******************************************************************************** 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/peb-1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrX:2210323-2210403 1.0000 80 chrX:2214601-2214681 1.0000 80 chrX:2212300-2212380 1.0000 80 chrX:2208761-2208841 1.0000 80 chrX:2215925-2216005 1.0000 80 chrV:12736362-12736442 1.0000 80 chrX:2219133-2219213 1.0000 80 chrX:2216802-2216882 1.0000 80 chrII:15203867-15203947 1.0000 80 chrI:527513-527593 1.0000 80 chrX:10194585-10194665 1.0000 80 chrII:7405444-7405524 1.0000 80 chrII:7406582-7406662 1.0000 80 chrIII:13779775-13779855 1.0000 80 chrV:6354438-6354518 1.0000 80 chrII:11200484-11200564 1.0000 80 chrV:13413481-13413561 1.0000 80 chrX:2215235-2215315 1.0000 80 chrX:11474332-11474412 1.0000 80 chrII:12965779-12965859 1.0000 80 chrII:9285084-9285164 1.0000 80 chrIV:10817210-10817290 1.0000 80 chrII:1238046-1238126 1.0000 80 chrIV:1371471-1371551 1.0000 80 chrII:2455041-2455121 1.0000 80 chrV:13414810-13414890 1.0000 80 chrI:6958827-6958907 1.0000 80 chrV:9287693-9287773 1.0000 80 chrII:66469-66549 1.0000 80 chrIV:1221184-1221264 1.0000 80 chrX:4905586-4905666 1.0000 80 chrX:12655422-12655502 1.0000 80 chrV:8653804-8653884 1.0000 80 chrV:6970173-6970253 1.0000 80 chrX:16157046-16157126 1.0000 80 chrX:9637415-9637495 1.0000 80 chrI:1000967-1001047 1.0000 80 chrX:11798189-11798269 1.0000 80 chrIV:10175318-10175398 1.0000 80 chrX:11465346-11465426 1.0000 80 chrIV:3636550-3636630 1.0000 80 chrII:7623667-7623747 1.0000 80 chrV:14366748-14366828 1.0000 80 chrIII:8132560-8132640 1.0000 80 chrIII:4552113-4552193 1.0000 80 chrX:10395746-10395826 1.0000 80 chrIV:8302085-8302165 1.0000 80 chrX:5480336-5480416 1.0000 80 chrI:9087335-9087415 1.0000 80 chrI:10409442-10409522 1.0000 80 chrII:5901815-5901895 1.0000 80 chrIV:4454890-4454970 1.0000 80 chrX:4971618-4971698 1.0000 80 chrI:10769948-10770028 1.0000 80 chrX:11299761-11299841 1.0000 80 chrI:1251648-1251728 1.0000 80 chrX:14297288-14297368 1.0000 80 chrI:6173111-6173191 1.0000 80 chrX:12656714-12656794 1.0000 80 chrV:10036456-10036536 1.0000 80 chrX:10372617-10372697 1.0000 80 chrIII:623893-623973 1.0000 80 chrV:4651801-4651881 1.0000 80 chrIV:8782370-8782450 1.0000 80 chrX:5812096-5812176 1.0000 80 chrV:10717231-10717311 1.0000 80 chrV:7978971-7979051 1.0000 80 chrX:5475291-5475371 1.0000 80 chrX:5686308-5686388 1.0000 80 chrI:13065859-13065939 1.0000 80 chrV:15661084-15661164 1.0000 80 chrIII:12178287-12178367 1.0000 80 chrX:9999850-9999930 1.0000 80 chrV:12529016-12529096 1.0000 80 chrII:11620092-11620172 1.0000 80 chrIV:14824887-14824967 1.0000 80 chrI:14320501-14320581 1.0000 80 chrII:10502922-10503002 1.0000 80 chrIV:11027800-11027880 1.0000 80 chrII:8751161-8751241 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_peb-1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/peb-1.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= 80 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= 6400 N= 80 sample: seed= 0 hsfrac= 0 searchsize= 6400 norand= no csites= 1000 Letter frequencies in dataset: A 0.243 C 0.247 G 0.267 T 0.242 Background letter frequencies (from file dataset with add-one prior applied): A 0.243 C 0.247 G 0.267 T 0.243 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GAAARAGA MEME-1 width = 8 sites = 40 llr = 279 E-value = 2.