 1.0000 80 chrII:8276256-8276336 1.0000 80 chrM:10372-10452 1.0000 80 chrII:13521435-13521515 1.0000 80 chrX:14228854-14228934 1.0000 80 chrI:7661017-7661097 1.0000 80 chrI:6210960-6211040 1.0000 80 chrIII:3377937-3378017 1.0000 80 chrIII:1894894-1894974 1.0000 80 chrII:2059124-2059204 1.0000 80 chrII:1302198-1302278 1.0000 80 chrX:4007934-4008014 1.0000 80 chrI:1228113-1228193 1.0000 80 chrX:15146534-15146614 1.0000 80 chrII:880864-880944 1.0000 80 chrI:9106214-9106294 1.0000 80 chrI:7159331-7159411 1.0000 80 chrII:10547828-10547908 1.0000 80 chrII:4706513-4706593 1.0000 80 chrII:4891515-4891595 1.0000 80 chrX:2089594-2089674 1.0000 80 chrI:13287313-13287393 1.0000 80 chrX:2435444-2435524 1.0000 80 chrIV:1708649-1708729 1.0000 80 chrV:8028950-8029030 1.0000 80 chrI:7058877-7058957 1.0000 80 chrI:1628729-1628809 1.0000 80 chrIII:2090872-2090952 1.0000 80 chrIV:7959193-7959273 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_lin-13/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/lin-13.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 0.288 C 0.217 G 0.23 T 0.265 Background letter frequencies (from file dataset with add-one prior applied): A 0.288 C 0.217 G 0.23 T 0.265 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF ACGCAAAC MEME-1 width = 8 sites = 23 llr = 234 E-value = 5.7e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A a:::a9a1 pos.-specific C :a:a:::9 probability G ::a::1:: matrix T :::::::: bits 2.2 *** 2.0 *** 1.8 **** ** 1.5 ***** ** Relative 1.3 ******** Entropy 1.1 ******** (14.7 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACGCAAAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:1894894-1894974 17 1.62e-05 cgccaatagt acgcaaac accgaggaac chrII:2250340-2250420 59 1.62e-05 cgccaaaagt acgcaaac atcgactaca chrIII:3307322-3307402 3 1.62e-05 gt acgcaaac accAGATCTT chrII:3087792-3087872 30 1.62e-05 CCTCGAGAAT ACGCAAAC ACACACAAAG chrII:1301127-1301207 63 1.62e-05 cctcaaaagt acgcaaac accaaacact chrII:14238078-14238158 9 1.62e-05 tgtctggt acgcaaac accgtggcgc chrII:1329764-1329844 62 1.62e-05 gtacgcaagt acgcaaac accgagcccc chrI:11965947-11966027 58 1.62e-05 GATGCAAAGT ACGCAAAC ACCCTGCGTA chrIII:1516749-1516829 18 1.62e-05 ggtgtctggt acgcaaac accgagggca chrIII:1611639-1611719 45 1.62e-05 tttcgaaagt acgcaaac accaaatagc chrIII:1938737-1938817 57 1.62e-05 CACTAAAAAT ACGCAAAC TGTGCATTTT chrIII:1898930-1899010 17 1.62e-05 cctcaaaagt acgcaaac accgaggctc chrII:1358183-1358263 35 1.62e-05 cttcgaaagt acgcaaac accaaACACC chrIII:1574796-1574876 1 1.62e-05 . acgcaaac accacggggg chrIII:1938180-1938260 51 1.62e-05 cctcaaaaat acgcaaac actgagcatc chrII:732592-732672 17 1.62e-05 caccaggagt acgcaaac accgactaca chrIII:1520041-1520121 46 1.62e-05 ggtgtcaggt acgcaaac accgcgggct chrII:4891515-4891595 4 2.91e-05 GAA ACGCAGAC ACTGAGAGCG chrX:17056734-17056814 51 2.91e-05 CGCTTGATGA ACGCAGAC GACATATGAT chrI:716714-716794 62 2.91e-05 GGTGAGAGAG ACGCAGAC ATCGAGATGA chrIII:2030882-2030962 10 5.05e-05 CTTCAGGCG ACGCAAAA AAAGAAGTAT chrI:12536134-12536214 58 5.05e-05 cgTACACTCT ACGCAAAA ATGCACAGAA chrIII:2393827-2393907 44 6.27e-05 ccccaaaagt ccgcaaac actgcggagt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:1894894-1894974 1.6e-05 16_[+1]_56 chrII:2250340-2250420 1.6e-05 58_[+1]_14 chrIII:3307322-3307402 1.6e-05 2_[+1]_70 chrII:3087792-3087872 1.6e-05 29_[+1]_43 chrII:1301127-1301207 1.6e-05 62_[+1]_10 chrII:14238078-14238158 1.6e-05 8_[+1]_64 chrII:1329764-1329844 1.6e-05 61_[+1]_11 chrI:11965947-11966027 1.6e-05 57_[+1]_15 chrIII:1516749-1516829 1.6e-05 17_[+1]_55 chrIII:1611639-1611719 1.6e-05 44_[+1]_28 chrIII:1938737-1938817 1.6e-05 56_[+1]_16 chrIII:1898930-1899010 1.6e-05 16_[+1]_56 chrII:1358183-1358263 1.6e-05 34_[+1]_38 chrIII:1574796-1574876 1.6e-05 [+1]_72 chrIII:1938180-1938260 1.6e-05 50_[+1]_22 chrII:732592-732672 1.6e-05 16_[+1]_56 chrIII:1520041-1520121 1.6e-05 45_[+1]_27 chrII:4891515-4891595 2.9e-05 3_[+1]_69 chrX:17056734-17056814 2.9e-05 50_[+1]_22 chrI:716714-716794 2.9e-05 61_[+1]_11 chrIII:2030882-2030962 5.1e-05 9_[+1]_63 chrI:12536134-12536214 5.1e-05 57_[+1]_15 chrIII:2393827-2393907 6.3e-05 43_[+1]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACGCAAAC width=8 seqs=23 chrIII:1894894-1894974 ( 17) ACGCAAAC 1 chrII:2250340-2250420 ( 59) ACGCAAAC 1 chrIII:3307322-3307402 ( 3) ACGCAAAC 1 chrII:3087792-3087872 ( 30) ACGCAAAC 1 chrII:1301127-1301207 ( 63) ACGCAAAC 1 chrII:14238078-14238158 ( 9) ACGCAAAC 1 chrII:1329764-1329844 ( 62) ACGCAAAC 1 chrI:11965947-11966027 ( 58) ACGCAAAC 1 chrIII:1516749-1516829 ( 18) ACGCAAAC 1 chrIII:1611639-1611719 ( 45) ACGCAAAC 1 chrIII:1938737-1938817 ( 57) ACGCAAAC 1 chrIII:1898930-1899010 ( 17) ACGCAAAC 1 chrII:1358183-1358263 ( 35) ACGCAAAC 1 chrIII:1574796-1574876 ( 1) ACGCAAAC 1 chrIII:1938180-1938260 ( 51) ACGCAAAC 1 chrII:732592-732672 ( 17) ACGCAAAC 1 chrIII:1520041-1520121 ( 46) ACGCAAAC 1 chrII:4891515-4891595 ( 4) ACGCAGAC 1 chrX:17056734-17056814 ( 51) ACGCAGAC 1 chrI:716714-716794 ( 62) ACGCAGAC 1 chrIII:2030882-2030962 ( 10) ACGCAAAA 1 chrI:12536134-12536214 ( 58) ACGCAAAA 1 chrIII:2393827-2393907 ( 44) CCGCAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.0332 E= 5.7e-013 173 -232 -1117 -1117 -1117 220 -1117 -1117 -1117 -1117 212 -1117 -1117 220 -1117 -1117 180 -1117 -1117 -1117 159 -1117 -82 -1117 180 -1117 -1117 -1117 -173 207 -1117 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 5.7e-013 0.956522 0.043478 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 1.000000 0.000000 0.000000 0.000000 0.869565 0.000000 0.130435 0.000000 1.000000 0.000000 0.000000 0.000000 0.086957 0.913043 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACGCAAAC MEME-1 regular expression -------------------------------------------------------------------------------- ACGCAAAC -------------------------------------------------------------------------------- Time 8.53 secs. ******************************************************************************** ******************************************************************************** MOTIF CTACAGTA MEME-2 width = 8 sites = 16 llr = 171 E-value = 4.6e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::a:9::a pos.-specific C a::a:::: probability G :::::a:: matrix T :a::1:a: bits 2.2 * * * 2.0 ** * ** 1.8 **** *** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (15.4 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTACAGTA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:2250340-2250420 72 1.82e-05 caaacatcga ctacagta c chrIV:1416328-1416408 40 1.82e-05 acttctgggg ctacagta actcggaagt chrII:14238078-14238158 42 1.82e-05 actatcgggg ctacagta acccggaaaa chrI:9383902-9383982 60 1.82e-05 GGTTGCGCAA CTACAGTA ACCCAGTGAA chrIII:1516749-1516829 52 1.82e-05 actattggcg ctacagta accccggcta chrII:2186937-2187017 6 1.82e-05 accga ctacagta cccccaaaca chrII:463164-463244 5 1.82e-05 gggg ctacagta acccgaaata chrIII:1563785-1563865 56 1.82e-05 gaaatccgtg ctacagta ccccgcgtgg chrIII:1587235-1587315 10 1.82e-05 cttttgggg ctacagta accccgaaaa chrI:13651954-13652034 69 1.82e-05 actttcgaag ctacagta cccc chrIII:1612725-1612805 37 1.82e-05 actttcggag ctacagta ccccataaat chrIII:1574796-1574876 37 1.82e-05 acttttggcg ctacagta accccgaaaa chrII:456541-456621 7 1.82e-05 ttggtg ctacagta ccccaaaatt chrII:732592-732672 30 1.82e-05 caaacaccga ctacagta ccccaaaaca chrIII:2482346-2482426 18 1.82e-05 gaaatcctac ctacagta acctggaaga chrV:18573300-18573380 40 3.49e-05 AGCCTAGAAA CTACTGTA TCGAGAAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:2250340-2250420 1.8e-05 71_[+2]_1 chrIV:1416328-1416408 1.8e-05 39_[+2]_33 chrII:14238078-14238158 1.8e-05 41_[+2]_31 chrI:9383902-9383982 1.8e-05 59_[+2]_13 chrIII:1516749-1516829 1.8e-05 51_[+2]_21 chrII:2186937-2187017 1.8e-05 5_[+2]_67 chrII:463164-463244 1.8e-05 4_[+2]_68 chrIII:1563785-1563865 1.8e-05 55_[+2]_17 chrIII:1587235-1587315 1.8e-05 9_[+2]_63 chrI:13651954-13652034 1.8e-05 68_[+2]_4 chrIII:1612725-1612805 1.8e-05 36_[+2]_36 chrIII:1574796-1574876 1.8e-05 36_[+2]_36 chrII:456541-456621 1.8e-05 6_[+2]_66 chrII:732592-732672 1.8e-05 29_[+2]_43 chrIII:2482346-2482426 1.8e-05 17_[+2]_55 chrV:18573300-18573380 3.5e-05 39_[+2]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTACAGTA width=8 seqs=16 chrII:2250340-2250420 ( 72) CTACAGTA 1 chrIV:1416328-1416408 ( 40) CTACAGTA 1 chrII:14238078-14238158 ( 42) CTACAGTA 1 chrI:9383902-9383982 ( 60) CTACAGTA 1 chrIII:1516749-1516829 ( 52) CTACAGTA 1 chrII:2186937-2187017 ( 6) CTACAGTA 1 chrII:463164-463244 ( 5) CTACAGTA 1 chrIII:1563785-1563865 ( 56) CTACAGTA 1 chrIII:1587235-1587315 ( 10) CTACAGTA 1 chrI:13651954-13652034 ( 69) CTACAGTA 1 chrIII:1612725-1612805 ( 37) CTACAGTA 1 chrIII:1574796-1574876 ( 37) CTACAGTA 1 chrII:456541-456621 ( 7) CTACAGTA 1 chrII:732592-732672 ( 30) CTACAGTA 1 chrIII:2482346-2482426 ( 18) CTACAGTA 1 chrV:18573300-18573380 ( 40) CTACTGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.1543 E= 