******************************************************************************** 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/emc.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:6406447-6406567 1.0000 120 chr3L:10866738-10866858 1.0000 120 chrX:10473695-10473815 1.0000 120 chr2R:17161069-17161189 1.0000 120 chr2R:13586384-13586504 1.0000 120 chrX:5084921-5085041 1.0000 120 chr3L:11258572-11258692 1.0000 120 chr3L:7861172-7861292 1.0000 120 chrX:3399482-3399602 1.0000 120 chr4:1181842-1181962 1.0000 120 chr2R:14488542-14488662 1.0000 120 chr3L:4186822-4186942 1.0000 120 chr3L:20395360-20395480 1.0000 120 chr2R:23554569-23554689 1.0000 120 chr2L:5946102-5946222 1.0000 120 chr2R:24748886-24749006 1.0000 120 chr2L:20078984-20079104 1.0000 120 chr3R:9055249-9055369 1.0000 120 chrX:6310527-6310647 1.0000 120 chr2L:18666064-18666184 1.0000 120 chr2L:6479775-6479895 1.0000 120 chr3R:20555136-20555256 1.0000 120 chr2L:8610926-8611046 1.0000 120 chr3L:8440862-8440982 1.0000 120 chr2R:20994820-20994940 1.0000 120 chr2R:12757519-12757639 1.0000 120 chr3L:20276746-20276866 1.0000 120 chr2R:21721032-21721152 1.0000 120 chr3R:28429716-28429836 1.0000 120 chr2R:18172396-18172516 1.0000 120 chr3L:1139530-1139650 1.0000 120 chr2L:5980994-5981114 1.0000 120 chr3L:4413160-4413280 1.0000 120 chr2L:10061478-10061598 1.0000 120 chr2R:7052513-7052633 1.0000 120 chr3R:11671888-11672008 1.0000 120 chr2L:6339630-6339750 1.0000 120 chrX:11137704-11137824 1.0000 120 chr3R:13683821-13683941 1.0000 120 chr3L:9972602-9972722 1.0000 120 chr3L:2265820-2265940 1.0000 120 chr3R:5063502-5063622 1.0000 120 chr2R:11453808-11453928 1.0000 120 chrX:13391257-13391377 1.0000 120 chr3R:25215268-25215388 1.0000 120 chr3L:3411742-3411862 1.0000 120 chrX:3390038-3390158 1.0000 120 chrX:10488013-10488133 1.0000 120 chr2R:7492691-7492811 1.0000 120 chrX:14839838-14839958 1.0000 120 chr2R:20832469-20832589 1.0000 120 chr3L:13923487-13923607 1.0000 120 chr2L:7037929-7038049 1.0000 120 chr2L:12467926-12468046 1.0000 120 chr2R:19129532-19129652 1.0000 120 chrX:20257387-20257507 1.0000 120 chrX:18405086-18405206 1.0000 120 chrX:1478437-1478557 1.0000 120 chr3L:21349040-21349160 1.0000 120 chr3L:14190116-14190236 1.0000 120 chr3R:5300742-5300862 1.0000 120 chr2R:17062633-17062753 1.0000 120 chr3L:18621226-18621346 1.0000 120 chr2L:20807761-20807881 1.0000 120 chrX:19505683-19505803 1.0000 120 chr3R:4220907-4221027 1.0000 120 chrX:15653643-15653763 1.0000 120 chr3L:4239602-4239722 1.0000 120 chrX:9137300-9137420 1.0000 120 chr2L:21156230-21156350 1.0000 120 chr3R:20948097-20948217 1.0000 120 chrX:1392915-1393035 1.0000 120 chr2R:6652963-6653083 1.0000 120 chr2L:21309984-21310104 1.0000 120 chr2L:19155111-19155231 1.0000 120 chr2L:283222-283342 1.0000 120 chr3R:26172131-26172251 1.0000 120 chr3L:21954609-21954729 1.0000 120 chr3R:23028651-23028771 1.0000 120 