******************************************************************************** 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/sma-9.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:10727754-10727834 1.0000 80 chrIV:6881394-6881474 1.0000 80 chrIV:11071044-11071124 1.0000 80 chrIV:8526226-8526306 1.0000 80 chrX:6178940-6179020 1.0000 80 chrX:2216688-2216768 1.0000 80 chrX:8477557-8477637 1.0000 80 chrII:5605547-5605627 1.0000 80 chrX:12795140-12795220 1.0000 80 chrX:8475328-8475408 1.0000 80 chrX:2240345-2240425 1.0000 80 chrIV:14594345-14594425 1.0000 80 chrII:13678876-13678956 1.0000 80 chrV:11888061-11888141 1.0000 80 chrX:5696371-5696451 1.0000 80 chrIV:14033498-14033578 1.0000 80 chrII:11836744-11836824 1.0000 80 chrI:12501388-12501468 1.0000 80 chrII:10650011-10650091 1.0000 80 chrV:6228666-6228746 1.0000 80 chrX:6491316-6491396 1.0000 80 chrV:5272859-5272939 1.0000 80 chrX:13081770-13081850 1.0000 80 chrIV:11915967-11916047 1.0000 80 chrV:3391177-3391257 1.0000 80 chrV:532136-532216 1.0000 80 chrIII:4099975-4100055 1.0000 80 chrX:4137988-4138068 1.0000 80 chrIII:12849394-12849474 1.0000 80 chrX:12872506-12872586 1.0000 80 chrV:11799544-11799624 1.0000 80 chrX:535942-536022 1.0000 80 chrX:4142258-4142338 1.0000 80 chrV:13081310-13081390 1.0000 80 chrX:13358685-13358765 1.0000 80 chrV:5049794-5049874 1.0000 80 chrV:6246674-6246754 1.0000 80 chrIV:5657162-5657242 1.0000 80 chrIV:13079241-13079321 1.0000 80 chrII:5330321-5330401 1.0000 80 chrIII:5552473-5552553 1.0000 80 chrX:17505895-17505975 1.0000 80 chrIV:5817559-5817639 1.0000 80 chrV:11802725-11802805 1.0000 80 chrV:14368580-14368660 1.0000 80 chrIII:1926558-1926638 1.0000 80 chrII:4745407-4745487 1.0000 80 chrI:5311904-5311984 1.0000 80 chrV:13658777-13658857 1.0000 80 chrIV:6097162-6097242 1.0000 80 chrX:17513706-17513786 1.0000 80 chrX:14790506-14790586 1.0000 80 chrX:6742211-6742291 1.0000 80 chrX:14560440-14560520 1.0000 80 chrX:6737776-6737856 1.0000 80 chrX:15707603-15707683 1.0000 80 chrV:10717244-10717324 1.0000 80 chrX:9551177-9551257 1.0000 80 chrX:14506048-14506128 1.0000 80 chrV:5768400-5768480 1.0000 80 chrIV:14611273-14611353 1.0000 80 chrII:5326373-5326453 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_sma-9/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/sma-9.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= 62 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= 4960 N= 62 sample: seed= 0 hsfrac= 0 searchsize= 4960 norand= no csites= 1000 Letter frequencies in dataset: A 0.274 C 0.231 G 0.225 T 0.269 Background letter frequencies (from file dataset with add-one prior applied): A 0.274 C 0.231 G 0.225 T 0.269 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCTGCGTC MEME-1 width = 8 sites = 12 llr = 111 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::3:: pos.