4.6e-007 -1064 220 -1064 -1064 -1064 -1064 -1064 192 180 -1064 -1064 -1064 -1064 220 -1064 -1064 170 -1064 -1064 -208 -1064 -1064 212 -1064 -1064 -1064 -1064 192 180 -1064 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 4.6e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.937500 0.000000 0.000000 0.062500 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAGTA MEME-2 regular expression -------------------------------------------------------------------------------- CTACAGTA -------------------------------------------------------------------------------- Time 12.25 secs. ******************************************************************************** ******************************************************************************** MOTIF AAATTTGA MEME-3 width = 8 sites = 52 llr = 393 E-value = 2.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 9a83:::8 pos.-specific C 1::::3:: probability G ::::::92 matrix T ::27a81: bits 2.2 2.0 * 1.8 * 1.5 * * * Relative 1.3 ** * * Entropy 1.1 *** **** (10.9 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAATTTGA consensus A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:1894894-1894974 60 2.94e-05 caattttctt aaatttga tggtagagct chrIII:3307322-3307402 67 2.94e-05 AAATTCTGGG AAATTTGA TTTTCA chrII:8603738-8603818 34 2.94e-05 ATTGCGCGTC AAATTTGA TGCACTGTGT chrII:14238078-14238158 57 2.94e-05 gtaacccgga aaatttga aaattgagct chrIV:5656131-5656211 73 2.94e-05 GCCTGGCGCC AAATTTGA chrIV:6330935-6331015 3 2.94e-05 TC AAATTTGA ATAGGCGAAT chrIII:72686-72766 67 2.94e-05 aatttgaGCA AAATTTGA CCCAAA chrIII:1587235-1587315 72 2.94e-05 ttcaggtgta aaatttga t chrII:2456315-2456395 44 2.94e-05 tttctgctca aaatttga aaatcacgta chrIII:1877319-1877399 31 2.94e-05 actattttga aaatttga gggtcccgcc chrI:1228113-1228193 69 8.56e-05 GTTGGAAGTg aaattcga aagg chrV:6228529-6228609 20 8.56e-05 AGATAATTGG AAAATTGA GACAGAATAG chrX:5213709-5213789 3 8.56e-05 AG AAAATTGA TTAGACACAC chrIII:2032423-2032503 30 8.56e-05 CTTGGAACAG AAATTCGA TCCCGCGGGA chrIII:984801-984881 64 8.56e-05 AAAACTTGAT aaattcga gttcagcgt chrIII:12847781-12847861 9 8.56e-05 ACGTTTCG AAAATTGA ACAAAGACCT chrIII:1612725-1612805 59 8.56e-05 ataaatgttc aaaattga gctagaaacc chrIII:1574796-1574876 59 8.56e-05 cgaaaatttc aaaattga gctagaagcc chrII:2250340-2250420 21 1.36e-04 tttctagctc aattttga aattttacgg chrII:1329764-1329844 17 1.36e-04 tttcctgcta aattttga tcattttggg chrIII:1611639-1611719 8 1.36e-04 tcactcc aattttga aaatttcggg chrI:13367720-13367800 24 1.36e-04 TCACGTGTCG AAATTTGG AGAAAACACC chrI:12571053-12571133 54 1.36e-04 TTTGCAAAAA AAATTTGG AGATGGTAGA chrV:18573300-18573380 14 1.36e-04 AAAATTGGTA AAATTTGG TGAAAACTAG chrIII:2393827-2393907 7 1.36e-04 aactca aattttga atttcgaagg chrIII:2150821-2150901 35 1.36e-04 gcgaaattta aattttga gctaagagcc chrIII:1938180-1938260 14 1.36e-04 tgctagcttg aattttga atttcccggg chrI:11930631-11930711 30 1.62e-04 AAACCTACAC AAAATCGA CCGTAGTGCG chrII:13298815-13298895 66 1.62e-04 ACGTCACTTT AAAATCGA GGGTAGG chrV:10960747-10960827 66 1.62e-04 TTTACCGACC AAAATCGA GATTCGG chrII:11542520-11542600 24 1.62e-04 CTTAAGAGTG AAAATCGA TGATGGAAGA chrIV:11913782-11913862 28 1.62e-04 ACCAGACATA AAAATCGA ATTACATGAT chrI:13287313-13287393 15 2.59e-04 GCAGAGGGGA AAAATTGG GCAAAAAAGG chrI:10103255-10103335 31 2.59e-04 TTATCATGCC AAAATTGG TCACACACAC chrIII:1608227-1608307 3 2.59e-04 AC AAATTCGG ATTCAGCACC chrIV:1276065-1276145 63 2.59e-04 TTTTGTCGTG AAATTCGG TGTTTGCACA chrI:12491172-12491252 59 2.59e-04 TCTGAATCAA AATATTGA TATTTCGCTA chrIII:1516749-1516829 2 2.59e-04 g aaattcgg tgtctggtac chrIII:70083-70163 67 2.59e-04 ATGGAACTCG AATTTCGA GTCAAA chrIII:1879604-1879684 57 2.59e-04 gactttgaaa aaaattgg gtcccgccgc chrII:732592-732672 69 2.59e-04 gacattggcg aatttcga gctg chrII:7056187-7056267 22 2.81e-04 GTGTAAGACA CAATTTGA GTCGATTAGT chrIII:1531912-1531992 71 2.81e-04 tgtttccgtg caatttga aa chrM:10372-10452 32 3.15e-04 ATAGAGCTTT AAATTTTA CTTGTTTAAA chrM:13156-13236 67 3.15e-04 TAAAAAGGtt aaatttta atagtg chrX:14228854-14228934 61 3.59e-04 AAAAGAAAAA ACATTTGA CCACTGAGCG chrIII:13767088-13767168 57 3.59e-04 CAAATTAACT ACATTTGA GACTATTTAA chrIII:2169647-2169727 71 4.46e-04 GAGATGGCAG CAAATTGA TA chrIII:1603892-1603972 15 5.11e-04 GAAAAAACGA AAAATTTA GTGTGGGATT chrIV:11479272-11479352 14 5.75e-04 GAAACAATGC GAATTTGA ATTAAAGTAT chrIV:1459554-1459634 19 6.46e-04 CATTTTCTCA AAATTTCA gagatccatc chrII:1302198-1302278 3 7.42e-04 CA AATTTTTA CCCATGTATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:1894894-1894974 