******************************************************************************** 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/org-1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:28851659-28851779 1.0000 120 chr3L:18881755-18881875 1.0000 120 chr3L:7349498-7349618 1.0000 120 chr3L:19845680-19845800 1.0000 120 chr2R:7953114-7953234 1.0000 120 chr2R:23668857-23668977 1.0000 120 chr2R:22508180-22508300 1.0000 120 chr2L:14527536-14527656 1.0000 120 chr3R:24007860-24007980 1.0000 120 chr2L:9864395-9864515 1.0000 120 chr3R:6353022-6353142 1.0000 120 chr2R:9756251-9756371 1.0000 120 chr2R:18202777-18202897 1.0000 120 chrX:4849528-4849648 1.0000 120 chr2R:12008872-12008992 1.0000 120 chrX:4970055-4970175 1.0000 120 chrX:4609839-4609959 1.0000 120 chr3R:15121956-15122076 1.0000 120 chr2R:12547614-12547734 1.0000 120 chr2R:12007914-12008034 1.0000 120 chr3L:22051590-22051710 1.0000 120 chr3L:11355704-11355824 1.0000 120 chr2L:13291183-13291303 1.0000 120 chr3L:15741930-15742050 1.0000 120 chr3L:3390723-3390843 1.0000 120 chr2R:8242600-8242720 1.0000 120 chr2R:11178516-11178636 1.0000 120 chr3L:11286798-11286918 1.0000 120 chr3R:12591809-12591929 1.0000 120 chr2L:18566880-18567000 1.0000 120 chrX:8542854-8542974 1.0000 120 chr3L:8584235-8584355 1.0000 120 chr3R:6665443-6665563 1.0000 120 chr2R:16096949-16097069 1.0000 120 chr3L:908508-908628 1.0000 120 chr3R:13892957-13893077 1.0000 120 chr3R:28959276-28959396 1.0000 120 chr2L:1207574-1207694 1.0000 120 chr3L:19190909-19191029 1.0000 120 chrX:8493671-8493791 1.0000 120 chr2L:3121810-3121930 1.0000 120 chr2L:1837815-1837935 1.0000 120 chr2R:11792737-11792857 1.0000 120 chrX:2708292-2708412 1.0000 120 chrX:779548-779668 1.0000 120 chr2R:7167952-7168072 1.0000 120 chr3L:12350437-12350557 1.0000 120 chr3R:8155853-8155973 1.0000 120 chr2R:18351749-18351869 1.0000 120 chr2L:3776047-3776167 1.0000 120 chr3L:16054161-16054281 1.0000 120 chr2R:11192597-11192717 1.0000 120 chr3R:26117763-26117883 1.0000 120 chr3L:20918998-20919118 1.0000 120 chr2R:24893715-24893835 1.0000 120 chr2R:24139249-24139369 1.0000 120 chr3R:25168409-25168529 1.0000 120 chr3R:23445392-23445512 1.0000 120 chr3R:30767245-30767365 1.0000 120 chr2R:21549073-21549193 1.0000 120 chr3R:8072751-8072871 1.0000 120 chr3R:6182622-6182742 1.0000 120 chr2L:8461933-8462053 1.0000 120 chr3R:31603839-31603959 1.0000 120 chrX:3745354-3745474 1.0000 120 chr2L:7957302-7957422 1.0000 120 chrX:966979-967099 1.0000 120 chr3L:3411776-3411896 1.0000 120 chrX:3288930-3289050 1.0000 120 chr3R:30718627-30718747 1.0000 120 chr3R:9675063-9675183 1.0000 120 chr2L:6088820-6088940 1.0000 120 chr2L:3435262-3435382 1.0000 120 chr3R:8784917-8785037 1.0000 120 chr3L:11540378-11540498 1.0000 120 chr3L:6612787-6612907 1.0000 120 chr3L:4220040-4220160 1.0000 120 chr2L:14499160-14499280 1.0000 120 chrX:13307403-13307523 1.0000 120 chr3R:20950398-20950518 1.0000 120 chr3R:28857386-28857506 1.0000 120 chrX:19166355-19166475 1.0000 120 chr3L:16310112-16310232 1.0000 120 chrX:16086345-16086465 1.0000 120 chr3R:29891311-29891431 1.0000 120 chr3R:16069401-16069521 1.0000 120 chrX:16385968-16386088 1.0000 120 chr2L:14245609-14245729 1.0000 120 chr2R:23567342-23567462 1.0000 120 