******************************************************************************** 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/alr-1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrX:11135144-11135224 1.0000 80 chrIV:5604641-5604721 1.0000 80 chrIII:6431916-6431996 1.0000 80 chrV:1154056-1154136 1.0000 80 chrX:12690502-12690582 1.0000 80 chrX:11137646-11137726 1.0000 80 chrX:11120908-11120988 1.0000 80 chrIII:3096235-3096315 1.0000 80 chrI:6579881-6579961 1.0000 80 chrV:6244860-6244940 1.0000 80 chrI:9721977-9722057 1.0000 80 chrX:10555559-10555639 1.0000 80 chrX:11129223-11129303 1.0000 80 chrX:11127375-11127455 1.0000 80 chrV:13656588-13656668 1.0000 80 chrX:5121987-5122067 1.0000 80 chrX:8378314-8378394 1.0000 80 chrII:8329068-8329148 1.0000 80 chrI:4254154-4254234 1.0000 80 chrX:7678550-7678630 1.0000 80 chrIV:7791422-7791502 1.0000 80 chrIII:4504442-4504522 1.0000 80 chrIII:4505878-4505958 1.0000 80 chrV:10274063-10274143 1.0000 80 chrV:126755-126835 1.0000 80 chrIV:5607461-5607541 1.0000 80 chrIV:8183500-8183580 1.0000 80 chrIII:8797540-8797620 1.0000 80 chrIII:5920128-5920208 1.0000 80 chrV:8359295-8359375 1.0000 80 chrIII:668466-668546 1.0000 80 chrX:6750330-6750410 1.0000 80 chrII:9603542-9603622 1.0000 80 chrI:6745563-6745643 1.0000 80 chrIII:623977-624057 1.0000 80 chrIII:8800127-8800207 1.0000 80 chrI:14708126-14708206 1.0000 80 chrV:13789554-13789634 1.0000 80 chrIV:443833-443913 1.0000 80 chrI:8813411-8813491 1.0000 80 chrII:13369390-13369470 1.0000 80 chrII:5326341-5326421 1.0000 80 chrII:6951511-6951591 1.0000 80 chrI:9373389-9373469 1.0000 80 chrI:8786823-8786903 1.0000 80 chrIII:5014102-5014182 1.0000 80 chrIV:11593707-11593787 1.0000 80 chrV:10466736-10466816 1.0000 80 chrX:10569020-10569100 1.0000 80 chrIII:8795644-8795724 1.0000 80 chrV:10353166-10353246 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_alr-1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/alr-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= 51 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= 4080 N= 51 sample: seed= 0 hsfrac= 0 searchsize= 4080 norand= no csites= 1000 Letter frequencies in dataset: A 0.277 C 0.232 G 0.216 T 0.275 Background letter frequencies (from file dataset with add-one prior applied): A 0.277 C 0.232 G 0.216 T 0.275 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTKCGTCT MEME-1 width = 8 sites = 18 llr = 147 E-value = 4.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::2: pos.-specific C a:2a:17: probability G :15:8::: matrix T :93:292a bits 2.2 * * 2.0 * * 1.8 * * * 1.5 * * * * Relative 1.3 ** *** * Entropy 1.1 ** *** * (11.8 bits) 0.9 ** *** * 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTGCGTCT consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:10466736-10466816 8 1.21e-05 ACACAAT CTGCGTCT CCGTGCTCTC chrV:13789554-13789634 39 1.21e-05 ATCTTTTTGT CTGCGTCT CGACGATACA chrIII:668466-668546 33 1.21e-05 ctcAGGTTTG CTGCGTCT CAGCGTTTCT chrI:4254154-4254234 34 1.21e-05 CCAAGTCTTT CTGCGTCT CTTAGTGCTC chrI:6579881-6579961 8 4.06e-05 TTTCTTC CTCCGTCT CTTCATTTCC chrX:12690502-12690582 38 4.06e-05 AGATAAGAAT CTCCGTCT TCCGAAAACG