chr2L:9938795-9938915 1.0000 120 chr2L:18377352-18377472 1.0000 120 chr2R:15114510-15114630 1.0000 120 chrX:5082970-5083090 1.0000 120 chr2R:23818412-23818532 1.0000 120 chr2L:7219987-7220107 1.0000 120 chr3R:24333314-24333434 1.0000 120 chr3L:6189706-6189826 1.0000 120 chr3L:7912038-7912158 1.0000 120 chr3R:5758972-5759092 1.0000 120 chr3R:5588282-5588402 1.0000 120 chr3L:21130975-21131095 1.0000 120 chr3L:11449028-11449148 1.0000 120 chrX:1322374-1322494 1.0000 120 chr2R:10117575-10117695 1.0000 120 chr2L:3042208-3042328 1.0000 120 chr3R:28887960-28888080 1.0000 120 chr2R:8900150-8900270 1.0000 120 chr3R:30796845-30796965 1.0000 120 chrX:6741217-6741337 1.0000 120 chr2L:18567757-18567877 1.0000 120 chr2L:11829426-11829546 1.0000 120 chr3L:22163770-22163890 1.0000 120 chrX:5285935-5286055 1.0000 120 chr3R:15472869-15472989 1.0000 120 chr2R:23856927-23857047 1.0000 120 chr3L:15626166-15626286 1.0000 120 chr3L:20309920-20310040 1.0000 120 chr2R:19669808-19669928 1.0000 120 chrX:10768250-10768370 1.0000 120 chr2R:15848058-15848178 1.0000 120 chr3L:9128129-9128249 1.0000 120 chr3R:10350839-10350959 1.0000 120 chr2R:9440437-9440557 1.0000 120 chr3R:20312985-20313105 1.0000 120 chr3R:27131488-27131608 1.0000 120 chr3R:13676274-13676394 1.0000 120 chrX:8113560-8113680 1.0000 120 chr3R:5474683-5474803 1.0000 120 chr2L:18443232-18443352 1.0000 120 chr3R:7813941-7814061 1.0000 120 chr3L:18870134-18870254 1.0000 120 chr2R:16608350-16608470 1.0000 120 chr3R:20835096-20835216 1.0000 120 chrX:2588747-2588867 1.0000 120 chr3R:12718269-12718389 1.0000 120 chr3R:20327987-20328107 1.0000 120 chr3L:16165784-16165904 1.0000 120 chr3R:5264746-5264866 1.0000 120 chrX:17881265-17881385 1.0000 120 chrX:1907876-1907996 1.0000 120 chr3R:4387636-4387756 1.0000 120 chr3L:11350992-11351112 1.0000 120 chr3L:16011783-16011903 1.0000 120 chr2R:11636052-11636172 1.0000 120 chr2R:18151498-18151618 1.0000 120 chr3R:31252708-31252828 1.0000 120 chr3R:23332758-23332878 1.0000 120 chr2L:7262175-7262295 1.0000 120 chrX:15599734-15599854 1.0000 120 chr2L:21657531-21657651 1.0000 120 chr2R:12605799-12605919 1.0000 120 chr3L:14762334-14762454 1.0000 120 chr3L:11483288-11483408 1.0000 120 chr3R:22356566-22356686 1.0000 120 chr3L:12572500-12572620 1.0000 120 chr2R:15991251-15991371 1.0000 120 chr2R:7466748-7466868 1.0000 120 chr2R:23067129-23067249 1.0000 120 chrX:8517358-8517478 1.0000 120 chr2L:2883099-2883219 1.0000 120 chr2R:18411946-18412066 1.0000 120 chrX:2094160-2094280 1.0000 120 chrX:20525091-20525211 1.0000 120 chr3R:23240388-23240508 1.0000 120 chr3R:7907468-7907588 1.0000 120 chr3R:12961601-12961721 1.0000 120 chr2R:17892982-17893102 1.0000 120 chr3R:20830387-20830507 1.0000 120 chr3R:29148206-29148326 1.0000 120 chr2R:19205331-19205451 1.0000 120 chr2R:17871989-17872109 1.0000 120 chr3R:26188837-26188957 1.0000 120 chr3R:15794521-15794641 1.0000 