2.9e-05 59_[+3]_13 chrIII:3307322-3307402 2.9e-05 66_[+3]_6 chrII:8603738-8603818 2.9e-05 33_[+3]_39 chrII:14238078-14238158 2.9e-05 56_[+3]_16 chrIV:5656131-5656211 2.9e-05 72_[+3] chrIV:6330935-6331015 2.9e-05 2_[+3]_70 chrIII:72686-72766 2.9e-05 66_[+3]_6 chrIII:1587235-1587315 2.9e-05 71_[+3]_1 chrII:2456315-2456395 2.9e-05 43_[+3]_29 chrIII:1877319-1877399 2.9e-05 30_[+3]_42 chrI:1228113-1228193 8.6e-05 68_[+3]_4 chrV:6228529-6228609 8.6e-05 19_[+3]_53 chrX:5213709-5213789 8.6e-05 2_[+3]_70 chrIII:2032423-2032503 8.6e-05 29_[+3]_43 chrIII:984801-984881 8.6e-05 63_[+3]_9 chrIII:12847781-12847861 8.6e-05 8_[+3]_64 chrIII:1612725-1612805 8.6e-05 58_[+3]_14 chrIII:1574796-1574876 8.6e-05 58_[+3]_14 chrII:2250340-2250420 0.00014 20_[+3]_52 chrII:1329764-1329844 0.00014 16_[+3]_56 chrIII:1611639-1611719 0.00014 7_[+3]_65 chrI:13367720-13367800 0.00014 23_[+3]_49 chrI:12571053-12571133 0.00014 53_[+3]_19 chrV:18573300-18573380 0.00014 13_[+3]_59 chrIII:2393827-2393907 0.00014 6_[+3]_66 chrIII:2150821-2150901 0.00014 34_[+3]_38 chrIII:1938180-1938260 0.00014 13_[+3]_59 chrI:11930631-11930711 0.00016 29_[+3]_43 chrII:13298815-13298895 0.00016 65_[+3]_7 chrV:10960747-10960827 0.00016 65_[+3]_7 chrII:11542520-11542600 0.00016 23_[+3]_49 chrIV:11913782-11913862 0.00016 27_[+3]_45 chrI:13287313-13287393 0.00026 14_[+3]_58 chrI:10103255-10103335 0.00026 30_[+3]_42 chrIII:1608227-1608307 0.00026 2_[+3]_70 chrIV:1276065-1276145 0.00026 62_[+3]_10 chrI:12491172-12491252 0.00026 58_[+3]_14 chrIII:1516749-1516829 0.00026 1_[+3]_71 chrIII:70083-70163 0.00026 66_[+3]_6 chrIII:1879604-1879684 0.00026 56_[+3]_16 chrII:732592-732672 0.00026 68_[+3]_4 chrII:7056187-7056267 0.00028 21_[+3]_51 chrIII:1531912-1531992 0.00028 70_[+3]_2 chrM:10372-10452 0.00031 31_[+3]_41 chrM:13156-13236 0.00031 66_[+3]_6 chrX:14228854-14228934 0.00036 60_[+3]_12 chrIII:13767088-13767168 0.00036 56_[+3]_16 chrIII:2169647-2169727 0.00045 70_[+3]_2 chrIII:1603892-1603972 0.00051 14_[+3]_58 chrIV:11479272-11479352 0.00058 13_[+3]_59 chrIV:1459554-1459634 0.00065 18_[+3]_54 chrII:1302198-1302278 0.00074 2_[+3]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAATTTGA width=8 seqs=52 chrIII:1894894-1894974 ( 60) AAATTTGA 1 chrIII:3307322-3307402 ( 67) AAATTTGA 1 chrII:8603738-8603818 ( 34) AAATTTGA 1 chrII:14238078-14238158 ( 57) AAATTTGA 1 chrIV:5656131-5656211 ( 73) AAATTTGA 1 chrIV:6330935-6331015 ( 3) AAATTTGA 1 chrIII:72686-72766 ( 67) AAATTTGA 1 chrIII:1587235-1587315 ( 72) AAATTTGA 1 chrII:2456315-2456395 ( 44) AAATTTGA 1 chrIII:1877319-1877399 ( 31) AAATTTGA 1 chrI:1228113-1228193 ( 69) AAATTCGA 1 chrV:6228529-6228609 ( 20) AAAATTGA 1 chrX:5213709-5213789 ( 3) AAAATTGA 1 chrIII:2032423-2032503 ( 30) AAATTCGA 1 chrIII:984801-984881 ( 64) AAATTCGA 1 chrIII:12847781-12847861 ( 9) AAAATTGA 1 chrIII:1612725-1612805 ( 59) AAAATTGA 1 chrIII:1574796-1574876 ( 59) AAAATTGA 1 chrII:2250340-2250420 ( 21) AATTTTGA 1 chrII:1329764-1329844 ( 17) AATTTTGA 1 chrIII:1611639-1611719 ( 8) AATTTTGA 1 chrI:13367720-13367800 ( 24) AAATTTGG 1 chrI:12571053-12571133 ( 54) AAATTTGG 1 chrV:18573300-18573380 ( 14) AAATTTGG 1 chrIII:2393827-2393907 ( 7) AATTTTGA 1 chrIII:2150821-2150901 ( 35) AATTTTGA 1 chrIII:1938180-1938260 ( 14) AATTTTGA 1 chrI:11930631-11930711 ( 30) AAAATCGA 1 chrII:13298815-13298895 ( 66) AAAATCGA 1 chrV:10960747-10960827 ( 66) AAAATCGA 1 chrII:11542520-11542600 ( 24) AAAATCGA 1 chrIV:11913782-11913862 ( 28) AAAATCGA 1 chrI:13287313-13287393 ( 15) AAAATTGG 1 chrI:10103255-10103335 ( 31) AAAATTGG 1 chrIII:1608227-1608307 ( 3) AAATTCGG 1 chrIV:1276065-1276145 ( 63) AAATTCGG 1 chrI:12491172-12491252 ( 59) AATATTGA 1 chrIII:1516749-1516829 ( 2) AAATTCGG 1 chrIII:70083-70163 ( 67) AATTTCGA 1 chrIII:1879604-1879684 ( 57) AAAATTGG 1 chrII:732592-732672 ( 69) AATTTCGA 1 chrII:7056187-7056267 ( 22) CAATTTGA 1 chrIII:1531912-1531992 ( 71) CAATTTGA 1 chrM:10372-10452 ( 32) AAATTTTA 1 chrM:13156-13236 ( 67) AAATTTTA 1 chrX:14228854-14228934 ( 61) ACATTTGA 1 chrIII:13767088-13767168 ( 57) ACATTTGA 1 chrIII:2169647-2169727 ( 71) CAAATTGA 1 chrIII:1603892-1603972 ( 15) AAAATTTA 1 chrIV:11479272-11479352 ( 14) GAATTTGA 1 chrIV:1459554-1459634 ( 19) AAATTTCA 1 chrII:1302198-1302278 ( 3) AATTTTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 8.20587 E= 2.8e-001 168 -191 -358 -1234 174 -250 -1234 -1234 149 -1234 -1234 -46 10 -1234 -1234 139 -1234 -1234 -1234 192 -1234 20 -1234 