-specific C :a:3a:28 probability G :::8:8:2 matrix T a:a:::8: bits 2.2 * * 1.9 *** * 1.7 *** * 1.5 *** * * Relative 1.3 ******** Entropy 1.1 ******** (13.4 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCTGCGTC consensus C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:1926558-1926638 30 1.21e-05 CATCGTGCTC TCTGCGTC TCTCGAACCG chrIV:5817559-5817639 37 1.21e-05 TCCGAATATC TCTGCGTC TCTTCATCTC chrV:532136-532216 60 1.21e-05 TGCAATAGTG TCTGCGTC TCTCTTTTCA chrIV:14033498-14033578 24 1.21e-05 GTGGCCGTTC TCTGCGTC TCTTCAGCCG chrII:13678876-13678956 5 1.21e-05 ACCA TCTGCGTC TCCACTGGAA chrX:14506048-14506128 62 2.46e-05 TTTTTTTTCA TCTCCGTC GTTTTCTCTC chrX:15707603-15707683 61 2.46e-05 GTCGGTTGTC TCTCCGTC ACTATTATTT chrX:9551177-9551257 48 3.94e-05 CGGCGCTCAC TCTGCATC TTATCCTCTC chrV:3391177-3391257 30 6.17e-05 ACATTCACAC TCTGCGTG TCTATCTGAC chrII:5330321-5330401 20 7.69e-05 tctctatgtg tctccatc tgtctctcAT chrV:6246674-6246754 50 1.12e-04 ACGCACCCGA TCTGCACC GCCCGCCGCC chrIV:11915967-11916047 4 1.37e-04 TTT TCTGCGCG ACACAAGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:1926558-1926638 1.2e-05 29_[+1]_43 chrIV:5817559-5817639 1.2e-05 36_[+1]_36 chrV:532136-532216 1.2e-05 59_[+1]_13 chrIV:14033498-14033578 1.2e-05 23_[+1]_49 chrII:13678876-13678956 1.2e-05 4_[+1]_68 chrX:14506048-14506128 2.5e-05 61_[+1]_11 chrX:15707603-15707683 2.5e-05 60_[+1]_12 chrX:9551177-9551257 3.9e-05 47_[+1]_25 chrV:3391177-3391257 6.2e-05 29_[+1]_43 chrII:5330321-5330401 7.7e-05 19_[+1]_53 chrV:6246674-6246754 0.00011 49_[+1]_23 chrIV:11915967-11916047 0.00014 3_[+1]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTGCGTC width=8 seqs=12 chrIII:1926558-1926638 ( 30) TCTGCGTC 1 chrIV:5817559-5817639 ( 37) TCTGCGTC 1 chrV:532136-532216 ( 60) TCTGCGTC 1 chrIV:14033498-14033578 ( 24) TCTGCGTC 1 chrII:13678876-13678956 ( 5) TCTGCGTC 1 chrX:14506048-14506128 ( 62) TCTCCGTC 1 chrX:15707603-15707683 ( 61) TCTCCGTC 1 chrX:9551177-9551257 ( 48) TCTGCATC 1 chrV:3391177-3391257 ( 30) TCTGCGTG 1 chrII:5330321-5330401 ( 20) TCTCCATC 1 chrV:6246674-6246754 ( 50) TCTGCACC 1 chrIV:11915967-11916047 ( 4) TCTGCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 9.00371 E= 1.4e-001 -1023 -1023 -1023 189 -1023 211 -1023 -1023 -1023 -1023 -1023 189 -1023 11 174 -1023 -1023 211 -1023 -1023 -13 -1023 174 -1023 -1023 -47 -1023 163 -1023 185 -43 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 1.4e-001 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGCGTC MEME-1 regular expression -------------------------------------------------------------------------------- TCT[GC]C[GA]TC -------------------------------------------------------------------------------- Time 1.33 secs. ******************************************************************************** ******************************************************************************** MOTIF ACAAAATG MEME-2 width = 8 sites = 15 llr = 128 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 73a8a9:: pos.-specific C 37:2:::: probability G :1:::1:a matrix T ::::::a: bits 2.2 * 1.9 * * ** 1.7 * * ** 1.5 * * ** Relative 1.3 ****** Entropy 1.1 * ****** (12.3 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACAAAATG consensus CA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:4142258-4142338 29 2.16e-05 TCGTCACAAT ACAAAATG TCACGCGATG chrV:5272859-5272939 65 2.16e-05 CGTGTGTGCC ACAAAATG CACTCTGA chrX:6491316-6491396 42 2.16e-05 TTTTAATTAT ACAAAATG GTGAGACCAG chrX:6178940-6179020 66 2.16e-05 ACATTAAATC ACAAAATG TAGATGA chrIV:8526226-8526306 18 2.16e-05 acacacacat acaAAATG AACCagaaga