******************************************************************************** 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/fly/fasta/RankLinear8.0_60/h.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrX:5891411-5891531 1.0000 120 chr2L:1168123-1168243 1.0000 120 chr2R:22887856-22887976 1.0000 120 chr2L:13391149-13391269 1.0000 120 chr3R:29802159-29802279 1.0000 120 chr3R:9011382-9011502 1.0000 120 chr3R:23320402-23320522 1.0000 120 chr2R:18137002-18137122 1.0000 120 chrX:624107-624227 1.0000 120 chr3R:14660018-14660138 1.0000 120 chr3R:13388137-13388257 1.0000 120 chr2R:5759411-5759531 1.0000 120 chr2R:22800867-22800987 1.0000 120 chr2R:22556244-22556364 1.0000 120 chr3R:23330678-23330798 1.0000 120 chr3R:23310890-23311010 1.0000 120 chr2R:20329903-20330023 1.0000 120 chr3L:3213410-3213530 1.0000 120 chr2R:15523883-15524003 1.0000 120 chr2L:19127867-19127987 1.0000 120 chr3R:5633892-5634012 1.0000 120 chr2L:557888-558008 1.0000 120 chr2R:17671938-17672058 1.0000 120 chr2L:21103265-21103385 1.0000 120 chr4:198882-199002 1.0000 120 chr3R:22028322-22028442 1.0000 120 chrX:14910630-14910750 1.0000 120 chr3R:16261894-16262014 1.0000 120 chr3R:24198306-24198426 1.0000 120 chr3R:23327856-23327976 1.0000 120 chrX:3084523-3084643 1.0000 120 chr2R:17848349-17848469 1.0000 120 chr2R:18276694-18276814 1.0000 120 chr3L:3403305-3403425 1.0000 120 chr3L:2571522-2571642 1.0000 120 chr2R:20273182-20273302 1.0000 120 chr2R:6669279-6669399 1.0000 120 chrX:11081956-11082076 1.0000 120 chr2L:11797171-11797291 1.0000 120 chr3R:25112654-25112774 1.0000 120 chr2L:19581155-19581275 1.0000 120 chrX:5694761-5694881 1.0000 120 chr2L:11123290-11123410 1.0000 120 chr3L:2567232-2567352 1.0000 120 chr3R:27272843-27272963 1.0000 120 chr3L:2534132-2534252 1.0000 120 chr2L:2194741-2194861 1.0000 120 chr2R:5350447-5350567 1.0000 120 chr3L:3417680-3417800 1.0000 120 chr2R:11410861-11410981 1.0000 120 chr3R:23332249-23332369 1.0000 120 chr3R:25678810-25678930 1.0000 120 chr2L:19134123-19134243 1.0000 120 chr3R:23257841-23257961 1.0000 120 chr2R:19373200-19373320 1.0000 120 chr3R:3750289-3750409 1.0000 120 chrX:16747041-16747161 1.0000 120 chr2L:13513089-13513209 1.0000 120 chrX:2121765-2121885 1.0000 120 chr2L:1117123-1117243 1.0000 120 chr3L:3159961-3160081 1.0000 120 chr2L:22247826-22247946 1.0000 120 chr3R:11312463-11312583 1.0000 120 chr3R:30056236-30056356 1.0000 120 ******************************************************************************** ******************************************************************************** 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/fly/inference_raw/MEME/RankLinear8.0_60_h/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/h.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= 64 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 7680 N= 64 sample: seed= 0 hsfrac= 0 searchsize= 7680 norand= no csites= 1000 Letter frequencies in dataset: A 0.234 C 0.253 G 0.244 T 0.269 Background letter frequencies (from file dataset with add-one prior applied): A 0.234 C 0.253 G 0.244 T 0.269 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGCWGCTG MEME-1 width = 8 sites = 33 llr = 237 E-value = 3.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::15::2: pos.