150 -1234 -350 198 -178 152 -1234 -41 -1234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 2.8e-001 0.923077 0.057692 0.019231 0.000000 0.961538 0.038462 0.000000 0.000000 0.807692 0.000000 0.000000 0.192308 0.307692 0.000000 0.000000 0.692308 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.019231 0.903846 0.076923 0.826923 0.000000 0.173077 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAATTTGA MEME-3 regular expression -------------------------------------------------------------------------------- AAA[TA]T[TC]GA -------------------------------------------------------------------------------- Time 15.87 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCGCCGC MEME-4 width = 8 sites = 15 llr = 149 E-value = 5.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a89:aa19 probability G :2:7::91 matrix T ::13:::: bits 2.2 * ** 2.0 * ** 1.8 * *** 1.5 *** **** Relative 1.3 ******** Entropy 1.1 ******** (14.3 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCCGCCGC consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:7159331-7159411 5 5.52e-06 GTGT CCCGCCGC GAAATCAAAA chrI:11930631-11930711 65 5.52e-06 CGCTGCGAGA CCCGCCGC GCGTTTGG chrIV:15984339-15984419 38 5.52e-06 CGCAATGCCT CCCGCCGC GAGTTGAGAG chrIII:1879604-1879684 67 5.52e-06 aaaattgggt cccgccgc gaaaac chrII:10547828-10547908 31 1.19e-05 CTCACAACCT CCCTCCGC TCATCACATA chrI:7661017-7661097 73 1.19e-05 TATCTCAGAA CCCTCCGC chrV:20423276-20423356 37 1.19e-05 CCTGTCTTCG CCCTCCGC TCTCTCACCG chrII:14043363-14043443 2 1.77e-05 C CGCGCCGC TTTCCCCGCC chrV:18622694-18622774 24 1.77e-05 TGCTGCTGGA CGCGCCGC GCAGCTTTAG chrII:12778503-12778583 25 1.77e-05 CCATTGCGCG CGCGCCGC CTCACACTCT chrIV:2603644-2603724 48 2.36e-05 GGGTTCGAGT CCCGCCGG CACATTATAG chrIII:1877319-1877399 56 2.36e-05 gccacgaaat cccgccgg gttactgtag chrIII:2032423-2032503 54 3.03e-05 GGGAGTGTCA CCTGCCGC TCCTCTATGC chrIII:1214843-1214923 59 4.23e-05 CTTTTCCAGT CCCGCCCC TTTAAGACGG chrI:15040268-15040348 48 5.68e-05 ATCAAATCCG CCTTCCGC TGTGCCGTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:7159331-7159411 5.5e-06 4_[+4]_68 chrI:11930631-11930711 5.5e-06 64_[+4]_8 chrIV:15984339-15984419 5.5e-06 37_[+4]_35 chrIII:1879604-1879684 5.5e-06 66_[+4]_6 chrII:10547828-10547908 1.2e-05 30_[+4]_42 chrI:7661017-7661097 1.2e-05 72_[+4] chrV:20423276-20423356 1.2e-05 36_[+4]_36 chrII:14043363-14043443 1.8e-05 1_[+4]_71 chrV:18622694-18622774 1.8e-05 23_[+4]_49 chrII:12778503-12778583 1.8e-05 24_[+4]_48 chrIV:2603644-2603724 2.4e-05 47_[+4]_25 chrIII:1877319-1877399 2.4e-05 55_[+4]_17 chrIII:2032423-2032503 3e-05 53_[+4]_19 chrIII:1214843-1214923 4.2e-05 58_[+4]_14 chrI:15040268-15040348 5.7e-05 47_[+4]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCGCCGC width=8 seqs=15 chrI:7159331-7159411 ( 5) CCCGCCGC 1 chrI:11930631-11930711 ( 65) CCCGCCGC 1 chrIV:15984339-15984419 ( 38) CCCGCCGC 1 chrIII:1879604-1879684 ( 67) CCCGCCGC 1 chrII:10547828-10547908 ( 31) CCCTCCGC 1 chrI:7661017-7661097 ( 73) CCCTCCGC 1 chrV:20423276-20423356 ( 37) CCCTCCGC 1 chrII:14043363-14043443 ( 2) CGCGCCGC 1 chrV:18622694-18622774 ( 24) CGCGCCGC 1 chrII:12778503-12778583 ( 25) CGCGCCGC 1 chrIV:2603644-2603724 ( 48) CCCGCCGG 1 chrIII:1877319-1877399 ( 56) CCCGCCGG 1 chrIII:2032423-2032503 ( 54) CCTGCCGC 1 chrIII:1214843-1214923 ( 59) CCCGCCCC 1 chrI:15040268-15040348 ( 48) CCTTCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.9536 E= 5.0e-001 -1055 220 -1055 -1055 -1055 188 -20 -1055 -1055 199 -1055 -99 -1055 -1055 167 1 -1055 220 -1055 -1055 -1055 220 -1055 -1055 -1055 -170 202 -1055 -1055 199 -78 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 5.0e-001 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.866667 0.000000 0.133333 0.000000 0.000000 0.733333 0.266667 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.066667 0.933333 0.000000 0.000000 0.866667 0.133333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCGCCGC MEME-4 regular expression -------------------------------------------------------------------------------- C[CG]C[GT]CCGC -------------------------------------------------------------------------------- Time 19.42 secs. ******************************************************************************** ******************************************************************************** MOTIF TACTGTAG MEME-5 width = 8 sites = 13 llr = 135 E-value = 8.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :a::::a: pos.