chrIII:623977-624057 41 8.48e-05 GTCGGTGTGT CTGCGTAT CTCTTTATGA chrII:9603542-9603622 25 8.48e-05 ATCTCACTCT CTGCGTTT CTCTTATTCC chrIV:8183500-8183580 28 8.48e-05 TTCGTATCGT CTGCGTTT GTGCACCACG chrIII:5014102-5014182 44 1.14e-04 ACTCCCCGGT CTTCTTCT CTCCTTTAAT chrIII:8797540-8797620 52 1.14e-04 CAGTGTATTT CTTCTTCT TCCTTTTCTT chrX:8378314-8378394 7 1.14e-04 tcttgt cttcttct ttccatttca chrII:8329068-8329148 57 1.51e-04 CAACGCGTCG CTTCGTAT GGTCTCGCAG chrX:10555559-10555639 13 1.51e-04 AGTGCTCGCC CTTCGTAT TCTTCCCCCT chrI:9721977-9722057 28 1.63e-04 TTGTCGCTGT CGTCGTCT TCGAAGCCGT chrV:126755-126835 55 1.90e-04 GGACAAACGC CTGCGCCT CTTCATTTCG chrV:10274063-10274143 19 1.90e-04 AGAAGACGTT CTCCTTCT TTTTTCCTTG chrI:14708126-14708206 24 3.15e-04 AACTGCCGCA CGGCGTTT TGCCATCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:10466736-10466816 1.2e-05 7_[+1]_65 chrV:13789554-13789634 1.2e-05 38_[+1]_34 chrIII:668466-668546 1.2e-05 32_[+1]_40 chrI:4254154-4254234 1.2e-05 33_[+1]_39 chrI:6579881-6579961 4.1e-05 7_[+1]_65 chrX:12690502-12690582 4.1e-05 37_[+1]_35 chrIII:623977-624057 8.5e-05 40_[+1]_32 chrII:9603542-9603622 8.5e-05 24_[+1]_48 chrIV:8183500-8183580 8.5e-05 27_[+1]_45 chrIII:5014102-5014182 0.00011 43_[+1]_29 chrIII:8797540-8797620 0.00011 51_[+1]_21 chrX:8378314-8378394 0.00011 6_[+1]_66 chrII:8329068-8329148 0.00015 56_[+1]_16 chrX:10555559-10555639 0.00015 12_[+1]_60 chrI:9721977-9722057 0.00016 27_[+1]_45 chrV:126755-126835 0.00019 54_[+1]_18 chrV:10274063-10274143 0.00019 18_[+1]_54 chrI:14708126-14708206 0.00032 23_[+1]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTKCGTCT width=8 seqs=18 chrV:10466736-10466816 ( 8) CTGCGTCT 1 chrV:13789554-13789634 ( 39) CTGCGTCT 1 chrIII:668466-668546 ( 33) CTGCGTCT 1 chrI:4254154-4254234 ( 34) CTGCGTCT 1 chrI:6579881-6579961 ( 8) CTCCGTCT 1 chrX:12690502-12690582 ( 38) CTCCGTCT 1 chrIII:623977-624057 ( 41) CTGCGTAT 1 chrII:9603542-9603622 ( 25) CTGCGTTT 1 chrIV:8183500-8183580 ( 28) CTGCGTTT 1 chrIII:5014102-5014182 ( 44) CTTCTTCT 1 chrIII:8797540-8797620 ( 52) CTTCTTCT 1 chrX:8378314-8378394 ( 7) CTTCTTCT 1 chrII:8329068-8329148 ( 57) CTTCGTAT 1 chrX:10555559-10555639 ( 13) CTTCGTAT 1 chrI:9721977-9722057 ( 28) CGTCGTCT 1 chrV:126755-126835 ( 55) CTGCGCCT 1 chrV:10274063-10274143 ( 19) CTCCTTCT 1 chrI:14708126-14708206 ( 24) CGGCGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3723 bayes= 8.53644 E= 4.1e-003 -1081 210 -1081 -1081 -1081 -1081 -96 169 -1081 -48 121 28 -1081 210 -1081 -1081 -1081 -1081 185 -31 -1081 -206 -1081 178 -73 152 -1081 -72 -1081 -1081 -1081 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 4.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.166667 0.500000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.055556 0.000000 0.944444 0.166667 0.666667 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTKCGTCT MEME-1 regular expression -------------------------------------------------------------------------------- CT[GT]C[GT]TCT -------------------------------------------------------------------------------- Time 2.01 secs. ******************************************************************************** ******************************************************************************** MOTIF GAAGRAAA MEME-2 width = 8 sites = 31 llr = 207 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a725a78 pos.