-specific C :29::6:: probability G 28::a1:a matrix T 7::5:28: bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 ** * * Entropy 1.0 ***** ** (10.4 bits) 0.8 ***** ** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGCAGCTG consensus GC T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:14910630-14910750 43 1.57e-05 CGGTTCTGCT TGCAGCTG CAGTTCCCGT chr2L:13513089-13513209 76 3.38e-05 ATGTTGTTGT TGCTGCTG CTGGTCCGCC chr3R:23332249-23332369 53 3.38e-05 TTAACTCTTC TGCTGCTG CTTCTTTTTT chr2L:11797171-11797291 105 3.38e-05 ACCctgctgt tgctgctg gtgatgct chr3L:2571522-2571642 17 3.38e-05 CAGCAGTCGA TGCTGCTG ACACCTTTCA chr3R:16261894-16262014 107 3.38e-05 CTTCTGCTTA TGCTGCTG AGCAGC chr4:198882-199002 44 3.38e-05 CAATTCTACT TGCTGCTG CAAAGCCCCA chr3R:30056236-30056356 31 6.49e-05 GGGATCCGAC TGCAGTTG CTTTGACCCC chr2R:19373200-19373320 31 1.31e-04 ctgcggctgc ggctgctg cactgcgctg chr3R:23257841-23257961 98 1.31e-04 TTGTTGTTAT TGCTGTTG CTGTAGACGG chr3R:27272843-27272963 76 1.31e-04 GATATCGGGA TGCTGTTG GCTTGCCGAA chr3R:24198306-24198426 90 1.31e-04 ctggttgtgg tgctgttg ctggtggtgg chr2R:22556244-22556364 1 1.31e-04 . TGCAGCAG GGGCTTCTTC chr2L:1117123-1117243 9 1.80e-04 GGCCAAAT TGCAGGTG TGGTTTCTAC chr3R:5633892-5634012 59 1.98e-04 CGCATCGACG TGCTGGTG AACAACGCCG chr3R:22028322-22028442 34 2.13e-04 AGTACTATCC GGCAGTTG ATCTGGACCT chr2L:21103265-21103385 108 2.60e-04 ACGGTTGTCC GCCAGCTG GACAT chr2R:17671938-17672058 104 2.60e-04 TGGTTCACAT TGAAGCTG ACCACCACC chr3R:23330678-23330798 94 2.60e-04 AAAATGCAAT TGAAGCTG TCCCAAGAAC chrX:624107-624227 51 2.60e-04 GTTCTGGTGT GCCAGCTG GAGACGCCCG chr3R:9011382-9011502 64 2.60e-04 AGAATGACTC GCCAGCTG CCGCACCACC chr2L:13391149-13391269 21 2.60e-04 CGATTTCTTA GCCAGCTG AAGCGGGACT chr3R:13388137-13388257 88 3.04e-04 GGAACCAAAA GGCAGCAG GAGGTGGACA chr2R:6669279-6669399 40 3.72e-04 ATTGCTCTTA TCCTGTTG CAGTGGAGGA chr3R:23320402-23320522 113 3.72e-04 CCCTCAAAAG TCCAGCAG chr2R:5759411-5759531 21 4.17e-04 GCTCTTTGAC GGCTGCAG GTACAACCGG chr2L:19581155-19581275 5 4.96e-04 CGGA TCCTGGTG GCGGTATACT chr2L:19134123-19134243 43 5.85e-04 GCATTCAACG TGAAGTTG CTCCAAAAAC chr2R:18276694-18276814 80 5.85e-04 CCTTGGCCTC TGCAGCGG TAATTGTGCG chr2R:22800867-22800987 94 5.85e-04 CATTCGCGTC TGCTGGAG CGTGCCGCCA chr3L:3213410-3213530 42 6.15e-04 CTGCAGGCCC TGGAGCTG CAGTTCCCTC chr2R:15523883-15524003 100 6.45e-04 ATTCACCCGC CGCTGCTG ACCCTGACGT chr3L:2567232-2567352 42 7.53e-04 TCGGGGGCCA TCCAGTAG GGAGTACCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:14910630-14910750 1.6e-05 42_[+1]_70 chr2L:13513089-13513209 3.4e-05 75_[+1]_37 chr3R:23332249-23332369 3.4e-05 52_[+1]_60 chr2L:11797171-11797291 3.4e-05 104_[+1]_8 chr3L:2571522-2571642 3.4e-05 16_[+1]_96 chr3R:16261894-16262014 3.4e-05 106_[+1]_6 chr4:198882-199002 3.4e-05 43_[+1]_69 chr3R:30056236-30056356 6.5e-05 30_[+1]_82 chr2R:19373200-19373320 0.00013 30_[+1]_82 chr3R:23257841-23257961 0.00013 97_[+1]_15 chr3R:27272843-27272963 0.00013 75_[+1]_37 chr3R:24198306-24198426 0.00013 89_[+1]_23 chr2R:22556244-22556364 0.00013 [+1]_112 chr2L:1117123-1117243 0.00018 8_[+1]_104 chr3R:5633892-5634012 0.0002 58_[+1]_54 chr3R:22028322-22028442 0.00021 33_[+1]_79 chr2L:21103265-21103385 0.00026 107_[+1]_5 chr2R:17671938-17672058 0.00026 103_[+1]_9 chr3R:23330678-23330798 0.00026 93_[+1]_19 chrX:624107-624227 0.00026 50_[+1]_62 chr3R:9011382-9011502 0.00026 63_[+1]_49 chr2L:13391149-13391269 0.00026 20_[+1]_92 chr3R:13388137-13388257 0.0003 87_[+1]_25 chr2R:6669279-6669399 0.00037 39_[+1]_73 chr3R:23320402-23320522 