-specific C ::a::::: probability G :::3a::a matrix T a::7:a:: bits 2.2 * * * 2.0 * * ** * 1.8 *** **** 1.5 *** **** Relative 1.3 *** **** Entropy 1.1 ******** (15.0 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TACTGTAG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:2250340-2250420 41 1.77e-05 ttttacgggt tactgtag cgccaaaagt chrII:1301127-1301207 45 1.77e-05 TATTTTgggt tactgtag cctcaaaagt chrII:1329764-1329844 36 1.77e-05 cattttgggg tactgtag ccccaatagt chrII:11978039-11978119 14 1.77e-05 GGGGGGTGTA TACTGTAG TTAGATACAA chrIII:1141603-1141683 66 1.77e-05 ccacgcgggg tactgtag ctctagt chrIII:1877319-1877399 66 1.77e-05 cccgccgggt tactgtag ttttcgc chrI:13651954-13652034 38 1.77e-05 tgtattgggg tactgtag ttggtgtttg chrII:1358183-1358263 17 1.77e-05 aattttgggg tactgtag cttcgaaagt chrIII:1938180-1938260 33 1.77e-05 tttcccgggg tactgtag cctcaaaaat chrIV:1416328-1416408 9 3.31e-05 ttctgggt tacggtag tcggtgtttg chrII:3087792-3087872 12 3.31e-05 CGAAAATGGT TACGGTAG CCTCGAGAAT chrIII:2393827-2393907 26 3.31e-05 tttcgaaggg tacggtag ccccaaaagt chrI:12536134-12536214 20 3.31e-05 actttcgggt tacggtag ccccaaaagt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:2250340-2250420 1.8e-05 40_[+5]_32 chrII:1301127-1301207 1.8e-05 44_[+5]_28 chrII:1329764-1329844 1.8e-05 35_[+5]_37 chrII:11978039-11978119 1.8e-05 13_[+5]_59 chrIII:1141603-1141683 1.8e-05 65_[+5]_7 chrIII:1877319-1877399 1.8e-05 65_[+5]_7 chrI:13651954-13652034 1.8e-05 37_[+5]_35 chrII:1358183-1358263 1.8e-05 16_[+5]_56 chrIII:1938180-1938260 1.8e-05 32_[+5]_40 chrIV:1416328-1416408 3.3e-05 8_[+5]_64 chrII:3087792-3087872 3.3e-05 11_[+5]_61 chrIII:2393827-2393907 3.3e-05 25_[+5]_47 chrI:12536134-12536214 3.3e-05 19_[+5]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TACTGTAG width=8 seqs=13 chrII:2250340-2250420 ( 41) TACTGTAG 1 chrII:1301127-1301207 ( 45) TACTGTAG 1 chrII:1329764-1329844 ( 36) TACTGTAG 1 chrII:11978039-11978119 ( 14) TACTGTAG 1 chrIII:1141603-1141683 ( 66) TACTGTAG 1 chrIII:1877319-1877399 ( 66) TACTGTAG 1 chrI:13651954-13652034 ( 38) TACTGTAG 1 chrII:1358183-1358263 ( 17) TACTGTAG 1 chrIII:1938180-1938260 ( 33) TACTGTAG 1 chrIV:1416328-1416408 ( 9) TACGGTAG 1 chrII:3087792-3087872 ( 12) TACGGTAG 1 chrIII:2393827-2393907 ( 26) TACGGTAG 1 chrI:12536134-12536214 ( 20) TACGGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.2095 E= 8.4e-001 -1035 -1035 -1035 192 180 -1035 -1035 -1035 -1035 220 -1035 -1035 -1035 -1035 42 139 -1035 -1035 212 -1035 -1035 -1035 -1035 192 180 -1035 -1035 -1035 -1035 -1035 212 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 8.4e-001 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.307692 0.692308 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACTGTAG MEME-5 regular expression -------------------------------------------------------------------------------- TAC[TG]GTAG -------------------------------------------------------------------------------- Time 22.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:11372695-11372775 7.05e-01 80 chrII:2221668-2221748 9.30e-01 80 chrIII:2482346-2482426 3.50e-03 17_[+2(1.82e-05)]_55 chrIII:1520041-1520121 3.27e-03 45_[+1(1.62e-05)]_27 chrII:732592-732672 1.84e-05 16_[+1(1.62e-05)]_5_[+2(1.82e-05)]_\ 43 chrV:14687357-14687437 6.22e-01 80 chrII:456541-456621 7.20e-04 6_[+2(1.82e-05)]_66 chrIII:1231340-1231420 3.31e-01 80 chrIII:1938180-1938260 7.39e-06 32_[+5(1.77e-05)]_10_[+1(1.62e-05)]_\ 22 chrI:12893117-12893197 9.78e-01 80 chrIV:1624599-1624679 7.62e-01 80 chrI:12536134-12536214 2.81e-04 19_[+5(3.31e-05)]_30_[+1(5.05e-05)]_\ 15 chrIII:1574796-1574876 6.86e-06 [+1(1.62e-05)]_28_[+2(1.82e-05)]_14_\ [+3(8.56e-05)]_14 chrII:1358183-1358263 2.55e-06 16_[+5(1.77e-05)]_10_[+1(1.62e-05)]_\ 12_[+1(7.99e-05)]_18 chrIII:2150821-2150901 3.84e-04 12_[+2(6.31e-05)]_60 chrX:343965-344045 7.40e-01 80 chrIII:1612725-1612805 8.65e-04 36_[+2(1.82e-05)]_14_[+3(8.56e-05)]_\ 14 chrI:13651954-13652034 7.63e-05 37_[+5(1.77e-05)]_23_[+2(1.82e-05)]_\ 4 chrIII:2393827-2393907 6.18e-05 25_[+5(3.31e-05)]_10_[+1(6.27e-05)]_\ 29 chrI:13642774-13642854 3.91e-01 80 chrIII:4236434-4236514 5.24e-01 80 chrIII:3887717-3887797 1.48e-01 80 chrIV:15107414-15107494 6.96e-02 80 chrIII:1877319-1877399 1.11e-06 30_[+3(2.94e-05)]_17_[+4(2.36e-05)]_\ 2_[+5(1.77e-05)]_7 chrI:1050817-1050897 2.83e-01 80 chrIII:7712064-7712144 6.01e-01 80 chrIV:2711443-2711523 2.32e-01 80 chrII:9656352-9656432 2.66e-01 80 chrII:14010939-14011019 6.84e-01 80 chrII:2456315-2456395 3.09e-02 