chr2L:11338389-11338509 1.0000 120 chr3L:614854-614974 1.0000 120 chrX:10628994-10629114 1.0000 120 chrX:5095820-5095940 1.0000 120 chrX:2591714-2591834 1.0000 120 chr2L:161278-161398 1.0000 120 chr2L:3507498-3507618 1.0000 120 chrX:7995310-7995430 1.0000 120 chrX:10718061-10718181 1.0000 120 chr3L:629567-629687 1.0000 120 chr2L:18625607-18625727 1.0000 120 chr2R:15034946-15035066 1.0000 120 chr2L:20758364-20758484 1.0000 120 chrX:13404053-13404173 1.0000 120 chr2L:2494667-2494787 1.0000 120 chr3L:13232884-13233004 1.0000 120 chrX:11146925-11147045 1.0000 120 chr2L:8080788-8080908 1.0000 120 chr3R:26121987-26122107 1.0000 120 chr2L:21623776-21623896 1.0000 120 chrX:7703058-7703178 1.0000 120 chr3R:14356765-14356885 1.0000 120 chr3R:5065117-5065237 1.0000 120 chr3L:19847091-19847211 1.0000 120 chr3L:3449830-3449950 1.0000 120 chr2L:8611013-8611133 1.0000 120 chr2L:6700858-6700978 1.0000 120 chr2L:18328863-18328983 1.0000 120 chr3L:8347479-8347599 1.0000 120 chr3L:13917969-13918089 1.0000 120 chr2L:11950048-11950168 1.0000 120 chr3R:9436719-9436839 1.0000 120 chr3L:15548932-15549052 1.0000 120 chr3L:14172680-14172800 1.0000 120 chr3L:6216079-6216199 1.0000 120 chr2R:16832812-16832932 1.0000 120 chrX:10573676-10573796 1.0000 120 chrX:16650538-16650658 1.0000 120 chr3R:21188044-21188164 1.0000 120 chrX:12925990-12926110 1.0000 120 chr3L:20471090-20471210 1.0000 120 chrX:9120959-9121079 1.0000 120 chr2L:20889901-20890021 1.0000 120 chr2L:1427973-1428093 1.0000 120 chr3L:721111-721231 1.0000 120 chrX:16854787-16854907 1.0000 120 chr2R:21178847-21178967 1.0000 120 chr2L:5196816-5196936 1.0000 120 chr2R:23180949-23181069 1.0000 120 chr2R:7054284-7054404 1.0000 120 chr3R:23947163-23947283 1.0000 120 chr2R:11601930-11602050 1.0000 120 chr2L:16690111-16690231 1.0000 120 chr2L:9190441-9190561 1.0000 120 chr3R:22108463-22108583 1.0000 120 chr2L:7871933-7872053 1.0000 120 chr3R:6008355-6008475 1.0000 120 chrX:8574846-8574966 1.0000 120 chr3R:22039589-22039709 1.0000 120 chrX:8141491-8141611 1.0000 120 chr2L:21218822-21218942 1.0000 120 chr2L:17583104-17583224 1.0000 120 chr3L:19575757-19575877 1.0000 120 chrX:8677526-8677646 1.0000 120 chr2R:8002202-8002322 1.0000 120 chr3R:23387042-23387162 1.0000 120 chr3L:11534071-11534191 1.0000 120 chr3L:3305612-3305732 1.0000 120 chrX:6375750-6375870 1.0000 120 chr3R:29068954-29069074 1.0000 120 chr2R:12772869-12772989 1.0000 120 chr3R:20276068-20276188 1.0000 120 chr3L:16202656-16202776 1.0000 120 chr3L:21961973-21962093 1.0000 120 chr3L:16061071-16061191 1.0000 120 chrX:4262805-4262925 1.0000 120 chr2L:18377250-18377370 1.0000 120 chr3R:19472377-19472497 1.0000 120 chr3R:17828860-17828980 1.0000 120 chr3L:16768391-16768511 1.0000 120 chrX:18900095-18900215 1.0000 120 chr3L:8689817-8689937 1.0000 120 chr3R:27138116-27138236 1.0000 120 chr3L:21007918-21008038 1.0000 120 chr2L:20881467-20881587 1.0000 120 chr3L:20389127-20389247 1.0000 120 chr3R:26280500-26280620 1.0000 120 chr2R:17533802-17533922 1.0000 120 chr3R:6667428-6667548 1.0000 120 chr2L:221997-222117 1.0000 120 chr3R:15644919-15645039 1.0000 120 chr4:226027-226147 1.0000 120 chr3R:15250630-15250750 1.0000 120 chr2R:20126219-20126339 1.0000 120 chr2L:10565848-10565968 1.0000 120 