0.00037 112_[+1] chr2R:5759411-5759531 0.00042 20_[+1]_92 chr2L:19581155-19581275 0.0005 4_[+1]_108 chr2L:19134123-19134243 0.00058 42_[+1]_70 chr2R:18276694-18276814 0.00058 79_[+1]_33 chr2R:22800867-22800987 0.00058 93_[+1]_19 chr3L:3213410-3213530 0.00061 41_[+1]_71 chr2R:15523883-15524003 0.00065 99_[+1]_13 chr3L:2567232-2567352 0.00075 41_[+1]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCWGCTG width=8 seqs=33 chrX:14910630-14910750 ( 43) TGCAGCTG 1 chr2L:13513089-13513209 ( 76) TGCTGCTG 1 chr3R:23332249-23332369 ( 53) TGCTGCTG 1 chr2L:11797171-11797291 ( 105) TGCTGCTG 1 chr3L:2571522-2571642 ( 17) TGCTGCTG 1 chr3R:16261894-16262014 ( 107) TGCTGCTG 1 chr4:198882-199002 ( 44) TGCTGCTG 1 chr3R:30056236-30056356 ( 31) TGCAGTTG 1 chr2R:19373200-19373320 ( 31) GGCTGCTG 1 chr3R:23257841-23257961 ( 98) TGCTGTTG 1 chr3R:27272843-27272963 ( 76) TGCTGTTG 1 chr3R:24198306-24198426 ( 90) TGCTGTTG 1 chr2R:22556244-22556364 ( 1) TGCAGCAG 1 chr2L:1117123-1117243 ( 9) TGCAGGTG 1 chr3R:5633892-5634012 ( 59) TGCTGGTG 1 chr3R:22028322-22028442 ( 34) GGCAGTTG 1 chr2L:21103265-21103385 ( 108) GCCAGCTG 1 chr2R:17671938-17672058 ( 104) TGAAGCTG 1 chr3R:23330678-23330798 ( 94) TGAAGCTG 1 chrX:624107-624227 ( 51) GCCAGCTG 1 chr3R:9011382-9011502 ( 64) GCCAGCTG 1 chr2L:13391149-13391269 ( 21) GCCAGCTG 1 chr3R:13388137-13388257 ( 88) GGCAGCAG 1 chr2R:6669279-6669399 ( 40) TCCTGTTG 1 chr3R:23320402-23320522 ( 113) TCCAGCAG 1 chr2R:5759411-5759531 ( 21) GGCTGCAG 1 chr2L:19581155-19581275 ( 5) TCCTGGTG 1 chr2L:19134123-19134243 ( 43) TGAAGTTG 1 chr2R:18276694-18276814 ( 80) TGCAGCGG 1 chr2R:22800867-22800987 ( 94) TGCTGGAG 1 chr3L:3213410-3213530 ( 42) TGGAGCTG 1 chr2R:15523883-15524003 ( 100) CGCTGCTG 1 chr3L:2567232-2567352 ( 42) TCCAGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7232 bayes= 8.53832 E= 3.1e+000 -1169 -306 -1 144 -1169 -6 163 -1169 -136 180 -301 -1169 114 -1169 -1169 85 -1169 -1169 203 -1169 -1169 133 -101 -15 -36 -1169 -301 155 -1169 -1169 203 -1169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 3.1e+000 0.000000 0.030303 0.242424 0.727273 0.000000 0.242424 0.757576 0.000000 0.090909 0.878788 0.030303 0.000000 0.515152 0.000000 0.000000 0.484848 0.000000 0.000000 1.000000 0.000000 0.000000 0.636364 0.121212 0.242424 0.181818 0.000000 0.030303 0.787879 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCWGCTG MEME-1 regular expression -------------------------------------------------------------------------------- [TG][GC]C[AT]G[CT]TG -------------------------------------------------------------------------------- Time 1.06 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAAKAAA MEME-2 width = 8 sites = 6 llr = 63 E-value = 5.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A aaa8:aaa pos.-specific C :::::::: probability G ::::7::: matrix T :::23::: bits 2.1 *** *** 1.9 *** *** 1.7 *** *** 1.5 **** *** Relative 1.3 **** *** Entropy 1.0 ******** (15.0 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAAGAAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:11410861-11410981 106 9.37e-06 TTCTTTATCC AAAAGAAA AAGGTTC chr2R:20273182-20273302 26 9.37e-06 ACCTGCCGGA AAAAGAAA TCAAATAATG chr4:198882-199002 73 9.37e-06 AATTTGAGTT AAAAGAAA CTTCATTTTG chr3L:3417680-3417800 5 1.97e-05 CCCA AAAATAAA CACTCACTTT chr3R:25112654-25112774 43 1.97e-05 AAGCTATGCA AAAATAAA GTACTCCAAA chr3R:27272843-27272963 