120 chr3L:18786810-18786930 1.0000 120 chr3R:19623760-19623880 1.0000 120 chr2L:13549216-13549336 1.0000 120 chr3R:31215918-31216038 1.0000 120 chr2L:2885183-2885303 1.0000 120 chr2R:10874719-10874839 1.0000 120 chr2R:7278199-7278319 1.0000 120 chrX:3363827-3363947 1.0000 120 chr3L:22868228-22868348 1.0000 120 chr2L:17470764-17470884 1.0000 120 chr3R:4970825-4970945 1.0000 120 chr3L:21177030-21177150 1.0000 120 chr3L:1861931-1862051 1.0000 120 chr3R:13999716-13999836 1.0000 120 chr3R:30601824-30601944 1.0000 120 chr2L:18152395-18152515 1.0000 120 chr3R:8670665-8670785 1.0000 120 chr3L:17016222-17016342 1.0000 120 chr3R:14036101-14036221 1.0000 120 chrX:20656794-20656914 1.0000 120 chr3R:14707057-14707177 1.0000 120 chrX:245795-245915 1.0000 120 chr3R:10109968-10110088 1.0000 120 chr3L:19687340-19687460 1.0000 120 chr3R:21487907-21488027 1.0000 120 chrX:1953057-1953177 1.0000 120 chr3L:6576857-6576977 1.0000 120 chrX:2534022-2534142 1.0000 120 chr2R:21076394-21076514 1.0000 120 chrX:6346958-6347078 1.0000 120 chr2R:8082817-8082937 1.0000 120 chr3L:7882299-7882419 1.0000 120 chr2R:5974466-5974586 1.0000 120 chr3L:2501932-2502052 1.0000 120 chr3L:21828319-21828439 1.0000 120 chr3L:1865311-1865431 1.0000 120 chr4:486667-486787 1.0000 120 chr2L:18138048-18138168 1.0000 120 chr3R:12369474-12369594 1.0000 120 chr2R:7565592-7565712 1.0000 120 chr3L:16004917-16005037 1.0000 120 chr2L:1986802-1986922 1.0000 120 chr2R:13577646-13577766 1.0000 120 chr3R:11458699-11458819 1.0000 120 chr2R:9862729-9862849 1.0000 120 chr3R:13779395-13779515 1.0000 120 chr3L:21347340-21347460 1.0000 120 chr2L:13515070-13515190 1.0000 120 chrX:7334185-7334305 1.0000 120 chr3R:8660409-8660529 1.0000 120 chr3R:5547766-5547886 1.0000 120 chr3L:14217822-14217942 1.0000 120 chr2L:9759044-9759164 1.0000 120 chrX:8114590-8114710 1.0000 120 chr3R:31977637-31977757 1.0000 120 chr3R:27407208-27407328 1.0000 120 chr3L:2733349-2733469 1.0000 120 chr2L:9490961-9491081 1.0000 120 chr3L:8768012-8768132 1.0000 120 chr2L:11269071-11269191 1.0000 120 chr2R:9137897-9138017 1.0000 120 chrX:2270729-2270849 1.0000 120 chr2R:23366586-23366706 1.0000 120 chrX:2919868-2919988 1.0000 120 chr3R:8663979-8664099 1.0000 120 chr2R:17215947-17216067 1.0000 120 chr3L:749584-749704 1.0000 120 chr3R:24771626-24771746 1.0000 120 chr3R:28332496-28332616 1.0000 120 chr2R:7489219-7489339 1.0000 120 chrX:3025645-3025765 1.0000 120 chrX:2070783-2070903 1.0000 120 chr3R:18439475-18439595 1.0000 120 chr3R:6368176-6368296 1.0000 120 chr2R:10158689-10158809 1.0000 120 chr3R:14473750-14473870 1.0000 120 chrX:19247471-19247591 1.0000 120 chr3L:563109-563229 1.0000 120 chrX:12217739-12217859 1.0000 120 chr2R:12150355-12150475 1.0000 120 chr2R:14164902-14165022 1.0000 120 chr2L:7434056-7434176 1.0000 120 chr3L:347172-347292 1.0000 120 chrX:7286223-7286343 1.0000 120 chr2L:8000769-8000889 1.0000 120 chr2L:6557476-6557596 1.0000 120 chr2R:14574973-14575093 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_emc/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/emc.