-specific C 2::1:::: probability G 8:355:32 matrix T :::21::: bits 2.2 2.0 1.8 * * 1.5 * * Relative 1.3 ** * * Entropy 1.1 ** *** (9.6 bits) 0.9 *** *** 0.7 *** **** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAGAAAA consensus C GAG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:11127375-11127455 51 1.64e-05 ACTCGGATTA GAAGGAAA ATAAGGAAAA chrIII:8795644-8795724 36 3.75e-05 TCCAATCGAT GAAGAAAA GACGACCCCA chrI:9373389-9373469 2 3.75e-05 G GAAGAAAA AACGAAGACG chrX:6750330-6750410 36 3.75e-05 GAGAATTTTT GAAGAAAA AAGCATTGTA chrIII:4505878-4505958 71 7.96e-05 AGAAAATGGA GAGGAAAA AA chrIII:623977-624057 70 9.60e-05 GGATAGGCAA GAAGAAGA GCA chrI:9721977-9722057 4 9.60e-05 AAA GAAGAAGA AGCTCGTTGT chrV:6244860-6244940 69 9.60e-05 CGAAGCATGA GAAGAAGA AGGA chrV:8359295-8359375 63 1.62e-04 TGACGTTTCA CAAGGAAA CATTTCAGAA chrIII:5920128-5920208 23 1.62e-04 CATCTTATTT CAAGGAAA CAAACACTTG chrI:8813411-8813491 2 1.96e-04 T GAATGAAA GTCAAGACTG chrI:14708126-14708206 72 2.71e-04 ATAATTAATG GAATAAAA C chrIII:8800127-8800207 20 2.71e-04 ttgagagaga gagggaga CATTGTCGAA chrX:11137646-11137726 2 2.71e-04 T GAAGAAAG GAGAAGTGAA chrX:12690502-12690582 5 2.71e-04 TTCG GAAGAAAG GAGGGCTCAT chrII:9603542-9603622 62 3.01e-04 TTTCATTTTT GAGAGAAA AGACAGTGTA chrIII:8797540-8797620 11 3.01e-04 tagagagaga gagagaaa gaCACTGACG chrII:13369390-13369470 11 4.96e-04 ATTCGCAACT GAACGAAA CAGTGTGGCA chrI:6745563-6745643 45 4.96e-04 GTTGAAGAAT GAAGGAGG TATTGGTGTC chrIV:7791422-7791502 36 4.96e-04 GCGCGAATTC GAACGAAA ATTTCAGTTG chrII:6951511-6951591 57 6.26e-04 GCAGGGACTC CAAAGAAA TCTAGATAGT chrV:126755-126835 3 6.71e-04 AA CAAAAAAA ATTCAAGTCT chrIII:3096235-3096315 42 7.42e-04 CAACATCTTC CAATGAAA TTCTGAGCAT chrI:8786823-8786903 50 8.48e-04 AAGAGAATTA GAGAAAGA TACAGAGAAA chrX:11120908-11120988 44 8.48e-04 CGATGCCTCG GAGGTAAA GTGATGGGCC chrV:10274063-10274143 4 9.19e-04 GAA GAAGTAGA AGACGTTCTC chrV:13656588-13656668 71 9.19e-04 AACGAGATCC GAATAAAG AA chrIV:5604641-5604721 25 9.63e-04 TGATGATGAT GATGGAAA AACCTCCATT chrV:10353166-10353246 11 1.25e-03 AAGGACGAAT CAAAAAGA CGACGGCGTA chrX:7678550-7678630 5 1.25e-03 AATG CAGTGAAA AGCATTCATC chrI:4254154-4254234 55 1.25e-03 AGTGCTCTTC GAGAAAAG AACGAGGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:11127375-11127455 1.6e-05 50_[+2]_22 chrIII:8795644-8795724 3.8e-05 35_[+2]_37 chrI:9373389-9373469 3.8e-05 1_[+2]_71 chrX:6750330-6750410 3.8e-05 35_[+2]_37 chrIII:4505878-4505958 8e-05 70_[+2]_2 chrIII:623977-624057 9.6e-05 69_[+2]_3 chrI:9721977-9722057 9.6e-05 3_[+2]_69 chrV:6244860-6244940 9.6e-05 68_[+2]_4 chrV:8359295-8359375 0.00016 62_[+2]_10 chrIII:5920128-5920208 0.00016 22_[+2]_50 chrI:8813411-8813491 0.0002 1_[+2]_71 chrI:14708126-14708206 0.00027 71_[+2]_1 chrIII:8800127-8800207 0.00027 19_[+2]_53 chrX:11137646-11137726 0.00027 1_[+2]_71 chrX:12690502-12690582 0.00027 4_[+2]_68 chrII:9603542-9603622 0.0003 61_[+2]_11 chrIII:8797540-8797620 0.0003 10_[+2]_62 chrII:13369390-13369470 0.0005 