43_[+3(2.94e-05)]_29 chrIII:2879865-2879945 6.58e-01 80 chrIII:1599047-1599127 4.05e-01 80 chrI:13637295-13637375 5.40e-01 80 chrIII:1898930-1899010 7.68e-03 16_[+1(1.62e-05)]_56 chrII:12344964-12345044 9.24e-01 80 chrM:13156-13236 6.14e-01 80 chrV:18573300-18573380 7.95e-04 39_[+2(3.49e-05)]_33 chrIII:1616415-1616495 2.01e-01 80 chrI:12571053-12571133 2.56e-01 80 chrIV:15059341-15059421 8.97e-01 80 chrIII:1587235-1587315 5.23e-04 9_[+2(1.82e-05)]_54_[+3(2.94e-05)]_\ 1 chrII:13298104-13298184 3.31e-01 80 chrIV:13893304-13893384 4.78e-01 80 chrII:10174531-10174611 4.72e-01 80 chrIV:1459554-1459634 3.86e-01 80 chrIII:1938737-1938817 5.07e-02 56_[+1(1.62e-05)]_16 chrIII:1988603-1988683 4.62e-01 80 chrII:11846030-11846110 3.84e-01 80 chrIII:2031367-2031447 7.37e-01 80 chrIII:12847781-12847861 2.41e-01 8_[+3(8.56e-05)]_64 chrI:1227877-1227957 1.18e-01 47_[+1(7.99e-05)]_25 chrI:13367720-13367800 8.81e-02 80 chrII:1334082-1334162 8.72e-01 80 chrIV:11479272-11479352 2.98e-01 80 chrV:13043346-13043426 8.55e-01 80 chrIII:6340183-6340263 9.49e-01 80 chrIII:1563785-1563865 2.67e-03 55_[+2(1.82e-05)]_17 chrV:18780798-18780878 3.73e-01 80 chrII:463164-463244 7.99e-03 4_[+2(1.82e-05)]_68 chrV:19550400-19550480 7.83e-01 80 chrIII:1603892-1603972 1.25e-01 80 chrI:11803293-11803373 4.39e-01 80 chrIII:1611639-1611719 8.96e-05 44_[+1(1.62e-05)]_28 chrI:13600644-13600724 1.49e-02 22_[+1(7.99e-05)]_50 chrV:3579898-3579978 9.34e-01 80 chrIII:1141603-1141683 3.00e-03 65_[+5(1.77e-05)]_7 chrV:20423276-20423356 1.37e-02 36_[+4(1.19e-05)]_36 chrII:10545460-10545540 7.82e-01 80 chrIII:5506042-5506122 7.02e-03 80 chrX:14978866-14978946 6.59e-01 80 chrIII:1879604-1879684 1.65e-03 66_[+4(5.52e-06)]_6 chrIII:70083-70163 1.44e-01 80 chrIV:4212846-4212926 7.32e-02 80 chrIV:14985314-14985394 2.88e-01 80 chrIV:2710308-2710388 9.83e-01 80 chrV:8179011-8179091 4.14e-01 80 chrIII:72686-72766 7.48e-02 66_[+3(2.94e-05)]_6 chrIII:1939974-1940054 5.74e-01 80 chrI:316179-316259 5.86e-01 80 chrI:12904112-12904192 7.73e-01 80 chrII:12346808-12346888 9.67e-01 80 chrII:7791169-7791249 7.29e-01 80 chrIII:7711042-7711122 8.15e-02 80 chrII:2186937-2187017 9.15e-04 5_[+2(1.82e-05)]_67 chrI:15040268-15040348 3.91e-02 47_[+4(5.68e-05)]_25 chrIII:1516749-1516829 1.68e-05 17_[+1(1.62e-05)]_26_[+2(1.82e-05)]_\ 21 chrII:12778503-12778583 1.03e-02 24_[+4(1.77e-05)]_48 chrIII:1602877-1602957 9.93e-01 80 chrIV:16181253-16181333 1.60e-01 80 chrI:13310826-13310906 9.91e-01 80 chrII:2735778-2735858 1.82e-01 80 chrI:716714-716794 3.56e-02 61_[+1(2.91e-05)]_11 chrI:545542-545622 9.18e-01 80 chrIII:1931768-1931848 6.33e-01 80 chrI:8027988-8028068 9.12e-01 80 chrV:18622694-18622774 8.13e-02 23_[+4(1.77e-05)]_49 chrIII:984801-984881 2.09e-01 63_[+3(8.56e-05)]_9 chrI:11965947-11966027 1.58e-02 57_[+1(1.62e-05)]_15 chrIII:2169647-2169727 5.93e-01 80 chrII:11978039-11978119 1.04e-02 13_[+5(1.77e-05)]_59 chrM:5266-5346 8.71e-01 80 chrI:12491172-12491252 2.73e-01 80 chrIV:15984339-15984419 8.79e-02 37_[+4(5.52e-06)]_35 chrX:11791516-11791596 8.49e-01 80 chrIV:11913782-11913862 3.64e-01 80 chrIII:10533438-10533518 3.04e-01 80 chrIII:9443078-9443158 5.22e-01 80 chrII:1329764-1329844 1.50e-06 35_[+5(1.77e-05)]_18_[+1(1.62e-05)]_\ 11 chrI:1229407-1229487 4.01e-01 80 chrIII:8867553-8867633 8.40e-01 80 chrII:10197260-10197340 1.69e-01 80 chrIV:6117908-6117988 3.53e-01 80 chrII:11542520-11542600 3.74e-01 80 chrII:2986118-2986198 8.36e-01 80 chrV:13411732-13411812 6.81e-01 80 chrV:7857954-7858034 5.10e-01 80 chrV:20413606-20413686 7.14e-01 80 chrIV:6330935-6331015 2.45e-02 2_[+3(2.94e-05)]_70 chrV:10960747-10960827 2.99e-01 80 chrII:2861528-2861608 2.49e-01 80 chrIV:5656131-5656211 2.50e-03 72_[+3(2.94e-05)] chrI:9383902-9383982 7.83e-03 59_[+2(1.82e-05)]_13 chrX:13108649-13108729 4.76e-01 80 chrII:14043363-14043443 1.19e-01 1_[+4(1.77e-05)]_71 chrIV:1276065-1276145 1.66e-01 80 chrX:3541033-3541113 4.26e-01 80 chrIII:1608227-1608307 1.87e-01 80 chrV:3588317-3588397 6.58e-01 80 chrII:14238078-14238158 5.70e-07 8_[+1(1.62e-05)]_25_[+2(1.82e-05)]_\ 7_[+3(2.94e-05)]_16 chrIV:2316948-2317028 8.04e-01 80 chrIII:1496070-1496150 4.20e-01 80 chrIV:11145812-11145892 9.54e-01 80 chrII:1301127-1301207 1.08e-04 44_[+5(1.77e-05)]_10_[+1(1.62e-05)]_\ 10 chrV:19050756-19050836 5.18e-01 80 chrV:7198514-7198594 9.71e-01 80 chrI:12893319-12893399 7.71e-01 80 chrV:19158817-19158897 9.00e-01 80 chrV:2664672-2664752 3.84e-01 80 chrIV:2603644-2603724 1.36e-01 