chrI:5311904-5311984 39 3.98e-05 GAGACAGAAA CCAAAATG ACGTCACGAA chrX:12795140-12795220 50 3.98e-05 ATTGTAATTA CCAAAATG CACATTGAAC chrV:532136-532216 39 8.36e-05 ATATGATTAC ACACAATG TTGTGCAATA chrIV:14594345-14594425 67 8.36e-05 CTGTTTTATC ACACAATG GAGTTT chrX:5696371-5696451 48 1.01e-04 AAGAAACGCA ACAAAGTG TGTGGTGGCG chrIV:13079241-13079321 12 1.23e-04 AGGCCAATTC CAAAAATG CACTTGTCAC chrX:13081770-13081850 17 1.23e-04 TAACTTTTCT CAAAAATG TGTTGAAATT chrX:6737776-6737856 32 1.81e-04 CGGAAACGTG AGAAAATG AGAAACGACG chrX:4137988-4138068 53 1.81e-04 AACTGAGTTC AAACAATG CTTTTTCTGG chrV:11888061-11888141 1 2.17e-04 . AAAAAGTG ATAAGAAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:4142258-4142338 2.2e-05 28_[+2]_44 chrV:5272859-5272939 2.2e-05 64_[+2]_8 chrX:6491316-6491396 2.2e-05 41_[+2]_31 chrX:6178940-6179020 2.2e-05 65_[+2]_7 chrIV:8526226-8526306 2.2e-05 17_[+2]_55 chrI:5311904-5311984 4e-05 38_[+2]_34 chrX:12795140-12795220 4e-05 49_[+2]_23 chrV:532136-532216 8.4e-05 38_[+2]_34 chrIV:14594345-14594425 8.4e-05 66_[+2]_6 chrX:5696371-5696451 0.0001 47_[+2]_25 chrIV:13079241-13079321 0.00012 11_[+2]_61 chrX:13081770-13081850 0.00012 16_[+2]_56 chrX:6737776-6737856 0.00018 31_[+2]_41 chrX:4137988-4138068 0.00018 52_[+2]_20 chrV:11888061-11888141 0.00022 [+2]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACAAAATG width=8 seqs=15 chrX:4142258-4142338 ( 29) ACAAAATG 1 chrV:5272859-5272939 ( 65) ACAAAATG 1 chrX:6491316-6491396 ( 42) ACAAAATG 1 chrX:6178940-6179020 ( 66) ACAAAATG 1 chrIV:8526226-8526306 ( 18) ACAAAATG 1 chrI:5311904-5311984 ( 39) CCAAAATG 1 chrX:12795140-12795220 ( 50) CCAAAATG 1 chrV:532136-532216 ( 39) ACACAATG 1 chrIV:14594345-14594425 ( 67) ACACAATG 1 chrX:5696371-5696451 ( 48) ACAAAGTG 1 chrIV:13079241-13079321 ( 12) CAAAAATG 1 chrX:13081770-13081850 ( 17) CAAAAATG 1 chrX:6737776-6737856 ( 32) AGAAAATG 1 chrX:4137988-4138068 ( 53) AAACAATG 1 chrV:11888061-11888141 ( 1) AAAAAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 8.90836 E= 1.6e+000 142 20 -1055 -1055 -4 153 -175 -1055 187 -1055 -1055 -1055 154 -21 -1055 -1055 187 -1055 -1055 -1055 166 -1055 -75 -1055 -1055 -1055 -1055 189 -1055 -1055 215 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 1.6e+000 0.733333 0.266667 0.000000 0.000000 0.266667 0.666667 0.066667 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.866667 0.000000 0.133333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACAAAATG MEME-2 regular expression -------------------------------------------------------------------------------- [AC][CA]A[AC]AATG -------------------------------------------------------------------------------- Time 1.99 secs. ******************************************************************************** ******************************************************************************** MOTIF CGTGTGTG MEME-3 width = 8 sites = 5 llr = 52 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::2::::: pos.