******************************************************************************** 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/Hr78.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:8047-8167 1.0000 120 chrM:11836-11956 1.0000 120 chrM:17583-17703 1.0000 120 chrM:4111-4231 1.0000 120 chrM:8284-8404 1.0000 120 chrM:1040-1160 1.0000 120 chr2R:24857325-24857445 1.0000 120 chrM:13791-13911 1.0000 120 chrM:840-960 1.0000 120 chr2L:6723705-6723825 1.0000 120 chrM:11563-11683 1.0000 120 chrM:10077-10197 1.0000 120 chrM:3896-4016 1.0000 120 chrM:14742-14862 1.0000 120 chr2L:3095017-3095137 1.0000 120 chr3L:4092850-4092970 1.0000 120 chr2R:4546600-4546720 1.0000 120 chrM:3011-3131 1.0000 120 chr3R:12712322-12712442 1.0000 120 chrM:4343-4463 1.0000 120 chr2L:7976801-7976921 1.0000 120 chr3R:20621842-20621962 1.0000 120 chr3L:24976002-24976122 1.0000 120 chrM:9045-9165 1.0000 120 chr3R:3623000-3623120 1.0000 120 chr3R:26717393-26717513 1.0000 120 chr4:570837-570957 1.0000 120 chr3R:6768359-6768479 1.0000 120 chr2L:22981728-22981848 1.0000 120 chrX:15760778-15760898 1.0000 120 chrX:22433052-22433172 1.0000 120 chr4:313993-314113 1.0000 120 chr3L:18088200-18088320 1.0000 120 chrX:16217416-16217536 1.0000 120 chr3L:26014145-26014265 1.0000 120 chr2L:740166-740286 1.0000 120 chr3L:24028384-24028504 1.0000 120 chrM:9767-9887 1.0000 120 chr3R:4400039-4400159 1.0000 120 chr2R:5307154-5307274 1.0000 120 chr4:314792-314912 1.0000 120 chrM:5991-6111 1.0000 120 chr3R:6908184-6908304 1.0000 120 chr3R:4232646-4232766 1.0000 120 chr2R:5604815-5604935 1.0000 120 chrM:6227-6347 1.0000 120 chr2L:16049723-16049843 1.0000 120 chr3R:21408504-21408624 1.0000 120 chr3L:25120587-25120707 1.0000 120 chrM:4561-4681 1.0000 120 chrM:12620-12740 1.0000 120 chr2L:12520349-12520469 1.0000 120 chrM:7098-7218 1.0000 120 chr3L:27083940-27084060 1.0000 120 chrX:2042386-2042506 1.0000 120 chr2L:10736065-10736185 1.0000 120 chrM:13373-13493 1.0000 120 chr2R:24337633-24337753 1.0000 120 chr2L:8478119-8478239 1.0000 120 chrX:14583297-14583417 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_Hr78/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/Hr78.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= 60 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= 7200 N= 60 sample: seed= 0 hsfrac= 0 searchsize= 7200 norand= no csites= 1000 Letter frequencies in dataset: A 0.344 C 0.169 G 0.144 T 0.343 Background letter frequencies (from file dataset with add-one prior applied): A 0.344 C 0.169 G 0.144 T 0.343 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTGCTTGC MEME-1 width = 8 sites = 13 llr = 134 E-value = 2.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :1::1::: pos.-specific C a::9:2:7 probability G ::a1:1a: matrix T :9::98:3 bits 2.8 * * 2.5 * * * 2.2 * ** * 2.0 * ** * Relative 1.7 * ** * Entropy 1.4 * ** ** (14.8 bits) 1.1 ***** ** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTGCTTGC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:24337633-24337753 22 4.04e-06 GATAGGTATA CTGCTTGC TTAAAAGTTC chr3R:21408504-21408624 56 4.04e-06 AGTTCTCTTG CTGCTTGC CGAAGCAGTT chr3R:6908184-6908304 53 4.04e-06 GCTTGCGCGT CTGCTTGC TTAGTGATCT chr3R:4400039-4400159 108 4.04e-06 TAATAGTTTT CTGCTTGC AATGT chr2L:740166-740286 57 4.04e-06 