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 395a47:a pos.-specific C ::3:1::: probability G 722:5:9: matrix T 1::::31: bits 2.0 * * 1.8 * * 1.6 * * 1.4 * * ** Relative 1.2 * * *** Entropy 1.0 * * *** (10.1 bits) 0.8 ** * *** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAAGAGA consensus A C AT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:7978971-7979051 33 1.61e-05 GAGATAGAGA GAAAGAGA ACGAAGGACG chrV:10717231-10717311 41 1.61e-05 ACGGCAGATG GAAAGAGA AGAAGATTTC chrIII:8132560-8132640 30 1.61e-05 AGTGAACGCG GAAAGAGA GTAATTAGAA chrI:6958827-6958907 27 1.61e-05 TCAATCCGGA GAAAGAGA GGGCGCAAAA chrV:13414810-13414890 27 1.61e-05 GAGGTGAAGA GAAAGAGA GAAACACTTT chrX:10372617-10372697 69 3.08e-05 GGTGAGATTA GAAAAAGA GATT chrII:8751161-8751241 3 6.33e-05 ag gaaagtga aaACAATTAG chrII:7405444-7405524 40 6.33e-05 ATTGAAACCG GAAAGTGA AATCGTTGCC chrIV:11027800-11027880 51 1.11e-04 GAGCAATGTA GACAAAGA TACGCAGAGA chrI:14320501-14320581 66 1.11e-04 gagagggaga gagagaga gagaTGC chrIII:623893-623973 52 1.11e-04 CGAAGTACGA GAGAGAGA CGCAGAGAGT chrIV:3636550-3636630 72 1.11e-04 gaggcgcaga gacaaaga c chrII:1238046-1238126 64 1.11e-04 TGGGACGGGA GAGAGAGA GGGGGGCGA chrX:10194585-10194665 22 1.11e-04 AGGTGGCAAG GACAAAGA GTGCGCGACG chrII:10502922-10503002 21 1.55e-04 AAAAATGGAA GAGAAAGA GCGCTCGTTT chrX:4971618-4971698 65 1.55e-04 CTGGTAAAGA GAGAAAGA CTGCGGCG chrX:12656714-12656794 58 2.01e-04 TCAGAGGCTG AACAGAGA AGGGAGCGAG chrI:10769948-10770028 56 2.48e-04 CTCTCGAACA AAAAGTGA ACGTGGTGTT chrII:11620092-11620172 55 2.96e-04 CACAGACAGT AAGAGAGA TAGAAATGAA chrX:5686308-5686388 27 2.96e-04 CACTATGGGC AAGAGAGA AGATAAAATG chrV:12736362-12736442 72 3.25e-04 TACAAGATGG AAAAATGA A chrIV:1221184-1221264 39 3.56e-04 TGGTGAATAG GGAAAAGA TGAAGGGCAT chrIII:12178287-12178367 58 3.71e-04 CCCCCAAGTG GACACAGA AAGAGCGATG chrII:7406582-7406662 70 4.01e-04 AGGGAGAAGC TAAAGAGA CAT chrI:527513-527593 14 4.01e-04 TGCCGAGGCA GAAACTGA GGACCGATCT chrIV:14824887-14824967 68 4.31e-04 AGACGGGGGA GAGACAGA ATCTG chrX:4905586-4905666 63 4.31e-04 CCGAGGGATT GAGACAGA GGCCAAGAGC chrI:6173111-6173191 68 4.59e-04 TGGCGATATT TAAAAAGA AGAAG chrX:9637415-9637495 41 4.59e-04 ATGCGGAAAA AACAGTGA GACACTTGAG chrII:9285084-9285164 67 4.59e-04 TGTTTATATA AACAGTGA GAGCTA chrV:13413481-13413561 51 4.92e-04 CAATCATTTC GAAAGATA TGAAGAGAAA chrII:15203867-15203947 55 4.92e-04 ACCAAAAGGT GGCAGAGA CGTGTGCTCC chrX:14297288-14297368 68 6.05e-04 GGGGAGAGCT GGCAAAGA GGCGA chrX:11299761-11299841 56 6.05e-04 GCCGGCGCTg agaagaga gcataggaaa chrI:9087335-9087415 33 6.05e-04 TTTCCGCGCG GAAAAATA GTGGAATACG chrX:2219133-2219213 49 6.98e-04 TCTGGCGCAA GACACTGA CAGTCGCCGC chrX:9999850-9999930 32 8.46e-04 CCACAATCAA TAAAATGA CAGCGGGCAT chrIII:13779775-13779855 23 1.02e-03 gagacctctc gaaaatta gtatggcact chrX:10395746-10395826 60 1.14e-03 TGATTGTCGC AGAAATGA GGCAAACGAG chrII:12965779-12965859 70 1.14e-03 TGGCGGCGGC AGAAATGA TGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:7978971-7979051 1.6e-05 32_[+1]_40 chrV:10717231-10717311 1.6e-05 40_[+1]_32 chrIII:8132560-8132640 1.6e-05 29_[+1]_43 chrI:6958827-6958907 1.6e-05 26_[+1]_46 chrV:13414810-13414890 1.6e-05 26_[+1]_46 chrX:10372617-10372697 3.1e-05 68_[+1]_4 chrII:8751161-8751241 6.3e-05 2_[+1]_70 chrII:7405444-7405524 6.3e-05 39_[+1]_33 chrIV:11027800-11027880 0.00011 50_[+1]_22 chrI:14320501-14320581 