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 0.292 C 0.201 G 0.205 T 0.302 Background letter frequencies (from file dataset with add-one prior applied): A 0.292 C 0.201 G 0.205 T 0.302 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CAGKGYTG MEME-1 width = 8 sites = 27 llr = 251 E-value = 2.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :a:::::: pos.-specific C a::236:: probability G ::a57::a matrix T :::3:4a: bits 2.3 * * * 2.1 * * * 1.9 *** * 1.6 *** ** Relative 1.4 *** * ** Entropy 1.2 *** * ** (13.4 bits) 0.9 *** **** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CAGGGCTG consensus TCT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:11269071-11269191 52 6.29e-06 TCTTATCCCA CAGGGCTG CATTAACATT chr3R:5547766-5547886 73 6.29e-06 CACGGTTGAC CAGGGCTG CACTAGCAAG chr3R:8660409-8660529 11 6.29e-06 TCTAAAAAAT CAGGGCTG CTTTAGCACG chr3R:4970825-4970945 11 6.29e-06 ATACAGTTAT CAGGGCTG CATAGGTCTT chr2L:2883099-2883219 28 6.29e-06 TAACATGTGC CAGGGCTG CAGAGTCCGT chr3L:11350992-11351112 21 6.29e-06 TACTGTTTCC CAGGGCTG CCAAATCAGA chr3R:20327987-20328107 35 6.29e-06 ATCGGCCGGC CAGGGCTG GTGGCGCTAG chr2L:18443232-18443352 74 6.29e-06 GTTTGGCAAC CAGGGCTG ACATTTTTAC chr2R:9137897-9138017 19 1.57e-05 AGAGCACACG CAGGGTTG CTTTCCCGTG chrX:5082970-5083090 60 1.57e-05 TAGTGTTGCG CAGGGTTG CATTCGGCGG chr2L:21309984-21310104 49 1.57e-05 ACCATCCCAT CAGGGTTG TCAAGCATTT chr3L:19687340-19687460 106 2.50e-05 CTGAACAGTC CAGTGCTG CAAGAGG chrX:245795-245915 41 2.50e-05 ACGCCTTTGC CAGTGCTG CCCTATCAAA chr2R:7466748-7466868 79 3.74e-05 CGTTTTCCGT CAGCGCTG GTCACACCGC chr3R:4220907-4221027 36 3.74e-05 GATGGTGAGC CAGGCCTG CGCGATCAAG chr2L:11829426-11829546 42 5.13e-05 ATCGGCTGGC CAGTGTTG GTAAACATTA chr2L:9938795-9938915 73 5.13e-05 GGAAATTAGT CAGTGTTG AAAAGCGAAT chr2R:20832469-20832589 97 5.13e-05 CAACAAAGCG CAGTGTTG TAAAGTGCCA chr2R:12757519-12757639 8 5.13e-05 TGACAAG CAGTGTTG GAAACGTCCT chr3R:14036101-14036221 82 6.98e-05 TGCTGCGTGT CAGCGTTG CCACCTGTCT chr3R:5758972-5759092 19 6.98e-05 AGAAATACCA CAGGCTTG TCAAACTATC chr2R:19129532-19129652 61 8.50e-05 GGTGGTTGTG CAGCCCTG CATCGCGTTG chr2L:7037929-7038049 66 8.50e-05 GTTTCGACTG CAGCCCTG GTTCTTGCAT chr2R:20994820-20994940 53 8.50e-05 ATCTAGTTTG CAGCCCTG GTACCGCTTT chr3R:27407208-27407328 21 1.05e-04 GTTTAAATGG CAGTCTTG TTTAATTACT chr3L:21954609-21954729 73 1.05e-04 gtgggcgttg cagtcttg tgcggtttat chr3R:13683821-13683941 26 1.05e-04 GGTGGCGTCA CAGGGGTG CTAGAGTTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:11269071-11269191 6.3e-06 51_[+1]_61 chr3R:5547766-5547886 6.3e-06 72_[+1]_40 chr3R:8660409-8660529 6.3e-06 10_[+1]_102 chr3R:4970825-4970945 6.3e-06 10_[+1]_102 chr2L:2883099-2883219 6.3e-06 