CAGAATCAGA CTGCTTGC CAGGTTAAGA chr3R:6768359-6768479 87 4.04e-06 TCACCACATA CTGCTTGC ATCGACAACT chr2R:24857325-24857445 82 4.04e-06 TGCTTGCACT CTGCTTGC GCACCATATG chr2L:8478119-8478239 57 1.59e-05 GCAGTTTTGA CTGCTTGT GTCTGCGAAC chr3L:18088200-18088320 44 1.59e-05 CATGTGCATA CTGCTTGT TGCACGAAAA chr4:570837-570957 96 2.34e-05 CTTTGTCATC CTGCTCGT TTACCCAAGT chr3R:12712322-12712442 82 4.06e-05 CTTGTTCACA CTGCACGC GACTTTCTTA chr2R:4546600-4546720 46 4.91e-05 GTGGTATAAG CTGGTGGC TCATGCTCTT chrM:9045-9165 83 6.89e-05 aaatataaaC CAGCTTGT AAACGTTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:24337633-24337753 4e-06 21_[+1]_91 chr3R:21408504-21408624 4e-06 55_[+1]_57 chr3R:6908184-6908304 4e-06 52_[+1]_60 chr3R:4400039-4400159 4e-06 107_[+1]_5 chr2L:740166-740286 4e-06 56_[+1]_56 chr3R:6768359-6768479 4e-06 86_[+1]_26 chr2R:24857325-24857445 4e-06 81_[+1]_31 chr2L:8478119-8478239 1.6e-05 56_[+1]_56 chr3L:18088200-18088320 1.6e-05 43_[+1]_69 chr4:570837-570957 2.3e-05 95_[+1]_17 chr3R:12712322-12712442 4.1e-05 81_[+1]_31 chr2R:4546600-4546720 4.9e-05 45_[+1]_67 chrM:9045-9165 6.9e-05 82_[+1]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGCTTGC width=8 seqs=13 chr2R:24337633-24337753 ( 22) CTGCTTGC 1 chr3R:21408504-21408624 ( 56) CTGCTTGC 1 chr3R:6908184-6908304 ( 53) CTGCTTGC 1 chr3R:4400039-4400159 ( 108) CTGCTTGC 1 chr2L:740166-740286 ( 57) CTGCTTGC 1 chr3R:6768359-6768479 ( 87) CTGCTTGC 1 chr2R:24857325-24857445 ( 82) CTGCTTGC 1 chr2L:8478119-8478239 ( 57) CTGCTTGT 1 chr3L:18088200-18088320 ( 44) CTGCTTGT 1 chr4:570837-570957 ( 96) CTGCTCGT 1 chr3R:12712322-12712442 ( 82) CTGCACGC 1 chr2R:4546600-4546720 ( 46) CTGGTGGC 1 chrM:9045-9165 ( 83) CAGCTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6780 bayes= 9.55523 E= 2.3e-006 -1035 257 -1035 -1035 -216 -1035 -1035 143 -1035 -1035 279 -1035 -1035 245 -91 -1035 -216 -1035 -1035 143 -1035 -13 -91 116 -1035 -1035 279 -1035 -1035 204 -1035 -16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 2.3e-006 0.000000 1.000000 0.000000 0.000000 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 1.000000 0.000000 0.000000 0.923077 0.076923 0.000000 0.076923 0.000000 0.000000 0.923077 0.000000 0.153846 0.076923 0.769231 0.000000 0.000000 1.000000 0.000000 0.000000 0.692308 0.000000 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCTTGC MEME-1 regular expression -------------------------------------------------------------------------------- CTGCTTG[CT] -------------------------------------------------------------------------------- Time 0.92 secs. ******************************************************************************** ******************************************************************************** MOTIF CAAGCAGT MEME-2 width = 8 sites = 13 llr = 127 E-value = 6.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :8a:19:: pos.