0.00011 65_[+1]_7 chrIII:623893-623973 0.00011 51_[+1]_21 chrIV:3636550-3636630 0.00011 71_[+1]_1 chrII:1238046-1238126 0.00011 63_[+1]_9 chrX:10194585-10194665 0.00011 21_[+1]_51 chrII:10502922-10503002 0.00015 20_[+1]_52 chrX:4971618-4971698 0.00015 64_[+1]_8 chrX:12656714-12656794 0.0002 57_[+1]_15 chrI:10769948-10770028 0.00025 55_[+1]_17 chrII:11620092-11620172 0.0003 54_[+1]_18 chrX:5686308-5686388 0.0003 26_[+1]_46 chrV:12736362-12736442 0.00033 71_[+1]_1 chrIV:1221184-1221264 0.00036 38_[+1]_34 chrIII:12178287-12178367 0.00037 57_[+1]_15 chrII:7406582-7406662 0.0004 69_[+1]_3 chrI:527513-527593 0.0004 13_[+1]_59 chrIV:14824887-14824967 0.00043 67_[+1]_5 chrX:4905586-4905666 0.00043 62_[+1]_10 chrI:6173111-6173191 0.00046 67_[+1]_5 chrX:9637415-9637495 0.00046 40_[+1]_32 chrII:9285084-9285164 0.00046 66_[+1]_6 chrV:13413481-13413561 0.00049 50_[+1]_22 chrII:15203867-15203947 0.00049 54_[+1]_18 chrX:14297288-14297368 0.0006 67_[+1]_5 chrX:11299761-11299841 0.0006 55_[+1]_17 chrI:9087335-9087415 0.0006 32_[+1]_40 chrX:2219133-2219213 0.0007 48_[+1]_24 chrX:9999850-9999930 0.00085 31_[+1]_41 chrIII:13779775-13779855 0.001 22_[+1]_50 chrX:10395746-10395826 0.0011 59_[+1]_13 chrII:12965779-12965859 0.0011 69_[+1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAAARAGA width=8 seqs=40 chrV:7978971-7979051 ( 33) GAAAGAGA 1 chrV:10717231-10717311 ( 41) GAAAGAGA 1 chrIII:8132560-8132640 ( 30) GAAAGAGA 1 chrI:6958827-6958907 ( 27) GAAAGAGA 1 chrV:13414810-13414890 ( 27) GAAAGAGA 1 chrX:10372617-10372697 ( 69) GAAAAAGA 1 chrII:8751161-8751241 ( 3) GAAAGTGA 1 chrII:7405444-7405524 ( 40) GAAAGTGA 1 chrIV:11027800-11027880 ( 51) GACAAAGA 1 chrI:14320501-14320581 ( 66) GAGAGAGA 1 chrIII:623893-623973 ( 52) GAGAGAGA 1 chrIV:3636550-3636630 ( 72) GACAAAGA 1 chrII:1238046-1238126 ( 64) GAGAGAGA 1 chrX:10194585-10194665 ( 22) GACAAAGA 1 chrII:10502922-10503002 ( 21) GAGAAAGA 1 chrX:4971618-4971698 ( 65) GAGAAAGA 1 chrX:12656714-12656794 ( 58) AACAGAGA 1 chrI:10769948-10770028 ( 56) AAAAGTGA 1 chrII:11620092-11620172 ( 55) AAGAGAGA 1 chrX:5686308-5686388 ( 27) AAGAGAGA 1 chrV:12736362-12736442 ( 72) AAAAATGA 1 chrIV:1221184-1221264 ( 39) GGAAAAGA 1 chrIII:12178287-12178367 ( 58) GACACAGA 1 chrII:7406582-7406662 ( 70) TAAAGAGA 1 chrI:527513-527593 ( 14) GAAACTGA 1 chrIV:14824887-14824967 ( 68) GAGACAGA 1 chrX:4905586-4905666 ( 63) GAGACAGA 1 chrI:6173111-6173191 ( 68) TAAAAAGA 1 chrX:9637415-9637495 ( 41) AACAGTGA 1 chrII:9285084-9285164 ( 67) AACAGTGA 1 chrV:13413481-13413561 ( 51) GAAAGATA 1 chrII:15203867-15203947 ( 55) GGCAGAGA 1 chrX:14297288-14297368 ( 68) GGCAAAGA 1 chrX:11299761-11299841 ( 56) AGAAGAGA 1 chrI:9087335-9087415 ( 33) GAAAAATA 1 chrX:2219133-2219213 ( 49) GACACTGA 1 chrX:9999850-9999930 ( 32) TAAAATGA 1 chrIII:13779775-13779855 ( 23) GAAAATTA 1 chrX:10395746-10395826 ( 60) AGAAATGA 1 chrII:12965779-12965859 ( 70) AGAAATGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 8.12809 E= 2.5e-006 4 -1197 134 -169 180 -1197 -83 -1197 111 2 -25 -1197 204 -1197 -1197 -1197 62 -98 91 -1197 152 -1197 -1197 31 -1197 -1197 179 -169 204 -1197 -1197 -1197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.5e-006 0.250000 0.000000 0.675000 0.075000 0.850000 0.000000 0.150000 0.000000 0.525000 0.250000 0.225000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.125000 0.500000 