chr3L:10847961-10848081 1.0000 120 chr2R:18994207-18994327 1.0000 120 chr2R:13999257-13999377 1.0000 120 chr2L:12487463-12487583 1.0000 120 chrX:7553523-7553643 1.0000 120 chr2L:11199183-11199303 1.0000 120 chr3L:772304-772424 1.0000 120 chr3L:16149806-16149926 1.0000 120 chr3L:10745718-10745838 1.0000 120 chr3R:24010902-24011022 1.0000 120 chr2R:7636674-7636794 1.0000 120 chr2L:19867064-19867184 1.0000 120 chr2R:15835444-15835564 1.0000 120 chr3L:6157654-6157774 1.0000 120 chr2L:21096500-21096620 1.0000 120 chr3L:22163857-22163977 1.0000 120 chr2R:13261849-13261969 1.0000 120 chr3L:1414155-1414275 1.0000 120 chr3R:10140407-10140527 1.0000 120 chr3R:10139759-10139879 1.0000 120 chrX:18921131-18921251 1.0000 120 chrX:10582181-10582301 1.0000 120 chr3R:20259549-20259669 1.0000 120 chr3R:28590647-28590767 1.0000 120 chr2R:9388631-9388751 1.0000 120 chrX:3690721-3690841 1.0000 120 chr2L:13905420-13905540 1.0000 120 chr3R:30304951-30305071 1.0000 120 chr2L:16275822-16275942 1.0000 120 chr3L:16640590-16640710 1.0000 120 chr2L:81290-81410 1.0000 120 chr2L:827716-827836 1.0000 120 chr3R:9701451-9701571 1.0000 120 chr3R:14714227-14714347 1.0000 120 chr2R:8615270-8615390 1.0000 120 chr3R:26444218-26444338 1.0000 120 chrX:4106931-4107051 1.0000 120 chrX:5698236-5698356 1.0000 120 chr2L:20911549-20911669 1.0000 120 chr3R:16223687-16223807 1.0000 120 chr2L:6339803-6339923 1.0000 120 chrX:8542143-8542263 1.0000 120 chrX:6614446-6614566 1.0000 120 chr3L:797018-797138 1.0000 120 chr2L:1123484-1123604 1.0000 120 chr3L:8751376-8751496 1.0000 120 chr3L:18226054-18226174 1.0000 120 chr2L:12351074-12351194 1.0000 120 chrX:16944177-16944297 1.0000 120 chrX:15312292-15312412 1.0000 120 chr3R:8744333-8744453 1.0000 120 chr3R:6468113-6468233 1.0000 120 chr3R:27988829-27988949 1.0000 120 chr2R:10303740-10303860 1.0000 120 chr3R:8867641-8867761 1.0000 120 chrX:15297093-15297213 1.0000 120 chr3L:20944302-20944422 1.0000 120 chr2L:11189161-11189281 1.0000 120 chr3R:31309411-31309531 1.0000 120 chr3L:10845221-10845341 1.0000 120 chr3R:21246582-21246702 1.0000 120 chr2L:20945416-20945536 1.0000 120 chr2R:21134453-21134573 1.0000 120 chrX:15384074-15384194 1.0000 120 chr3L:642927-643047 1.0000 120 chr2R:11738686-11738806 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_org-1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/org-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= 250 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= 30000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 30000 norand= no csites= 1000 Letter frequencies in dataset: A 0.319 C 0.185 G 0.184 T 0.312 Background letter frequencies (from file dataset with add-one prior applied): A 0.319 C 0.185 G 0.184 T 0.312 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCAGCCGC MEME-1 width = 8 sites = 2 llr = 26 E-value = 2.7e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C aa::aa:a probability G :::a::a: matrix T :::::::: bits 2.4 ** ***** 2.2 ** ***** 2.0 ** ***** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (18.7 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCAGCCGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:6008355-6008475 44 2.34e-06 GCAAGTTGCC CCAGCCGC AGGCAGTCGG chr3L:22051590-22051710 