27_[+1]_85 chr3L:11350992-11351112 6.3e-06 20_[+1]_92 chr3R:20327987-20328107 6.3e-06 34_[+1]_78 chr2L:18443232-18443352 6.3e-06 73_[+1]_39 chr2R:9137897-9138017 1.6e-05 18_[+1]_94 chrX:5082970-5083090 1.6e-05 59_[+1]_53 chr2L:21309984-21310104 1.6e-05 48_[+1]_64 chr3L:19687340-19687460 2.5e-05 105_[+1]_7 chrX:245795-245915 2.5e-05 40_[+1]_72 chr2R:7466748-7466868 3.7e-05 78_[+1]_34 chr3R:4220907-4221027 3.7e-05 35_[+1]_77 chr2L:11829426-11829546 5.1e-05 41_[+1]_71 chr2L:9938795-9938915 5.1e-05 72_[+1]_40 chr2R:20832469-20832589 5.1e-05 96_[+1]_16 chr2R:12757519-12757639 5.1e-05 7_[+1]_105 chr3R:14036101-14036221 7e-05 81_[+1]_31 chr3R:5758972-5759092 7e-05 18_[+1]_94 chr2R:19129532-19129652 8.5e-05 60_[+1]_52 chr2L:7037929-7038049 8.5e-05 65_[+1]_47 chr2R:20994820-20994940 8.5e-05 52_[+1]_60 chr3R:27407208-27407328 0.00011 20_[+1]_92 chr3L:21954609-21954729 0.00011 72_[+1]_40 chr3R:13683821-13683941 0.00011 25_[+1]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGKGYTG width=8 seqs=27 chr2L:11269071-11269191 ( 52) CAGGGCTG 1 chr3R:5547766-5547886 ( 73) CAGGGCTG 1 chr3R:8660409-8660529 ( 11) CAGGGCTG 1 chr3R:4970825-4970945 ( 11) CAGGGCTG 1 chr2L:2883099-2883219 ( 28) CAGGGCTG 1 chr3L:11350992-11351112 ( 21) CAGGGCTG 1 chr3R:20327987-20328107 ( 35) CAGGGCTG 1 chr2L:18443232-18443352 ( 74) CAGGGCTG 1 chr2R:9137897-9138017 ( 19) CAGGGTTG 1 chrX:5082970-5083090 ( 60) CAGGGTTG 1 chr2L:21309984-21310104 ( 49) CAGGGTTG 1 chr3L:19687340-19687460 ( 106) CAGTGCTG 1 chrX:245795-245915 ( 41) CAGTGCTG 1 chr2R:7466748-7466868 ( 79) CAGCGCTG 1 chr3R:4220907-4221027 ( 36) CAGGCCTG 1 chr2L:11829426-11829546 ( 42) CAGTGTTG 1 chr2L:9938795-9938915 ( 73) CAGTGTTG 1 chr2R:20832469-20832589 ( 97) CAGTGTTG 1 chr2R:12757519-12757639 ( 8) CAGTGTTG 1 chr3R:14036101-14036221 ( 82) CAGCGTTG 1 chr3R:5758972-5759092 ( 19) CAGGCTTG 1 chr2R:19129532-19129652 ( 61) CAGCCCTG 1 chr2L:7037929-7038049 ( 66) CAGCCCTG 1 chr2R:20994820-20994940 ( 53) CAGCCCTG 1 chr3R:27407208-27407328 ( 21) CAGTCTTG 1 chr3L:21954609-21954729 ( 73) CAGTCTTG 1 chr3R:13683821-13683941 ( 26) CAGGGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.2246 E= 2.2e-002 -1140 231 -1140 -1140 178 -1140 -1140 -1140 -1140 -1140 229 -1140 -1140 -12 134 -3 -1140 37 185 -1140 -1140 147 -247 43 -1140 -1140 -1140 173 -1140 -1140 229 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.2e-002 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 0.185185 0.518519 0.296296 0.000000 0.259259 0.740741 0.000000 0.000000 0.555556 0.037037 0.407407 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGKGYTG MEME-1 regular expression -------------------------------------------------------------------------------- CAG[GT][GC][CT]TG -------------------------------------------------------------------------------- Time 7.50 secs. ******************************************************************************** ******************************************************************************** MOTIF YATCGATR MEME-2 width = 8 sites = 37 llr = 311 E-value = 5.