-specific C 82::8::: probability G 2::a21a1 matrix T :::::::9 bits 2.8 * * 2.5 * * 2.2 * * 2.0 * * * Relative 1.7 * ** * Entropy 1.4 * *** * (14.1 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CAAGCAGT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:16049723-16049843 53 8.27e-06 AAGGGGAAAT CAAGCAGT GGAAGGGGAA chr2L:740166-740286 11 8.27e-06 TGCACTGCTT CAAGCAGT TATATTCGTA chr3L:18088200-18088320 70 8.27e-06 AAACGCATGC CAAGCAGT TCAAATCCAG chr3R:6768359-6768479 55 8.27e-06 GATCCCTGGT CAAGCAGT TTTGCAAACG chr3L:4092850-4092970 72 8.27e-06 TCAACCGTGG CAAGCAGT GCATAACCGC chr2L:3095017-3095137 55 8.27e-06 GTGCGTGCAG CAAGCAGT GCCAGAAAGC chr3R:21408504-21408624 65 1.94e-05 GCTGCTTGCC GAAGCAGT TGATGCGCTG chr3L:24028384-24028504 29 1.94e-05 TAGCCAACCA GAAGCAGT CAAACGTAGT chr2L:8478119-8478239 1 2.64e-05 . CAAGGAGT TAACTAAGCA chr3R:6908184-6908304 76 3.34e-05 GATCTAATAT CAAGCAGG AAACACAATA chr3R:12712322-12712442 53 5.56e-05 GTTTACACCG CCAGCGGT CCCACTGAAA chr2R:24337633-24337753 68 7.24e-05 GCCATCTAGG CAAGAAGT TATGAGTATA chrX:15760778-15760898 6 8.27e-05 CATTT GCAGGAGT GTCCATAAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:16049723-16049843 8.3e-06 52_[+2]_60 chr2L:740166-740286 8.3e-06 10_[+2]_102 chr3L:18088200-18088320 8.3e-06 69_[+2]_43 chr3R:6768359-6768479 8.3e-06 54_[+2]_58 chr3L:4092850-4092970 8.3e-06 71_[+2]_41 chr2L:3095017-3095137 8.3e-06 54_[+2]_58 chr3R:21408504-21408624 1.9e-05 64_[+2]_48 chr3L:24028384-24028504 1.9e-05 28_[+2]_84 chr2L:8478119-8478239 2.6e-05 [+2]_112 chr3R:6908184-6908304 3.3e-05 75_[+2]_37 chr3R:12712322-12712442 5.6e-05 52_[+2]_60 chr2R:24337633-24337753 7.2e-05 67_[+2]_45 chrX:15760778-15760898 8.3e-05 5_[+2]_107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAAGCAGT width=8 seqs=13 chr2L:16049723-16049843 ( 53) CAAGCAGT 1 chr2L:740166-740286 ( 11) CAAGCAGT 1 chr3L:18088200-18088320 ( 70) CAAGCAGT 1 chr3R:6768359-6768479 ( 55) CAAGCAGT 1 chr3L:4092850-4092970 ( 72) CAAGCAGT 1 chr2L:3095017-3095137 ( 55) CAAGCAGT 1 chr3R:21408504-21408624 ( 65) GAAGCAGT 1 chr3L:24028384-24028504 ( 29) GAAGCAGT 1 chr2L:8478119-8478239 ( 1) CAAGGAGT 1 chr3R:6908184-6908304 ( 76) CAAGCAGG 1 chr3R:12712322-12712442 ( 53) CCAGCGGT 1 chr2R:24337633-24337753 ( 68) CAAGAAGT 1 chrX:15760778-15760898 ( 6) GCAGGAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6780 bayes= 9.55523 E= 6.7e-003 -1035 219 68 -1035 130 -13 -1035 -1035 154 -1035 -1035 -1035 -1035 -1035 279 -1035 -216 219 9 -1035 142 -1035 -91 -1035 -1035 -1035 279 -1035 -1035 -1035 -91 143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 6.7e-003 0.000000 0.769231 0.230769 0.000000 0.846154 0.153846 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.076923 0.769231 0.153846 0.000000 0.923077 0.000000 0.076923 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.076923 0.923077 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAGCAGT MEME-2 regular expression -------------------------------------------------------------------------------- [CG]AAGCAGT -------------------------------------------------------------------------------- Time 1.73 secs. ******************************************************************************** ******************************************************************************** MOTIF KGGCGCCR MEME-3 width = 8 sites = 8 llr = 86 E-value = 3.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1::1:::5 pos.