0.000000 0.700000 0.000000 0.000000 0.300000 0.000000 0.000000 0.925000 0.075000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAARAGA MEME-1 regular expression -------------------------------------------------------------------------------- [GA]A[ACG]A[GA][AT]GA -------------------------------------------------------------------------------- Time 1.83 secs. ******************************************************************************** ******************************************************************************** MOTIF CTYTTTCT MEME-2 width = 8 sites = 23 llr = 187 E-value = 5.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::1:: pos.-specific C 934:2:a1 probability G :::::::: matrix T 176a89:9 bits 2.0 * 1.8 * * 1.6 * ** 1.4 * * *** Relative 1.2 ** ***** Entropy 1.0 ******** (11.7 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTTTTTCT consensus CC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:12529016-12529096 26 1.26e-05 GGCATACTCT CTTTTTCT GTTTTTCTAT chrI:6173111-6173191 2 1.26e-05 T CTTTTTCT ACTCATTCCT chrX:11798189-11798269 6 1.26e-05 CACGT CTTTTTCT ACTTCGTGTC chrX:2208761-2208841 27 1.26e-05 ATTTGATCGT CTTTTTCT TTGCATTGAA chrI:13065859-13065939 61 2.53e-05 CTCTTTCTCT CTCTTTCT GTTGCGCCAC chrIII:4552113-4552193 1 2.53e-05 . CTCTTTCT GTGTCTGTCT chrII:66469-66549 43 2.53e-05 TCGGTCTACA CTCTTTCT ACGTTATATT chrV:9287693-9287773 18 2.53e-05 TTCAACTCTC CTCTTTCT GGAGAGGGCT chrI:10409442-10409522 2 5.11e-05 C CCCTTTCT GTCGGCGTTT chrII:1238046-1238126 19 5.11e-05 ACTGCCGGTG CCCTTTCT CCCGCTGTCG chrX:2214601-2214681 30 5.11e-05 TTTGGAGACC CCCTTTCT GGTGCCTATT chrX:9999850-9999930 4 8.92e-05 ttc ttttttct tttttttcCG chrII:11200484-11200564 16 8.92e-05 ATCGTTCTCC CTCTCTCT TCAATTTGCC chrX:12656714-12656794 34 1.02e-04 CTCCCCTTCA CCTTCTCT CTATCATCAG chrV:14366748-14366828 46 1.02e-04 GGCGCGCGCG CCTTCTCT CCGTGCCGCC chrIII:13779775-13779855 73 1.27e-04 aatagtcttg cttttact chrX:10395746-10395826 17 1.66e-04 TTCTTCTCCC TCTTTTCT CTCATTCAAA chrII:9285084-9285164 36 1.92e-04 TCGCCGACGT CTCTTTCC GCCGCAGACA chrIV:4454890-4454970 48 2.04e-04 TTCTCTGCAT CTTTTCCT TGCCTGTCTG chrIV:1371471-1371551 12 2.43e-04 CTCTCCCATG CTTCTTCT TCTAGATGAC chrX:5812096-5812176 14 2.68e-04 GACCACCCTG TTTTCTCT GCCGCACGGC chrV:13414810-13414890 73 2.68e-04 TATCAATTGT CCTTTTCC chrX:2219133-2219213 73 3.46e-04 CCGCCATCCA CTTTCACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:12529016-12529096 1.3e-05 25_[+2]_47 chrI:6173111-6173191 1.3e-05 1_[+2]_71 chrX:11798189-11798269 1.3e-05 5_[+2]_67 chrX:2208761-2208841 1.3e-05 26_[+2]_46 chrI:13065859-13065939 2.5e-05 60_[+2]_12 chrIII:4552113-4552193 2.5e-05 [+2]_72 chrII:66469-66549 2.5e-05 42_[+2]_30 chrV:9287693-9287773 2.5e-05 17_[+2]_55 chrI:10409442-10409522 5.1e-05 1_[+2]_71 chrII:1238046-1238126 5.1e-05 18_[+2]_54 chrX:2214601-2214681 5.1e-05 29_[+2]_43 chrX:9999850-9999930 8.9e-05 3_[+2]_69 chrII:11200484-11200564 8.9e-05 15_[+2]_57 chrX:12656714-12656794 0.0001 33_[+2]_39 chrV:14366748-14366828 0.0001 45_[+2]_27 chrIII:13779775-13779855 0.00013 72_[+2] chrX:10395746-10395826 0.00017 16_[+2]_56 chrII:9285084-9285164 0.00019 35_[+2]_37 chrIV:4454890-4454970 0.0002 47_[+2]_25 chrIV:1371471-1371551 0.00024 11_[+2]_61 chrX:5812096-5812176 0.00027 13_[+2]_59 chrV:13414810-13414890 0.00027 72_[+2] chrX:2219133-2219213 0.00035 