-specific C 8::::::: probability G 2a:a:a:a matrix T ::8:a:a: bits 2.2 * * * * 1.9 * ***** 1.7 * ***** 1.5 * ***** Relative 1.3 ** ***** Entropy 1.1 ******** (15.0 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGTGTGTG consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:9551177-9551257 28 1.15e-05 CTAGCGCGCG CGTGTGTG CCCGGCGCTC chrV:5049794-5049874 9 1.15e-05 GAGGGCCC CGTGTGTG GTATAAAACA chrV:5272859-5272939 55 1.15e-05 GACACAGAAA CGTGTGTG CCACAAAATG chrX:15707603-15707683 41 3.45e-05 GTCCCCCTGC GGTGTGTG GTGTCGGTTG chrII:13678876-13678956 52 3.45e-05 GAACACCATT CGAGTGTG GTTGTGTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:9551177-9551257 1.2e-05 27_[+3]_45 chrV:5049794-5049874 1.2e-05 8_[+3]_64 chrV:5272859-5272939 1.2e-05 54_[+3]_18 chrX:15707603-15707683 3.4e-05 40_[+3]_32 chrII:13678876-13678956 3.4e-05 51_[+3]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGTGTGTG width=8 seqs=5 chrX:9551177-9551257 ( 28) CGTGTGTG 1 chrV:5049794-5049874 ( 9) CGTGTGTG 1 chrV:5272859-5272939 ( 55) CGTGTGTG 1 chrX:15707603-15707683 ( 41) GGTGTGTG 1 chrII:13678876-13678956 ( 52) CGAGTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 10.0723 E= 1.2e+003 -897 179 -17 -897 -897 -897 215 -897 -46 -897 -897 157 -897 -897 215 -897 -897 -897 -897 189 -897 -897 215 -897 -897 -897 -897 189 -897 -897 215 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.2e+003 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.000000 0.800000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGTGTG MEME-3 regular expression -------------------------------------------------------------------------------- [CG]G[TA]GTGTG -------------------------------------------------------------------------------- Time 2.62 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGCCCSG MEME-4 width = 8 sites = 3 llr = 33 E-value = 6.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C aa:aaa3: probability G ::a:::7a matrix T :::::::: bits 2.2 ****** * 1.9 ****** * 1.7 ****** * 1.5 ****** * Relative 1.3 ******** Entropy 1.1 ******** (16.1 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCGCCCGG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:4142258-4142338 6 7.49e-06 TCTGG CCGCCCGG ATGTTTCGTC chrX:5696371-5696451 27 7.49e-06 GCTAGCTCGC CCGCCCGG TTCAAGAAAC chrIV:14033498-14033578 54 1.52e-05 ACCAATCTCT CCGCCCCG TCTCTTCCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:4142258-4142338 7.5e-06 5_[+4]_67 chrX:5696371-5696451 7.5e-06 26_[+4]_46 chrIV:14033498-14033578 1.5e-05 53_[+4]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGCCCSG width=8 seqs=3 chrX:4142258-4142338 ( 6) CCGCCCGG 1 chrX:5696371-5696451 ( 27) CCGCCCGG 1 chrIV:14033498-14033578 ( 54) CCGCCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 10.2168 E= 6.2e+003 -823 211 -823 -823 -823 211 -823 -823 -823 -823 215 -823 -823 211 -823 -823 -823 211 -823 -823 -823 211 -823 -823 -823 52 157 -823 -823 -823 215 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 6.2e+003 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 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCCCSG MEME-4 regular expression -------------------------------------------------------------------------------- CCGCCC[GC]G -------------------------------------------------------------------------------- Time 3.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GRVAGAGA MEME-5 width = 8 sites = 15 llr = 119 E-value = 8.