29 3.05e-05 CCGCGGAGCG AAATGAAA TGTACAGCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:11410861-11410981 9.4e-06 105_[+2]_7 chr2R:20273182-20273302 9.4e-06 25_[+2]_87 chr4:198882-199002 9.4e-06 72_[+2]_40 chr3L:3417680-3417800 2e-05 4_[+2]_108 chr3R:25112654-25112774 2e-05 42_[+2]_70 chr3R:27272843-27272963 3e-05 28_[+2]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAKAAA width=8 seqs=6 chr2R:11410861-11410981 ( 106) AAAAGAAA 1 chr2R:20273182-20273302 ( 26) AAAAGAAA 1 chr4:198882-199002 ( 73) AAAAGAAA 1 chr3L:3417680-3417800 ( 5) AAAATAAA 1 chr3R:25112654-25112774 ( 43) AAAATAAA 1 chr3R:27272843-27272963 ( 29) AAATGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7232 bayes= 11.3342 E= 5.6e+002 209 -923 -923 -923 209 -923 -923 -923 209 -923 -923 -923 183 -923 -923 -69 -923 -923 145 31 209 -923 -923 -923 209 -923 -923 -923 209 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 5.6e+002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 0.666667 0.333333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-2 regular expression -------------------------------------------------------------------------------- AAAA[GT]AAA -------------------------------------------------------------------------------- Time 1.95 secs. ******************************************************************************** ******************************************************************************** MOTIF CSAAAGCA MEME-3 width = 8 sites = 9 llr = 83 E-value = 5.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1:999::a pos.-specific C 961:::a: probability G :4:11a:: matrix T :::::::: bits 2.1 * * 1.9 *** 1.7 ****** 1.5 * ****** Relative 1.3 * ****** Entropy 1.0 ******** (13.4 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCAAAGCA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:11312463-11312583 43 1.18e-05 GCTCTTAAAT CCAAAGCA TGCCTAGTTT chr3R:25112654-25112774 56 1.18e-05 ATAAAGTACT CCAAAGCA TTTTCGTTCG chr3R:16261894-16262014 60 1.18e-05 TTGAAGGTTA CCAAAGCA CATAAGTTAA chrX:16747041-16747161 70 2.33e-05 TAATCCGCAA CGAAAGCA ACCAATTCAC chr2R:22556244-22556364 55 2.33e-05 GTTCAAGGAT CGAAAGCA AAGCATGCAG chr3L:2534132-2534252 74 3.42e-05 TTCAGCACAC ACAAAGCA CAACACACAC chr2L:11797171-11797291 19 5.89e-05 GCGGCACGTG CCAGAGCA CTTGGGTCAC chr2L:2194741-2194861 34 1.06e-04 ATGGGGGCGG CGAAGGCA AGACTTTGGA chr2L:21103265-21103385 89 1.18e-04 GCTCCTAAAC CGCAAGCA CACGGTTGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:11312463-11312583 1.2e-05 42_[+3]_70 chr3R:25112654-25112774 1.2e-05 55_[+3]_57 chr3R:16261894-16262014 1.2e-05 59_[+3]_53 chrX:16747041-16747161 2.3e-05 69_[+3]_43 chr2R:22556244-22556364 2.3e-05 54_[+3]_58 chr3L:2534132-2534252 3.4e-05 73_[+3]_39 chr2L:11797171-11797291 5.9e-05 18_[+3]_94 chr2L:2194741-2194861 0.00011 33_[+3]_79 chr2L:21103265-21103385 0.00012 88_[+3]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CSAAAGCA width=8 seqs=9 chr3R:11312463-11312583 ( 43) CCAAAGCA 1 chr3R:25112654-25112774 ( 56) CCAAAGCA 1 chr3R:16261894-16262014 ( 60) CCAAAGCA 1 chrX:16747041-16747161 ( 70) CGAAAGCA 1 chr2R:22556244-22556364 ( 55) CGAAAGCA 1 chr3L:2534132-2534252 ( 74) ACAAAGCA 1 chr2L:11797171-11797291 ( 19) CCAGAGCA 1 chr2L:2194741-2194861 ( 34) CGAAGGCA 1 chr2L:21103265-21103385 ( 89) CGCAAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7232 bayes= 10.4973 E= 5.2e+003 -107 181 -982 -982 -982 