34 2.34e-06 TTTTTTGCCC CCAGCCGC CAACCCCGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:6008355-6008475 2.3e-06 43_[+1]_69 chr3L:22051590-22051710 2.3e-06 33_[+1]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCAGCCGC width=8 seqs=2 chr3R:6008355-6008475 ( 44) CCAGCCGC 1 chr3L:22051590-22051710 ( 34) CCAGCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.7e+005 -765 243 -765 -765 -765 243 -765 -765 164 -765 -765 -765 -765 -765 243 -765 -765 243 -765 -765 -765 243 -765 -765 -765 -765 243 -765 -765 243 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.7e+005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCGC MEME-1 regular expression -------------------------------------------------------------------------------- CCAGCCGC -------------------------------------------------------------------------------- Time 7.41 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGGCCGG MEME-2 width = 8 sites = 2 llr = 27 E-value = 1.1e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C aa::aa:: probability G ::aa::aa matrix T :::::::: bits 2.4 ******** 2.2 ******** 2.0 ******** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (19.5 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCGGCCGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:12925990-12926110 113 1.34e-06 CACTTGGCCA CCGGCCGG chr2R:7953114-7953234 8 1.34e-06 CCGGACT CCGGCCGG AATCTAATTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:12925990-12926110 1.3e-06 112_[+2] chr2R:7953114-7953234 1.3e-06 7_[+2]_105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGGCCGG width=8 seqs=2 chrX:12925990-12926110 ( 113) CCGGCCGG 1 chr2R:7953114-7953234 ( 8) CCGGCCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.1e+005 -765 243 -765 -765 -765 243 -765 -765 -765 -765 243 -765 -765 -765 243 -765 -765 243 -765 -765 -765 243 -765 -765 -765 -765 243 -765 -765 -765 243 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.1e+005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGCCGG MEME-2 regular expression -------------------------------------------------------------------------------- CCGGCCGG -------------------------------------------------------------------------------- Time 13.67 secs. ******************************************************************************** ******************************************************************************** MOTIF CGCCTGCC MEME-3 width = 8 sites = 2 llr = 26 E-value = 2.0e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a:aa::aa probability G :a:::a:: matrix T ::::a::: bits 2.4 **** *** 2.2 **** *** 2.0 **** *** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (18.7 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CGCCTGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:6700858-6700978 22 2.29e-06 TCGGTTATTT CGCCTGCC ACAGATTACA chr2R:23567342-23567462 29 2.29e-06 TGTTTGTATT CGCCTGCC AGCCGGCAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:6700858-6700978 2.3e-06 21_[+3]_91 chr2R:23567342-23567462 2.3e-06 28_[+3]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGCCTGCC width=8 seqs=2 chr2L:6700858-6700978 ( 22) CGCCTGCC 1 chr2R:23567342-23567462 ( 29) CGCCTGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 2.0e+005 -765 243 -765 -765 -765 -765 243 -765 -765 243 -765 -765 -765 243 -765 -765 -765 -765 -765 168 -765 -765 243 -765 -765 243 -765 -765 -765 243 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.0e+005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTGCC MEME-3 regular expression -------------------------------------------------------------------------------- CGCCTGCC -------------------------------------------------------------------------------- Time 19.93 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCCAGC MEME-4 width = 8 sites = 2 llr = 26 E-value = 2.7e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C :a:aa::a probability G a:a:::a: matrix T :::::::: bits 2.4 ***** ** 2.2 ***** ** 2.0 ***** ** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (18.7 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCGCCAGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:6612787-6612907 82 2.33e-06 CGTACACAAA GCGCCAGC GACAATTACA chr2R:21549073-21549193 112 2.33e-06 TGCGCATTGT GCGCCAGC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:6612787-6612907 2.3e-06 81_[+4]_31 chr2R:21549073-21549193 2.3e-06 111_[+4]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCCAGC width=8 seqs=2 chr3L:6612787-6612907 ( 82) GCGCCAGC 1 chr2R:21549073-21549193 ( 112) GCGCCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.0201 E= 2.7e+005 -765 -765 243 -765 -765 243 -765 -765 -765 -765 243 -765 -765 243 -765 -765 -765 243 -765 -765 164 -765 -765 -765 -765 -765 243 -765 -765 243 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.7e+005 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCCAGC MEME-4 regular expression -------------------------------------------------------------------------------- GCGCCAGC -------------------------------------------------------------------------------- Time 26.22 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGRGC MEME-5 width = 8 sites = 2 llr = 25 E-value = 5.6e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::5:: pos.-specific C ::a::::a probability G aa:aa5a: matrix T :::::::: bits 2.4 ***** ** 2.2 ***** ** 2.0 ***** ** 1.7 ***** ** Relative 1.5 ***** ** Entropy 1.2 ***** ** (18.1 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGCGGAGC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:7553523-7553643 110 1.33e-06 TGGGCGAAGG GGCGGGGC GAA chr3L:3390723-3390843 23 3.63e-06 gtGTTACAGG GGCGGAGC AGGCGGCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:7553523-7553643 1.3e-06 109_[+5]_3 chr3L:3390723-3390843 3.6e-06 22_[+5]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGGRGC width=8 seqs=2 chrX:7553523-7553643 ( 110) GGCGGGGC 1 chr3L:3390723-3390843 ( 23) GGCGGAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 5.6e+005 -765 -765 243 -765 -765 -765 243 -765 -765 243 -765 -765 -765 -765 243 -765 -765 -765 243 -765 65 -765 144 -765 -765 -765 243 -765 -765 243 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.6e+005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGRGC MEME-5 regular expression -------------------------------------------------------------------------------- GGCGG[AG]GC -------------------------------------------------------------------------------- Time 32.