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2a:::a:6 pos.-specific C 3::a:::: probability G ::1:a::3 matrix T 5:9:::a1 bits 2.3 ** 2.1 ** 1.9 * *** 1.6 * **** Relative 1.4 * **** Entropy 1.2 ****** (12.1 bits) 0.9 ****** 0.7 ****** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TATCGATA consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:8663979-8664099 86 2.83e-05 GACGTTAAAG TATCGATA CATTTAGTGC chr3L:22868228-22868348 78 2.83e-05 GGCACCAGGG TATCGATA GGCAGTTACG chr3R:31215918-31216038 18 2.83e-05 GCGCAATTGT TATCGATA AGCAGATCTA chr3R:12961601-12961721 63 2.83e-05 CGATGTCAGC TATCGATA AGTGCAGAAC chrX:10768250-10768370 29 2.83e-05 TTGCTGGTTT TATCGATA AGCACTCGCA chr2R:23856927-23857047 1 2.83e-05 . TATCGATA GCTTTGCTAT chrX:6741217-6741337 54 2.83e-05 GCTATATCGA TATCGATA AGTTATCGCA chr2R:8900150-8900270 85 2.83e-05 AACGCCAACT TATCGATA CTTTATCGAG chr3R:13683821-13683941 103 2.83e-05 TCTGGCCGAG TATCGATA CGCAGATATT chrX:11137704-11137824 105 2.83e-05 CGCGCTTGTC TATCGATA CTATAATC chrX:2270729-2270849 63 4.81e-05 TGTATCGGCA TATCGATG GTTGCGCAAG chr3R:5547766-5547886 54 4.81e-05 GGCCCGCCAG TATCGATG GCACGGTTGA chr3R:8660409-8660529 31 4.81e-05 TTAGCACGTA TATCGATG AGGAATCGAT chr3R:4220907-4221027 22 4.81e-05 CAGCGCCACA TATCGATG GTGAGCCAGG chr2R:17062633-17062753 77 4.81e-05 CGCCGGCATA TATCGATG AATGAAGATC chr2R:19129532-19129652 18 4.81e-05 CTTTGATAAT TATCGATG CACCGATTAC chr2L:18138048-18138168 44 6.69e-05 GATGAATACT CATCGATA GTCCGATAGG chr2L:2883099-2883219 50 6.69e-05 GTCCGTGGCT CATCGATA ACGTTAACCA chr3R:22356566-22356686 99 6.69e-05 ACGAAACAAA CATCGATA TTTCACAGCT chr3R:28887960-28888080 65 6.69e-05 CATTACTCAA CATCGATA TCAACAAAAC chr3L:21954609-21954729 7 6.69e-05 ctggga catcgata gatattgggg chr2R:10117575-10117695 96 8.01e-05 TTGTCGGTGC CATCGATG CGCTTCCAGC chrX:10473695-10473815 72 8.01e-05 GGACTCTATG CATCGATG CCGACAAAAA chr3L:347172-347292 4 1.07e-04 TTT AATCGATA TATCGTACAT chr2L:283222-283342 72 1.07e-04 TTTAAAGCCA AATCGATA TGATAGCGCC chr2L:21156230-21156350 58 1.27e-04 TAAATCGATT AATCGATG CTTGCGCACA chr2L:5980994-5981114 40 1.27e-04 CGCTCGAAAC AATCGATG TGTGCCAAAA chrX:245795-245915 60 1.75e-04 CCTATCAAAT TAGCGATA GCTAAATTGG chr2R:17871989-17872109 42 1.75e-04 CCCCTGCATA TATCGATT GATTTTGTCT chr3R:20327987-20328107 84 1.75e-04 CGATAACAGC TATCGATT ATTTGGACAC chrX:20257387-20257507 106 1.75e-04 TGTCAATCGT TATCGATT AGATTCA chrX:3363827-3363947 53 2.21e-04 TCAAAGTTAT CATCGATT TCATCATTAA chr2L:7037929-7038049 48 2.21e-04 TATCGGTGCA CAGCGATA GTTTCGACTG chrX:13391257-13391377 15 2.30e-04 AGTTGGTACT CAGCGATG GTTAAATGGG chr3R:10109968-10110088 102 2.76e-04 TGTTTGGCCC AAGCGATA AATTTGTGAA chr3L:16011783-16011903 17 2.76e-04 GTAGTCGCGC AAGCGATA GATCTCATGC