113 86 -982 192 -119 -982 -982 192 -982 -113 -982 192 -982 -113 -982 -982 -982 203 -982 -982 198 -982 -982 209 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 5.2e+003 0.111111 0.888889 0.000000 0.000000 0.000000 0.555556 0.444444 0.000000 0.888889 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSAAAGCA MEME-3 regular expression -------------------------------------------------------------------------------- C[CG]AAAGCA -------------------------------------------------------------------------------- Time 2.81 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGGCGG MEME-4 width = 8 sites = 4 llr = 43 E-value = 7.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:::3: pos.-specific C :::::a:: probability G aa:aa:8a matrix T :::::::: bits 2.1 ***** * 1.9 ****** * 1.7 ****** * 1.5 ****** * Relative 1.3 ******** Entropy 1.0 ******** (15.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GGAGGCGG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:16747041-16747161 105 1.25e-05 ATTGAAATGG GGAGGCGG CAGGTTAA chr3R:27272843-27272963 51 1.25e-05 CAGCCGCGGA GGAGGCGG AAACCAGGAT chr2L:19581155-19581275 92 1.25e-05 GGGACGCAAT GGAGGCGG AAACGGATAT chr2L:557888-558008 85 2.45e-05 CTGGACAATG GGAGGCAG TGATCCGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:16747041-16747161 1.2e-05 104_[+4]_8 chr3R:27272843-27272963 1.2e-05 50_[+4]_62 chr2L:19581155-19581275 1.2e-05 91_[+4]_21 chr2L:557888-558008 2.4e-05 84_[+4]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGGCGG width=8 seqs=4 chrX:16747041-16747161 ( 105) GGAGGCGG 1 chr3R:27272843-27272963 ( 51) GGAGGCGG 1 chr2L:19581155-19581275 ( 92) GGAGGCGG 1 chr2L:557888-558008 ( 85) GGAGGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7232 bayes= 10.8194 E= 7.4e+004 -865 -865 203 -865 -865 -865 203 -865 209 -865 -865 -865 -865 -865 203 -865 -865 -865 203 -865 -865 198 -865 -865 9 -865 162 -865 -865 -865 203 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 7.4e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCGG MEME-4 regular expression -------------------------------------------------------------------------------- GGAGGC[GA]G -------------------------------------------------------------------------------- Time 3.63 secs. ******************************************************************************** ******************************************************************************** MOTIF CAACAAGA MEME-5 width = 8 sites = 2 llr = 23 E-value = 2.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :aa:aa:a pos.-specific C a::a:::: probability G ::::::a: matrix T :::::::: bits 2.1 ** **** 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.0 ******** (16.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CAACAAGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:9011382-9011502 49 1.10e-05 TGAATTGGGC CAACAAGA ATGACTCGCC chr2L:13391149-13391269 43 1.10e-05 GGGACTATCC CAACAAGA CCGATTTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:9011382-9011502 1.1e-05 48_[+5]_64 chr2L:13391149-13391269 1.1e-05 42_[+5]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAACAAGA width=8 seqs=2 chr3R:9011382-9011502 ( 49) CAACAAGA 1 chr2L:13391149-13391269 ( 43) CAACAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7232 bayes= 10.9715 E= 2.1e+004 -765 198 -765 -765 209 -765 -765 -765 209 -765 -765 -765 -765 198 -765 -765 209 -765 -765 -765 209 -765 -765 -765 -765 -765 203 -765 209 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.1e+004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAACAAGA MEME-5 regular expression -------------------------------------------------------------------------------- CAACAAGA -------------------------------------------------------------------------------- Time 4.