-specific C ::39:9a1 probability G 5a8:a1:4 matrix T 4::::::: bits 2.8 * * 2.5 * * * 2.2 * * * 2.0 ****** Relative 1.7 ****** Entropy 1.4 ****** (15.5 bits) 1.1 ****** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGCGCCA consensus T C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:740166-740286 106 1.01e-06 CACATGTAGA GGGCGCCA CTGAGGA chr2R:24857325-24857445 99 1.01e-06 CGCACCATAT GGGCGCCA ACTTCAAATT chr3R:20621842-20621962 82 1.72e-06 GCATGCTGAC TGGCGCCG TGGATTTTGA chr2R:24337633-24337753 54 4.13e-06 ATAACTTATG TGGCGCCA TCTAGGCAAG chr2R:5307154-5307274 66 8.21e-06 ATATGGTTTT TGCCGCCG TAAGAATAGG chrX:16217416-16217536 15 9.23e-06 gcgagagaga gggagccg gagcacaaga chr3R:4400039-4400159 4 1.87e-05 CAC AGGCGCCC AATGTCAAAA chr2L:7976801-7976921 64 2.04e-05 acGCGACGAA GGCCGGCA GACAGAGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:740166-740286 1e-06 105_[+3]_7 chr2R:24857325-24857445 1e-06 98_[+3]_14 chr3R:20621842-20621962 1.7e-06 81_[+3]_31 chr2R:24337633-24337753 4.1e-06 53_[+3]_59 chr2R:5307154-5307274 8.2e-06 65_[+3]_47 chrX:16217416-16217536 9.2e-06 14_[+3]_98 chr3R:4400039-4400159 1.9e-05 3_[+3]_109 chr2L:7976801-7976921 2e-05 63_[+3]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KGGCGCCR width=8 seqs=8 chr2L:740166-740286 ( 106) GGGCGCCA 1 chr2R:24857325-24857445 ( 99) GGGCGCCA 1 chr3R:20621842-20621962 ( 82) TGGCGCCG 1 chr2R:24337633-24337753 ( 54) TGGCGCCA 1 chr2R:5307154-5307274 ( 66) TGCCGCCG 1 chrX:16217416-16217536 ( 15) GGGAGCCG 1 chr3R:4400039-4400159 ( 4) AGGCGCCC 1 chr2L:7976801-7976921 ( 64) GGCCGGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6780 bayes= 11.0483 E= 3.9e-001 -146 -965 179 13 -965 -965 279 -965 -965 57 238 -965 -146 237 -965 -965 -965 -965 279 -965 -965 237 -21 -965 -965 257 -965 -965 54 -43 138 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 3.9e-001 0.125000 0.000000 0.500000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.125000 0.375000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGCGCCR MEME-3 regular expression -------------------------------------------------------------------------------- [GT]G[GC]CGCC[AG] -------------------------------------------------------------------------------- Time 2.53 secs. ******************************************************************************** ******************************************************************************** MOTIF KCACTGCT MEME-4 width = 8 sites = 10 llr = 100 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :28::::: pos.-specific C :81a1:a: probability G 6:1::a:: matrix T 4:::9::a bits 2.8 * 2.5 * ** 2.2 * ** 2.0 * ** Relative 1.7 * * *** Entropy 1.4 ** * *** (14.5 bits) 1.1 ** ***** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCACTGCT consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:24337633-24337753 90 4.05e-06 AGTATATGGT GCACTGCT TGGGAAAGGT chr3R:21408504-21408624 101 4.05e-06 AGCAGTTGAT GCACTGCT TGCACATTGC chr2L:740166-740286 2 4.05e-06 T GCACTGCT TCAAGCAGTT chr2R:24857325-24857445 68 4.05e-06 ACCTGCTTTG GCACTGCT TGCACTCTGC chr3L:4092850-4092970 54 1.54e-05 AGGAACCGTT TCACTGCT TCAACCGTGG chr3R:4232646-4232766 84 1.74e-05 AGCACTTTTG GCCCTGCT TTAAATATAT chr3R:6908184-6908304 38 2.76e-05 TGATCTGCGT GAACTGCT TGCGCGTCTG chrX:16217416-16217536 104 3.17e-05 ACGTAATTTG TCGCTGCT GCGACGTCA chr2L:22981728-22981848 95 4.20e-05 AAAATTATTA TCACCGCT GTTGTTTGCT chr3L:18088200-18088320 10 6.61e-05 TGAAGATGT TAACTGCT TTATTCGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:24337633-24337753 4.1e-06 89_[+4]_23 chr3R:21408504-21408624 4.1e-06 100_[+4]_12 chr2L:740166-740286 