72_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTYTTTCT width=8 seqs=23 chrV:12529016-12529096 ( 26) CTTTTTCT 1 chrI:6173111-6173191 ( 2) CTTTTTCT 1 chrX:11798189-11798269 ( 6) CTTTTTCT 1 chrX:2208761-2208841 ( 27) CTTTTTCT 1 chrI:13065859-13065939 ( 61) CTCTTTCT 1 chrIII:4552113-4552193 ( 1) CTCTTTCT 1 chrII:66469-66549 ( 43) CTCTTTCT 1 chrV:9287693-9287773 ( 18) CTCTTTCT 1 chrI:10409442-10409522 ( 2) CCCTTTCT 1 chrII:1238046-1238126 ( 19) CCCTTTCT 1 chrX:2214601-2214681 ( 30) CCCTTTCT 1 chrX:9999850-9999930 ( 4) TTTTTTCT 1 chrII:11200484-11200564 ( 16) CTCTCTCT 1 chrX:12656714-12656794 ( 34) CCTTCTCT 1 chrV:14366748-14366828 ( 46) CCTTCTCT 1 chrIII:13779775-13779855 ( 73) CTTTTACT 1 chrX:10395746-10395826 ( 17) TCTTTTCT 1 chrII:9285084-9285164 ( 36) CTCTTTCC 1 chrIV:4454890-4454970 ( 48) CTTTTCCT 1 chrIV:1371471-1371551 ( 12) CTTCTTCT 1 chrX:5812096-5812176 ( 14) TTTTCTCT 1 chrV:13414810-13414890 ( 73) CCTTTTCC 1 chrX:2219133-2219213 ( 73) CTTTCACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 9.87795 E= 5.6e-004 -1117 181 -1117 -89 -1117 30 -1117 152 -1117 66 -1117 133 -1117 -251 -1117 198 -1117 -19 -1117 169 -148 -251 -1117 184 -1117 201 -1117 -1117 -1117 -151 -1117 191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 5.6e-004 0.000000 0.869565 0.000000 0.130435 0.000000 0.304348 0.000000 0.695652 0.000000 0.391304 0.000000 0.608696 0.000000 0.043478 0.000000 0.956522 0.000000 0.217391 0.000000 0.782609 0.086957 0.043478 0.000000 0.869565 0.000000 1.000000 0.000000 0.000000 0.000000 0.086957 0.000000 0.913043 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTTTCT MEME-2 regular expression -------------------------------------------------------------------------------- C[TC][TC]T[TC]TCT -------------------------------------------------------------------------------- Time 2.63 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGCRG MEME-3 width = 8 sites = 19 llr = 151 E-value = 3.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :1:1::4: pos.-specific C 3:9::a2: probability G 7919a:3a matrix T ::::::1: bits 2.0 * 1.8 ** * 1.6 ** * 1.4 ***** * Relative 1.2 ***** * Entropy 1.0 ****** * (11.4 bits) 0.8 ****** * 0.6 ****** * 0.4 ****** * 0.2 ******** 0.0 -------- Multilevel GGCGGCAG consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:4971618-4971698 39 2.01e-05 GGAGGGCGGA GGCGGCAG ACAATGGCCT chrV:8653804-8653884 23 2.01e-05 CTACAGCGGT GGCGGCAG CGGATCAAAA chrIII:623893-623973 9 4.22e-05 CCGATGCC GGCGGCGG GCGTGTGACA chrI:1251648-1251728 73 4.22e-05 TTTCCAACCC GGCGGCGG chrII:2455041-2455121 3 4.22e-05 CC GGCGGCGG GCCGACACAG chrII:12965779-12965859 61 4.22e-05 AGCGCTCTGT GGCGGCGG CAGAAATGAT chrIV:3636550-3636630 4 6.08e-05 CCG CGCGGCAG AGAGGCACGA chrX:2216802-2216882 61 6.08e-05 ATGGCAGGCA CGCGGCAG CGCGCGCGGG chrV:4651801-4651881 59 8.13e-05 TCGCGGCAAC GGCGGCCG AGCGAGTTTT chrI:14320501-14320581 47 1.02e-04 TGCTAAACGG CGCGGCGg agagagggag chrV:14366748-14366828 25 1.22e-04 TGGCACAGGA GGCGGCTG AGGGGCGCGC chrIV:8302085-8302165 65 1.41e-04 CTTCGCGCCC CGCGGCCG AAAACCAG chrV:10717231-10717311 30 1.77e-04 CACTTCTGCA GACGGCAG ATGGAAAGAG chrX:11299761-11299841 16 1.77e-04 CTCCCTCCCT GGCAGCAG GTCGGGTCTC chrII:1238046-1238126 41 1.96e-04 CTGTCGCTGC CGCGGCTG GCACTTGGGA chrV:10036456-10036536 64 2.18e-04 CAAAACCCGT GGGGGCAG CCCCGCAAA chrV:12736362-12736442 21 2.18e-04 TCAGTACCTG GGGGGCAG