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:5891411-5891531 9.99e-01 120 chr2L:1168123-1168243 6.34e-01 120 chr2R:22887856-22887976 6.10e-01 120 chr2L:13391149-13391269 5.82e-03 42_[+5(1.10e-05)]_70 chr3R:29802159-29802279 8.89e-01 120 chr3R:9011382-9011502 8.60e-03 48_[+5(1.10e-05)]_64 chr3R:23320402-23320522 3.47e-02 120 chr2R:18137002-18137122 8.32e-01 120 chrX:624107-624227 1.98e-01 120 chr3R:14660018-14660138 6.36e-01 120 chr3R:13388137-13388257 1.57e-02 120 chr2R:5759411-5759531 2.18e-01 120 chr2R:22800867-22800987 5.65e-01 120 chr2R:22556244-22556364 2.99e-03 54_[+3(2.33e-05)]_58 chr3R:23330678-23330798 6.86e-02 120 chr3R:23310890-23311010 7.57e-01 120 chr2R:20329903-20330023 2.49e-01 120 chr3L:3213410-3213530 6.93e-01 120 chr2R:15523883-15524003 6.55e-01 120 chr2L:19127867-19127987 3.29e-01 120 chr3R:5633892-5634012 3.48e-02 120 chr2L:557888-558008 4.48e-02 84_[+4(2.45e-05)]_28 chr2R:17671938-17672058 3.42e-01 120 chr2L:21103265-21103385 3.68e-02 120 chr4:198882-199002 1.25e-03 43_[+1(3.38e-05)]_21_[+2(9.37e-06)]_\ 40 chr3R:22028322-22028442 4.03e-01 120 chrX:14910630-14910750 1.53e-01 42_[+1(1.57e-05)]_70 chr3R:16261894-16262014 1.74e-03 59_[+3(1.18e-05)]_39_[+1(3.38e-05)]_\ 6 chr3R:24198306-24198426 2.48e-01 120 chr3R:23327856-23327976 1.06e-01 120 chrX:3084523-3084643 1.77e-01 120 chr2R:17848349-17848469 9.87e-01 120 chr2R:18276694-18276814 2.45e-01 120 chr3L:3403305-3403425 3.50e-01 120 chr3L:2571522-2571642 9.90e-02 16_[+1(3.38e-05)]_96 chr2R:20273182-20273302 1.09e-02 25_[+2(9.37e-06)]_87 chr2R:6669279-6669399 1.13e-01 120 chrX:11081956-11082076 8.02e-01 120 chr2L:11797171-11797291 1.76e-03 18_[+3(5.89e-05)]_39_[+1(3.38e-05)]_\ 31_[+1(3.38e-05)]_8 chr3R:25112654-25112774 3.96e-04 42_[+2(1.97e-05)]_5_[+3(1.18e-05)]_\ 57 chr2L:19581155-19581275 1.29e-02 91_[+4(1.25e-05)]_21 chrX:5694761-5694881 7.48e-01 120 chr2L:11123290-11123410 3.75e-01 120 chr3L:2567232-2567352 5.41e-02 120 chr3R:27272843-27272963 1.73e-04 28_[+2(3.05e-05)]_14_[+4(1.25e-05)]_\ 62 chr3L:2534132-2534252 2.08e-03 73_[+3(3.42e-05)]_39 chr2L:2194741-2194861 6.99e-02 120 chr2R:5350447-5350567 8.43e-02 120 chr3L:3417680-3417800 5.22e-02 4_[+2(1.97e-05)]_108 chr2R:11410861-11410981 3.71e-02 105_[+2(9.37e-06)]_7 chr3R:23332249-23332369 1.85e-01 52_[+1(3.38e-05)]_60 chr3R:25678810-25678930 9.78e-01 120 chr2L:19134123-19134243 1.64e-01 120 chr3R:23257841-23257961 5.53e-02 120 chr2R:19373200-19373320 1.68e-01 120 chr3R:3750289-3750409 8.59e-01 120 chrX:16747041-16747161 1.65e-04 69_[+3(2.33e-05)]_27_[+4(1.25e-05)]_\ 8 chr2L:13513089-13513209 1.57e-01 51_[+1(3.38e-05)]_16_[+1(3.38e-05)]_\ 37 chrX:2121765-2121885 3.48e-02 120 chr2L:1117123-1117243 2.61e-01 120 chr3L:3159961-3160081 7.62e-01 120 chr2L:22247826-22247946 3.59e-01 120 chr3R:11312463-11312583 1.09e-01 42_[+3(1.18e-05)]_70 chr3R:30056236-30056356 1.68e-01 30_[+1(6.49e-05)]_82 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n06.farnam.hpc.yale.internal ********************************************************************************