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 Description -------------------------------------------------------------------------------- Simplified A 253a:a3a pos.-specific C ::4::::: probability G 833:a:7: matrix T :1:::::: bits 2.2 * 1.9 *** * 1.7 *** * 1.5 *** * Relative 1.3 * ***** Entropy 1.1 * ***** (11.4 bits) 0.9 * ***** 0.6 ** ***** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GACAGAGA consensus AGA A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:10717244-10717324 28 5.90e-05 ACGGCAGATG GAAAGAGA AGAAGATTTC chrX:14790506-14790586 17 5.90e-05 GGTAGGAGAA GAGAGAGA TAGATGACAG chrI:12501388-12501468 52 5.90e-05 CGAATTCGGG GAAAGAGA TATTTTCGAA chrV:11888061-11888141 13 5.90e-05 AAAGTGATAA GAAAGAGA TAGTATGTGT chrIV:11915967-11916047 32 8.54e-05 GTGTGTAGGT GGAAGAGA CGGAGAGATG chrIV:8526226-8526306 51 8.54e-05 aaattgacaa ggaagaga agagaagaga chrI:5311904-5311984 31 1.03e-04 TCCTCTCCGA GACAGAAA CCAAAATGAC chrII:5330321-5330401 73 1.03e-04 ATTTCAAAAC GACAGAAA chrX:14506048-14506128 32 1.18e-04 GCAGGAGCGT GTCAGAGA GGCCCGACAG chrX:5696371-5696451 71 1.18e-04 TGGCGTGTTT GTCAGAGA AC chrV:14368580-14368660 1 1.90e-04 . AACAGAGA GTGCGAACGA chrX:8475328-8475408 18 1.90e-04 GAGTTCAACA AACAGAGA ACACTGCCAG chrV:11802725-11802805 29 2.68e-04 GCAGAAATTG GGGAGAAA CGAGGTTGCA chrII:5605547-5605627 44 2.68e-04 TTTTTGAAAC GGGAGAAA AGAACCTATC chrIV:5657162-5657242 67 3.39e-04 TCACAAGACG AGGAGAGA TGGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:10717244-10717324 5.9e-05 27_[+5]_45 chrX:14790506-14790586 5.9e-05 16_[+5]_56 chrI:12501388-12501468 5.9e-05 51_[+5]_21 chrV:11888061-11888141 5.9e-05 12_[+5]_60 chrIV:11915967-11916047 8.5e-05 31_[+5]_41 chrIV:8526226-8526306 8.5e-05 50_[+5]_22 chrI:5311904-5311984 0.0001 30_[+5]_42 chrII:5330321-5330401 0.0001 72_[+5] chrX:14506048-14506128 0.00012 31_[+5]_41 chrX:5696371-5696451 0.00012 70_[+5]_2 chrV:14368580-14368660 0.00019 [+5]_72 chrX:8475328-8475408 0.00019 17_[+5]_55 chrV:11802725-11802805 0.00027 28_[+5]_44 chrII:5605547-5605627 0.00027 43_[+5]_29 chrIV:5657162-5657242 0.00034 66_[+5]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GRVAGAGA width=8 seqs=15 chrV:10717244-10717324 ( 28) GAAAGAGA 1 chrX:14790506-14790586 ( 17) GAGAGAGA 1 chrI:12501388-12501468 ( 52) GAAAGAGA 1 chrV:11888061-11888141 ( 13) GAAAGAGA 1 chrIV:11915967-11916047 ( 32) GGAAGAGA 1 chrIV:8526226-8526306 ( 51) GGAAGAGA 1 chrI:5311904-5311984 ( 31) GACAGAAA 1 chrII:5330321-5330401 ( 73) GACAGAAA 1 chrX:14506048-14506128 ( 32) GTCAGAGA 1 chrX:5696371-5696451 ( 71) GTCAGAGA 1 chrV:14368580-14368660 ( 1) AACAGAGA 1 chrX:8475328-8475408 ( 18) AACAGAGA 1 chrV:11802725-11802805 ( 29) GGGAGAAA 1 chrII:5605547-5605627 ( 44) GGGAGAAA 1 chrIV:5657162-5657242 ( 67) AGGAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4526 bayes= 8.90836 E= 8.5e+003 -46 -1055 183 -1055 96 -1055 57 -101 28 79 25 -1055 187 -1055 -1055 -1055 -1055 -1055 215 -1055 187 -1055 -1055 -1055 -4 -1055 171 -1055 187 -1055 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 8.5e+003 0.200000 0.000000 0.800000 0.000000 0.533333 0.000000 0.333333 0.133333 0.333333 0.400000 0.266667 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 0.266667 0.000000 0.733333 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRVAGAGA MEME-5 regular expression -------------------------------------------------------------------------------- [GA][AG][CAG]AGA[GA]A -------------------------------------------------------------------------------- Time 3.