10_[+2]_62 chrI:6745563-6745643 0.0005 44_[+2]_28 chrIV:7791422-7791502 0.0005 35_[+2]_37 chrII:6951511-6951591 0.00063 56_[+2]_16 chrV:126755-126835 0.00067 2_[+2]_70 chrIII:3096235-3096315 0.00074 41_[+2]_31 chrI:8786823-8786903 0.00085 49_[+2]_23 chrX:11120908-11120988 0.00085 43_[+2]_29 chrV:10274063-10274143 0.00092 3_[+2]_69 chrV:13656588-13656668 0.00092 70_[+2]_2 chrIV:5604641-5604721 0.00096 24_[+2]_48 chrV:10353166-10353246 0.0012 10_[+2]_62 chrX:7678550-7678630 0.0012 4_[+2]_68 chrI:4254154-4254234 0.0012 54_[+2]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAAGRAAA width=8 seqs=31 chrX:11127375-11127455 ( 51) GAAGGAAA 1 chrIII:8795644-8795724 ( 36) GAAGAAAA 1 chrI:9373389-9373469 ( 2) GAAGAAAA 1 chrX:6750330-6750410 ( 36) GAAGAAAA 1 chrIII:4505878-4505958 ( 71) GAGGAAAA 1 chrIII:623977-624057 ( 70) GAAGAAGA 1 chrI:9721977-9722057 ( 4) GAAGAAGA 1 chrV:6244860-6244940 ( 69) GAAGAAGA 1 chrV:8359295-8359375 ( 63) CAAGGAAA 1 chrIII:5920128-5920208 ( 23) CAAGGAAA 1 chrI:8813411-8813491 ( 2) GAATGAAA 1 chrI:14708126-14708206 ( 72) GAATAAAA 1 chrIII:8800127-8800207 ( 20) GAGGGAGA 1 chrX:11137646-11137726 ( 2) GAAGAAAG 1 chrX:12690502-12690582 ( 5) GAAGAAAG 1 chrII:9603542-9603622 ( 62) GAGAGAAA 1 chrIII:8797540-8797620 ( 11) GAGAGAAA 1 chrII:13369390-13369470 ( 11) GAACGAAA 1 chrI:6745563-6745643 ( 45) GAAGGAGG 1 chrIV:7791422-7791502 ( 36) GAACGAAA 1 chrII:6951511-6951591 ( 57) CAAAGAAA 1 chrV:126755-126835 ( 3) CAAAAAAA 1 chrIII:3096235-3096315 ( 42) CAATGAAA 1 chrI:8786823-8786903 ( 50) GAGAAAGA 1 chrX:11120908-11120988 ( 44) GAGGTAAA 1 chrV:10274063-10274143 ( 4) GAAGTAGA 1 chrV:13656588-13656668 ( 71) GAATAAAG 1 chrIV:5604641-5604721 ( 25) GATGGAAA 1 chrV:10353166-10353246 ( 11) CAAAAAGA 1 chrX:7678550-7678630 ( 5) CAGTGAAA 1 chrI:4254154-4254234 ( 55) GAGAAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3723 bayes= 8.20201 E= 1.5e-001 -1160 -4 184 -1160 185 -1160 -1160 -1160 136 -1160 26 -309 -29 -185 135 -77 81 -1160 107 -209 185 -1160 -1160 -1160 142 -1160 26 -1160 160 -1160 -42 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.5e-001 0.000000 0.225806 0.774194 0.000000 1.000000 0.000000 0.000000 0.000000 0.709677 0.000000 0.258065 0.032258 0.225806 0.064516 0.548387 0.161290 0.483871 0.000000 0.451613 0.064516 1.000000 0.000000 0.000000 0.000000 0.741935 0.000000 0.258065 0.000000 0.838710 0.000000 0.161290 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGRAAA MEME-2 regular expression -------------------------------------------------------------------------------- [GC]A[AG][GA][AG]A[AG]A -------------------------------------------------------------------------------- Time 2.56 secs. ******************************************************************************** ******************************************************************************** MOTIF TTGCGCAC MEME-3 width = 8 sites = 6 llr = 60 E-value = 4.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::8: pos.