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:28851659-28851779 1.32e-01 120 chr3L:18881755-18881875 1.14e-01 120 chr3L:7349498-7349618 6.04e-01 120 chr3L:19845680-19845800 7.99e-01 120 chr2R:7953114-7953234 1.85e-05 7_[+2(1.34e-06)]_105 chr2R:23668857-23668977 2.09e-03 43_[+3(7.81e-05)]_69 chr2R:22508180-22508300 1.00e+00 120 chr2L:14527536-14527656 3.28e-01 120 chr3R:24007860-24007980 9.09e-01 120 chr2L:9864395-9864515 6.95e-01 120 chr3R:6353022-6353142 8.56e-01 120 chr2R:9756251-9756371 6.55e-01 120 chr2R:18202777-18202897 5.28e-02 120 chrX:4849528-4849648 5.69e-02 48_[+4(7.93e-05)]_64 chr2R:12008872-12008992 2.55e-02 120 chrX:4970055-4970175 1.00e+00 120 chrX:4609839-4609959 7.25e-01 120 chr3R:15121956-15122076 8.06e-01 120 chr2R:12547614-12547734 8.86e-01 120 chr2R:12007914-12008034 2.58e-01 120 chr3L:22051590-22051710 4.11e-05 33_[+1(2.34e-06)]_79 chr3L:11355704-11355824 6.49e-01 120 chr2L:13291183-13291303 2.91e-01 120 chr3L:15741930-15742050 8.81e-01 120 chr3L:3390723-3390843 1.06e-03 22_[+5(3.63e-06)]_90 chr2R:8242600-8242720 6.65e-02 120 chr2R:11178516-11178636 7.63e-01 120 chr3L:11286798-11286918 9.03e-01 120 chr3R:12591809-12591929 9.75e-01 120 chr2L:18566880-18567000 9.96e-01 120 chrX:8542854-8542974 1.00e+00 120 chr3L:8584235-8584355 5.77e-01 120 chr3R:6665443-6665563 4.10e-02 120 chr2R:16096949-16097069 9.52e-01 120 chr3L:908508-908628 8.41e-01 120 chr3R:13892957-13893077 9.99e-01 120 chr3R:28959276-28959396 9.99e-01 120 chr2L:1207574-1207694 9.99e-01 120 chr3L:19190909-19191029 9.94e-01 120 chrX:8493671-8493791 9.28e-01 120 chr2L:3121810-3121930 3.71e-01 120 chr2L:1837815-1837935 2.63e-03 6_[+1(7.96e-05)]_106 chr2R:11792737-11792857 7.99e-02 120 chrX:2708292-2708412 1.82e-01 120 chrX:779548-779668 9.99e-01 120 chr2R:7167952-7168072 6.90e-03 120 chr3L:12350437-12350557 1.16e-01 10_[+5(4.84e-05)]_102 chr3R:8155853-8155973 8.85e-01 120 chr2R:18351749-18351869 6.88e-01 120 chr2L:3776047-3776167 9.38e-01 120 chr3L:16054161-16054281 9.39e-01 120 chr2R:11192597-11192717 6.56e-01 120 chr3R:26117763-26117883 9.26e-01 120 chr3L:20918998-20919118 9.36e-01 120 chr2R:24893715-24893835 9.97e-01 120 chr2R:24139249-24139369 2.32e-01 120 chr3R:25168409-25168529 9.96e-01 120 chr3R:23445392-23445512 4.77e-01 120 chr3R:30767245-30767365 7.66e-03 38_[+3(7.81e-05)]_74 chr2R:21549073-21549193 8.32e-05 111_[+4(2.33e-06)]_1 chr3R:8072751-8072871 8.01e-01 120 chr3R:6182622-6182742 7.48e-01 120 chr2L:8461933-8462053 9.86e-01 120 chr3R:31603839-31603959 8.31e-03 108_[+3(7.81e-05)]_4 chrX:3745354-3745474 1.00e+00 120 chr2L:7957302-7957422 3.74e-01 120 chrX:966979-967099 1.00e+00 120 chr3L:3411776-3411896 9.98e-01 120 chrX:3288930-3289050 6.39e-01 120 chr3R:30718627-30718747 9.77e-01 120 chr3R:9675063-9675183 9.98e-01 120 chr2L:6088820-6088940 1.00e+00 120 chr2L:3435262-3435382 1.26e-02 106_[+3(7.81e-05)]_6 chr3R:8784917-8785037 1.00e+00 120 chr3L:11540378-11540498 7.52e-01 120 chr3L:6612787-6612907 1.20e-03 81_[+4(2.33e-06)]_31 chr3L:4220040-4220160 3.40e-01 120 chr2L:14499160-14499280 9.71e-01 120 chrX:13307403-13307523 7.04e-01 120 chr3R:20950398-20950518 3.15e-01 120 chr3R:28857386-28857506 1.00e+00 120 chrX:19166355-19166475 5.45e-01 120 chr3L:16310112-16310232 7.92e-01 120 