47_[+4(2.36e-05)]_25 chrX:16721966-16722046 2.84e-01 80 chrIII:11463932-11464012 9.63e-01 80 chrIII:1531912-1531992 2.69e-01 80 chrII:7056187-7056267 2.76e-01 80 chrII:1141850-1141930 6.91e-01 80 chrII:12666177-12666257 7.08e-01 80 chrIII:12317615-12317695 7.25e-01 80 chrIII:2032423-2032503 4.44e-03 29_[+3(8.56e-05)]_16_[+4(3.03e-05)]_\ 19 chrIII:2030882-2030962 1.08e-01 9_[+1(5.05e-05)]_63 chrIV:2704166-2704246 6.56e-01 80 chrX:11482892-11482972 8.55e-01 80 chrIV:3012593-3012673 8.90e-01 80 chrI:2875223-2875303 9.49e-01 80 chrIII:11084179-11084259 5.71e-01 80 chrIII:8242981-8243061 9.34e-01 80 chrI:10103255-10103335 1.83e-01 80 chrIII:1533737-1533817 2.41e-01 80 chrI:3152682-3152762 8.57e-01 80 chrV:14350511-14350591 8.54e-01 80 chrIII:5917568-5917648 6.96e-01 80 chrII:3087792-3087872 9.06e-04 11_[+5(3.31e-05)]_10_[+1(1.62e-05)]_\ 43 chrIII:13542680-13542760 8.37e-01 80 chrIII:1208017-1208097 9.27e-03 80 chrV:2277425-2277505 4.67e-01 80 chrI:6163487-6163567 9.10e-01 80 chrII:8603738-8603818 1.28e-01 33_[+3(2.94e-05)]_39 chrX:5213709-5213789 1.14e-01 2_[+3(8.56e-05)]_70 chrX:10576615-10576695 9.52e-02 80 chrIII:7358752-7358832 4.04e-01 80 chrV:6228529-6228609 3.34e-01 19_[+3(8.56e-05)]_53 chrIII:3307322-3307402 3.00e-03 2_[+1(1.62e-05)]_56_[+3(2.94e-05)]_\ 6 chrII:9934187-9934267 7.16e-01 80 chrIII:1820969-1821049 1.53e-01 80 chrII:12542774-12542854 9.91e-01 80 chrIII:3503618-3503698 6.87e-01 80 chrX:17056734-17056814 8.81e-03 50_[+1(2.91e-05)]_22 chrIV:1416328-1416408 1.35e-03 8_[+5(3.31e-05)]_23_[+2(1.82e-05)]_\ 33 chrIV:2801145-2801225 2.26e-01 80 chrIII:1214843-1214923 2.44e-01 58_[+4(4.23e-05)]_14 chrI:14662980-14663060 4.80e-01 80 chrIII:1600840-1600920 5.17e-01 80 chrX:4997850-4997930 9.97e-01 80 chrV:5835625-5835705 5.88e-01 80 chrI:4653966-4654046 4.74e-01 80 chrIII:11981747-11981827 8.61e-01 80 chrIII:5196598-5196678 9.26e-01 80 chrIII:2760827-2760907 5.39e-01 80 chrII:13298815-13298895 2.65e-01 80 chrIII:9240126-9240206 8.70e-01 80 chrII:8484603-8484683 4.98e-01 80 chrII:13678436-13678516 6.56e-01 80 chrII:1335679-1335759 8.64e-01 80 chrIV:5665504-5665584 2.46e-01 80 chrIII:13767088-13767168 1.52e-01 80 chrV:18354397-18354477 9.91e-01 80 chrII:13575688-13575768 4.32e-01 80 chrI:10565943-10566023 1.26e-01 80 chrII:2970607-2970687 4.13e-01 80 chrII:873542-873622 8.12e-01 80 chrIV:3741272-3741352 3.01e-01 80 chrIII:11834901-11834981 2.42e-01 80 chrI:11977966-11978046 5.76e-01 80 chrV:18346238-18346318 1.53e-02 80 chrV:19207081-19207161 6.17e-01 80 chrX:15610594-15610674 7.34e-01 80 chrII:10543768-10543848 7.50e-01 80 chrII:7669572-7669652 5.87e-01 80 chrV:15982919-15982999 2.08e-01 80 chrIV:16490174-16490254 6.44e-01 80 chrIV:9993879-9993959 6.59e-01 80 chrII:2250340-2250420 3.52e-07 40_[+5(1.77e-05)]_10_[+1(1.62e-05)]_\ 5_[+2(1.82e-05)]_1 chrM:1786-1866 5.04e-01 80 chrIV:11820723-11820803 8.26e-01 80 chrIII:1533266-1533346 3.17e-01 80 chrIV:2655183-2655263 5.13e-01 80 chrI:9168581-9168661 6.39e-01 80 chrV:10169060-10169140 4.54e-01 80 chrII:7350465-7350545 4.69e-01 80 chrI:11930631-11930711 1.52e-05 64_[+4(5.52e-06)]_8 chrII:13079102-13079182 9.49e-01 80 chrIII:3104704-3104784 9.68e-01 80 chrIII:1744646-1744726 3.79e-01 80 chrII:13836057-13836137 2.94e-01 80 chrII:8276256-8276336 4.04e-01 80 chrM:10372-10452 3.23e-01 80 chrII:13521435-13521515 2.34e-01 80 chrX:14228854-14228934 4.30e-01 80 chrI:7661017-7661097 7.27e-02 72_[+4(1.19e-05)] chrI:6210960-6211040 2.10e-01 80 chrIII:3377937-3378017 7.37e-01 80 chrIII:1894894-1894974 7.59e-04 16_[+1(1.62e-05)]_35_[+3(2.94e-05)]_\ 13 chrII:2059124-2059204 1.23e-01 80 chrII:1302198-1302278 5.71e-01 80 chrX:4007934-4008014 9.88e-01 80 chrI:1228113-1228193 4.79e-03 68_[+3(8.56e-05)]_4 chrX:15146534-15146614 5.14e-01 80 chrII:880864-880944 8.93e-01 80 chrI:9106214-9106294 9.48e-01 80 chrI:7159331-7159411 1.80e-02 4_[+4(5.52e-06)]_68 chrII:10547828-10547908 3.58e-02 30_[+4(1.19e-05)]_42 chrII:4706513-4706593 8.90e-02 80 chrII:4891515-4891595 9.24e-02 3_[+1(2.91e-05)]_69 chrX:2089594-2089674 6.61e-01 80 chrI:13287313-13287393 3.61e-01 80 chrX:2435444-2435524 5.13e-01 80 chrIV:1708649-1708729 7.29e-01 80 chrV:8028950-8029030 7.16e-02 80 chrI:7058877-7058957 8.82e-02 80 chrI:1628729-1628809 3.62e-01 80 chrIII:2090872-2090952 8.98e-01 80 chrIV:7959193-7959273 6.76e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n06.farnam.hpc.yale.internal ********************************************************************************