-specific C :::8:8:a probability G ::a:a22: matrix T aa:2:::: bits 2.2 * * * 2.0 * * * 1.8 *** * * 1.5 *** ** * Relative 1.3 ******** Entropy 1.1 ******** (14.4 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTGCGCAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:10466736-10466816 72 1.22e-05 AATTTTTCAT TTGCGCAC G chrV:8359295-8359375 41 1.22e-05 TCTCGTGTCT TTGCGCAC ATCTTGACGT chrV:1154056-1154136 22 1.22e-05 CACCGACGCA TTGCGCAC ACCACCAGTC chrX:11129223-11129303 53 2.17e-05 CATCGCTAAA TTGCGCGC ATCTTCTTGC chrV:126755-126835 41 3.31e-05 GTGACGGTGT TTGCGGAC AAACGCCTGC chrIV:443833-443913 58 4.76e-05 GAGAATTTGT TTGTGCAC TCCTCTCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:10466736-10466816 1.2e-05 71_[+3]_1 chrV:8359295-8359375 1.2e-05 40_[+3]_32 chrV:1154056-1154136 1.2e-05 21_[+3]_51 chrX:11129223-11129303 2.2e-05 52_[+3]_20 chrV:126755-126835 3.3e-05 40_[+3]_32 chrIV:443833-443913 4.8e-05 57_[+3]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTGCGCAC width=8 seqs=6 chrV:10466736-10466816 ( 72) TTGCGCAC 1 chrV:8359295-8359375 ( 41) TTGCGCAC 1 chrV:1154056-1154136 ( 22) TTGCGCAC 1 chrX:11129223-11129303 ( 53) TTGCGCGC 1 chrV:126755-126835 ( 41) TTGCGGAC 1 chrIV:443833-443913 ( 58) TTGTGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3723 bayes= 9.72304 E= 4.8e+002 -923 -923 -923 186 -923 -923 -923 186 -923 -923 221 -923 -923 184 -923 -72 -923 -923 221 -923 -923 184 -37 -923 159 -923 -37 -923 -923 210 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 4.8e+002 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 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGCGCAC MEME-3 regular expression -------------------------------------------------------------------------------- TTGCGCAC -------------------------------------------------------------------------------- Time 3.06 secs. ******************************************************************************** ******************************************************************************** MOTIF TCHTCTTC MEME-4 width = 8 sites = 16 llr = 123 E-value = 2.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::3::33: pos.-specific C :64:a::a probability G :2:::::: matrix T a23a:78: bits 2.2 * * 2.0 * * 1.8 * ** * 1.5 * ** * Relative 1.3 * ** * Entropy 1.1 * ** ** (11.1 bits) 0.9 * ***** 0.7 ** ***** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCCTCTTC consensus A AA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:10569020-10569100 19 1.66e-05 TTTTATTCTC TCCTCTTC TCTATTTCTC chrII:5326341-5326421 22 1.66e-05 GTTTTCTGTT TCCTCTTC ACTTTGAACG chrX:10555559-10555639 46 1.66e-05 CTCCTTTTCG TCCTCTTC GTTGTGGCCG chrX:8378314-8378394 52 5.60e-05 ctccttctcc tcatcttc ttttcatcac chrI:4254154-4254234 47 1.45e-04 CGTCTCTTAG TGCTCTTC GAGAAAAGAA chrX:11129223-11129303 39 1.45e-04 TTACAAATCA TCATCATC GCTAAATTGC chrI:6579881-6579961 32 1.45e-04 TTCCTTAACT TCTTCATC CTCCCGTTCC chrIII:3096235-3096315 13 1.45e-04 ATTTCTTGTC TCTTCATC CTACACCCCC chrX:11135144-11135224 20 1.45e-04 AAGTAGGTAT TCATCATC AAAAATTGAA chrV:10466736-10466816 24 2.41e-04 CTCCGTGCTC TCATCTAC CATTATGTCT chrIV:5607461-5607541 8 2.41e-04 AGCTGAG TGTTCTTC TCTCTGTCAA chrIII:8797540-8797620 63 2.87e-04 TTCTTCTTCC TTTTCTTC CATACACAAT chrIV:8183500-8183580 13 2.87e-04 TCTTTCGCTC TTTTCTTC GTATCGTCTG chrX:12690502-12690582 19 4.32e-04 AAAGGAGGGC TCATCAAC AAGATAAGAA