chrX:16086345-16086465 2.62e-01 120 chr3R:29891311-29891431 2.02e-02 120 chr3R:16069401-16069521 2.24e-01 120 chrX:16385968-16386088 5.28e-01 120 chr2L:14245609-14245729 9.96e-01 120 chr2R:23567342-23567462 1.41e-06 28_[+3(2.29e-06)]_84 chr2L:11338389-11338509 9.96e-01 120 chr3L:614854-614974 2.67e-01 120 chrX:10628994-10629114 1.00e+00 120 chrX:5095820-5095940 9.28e-01 120 chrX:2591714-2591834 6.87e-01 120 chr2L:161278-161398 4.24e-01 120 chr2L:3507498-3507618 9.51e-01 120 chrX:7995310-7995430 9.96e-02 120 chrX:10718061-10718181 9.96e-01 120 chr3L:629567-629687 9.31e-01 120 chr2L:18625607-18625727 9.18e-01 120 chr2R:15034946-15035066 2.63e-03 71_[+4(7.93e-05)]_41 chr2L:20758364-20758484 8.80e-01 120 chrX:13404053-13404173 9.55e-01 120 chr2L:2494667-2494787 5.45e-01 120 chr3L:13232884-13233004 1.23e-01 120 chrX:11146925-11147045 1.13e-01 120 chr2L:8080788-8080908 8.80e-01 120 chr3R:26121987-26122107 9.87e-01 120 chr2L:21623776-21623896 9.90e-01 120 chrX:7703058-7703178 1.00e+00 120 chr3R:14356765-14356885 9.86e-01 120 chr3R:5065117-5065237 8.81e-01 120 chr3L:19847091-19847211 7.55e-01 120 chr3L:3449830-3449950 9.46e-01 120 chr2L:8611013-8611133 9.69e-01 120 chr2L:6700858-6700978 9.38e-05 21_[+3(2.29e-06)]_91 chr2L:18328863-18328983 8.33e-01 120 chr3L:8347479-8347599 6.59e-03 72_[+4(7.93e-05)]_40 chr3L:13917969-13918089 9.47e-01 120 chr2L:11950048-11950168 1.00e+00 120 chr3R:9436719-9436839 8.59e-02 120 chr3L:15548932-15549052 6.04e-01 120 chr3L:14172680-14172800 1.00e+00 120 chr3L:6216079-6216199 8.82e-01 120 chr2R:16832812-16832932 3.02e-01 120 chrX:10573676-10573796 1.00e+00 120 chrX:16650538-16650658 9.86e-01 120 chr3R:21188044-21188164 4.70e-01 120 chrX:12925990-12926110 5.84e-05 112_[+2(1.34e-06)] chr3L:20471090-20471210 5.35e-01 120 chrX:9120959-9121079 9.99e-01 120 chr2L:20889901-20890021 6.65e-02 120 chr2L:1427973-1428093 9.50e-01 120 chr3L:721111-721231 9.57e-01 120 chrX:16854787-16854907 4.67e-01 120 chr2R:21178847-21178967 1.17e-03 120 chr2L:5196816-5196936 4.58e-02 23_[+5(4.84e-05)]_89 chr2R:23180949-23181069 2.91e-01 120 chr2R:7054284-7054404 9.87e-01 120 chr3R:23947163-23947283 5.93e-01 120 chr2R:11601930-11602050 9.76e-01 120 chr2L:16690111-16690231 9.50e-01 120 chr2L:9190441-9190561 6.54e-01 120 chr3R:22108463-22108583 9.99e-01 120 chr2L:7871933-7872053 9.74e-01 120 chr3R:6008355-6008475 4.89e-07 43_[+1(2.34e-06)]_9_[+5(4.84e-05)]_\ 52 chrX:8574846-8574966 1.00e+00 120 chr3R:22039589-22039709 1.00e+00 120 chrX:8141491-8141611 1.67e-01 43_[+1(7.96e-05)]_69 chr2L:21218822-21218942 8.33e-01 120 chr2L:17583104-17583224 9.01e-01 120 chr3L:19575757-19575877 6.71e-02 120 chrX:8677526-8677646 8.29e-01 120 chr2R:8002202-8002322 3.73e-01 120 chr3R:23387042-23387162 1.00e+00 120 chr3L:11534071-11534191 9.99e-01 120 chr3L:3305612-3305732 2.89e-01 120 chrX:6375750-6375870 8.86e-01 120 chr3R:29068954-29069074 9.75e-01 120 chr2R:12772869-12772989 9.87e-01 120 chr3R:20276068-20276188 2.56e-01 120 chr3L:16202656-16202776 1.00e+00 120 chr3L:21961973-21962093 4.93e-01 120 chr3L:16061071-16061191 5.39e-01 120 chrX:4262805-4262925 5.81e-01 120 chr2L:18377250-18377370 7.98e-01 120 chr3R:19472377-19472497 2.56e-01 120 chr3R:17828860-17828980 6.86e-01 120 chr3L:16768391-16768511 