TAACTAGGTA chrX:2215235-2215315 40 3.73e-04 TGTCTTAGTT GGCAGCCG GTTGGTGCCT chrX:5812096-5812176 26 4.10e-04 TTCTCTGCCG CACGGCGG AGCTAGCCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:4971618-4971698 2e-05 38_[+3]_34 chrV:8653804-8653884 2e-05 22_[+3]_50 chrIII:623893-623973 4.2e-05 8_[+3]_64 chrI:1251648-1251728 4.2e-05 72_[+3] chrII:2455041-2455121 4.2e-05 2_[+3]_70 chrII:12965779-12965859 4.2e-05 60_[+3]_12 chrIV:3636550-3636630 6.1e-05 3_[+3]_69 chrX:2216802-2216882 6.1e-05 60_[+3]_12 chrV:4651801-4651881 8.1e-05 58_[+3]_14 chrI:14320501-14320581 0.0001 46_[+3]_26 chrV:14366748-14366828 0.00012 24_[+3]_48 chrIV:8302085-8302165 0.00014 64_[+3]_8 chrV:10717231-10717311 0.00018 29_[+3]_43 chrX:11299761-11299841 0.00018 15_[+3]_57 chrII:1238046-1238126 0.0002 40_[+3]_32 chrV:10036456-10036536 0.00022 63_[+3]_9 chrV:12736362-12736442 0.00022 20_[+3]_52 chrX:2215235-2215315 0.00037 39_[+3]_33 chrX:5812096-5812176 0.00041 25_[+3]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGGCRG width=8 seqs=19 chrX:4971618-4971698 ( 39) GGCGGCAG 1 chrV:8653804-8653884 ( 23) GGCGGCAG 1 chrIII:623893-623973 ( 9) GGCGGCGG 1 chrI:1251648-1251728 ( 73) GGCGGCGG 1 chrII:2455041-2455121 ( 3) GGCGGCGG 1 chrII:12965779-12965859 ( 61) GGCGGCGG 1 chrIV:3636550-3636630 ( 4) CGCGGCAG 1 chrX:2216802-2216882 ( 61) CGCGGCAG 1 chrV:4651801-4651881 ( 59) GGCGGCCG 1 chrI:14320501-14320581 ( 47) CGCGGCGG 1 chrV:14366748-14366828 ( 25) GGCGGCTG 1 chrIV:8302085-8302165 ( 65) CGCGGCCG 1 chrV:10717231-10717311 ( 30) GACGGCAG 1 chrX:11299761-11299841 ( 16) GGCAGCAG 1 chrII:1238046-1238126 ( 41) CGCGGCTG 1 chrV:10036456-10036536 ( 64) GGGGGCAG 1 chrV:12736362-12736442 ( 21) GGGGGCAG 1 chrX:2215235-2215315 ( 40) GGCAGCCG 1 chrX:5812096-5812176 ( 26) CACGGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 8.45453 E= 3.2e+002 -1089 35 136 -1089 -121 -1089 175 -1089 -1089 185 -134 -1089 -121 -1089 175 -1089 -1089 -1089 191 -1089 -1089 201 -1089 -1089 79 -65 24 -120 -1089 -1089 191 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.2e+002 0.000000 0.315789 0.684211 0.000000 0.105263 0.000000 0.894737 0.000000 0.000000 0.894737 0.105263 0.000000 0.105263 0.000000 0.894737 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.421053 0.157895 0.315789 0.105263 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-3 regular expression -------------------------------------------------------------------------------- [GC]GCGGC[AG]G -------------------------------------------------------------------------------- Time 3.40 secs. ******************************************************************************** ******************************************************************************** MOTIF TCATTTTT MEME-4 width = 8 sites = 2 llr = 23 E-value = 7.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C :a:::::: probability G :::::::: matrix T a::aaaaa bits 2.0 ******** 1.8 ******** 1.6 ******** 1.4 ******** Relative 1.2 ******** Entropy 1.0 ******** (16.3 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCATTTTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:4905586-4905666 6 1.24e-05 TTGTG TCATTTTT TGAGCGCGCT chrX:2214601-2214681 61 1.24e-05 AAAACTTGCT TCATTTTT GGTCACTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:4905586-4905666 1.2e-05 5_[+4]_67 chrX:2214601-2214681 1.2e-05 