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:10727754-10727834 7.01e-01 80 chrIV:6881394-6881474 8.78e-02 80 chrIV:11071044-11071124 1.00e+00 80 chrIV:8526226-8526306 1.05e-02 17_[+2(2.16e-05)]_25_[+5(8.54e-05)]_\ 22 chrX:6178940-6179020 1.40e-01 65_[+2(2.16e-05)]_7 chrX:2216688-2216768 4.44e-01 80 chrX:8477557-8477637 4.98e-01 80 chrII:5605547-5605627 4.15e-01 80 chrX:12795140-12795220 2.73e-01 49_[+2(3.98e-05)]_23 chrX:8475328-8475408 1.39e-01 80 chrX:2240345-2240425 3.96e-01 80 chrIV:14594345-14594425 3.18e-01 66_[+2(8.36e-05)]_6 chrII:13678876-13678956 1.61e-03 4_[+1(1.21e-05)]_39_[+3(3.45e-05)]_\ 21 chrV:11888061-11888141 8.19e-03 12_[+5(5.90e-05)]_60 chrX:5696371-5696451 9.49e-07 26_[+4(7.49e-06)]_17_[+3(9.25e-05)]_\ 21 chrIV:14033498-14033578 1.33e-03 23_[+1(1.21e-05)]_22_[+4(1.52e-05)]_\ 19 chrII:11836744-11836824 9.00e-01 80 chrI:12501388-12501468 7.92e-02 51_[+5(5.90e-05)]_21 chrII:10650011-10650091 9.29e-01 80 chrV:6228666-6228746 4.86e-01 80 chrX:6491316-6491396 5.80e-02 41_[+2(2.16e-05)]_31 chrV:5272859-5272939 1.10e-04 54_[+3(1.15e-05)]_2_[+2(2.16e-05)]_\ 8 chrX:13081770-13081850 2.91e-01 80 chrIV:11915967-11916047 1.02e-03 31_[+5(8.54e-05)]_41 chrV:3391177-3391257 5.42e-03 29_[+1(6.17e-05)]_43 chrV:532136-532216 1.34e-03 38_[+2(8.36e-05)]_13_[+1(1.21e-05)]_\ 13 chrIII:4099975-4100055 1.59e-01 80 chrX:4137988-4138068 1.17e-01 80 chrIII:12849394-12849474 5.99e-01 80 chrX:12872506-12872586 6.30e-02 80 chrV:11799544-11799624 3.50e-01 80 chrX:535942-536022 6.32e-01 80 chrX:4142258-4142338 4.31e-04 5_[+4(7.49e-06)]_15_[+2(2.16e-05)]_\ 44 chrV:13081310-13081390 9.67e-01 80 chrX:13358685-13358765 5.15e-01 80 chrV:5049794-5049874 4.82e-03 8_[+3(1.15e-05)]_64 chrV:6246674-6246754 3.54e-03 80 chrIV:5657162-5657242 5.84e-02 80 chrIV:13079241-13079321 1.65e-01 80 chrII:5330321-5330401 8.03e-03 19_[+1(7.69e-05)]_53 chrIII:5552473-5552553 4.00e-01 80 chrX:17505895-17505975 4.07e-01 80 chrIV:5817559-5817639 1.09e-01 36_[+1(1.21e-05)]_36 chrV:11802725-11802805 1.41e-01 80 chrV:14368580-14368660 1.38e-03 80 chrIII:1926558-1926638 1.31e-01 29_[+1(1.21e-05)]_10_[+1(3.94e-05)]_\ 25 chrII:4745407-4745487 6.87e-01 80 chrI:5311904-5311984 8.98e-04 38_[+2(3.98e-05)]_34 chrV:13658777-13658857 8.80e-01 80 chrIV:6097162-6097242 9.70e-01 80 chrX:17513706-17513786 2.20e-01 80 chrX:14790506-14790586 1.79e-01 16_[+5(5.90e-05)]_56 chrX:6742211-6742291 3.95e-01 80 chrX:14560440-14560520 4.12e-01 80 chrX:6737776-6737856 3.60e-02 80 chrX:15707603-15707683 2.59e-03 40_[+3(3.45e-05)]_12_[+1(2.46e-05)]_\ 12 chrV:10717244-10717324 1.05e-01 27_[+5(5.90e-05)]_45 chrX:9551177-9551257 1.08e-03 27_[+3(1.15e-05)]_12_[+1(3.94e-05)]_\ 25 chrX:14506048-14506128 1.37e-03 61_[+1(2.46e-05)]_11 chrV:5768400-5768480 8.91e-01 80 chrIV:14611273-14611353 9.36e-02 80 chrII:5326373-5326453 3.60e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n06.farnam.hpc.yale.internal ********************************************************************************