4.1e-06 1_[+4]_111 chr2R:24857325-24857445 4.1e-06 67_[+4]_45 chr3L:4092850-4092970 1.5e-05 53_[+4]_59 chr3R:4232646-4232766 1.7e-05 83_[+4]_29 chr3R:6908184-6908304 2.8e-05 37_[+4]_75 chrX:16217416-16217536 3.2e-05 103_[+4]_9 chr2L:22981728-22981848 4.2e-05 94_[+4]_18 chr3L:18088200-18088320 6.6e-05 9_[+4]_103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KCACTGCT width=8 seqs=10 chr2R:24337633-24337753 ( 90) GCACTGCT 1 chr3R:21408504-21408624 ( 101) GCACTGCT 1 chr2L:740166-740286 ( 2) GCACTGCT 1 chr2R:24857325-24857445 ( 68) GCACTGCT 1 chr3L:4092850-4092970 ( 54) TCACTGCT 1 chr3R:4232646-4232766 ( 84) GCCCTGCT 1 chr3R:6908184-6908304 ( 38) GAACTGCT 1 chrX:16217416-16217536 ( 104) TCGCTGCT 1 chr2L:22981728-22981848 ( 95) TCACCGCT 1 chr3L:18088200-18088320 ( 10) TAACTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6780 bayes= 10.3475 E= 1.6e+000 -997 -997 206 22 -78 224 -997 -997 122 -75 -53 -997 -997 257 -997 -997 -997 -75 -997 139 -997 -997 279 -997 -997 257 -997 -997 -997 -997 -997 154 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 1.6e+000 0.000000 0.000000 0.600000 0.400000 0.200000 0.800000 0.000000 0.000000 0.800000 0.100000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACTGCT MEME-4 regular expression -------------------------------------------------------------------------------- [GT][CA]ACTGCT -------------------------------------------------------------------------------- Time 3.36 secs. ******************************************************************************** ******************************************************************************** MOTIF CGAGAGAG MEME-5 width = 8 sites = 4 llr = 48 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::a:a:a: pos.-specific C a::::::: probability G :a:8:a:a matrix T :::3:::: bits 2.8 * * * 2.5 ** * * 2.2 ** * * 2.0 ** * * Relative 1.7 ******** Entropy 1.4 ******** (17.2 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CGAGAGAG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:16217416-16217536 6 2.96e-06 cagag cgagagag agggagccgg chr2L:7976801-7976921 110 2.96e-06 AGACGATGGG CGAGAGAG AAA chr2L:3095017-3095137 91 2.96e-06 TGTTGCTGGT CGAGAGAG CGCAACATGT chr2L:12520349-12520469 27 1.00e-05 GACAATATTC CGATAGAG GGCTATGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:16217416-16217536 3e-06 5_[+5]_107 chr2L:7976801-7976921 3e-06 109_[+5]_3 chr2L:3095017-3095137 3e-06 90_[+5]_22 chr2L:12520349-12520469 1e-05 26_[+5]_86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGAGAGAG width=8 seqs=4 chrX:16217416-16217536 ( 6) CGAGAGAG 1 chr2L:7976801-7976921 ( 110) CGAGAGAG 1 chr2L:3095017-3095137 ( 91) CGAGAGAG 1 chr2L:12520349-12520469 ( 27) CGATAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6780 bayes= 10.7262 E= 1.0e+003 -865 256 -865 -865 -865 -865 279 -865 154 -865 -865 -865 -865 -865 238 -46 154 -865 -865 -865 -865 -865 279 -865 154 -865 -865 -865 -865 -865 279 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.0e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 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 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGAGAG MEME-5 regular expression -------------------------------------------------------------------------------- CGA[GT]AGAG -------------------------------------------------------------------------------- Time 4.15 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:8047-8167 1.00e+00 120 chrM:11836-11956 1.00e+00 120 chrM:17583-17703 1.00e+00 120 chrM:4111-4231 4.86e-01 120 chrM:8284-8404 6.21e-01 120 chrM:1040-1160 9.95e-01 120 chr2R:24857325-24857445 1.40e-07 47_[+4(1.54e-05)]_15_[+1(4.04e-06)]_\ 3_[+1(4.04e-06)]_9_[+3(1.01e-06)]_14 chrM:13791-13911 7.95e-01 120 chrM:840-960 1.00e+00 120 chr2L:6723705-6723825 6.82e-01 120 chrM:11563-11683 9.99e-01 120 chrM:10077-10197 6.64e-01 120 chrM:3896-4016 9.99e-01 120 chrM:14742-14862 9.90e-01 120 chr2L:3095017-3095137 1.24e-05 54_[+2(8.27e-06)]_28_[+5(2.96e-06)]_\ 22 chr3L:4092850-4092970 6.62e-05 53_[+4(1.54e-05)]_10_[+2(8.27e-06)]_\ 12_[+4(6.61e-05)]_21 chr2R:4546600-4546720 1.20e-01 45_[+1(4.91e-05)]_67 chrM:3011-3131 2.45e-01 120 chr3R:12712322-12712442 5.69e-04 52_[+2(5.56e-05)]_21_[+1(4.06e-05)]_\ 31 chrM:4343-4463 9.79e-01 120 chr2L:7976801-7976921 5.09e-04 63_[+3(2.04e-05)]_38_[+5(2.96e-06)]_\ 3 chr3R:20621842-20621962 4.69e-03 81_[+3(1.72e-06)]_31 chr3L:24976002-24976122 9.41e-01 120 chrM:9045-9165 3.18e-01 82_[+1(6.89e-05)]_30 chr3R:3623000-3623120 9.74e-01 120 chr3R:26717393-26717513 7.96e-01 120 chr4:570837-570957 1.68e-01 95_[+1(2.34e-05)]_17 chr3R:6768359-6768479 4.47e-05 54_[+2(8.27e-06)]_24_[+1(4.04e-06)]_\ 8_[+1(1.59e-05)]_10 chr2L:22981728-22981848 4.59e-02 94_[+4(4.20e-05)]_18 chrX:15760778-15760898 5.57e-02 5_[+2(8.27e-05)]_107 chrX:22433052-22433172 1.00e+00 120 chr4:313993-314113 9.74e-01 120 chr3L:18088200-18088320 5.03e-05 9_[+4(6.61e-05)]_26_[+1(1.59e-05)]_\ 18_[+2(8.27e-06)]_43 chrX:16217416-16217536 1.55e-07 5_[+5(2.96e-06)]_1_[+3(9.23e-06)]_\ 19_[+5(5.20e-05)]_3_[+5(2.69e-05)]_43_[+4(3.17e-05)]_9 chr3L:26014145-26014265 4.19e-01 120 chr2L:740166-740286 4.45e-10 1_[+4(4.05e-06)]_1_[+2(8.27e-06)]_\ 38_[+1(4.04e-06)]_41_[+3(1.01e-06)]_7 chr3L:24028384-24028504 1.19e-02 28_[+2(1.94e-05)]_84 chrM:9767-9887 1.00e+00 120 chr3R:4400039-4400159 4.82e-04 3_[+3(1.87e-05)]_96_[+1(4.04e-06)]_\ 5 chr2R:5307154-5307274 2.79e-02 65_[+3(8.21e-06)]_47 chr4:314792-314912 1.70e-01 120 chrM:5991-6111 4.84e-01 120 chr3R:6908184-6908304 8.05e-06 40_[+1(4.04e-06)]_4_[+1(4.04e-06)]_\ 15_[+2(3.34e-05)]_37 chr3R:4232646-4232766 5.26e-02 83_[+4(1.74e-05)]_29 chr2R:5604815-5604935 8.52e-01 120 chrM:6227-6347 1.00e+00 120 chr2L:16049723-16049843 7.52e-03 13_[+2(1.94e-05)]_31_[+2(8.27e-06)]_\ 60 chr3R:21408504-21408624 4.18e-07 55_[+1(4.04e-06)]_1_[+2(1.94e-05)]_\ 4_[+4(1.54e-05)]_4_[+2(1.94e-05)]_7_[+1(4.04e-06)]_9 chr3L:25120587-25120707 2.83e-01 120 chrM:4561-4681 7.15e-01 120 chrM:12620-12740 8.04e-01 120 chr2L:12520349-12520469 2.00e-02 26_[+5(1.00e-05)]_86 chrM:7098-7218 6.09e-01 120 chr3L:27083940-27084060 3.93e-01 120 chrX:2042386-2042506 8.57e-01 120 chr2L:10736065-10736185 4.87e-01 120 chrM:13373-13493 9.56e-01 120 chr2R:24337633-24337753 7.07e-09 21_[+1(4.04e-06)]_24_[+3(4.13e-06)]_\ 6_[+2(7.24e-05)]_14_[+4(4.05e-06)]_13_[+1(1.59e-05)]_2 chr2L:8478119-8478239 1.13e-04 [+2(2.64e-05)]_48_[+1(1.59e-05)]_56 chrX:14583297-14583417 3.89e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n05.farnam.hpc.yale.internal ********************************************************************************