chrIII:6431916-6431996 45 4.32e-04 CATACAAGTG TGCTCTAC TGAACAGCTA chrV:13789554-13789634 17 4.99e-04 ACTCTATGTT TTCTCTAC TTCCATCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:10569020-10569100 1.7e-05 18_[+4]_54 chrII:5326341-5326421 1.7e-05 21_[+4]_51 chrX:10555559-10555639 1.7e-05 45_[+4]_27 chrX:8378314-8378394 5.6e-05 51_[+4]_21 chrI:4254154-4254234 0.00014 46_[+4]_26 chrX:11129223-11129303 0.00014 38_[+4]_34 chrI:6579881-6579961 0.00014 31_[+4]_41 chrIII:3096235-3096315 0.00014 12_[+4]_60 chrX:11135144-11135224 0.00014 19_[+4]_53 chrV:10466736-10466816 0.00024 23_[+4]_49 chrIV:5607461-5607541 0.00024 7_[+4]_65 chrIII:8797540-8797620 0.00029 62_[+4]_10 chrIV:8183500-8183580 0.00029 12_[+4]_60 chrX:12690502-12690582 0.00043 18_[+4]_54 chrIII:6431916-6431996 0.00043 44_[+4]_28 chrV:13789554-13789634 0.0005 16_[+4]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCHTCTTC width=8 seqs=16 chrX:10569020-10569100 ( 19) TCCTCTTC 1 chrII:5326341-5326421 ( 22) TCCTCTTC 1 chrX:10555559-10555639 ( 46) TCCTCTTC 1 chrX:8378314-8378394 ( 52) TCATCTTC 1 chrI:4254154-4254234 ( 47) TGCTCTTC 1 chrX:11129223-11129303 ( 39) TCATCATC 1 chrI:6579881-6579961 ( 32) TCTTCATC 1 chrIII:3096235-3096315 ( 13) TCTTCATC 1 chrX:11135144-11135224 ( 20) TCATCATC 1 chrV:10466736-10466816 ( 24) TCATCTAC 1 chrIV:5607461-5607541 ( 8) TGTTCTTC 1 chrIII:8797540-8797620 ( 63) TTTTCTTC 1 chrIV:8183500-8183580 ( 13) TTTTCTTC 1 chrX:12690502-12690582 ( 19) TCATCAAC 1 chrIII:6431916-6431996 ( 45) TGCTCTAC 1 chrV:13789554-13789634 ( 17) TTCTCTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3723 bayes= 8.59549 E= 2.5e+003 -1064 -1064 -1064 186 -1064 143 -20 -55 18 69 -1064 18 -1064 -1064 -1064 186 -1064 210 -1064 -1064 18 -1064 -1064 132 -15 -1064 -1064 145 -1064 210 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 2.5e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.187500 0.187500 0.312500 0.375000 0.000000 0.312500 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.312500 0.000000 0.000000 0.687500 0.250000 0.000000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCHTCTTC MEME-4 regular expression -------------------------------------------------------------------------------- TC[CAT]TC[TA][TA]C -------------------------------------------------------------------------------- Time 3.59 secs. ******************************************************************************** ******************************************************************************** MOTIF GACGCGCG MEME-5 width = 8 sites = 2 llr = 24 E-value = 3.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :a:::::: pos.-specific C ::a:a:a: probability G a::a:a:a matrix T :::::::: bits 2.2 * ****** 2.0 * ****** 1.8 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (17.0 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GACGCGCG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:8329068-8329148 30 7.53e-06 GAATATTTTC GACGCGCG ACGCACACGC chrV:6244860-6244940 27 7.53e-06 CATTGCACCG GACGCGCG CAAAGTACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:8329068-8329148 7.5e-06 29_[+5]_43 chrV:6244860-6244940 7.5e-06 