6.87e-01 120 chrX:18900095-18900215 1.00e+00 120 chr3L:8689817-8689937 2.00e-02 120 chr3R:27138116-27138236 7.52e-01 120 chr3L:21007918-21008038 9.64e-01 120 chr2L:20881467-20881587 5.87e-01 120 chr3L:20389127-20389247 9.54e-01 120 chr3R:26280500-26280620 9.96e-01 120 chr2R:17533802-17533922 1.00e+00 120 chr3R:6667428-6667548 1.00e+00 120 chr2L:221997-222117 2.93e-01 120 chr3R:15644919-15645039 6.10e-01 120 chr4:226027-226147 9.69e-01 120 chr3R:15250630-15250750 1.00e+00 120 chr2R:20126219-20126339 1.47e-01 120 chr2L:10565848-10565968 9.87e-01 120 chr3L:10847961-10848081 9.98e-01 120 chr2R:18994207-18994327 1.00e+00 120 chr2R:13999257-13999377 9.96e-01 120 chr2L:12487463-12487583 2.25e-01 120 chrX:7553523-7553643 1.67e-05 74_[+2(4.88e-05)]_27_[+5(1.33e-06)]_\ 3 chr2L:11199183-11199303 9.78e-01 120 chr3L:772304-772424 9.94e-01 120 chr3L:16149806-16149926 9.96e-01 120 chr3L:10745718-10745838 1.00e+00 120 chr3R:24010902-24011022 9.22e-01 120 chr2R:7636674-7636794 3.71e-01 120 chr2L:19867064-19867184 9.92e-01 120 chr2R:15835444-15835564 1.00e+00 120 chr3L:6157654-6157774 9.99e-01 120 chr2L:21096500-21096620 1.00e+00 120 chr3L:22163857-22163977 9.42e-02 120 chr2R:13261849-13261969 1.00e+00 120 chr3L:1414155-1414275 8.15e-01 120 chr3R:10140407-10140527 1.00e+00 120 chr3R:10139759-10139879 3.05e-01 120 chrX:18921131-18921251 4.74e-01 120 chrX:10582181-10582301 3.43e-01 120 chr3R:20259549-20259669 9.97e-01 120 chr3R:28590647-28590767 2.35e-01 120 chr2R:9388631-9388751 9.99e-01 120 chrX:3690721-3690841 5.89e-01 120 chr2L:13905420-13905540 9.94e-01 120 chr3R:30304951-30305071 9.91e-01 120 chr2L:16275822-16275942 9.60e-01 120 chr3L:16640590-16640710 9.47e-01 120 chr2L:81290-81410 4.68e-01 120 chr2L:827716-827836 4.77e-01 120 chr3R:9701451-9701571 3.74e-01 120 chr3R:14714227-14714347 7.76e-03 71_[+4(7.93e-05)]_41 chr2R:8615270-8615390 2.67e-02 25_[+3(7.81e-05)]_87 chr3R:26444218-26444338 9.99e-01 120 chrX:4106931-4107051 9.90e-01 120 chrX:5698236-5698356 9.60e-01 120 chr2L:20911549-20911669 1.07e-01 120 chr3R:16223687-16223807 5.45e-01 120 chr2L:6339803-6339923 5.78e-01 120 chrX:8542143-8542263 1.00e+00 120 chrX:6614446-6614566 9.99e-01 120 chr3L:797018-797138 9.87e-01 120 chr2L:1123484-1123604 7.56e-01 120 chr3L:8751376-8751496 1.00e+00 120 chr3L:18226054-18226174 1.00e+00 120 chr2L:12351074-12351194 1.00e+00 120 chrX:16944177-16944297 1.00e+00 120 chrX:15312292-15312412 9.58e-01 120 chr3R:8744333-8744453 9.95e-01 120 chr3R:6468113-6468233 1.00e+00 120 chr3R:27988829-27988949 1.00e+00 120 chr2R:10303740-10303860 1.27e-02 65_[+3(7.81e-05)]_47 chr3R:8867641-8867761 6.08e-01 120 chrX:15297093-15297213 1.00e+00 120 chr3L:20944302-20944422 5.02e-02 87_[+4(7.93e-05)]_25 chr2L:11189161-11189281 5.02e-01 120 chr3R:31309411-31309531 4.75e-01 120 chr3L:10845221-10845341 2.13e-01 43_[+5(4.84e-05)]_69 chr3R:21246582-21246702 2.42e-01 107_[+4(7.93e-05)]_5 chr2L:20945416-20945536 1.00e+00 120 chr2R:21134453-21134573 6.32e-01 120 chrX:15384074-15384194 9.90e-01 120 chr3L:642927-643047 3.92e-01 120 chr2R:11738686-11738806 9.71e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n12.farnam.hpc.yale.internal ********************************************************************************