60_[+4]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCATTTTT width=8 seqs=2 chrX:4905586-4905666 ( 6) TCATTTTT 1 chrX:2214601-2214681 ( 61) TCATTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 11.5113 E= 7.9e+003 -765 -765 -765 204 -765 201 -765 -765 203 -765 -765 -765 -765 -765 -765 204 -765 -765 -765 204 -765 -765 -765 204 -765 -765 -765 204 -765 -765 -765 204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.9e+003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATTTTT MEME-4 regular expression -------------------------------------------------------------------------------- TCATTTTT -------------------------------------------------------------------------------- Time 4.26 secs. ******************************************************************************** ******************************************************************************** MOTIF CGCAGAGA MEME-5 width = 8 sites = 7 llr = 70 E-value = 2.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a:a:a pos.-specific C a:7:::1: probability G :a::a:9: matrix T ::3::::: bits 2.0 * * * * 1.8 ** *** * 1.6 ** *** * 1.4 ** ***** Relative 1.2 ******** Entropy 1.0 ******** (14.4 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGCAGAGA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:11027800-11027880 61 1.67e-05 GACAAAGATA CGCAGAGA ATGCCGTTGA chrIII:623893-623973 60 1.67e-05 GAGAGAGAGA CGCAGAGA GTTCGAGCAA chrX:9637415-9637495 62 1.67e-05 ACTTGAGAGG CGCAGAGA AAACAAAACT chrII:2455041-2455121 58 1.67e-05 ACGTGAGAGA CGCAGAGA ACTCTTTGGC chrX:5686308-5686388 53 3.31e-05 TGAAGAGATG CGTAGAGA AAATTGGACT chrV:7978971-7979051 51 3.31e-05 ACGAAGGACG CGTAGAGA TAAAGGTATG chrII:9285084-9285164 46 4.85e-05 CTCTTTCCGC CGCAGACA ATTTGTTTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:11027800-11027880 1.7e-05 60_[+5]_12 chrIII:623893-623973 1.7e-05 59_[+5]_13 chrX:9637415-9637495 1.7e-05 61_[+5]_11 chrII:2455041-2455121 1.7e-05 57_[+5]_15 chrX:5686308-5686388 3.3e-05 52_[+5]_20 chrV:7978971-7979051 3.3e-05 50_[+5]_22 chrII:9285084-9285164 4.8e-05 45_[+5]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGCAGAGA width=8 seqs=7 chrIV:11027800-11027880 ( 61) CGCAGAGA 1 chrIII:623893-623973 ( 60) CGCAGAGA 1 chrX:9637415-9637495 ( 62) CGCAGAGA 1 chrII:2455041-2455121 ( 58) CGCAGAGA 1 chrX:5686308-5686388 ( 53) CGTAGAGA 1 chrV:7978971-7979051 ( 51) CGTAGAGA 1 chrII:9285084-9285164 ( 46) CGCAGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5840 bayes= 9.54635 E= 2.1e+004 -945 201 -945 -945 -945 -945 191 -945 -945 153 -945 24 204 -945 -945 -945 -945 -945 191 -945 204 -945 -945 -945 -945 -79 168 -945 204 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.1e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.000000 0.285714 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCAGAGA MEME-5 regular expression -------------------------------------------------------------------------------- CG[CT]AGAGA -------------------------------------------------------------------------------- Time 5.