26_[+5]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GACGCGCG width=8 seqs=2 chrII:8329068-8329148 ( 30) GACGCGCG 1 chrV:6244860-6244940 ( 27) GACGCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3723 bayes= 10.8615 E= 3.9e+003 -765 -765 221 -765 185 -765 -765 -765 -765 210 -765 -765 -765 -765 221 -765 -765 210 -765 -765 -765 -765 221 -765 -765 210 -765 -765 -765 -765 221 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.9e+003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCGCG MEME-5 regular expression -------------------------------------------------------------------------------- GACGCGCG -------------------------------------------------------------------------------- Time 4.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:11135144-11135224 3.52e-02 80 chrIV:5604641-5604721 2.32e-01 80 chrIII:6431916-6431996 1.96e-01 80 chrV:1154056-1154136 5.01e-02 21_[+3(1.22e-05)]_51 chrX:12690502-12690582 2.63e-03 37_[+1(4.06e-05)]_35 chrX:11137646-11137726 3.31e-01 80 chrX:11120908-11120988 5.76e-01 80 chrIII:3096235-3096315 6.32e-02 80 chrI:6579881-6579961 1.55e-02 7_[+1(4.06e-05)]_65 chrV:6244860-6244940 2.24e-03 26_[+5(7.53e-06)]_34_[+2(9.60e-05)]_\ 4 chrI:9721977-9722057 1.25e-03 3_[+2(9.60e-05)]_69 chrX:10555559-10555639 3.13e-04 45_[+4(1.66e-05)]_27 chrX:11129223-11129303 2.04e-03 52_[+3(2.17e-05)]_20 chrX:11127375-11127455 9.27e-02 50_[+2(1.64e-05)]_22 chrV:13656588-13656668 7.34e-01 80 chrX:5121987-5122067 8.58e-01 80 chrX:8378314-8378394 2.19e-02 5_[+4(5.60e-05)]_38_[+4(5.60e-05)]_\ 21 chrII:8329068-8329148 9.70e-04 29_[+5(7.53e-06)]_43 chrI:4254154-4254234 2.60e-04 33_[+1(1.21e-05)]_39 chrX:7678550-7678630 2.35e-01 80 chrIV:7791422-7791502 4.21e-01 80 chrIII:4504442-4504522 9.66e-01 80 chrIII:4505878-4505958 2.15e-01 70_[+2(7.96e-05)]_2 chrV:10274063-10274143 1.53e-02 80 chrV:126755-126835 1.16e-04 40_[+3(3.31e-05)]_32 chrIV:5607461-5607541 1.13e-01 80 chrIV:8183500-8183580 1.10e-03 33_[+3(4.76e-05)]_39 chrIII:8797540-8797620 1.50e-03 50_[+4(5.60e-05)]_22 chrIII:5920128-5920208 8.35e-02 80 chrV:8359295-8359375 3.17e-03 40_[+3(1.22e-05)]_32 chrIII:668466-668546 6.46e-02 32_[+1(1.21e-05)]_40 chrX:6750330-6750410 8.11e-02 35_[+2(3.75e-05)]_37 chrII:9603542-9603622 3.98e-03 24_[+1(8.48e-05)]_48 chrI:6745563-6745643 8.14e-02 80 chrIII:623977-624057 1.43e-02 40_[+1(8.48e-05)]_21_[+2(9.60e-05)]_\ 3 chrIII:8800127-8800207 3.11e-01 80 chrI:14708126-14708206 4.54e-03 80 chrV:13789554-13789634 1.39e-02 38_[+1(1.21e-05)]_34 chrIV:443833-443913 3.96e-02 57_[+3(4.76e-05)]_15 chrI:8813411-8813491 1.14e-02 80 chrII:13369390-13369470 2.99e-02 80 chrII:5326341-5326421 7.65e-02 21_[+4(1.66e-05)]_51 chrII:6951511-6951591 3.28e-01 80 chrI:9373389-9373469 1.90e-01 1_[+2(3.75e-05)]_59_[+2(9.60e-05)]_\ 4 chrI:8786823-8786903 2.22e-01 80 chrIII:5014102-5014182 9.43e-03 42_[+4(5.60e-05)]_30 chrIV:11593707-11593787 8.84e-01 80 chrV:10466736-10466816 3.95e-05 7_[+1(1.21e-05)]_56_[+3(1.22e-05)]_\ 1 chrX:10569020-10569100 2.17e-03 18_[+4(1.66e-05)]_54 chrIII:8795644-8795724 1.40e-01 35_[+2(3.75e-05)]_11_[+2(5.03e-05)]_\ 18 chrV:10353166-10353246 2.38e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************