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:2210323-2210403 7.91e-01 80 chrX:2214601-2214681 3.13e-03 29_[+2(5.11e-05)]_23_[+4(1.24e-05)]_\ 12 chrX:2212300-2212380 1.47e-01 80 chrX:2208761-2208841 3.89e-03 26_[+2(1.26e-05)]_46 chrX:2215925-2216005 2.67e-01 80 chrV:12736362-12736442 3.25e-02 80 chrX:2219133-2219213 4.35e-02 80 chrX:2216802-2216882 4.36e-02 60_[+3(6.08e-05)]_12 chrII:15203867-15203947 4.10e-02 80 chrI:527513-527593 1.39e-01 80 chrX:10194585-10194665 8.90e-02 80 chrII:7405444-7405524 2.98e-02 39_[+1(6.33e-05)]_33 chrII:7406582-7406662 5.03e-01 80 chrIII:13779775-13779855 5.79e-02 80 chrV:6354438-6354518 4.78e-01 80 chrII:11200484-11200564 1.08e-01 15_[+2(8.92e-05)]_57 chrV:13413481-13413561 1.70e-01 80 chrX:2215235-2215315 5.58e-01 80 chrX:11474332-11474412 7.04e-01 80 chrII:12965779-12965859 1.45e-02 63_[+3(2.01e-05)]_9 chrII:9285084-9285164 5.73e-04 45_[+5(4.85e-05)]_27 chrIV:10817210-10817290 8.31e-01 80 chrII:1238046-1238126 2.21e-04 18_[+2(5.11e-05)]_54 chrIV:1371471-1371551 1.82e-01 80 chrII:2455041-2455121 1.93e-03 2_[+3(4.22e-05)]_47_[+5(1.67e-05)]_\ 15 chrV:13414810-13414890 1.46e-03 26_[+1(1.61e-05)]_46 chrI:6958827-6958907 1.05e-03 26_[+1(1.61e-05)]_46 chrV:9287693-9287773 4.44e-02 17_[+2(2.53e-05)]_55 chrII:66469-66549 4.89e-02 42_[+2(2.53e-05)]_30 chrIV:1221184-1221264 4.07e-01 80 chrX:4905586-4905666 9.75e-03 5_[+4(1.24e-05)]_67 chrX:12655422-12655502 5.54e-01 80 chrV:8653804-8653884 1.12e-01 22_[+3(2.01e-05)]_50 chrV:6970173-6970253 3.55e-01 80 chrX:16157046-16157126 3.93e-01 80 chrX:9637415-9637495 2.10e-02 61_[+5(1.67e-05)]_11 chrI:1000967-1001047 9.86e-01 80 chrX:11798189-11798269 1.78e-02 5_[+2(1.26e-05)]_67 chrIV:10175318-10175398 8.90e-01 80 chrX:11465346-11465426 3.87e-01 80 chrIV:3636550-3636630 1.91e-04 3_[+3(6.08e-05)]_54_[+5(1.67e-05)]_\ 7 chrII:7623667-7623747 6.81e-01 80 chrV:14366748-14366828 2.72e-02 80 chrIII:8132560-8132640 2.91e-02 29_[+1(1.61e-05)]_43 chrIII:4552113-4552193 7.45e-03 [+2(2.53e-05)]_72 chrX:10395746-10395826 3.46e-03 80 chrIV:8302085-8302165 2.79e-01 80 chrX:5480336-5480416 4.36e-01 80 chrI:9087335-9087415 3.92e-02 80 chrI:10409442-10409522 1.45e-01 1_[+2(5.11e-05)]_71 chrII:5901815-5901895 9.69e-01 80 chrIV:4454890-4454970 9.94e-02 80 chrX:4971618-4971698 2.40e-03 38_[+3(2.01e-05)]_34 chrI:10769948-10770028 2.91e-02 80 chrX:11299761-11299841 1.88e-03 80 chrI:1251648-1251728 6.82e-02 72_[+3(4.22e-05)] chrX:14297288-14297368 1.16e-01 80 chrI:6173111-6173191 6.26e-03 1_[+2(1.26e-05)]_71 chrX:12656714-12656794 8.63e-03 80 chrV:10036456-10036536 4.21e-01 80 chrX:10372617-10372697 1.15e-02 68_[+1(3.08e-05)]_4 chrIII:623893-623973 1.25e-04 8_[+3(4.22e-05)]_43_[+5(1.67e-05)]_\ 13 chrV:4651801-4651881 5.92e-02 58_[+3(8.13e-05)]_14 chrIV:8782370-8782450 3.20e-01 80 chrX:5812096-5812176 4.31e-02 80 chrV:10717231-10717311 1.30e-03 40_[+1(1.61e-05)]_32 chrV:7978971-7979051 4.33e-03 32_[+1(1.61e-05)]_10_[+5(3.31e-05)]_\ 22 chrX:5475291-5475371 1.00e+00 80 chrX:5686308-5686388 1.01e-02 52_[+5(3.31e-05)]_20 chrI:13065859-13065939 2.71e-02 50_[+2(2.53e-05)]_2_[+2(2.53e-05)]_\ 12 chrV:15661084-15661164 2.84e-01 80 chrIII:12178287-12178367 3.30e-01 80 chrX:9999850-9999930 1.07e-03 3_[+2(8.92e-05)]_69 chrV:12529016-12529096 6.64e-02 25_[+2(1.26e-05)]_27_[+2(6.38e-05)]_\ 12 chrII:11620092-11620172 4.51e-02 80 chrIV:14824887-14824967 5.89e-02 80 chrI:14320501-14320581 8.90e-04 51_[+5(9.80e-05)]_21 chrII:10502922-10503002 6.23e-03 80 chrIV:11027800-11027880 1.08e-03 60_[+5(1.67e-05)]_12 chrII:8751161-8751241 1.76e-01 2_[+1(6.33e-05)]_70 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n12.farnam.hpc.yale.internal ********************************************************************************