chrX:2588747-2588867 113 2.76e-04 GTCGTGGGAA AATCGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:8663979-8664099 2.8e-05 85_[+2]_27 chr3L:22868228-22868348 2.8e-05 77_[+2]_35 chr3R:31215918-31216038 2.8e-05 17_[+2]_95 chr3R:12961601-12961721 2.8e-05 62_[+2]_50 chrX:10768250-10768370 2.8e-05 28_[+2]_84 chr2R:23856927-23857047 2.8e-05 [+2]_112 chrX:6741217-6741337 2.8e-05 53_[+2]_59 chr2R:8900150-8900270 2.8e-05 84_[+2]_28 chr3R:13683821-13683941 2.8e-05 102_[+2]_10 chrX:11137704-11137824 2.8e-05 104_[+2]_8 chrX:2270729-2270849 4.8e-05 62_[+2]_50 chr3R:5547766-5547886 4.8e-05 53_[+2]_59 chr3R:8660409-8660529 4.8e-05 30_[+2]_82 chr3R:4220907-4221027 4.8e-05 21_[+2]_91 chr2R:17062633-17062753 4.8e-05 76_[+2]_36 chr2R:19129532-19129652 4.8e-05 17_[+2]_95 chr2L:18138048-18138168 6.7e-05 43_[+2]_69 chr2L:2883099-2883219 6.7e-05 49_[+2]_63 chr3R:22356566-22356686 6.7e-05 98_[+2]_14 chr3R:28887960-28888080 6.7e-05 64_[+2]_48 chr3L:21954609-21954729 6.7e-05 6_[+2]_106 chr2R:10117575-10117695 8e-05 95_[+2]_17 chrX:10473695-10473815 8e-05 71_[+2]_41 chr3L:347172-347292 0.00011 3_[+2]_109 chr2L:283222-283342 0.00011 71_[+2]_41 chr2L:21156230-21156350 0.00013 57_[+2]_55 chr2L:5980994-5981114 0.00013 39_[+2]_73 chrX:245795-245915 0.00018 59_[+2]_53 chr2R:17871989-17872109 0.00018 41_[+2]_71 chr3R:20327987-20328107 0.00018 83_[+2]_29 chrX:20257387-20257507 0.00018 105_[+2]_7 chrX:3363827-3363947 0.00022 52_[+2]_60 chr2L:7037929-7038049 0.00022 47_[+2]_65 chrX:13391257-13391377 0.00023 14_[+2]_98 chr3R:10109968-10110088 0.00028 101_[+2]_11 chr3L:16011783-16011903 0.00028 16_[+2]_96 chrX:2588747-2588867 0.00028 112_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YATCGATR width=8 seqs=37 chr3R:8663979-8664099 ( 86) TATCGATA 1 chr3L:22868228-22868348 ( 78) TATCGATA 1 chr3R:31215918-31216038 ( 18) TATCGATA 1 chr3R:12961601-12961721 ( 63) TATCGATA 1 chrX:10768250-10768370 ( 29) TATCGATA 1 chr2R:23856927-23857047 ( 1) TATCGATA 1 chrX:6741217-6741337 ( 54) TATCGATA 1 chr2R:8900150-8900270 ( 85) TATCGATA 1 chr3R:13683821-13683941 ( 103) TATCGATA 1 chrX:11137704-11137824 ( 105) TATCGATA 1 chrX:2270729-2270849 ( 63) TATCGATG 1 chr3R:5547766-5547886 ( 54) TATCGATG 1 chr3R:8660409-8660529 ( 31) TATCGATG 1 chr3R:4220907-4221027 ( 22) TATCGATG 1 chr2R:17062633-17062753 ( 77) TATCGATG 1 chr2R:19129532-19129652 ( 18) TATCGATG 1 chr2L:18138048-18138168 ( 44) CATCGATA 1 chr2L:2883099-2883219 ( 50) CATCGATA 1 chr3R:22356566-22356686 ( 99) CATCGATA 1 chr3R:28887960-28888080 ( 65) CATCGATA 1 chr3L:21954609-21954729 ( 7) CATCGATA 1 chr2R:10117575-10117695 ( 96) CATCGATG 1 chrX:10473695-10473815 ( 72) CATCGATG 1 chr3L:347172-347292 ( 4) AATCGATA 1 chr2L:283222-283342 ( 72) AATCGATA 1 chr2L:21156230-21156350 ( 58) AATCGATG 1 chr2L:5980994-5981114 ( 40) AATCGATG 1 chrX:245795-245915 ( 60) TAGCGATA 1 chr2R:17871989-17872109 ( 42) TATCGATT 1 chr3R:20327987-20328107 ( 84) TATCGATT 1 chrX:20257387-20257507 ( 106) TATCGATT 1 chrX:3363827-3363947 ( 53) CATCGATT 1 chr2L:7037929-7038049 ( 48) CAGCGATA 1 chrX:13391257-13391377 ( 15) CAGCGATG 1 chr3R:10109968-10110088 ( 102) AAGCGATA 1 chr3L:16011783-16011903 ( 17) AAGCGATA 1 chrX:2588747-2588867 ( 113) AATCGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 9.73988 E= 5.9e+002 -62 43 -1185 84 178 -1185 -1185 -1185 -1185 -1185 -60 152 -1185 231 -1185 -1185 -1185 -1185 229 -1185 178 -1185 -1185 -1185 -1185 -1185 -1185 173 96 -1185 54 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 5.9e+002 0.189189 0.270270 0.000000 0.540541 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.135135 0.864865 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 0.000000 1.000000 0.567568 0.000000 0.297297 0.135135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATCGATR MEME-2 regular expression -------------------------------------------------------------------------------- [TC]ATCGAT[AG] -------------------------------------------------------------------------------- Time 13.94 secs. ******************************************************************************** ******************************************************************************** MOTIF CTGGCAAC MEME-3 width = 8 sites = 31 llr = 269 E-value = 5.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::873 pos.-specific C 6::1a2:7 probability G 2:a9::3: matrix T 2a:::::: bits 2.3 * * 2.1 * * 1.9 *** 1.6 **** Relative 1.4 **** Entropy 1.2 ******* (12.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTGGCAAC consensus CGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:19505683-19505803 108 8.79e-06 ATCGGCTGAG CTGGCAAC CCTGA chr2R:20994820-20994940 92 8.79e-06 GTGTGGCAGT CTGGCAAC CCTACACTGA chr2L:6479775-6479895 95 8.79e-06 AACGCGTGGG CTGGCAAC ACTGGCAGAG chr3L:1865311-1865431 106 1.50e-05 ACCAAGCAGG CTGGCAGC CACCCCC chr3R:30601824-30601944 83 1.50e-05 AGCCATCCTT CTGGCAGC ACTAGTTGGG chr3L:18870134-18870254 111 1.50e-05 TTTAACTGAT CTGGCAGC GC chrX:1322374-1322494 57 1.50e-05 CTGCTCCGCT CTGGCAGC ACTTTTCCGG chr3R:10109968-10110088 55 2.10e-05 GCGCGCGTTA CTGGCCAC TTCGGATGGT chr3R:12961601-12961721 98 2.10e-05 TTCTTTCAGC CTGGCCAC CCTGCTGGTG chrX:2094160-2094280 86 2.10e-05 CTTAAATCGA CTGGCCAC ACCGCACAGC chr3R:8660409-8660529 106 4.27e-05 GCGGCGGTTA CTGGCAAA GACTCCG chr3L:21347340-21347460 63 4.27e-05 AGAGCTGATT CTGGCAAA CCAGGGAAGC chr3R:28887960-28888080 2 4.27e-05 T GTGGCAAC TGCTTACTCT chr3L:21954609-21954729 107 4.27e-05 tagagtggga gtggcaaC ATGGGC chr3R:5063502-5063622 113 4.27e-05 ATTAAAGCAG CTGGCAAA chr2L:17470764-17470884 109 6.02e-05 ACGTTTTCTT TTGGCAAC AAGC chr2L:2883099-2883219 84 6.02e-05 GGCCACACTT TTGGCAAC GGTAATTTAG chr2L:18443232-18443352 66 6.02e-05 ACTAGCGTGT TTGGCAAC CAGGGCTGAC chr3R:6368176-6368296 50 7.54e-05 GAAAGGCTAT GTGGCAGC ACATGAATGT chr3R:20830387-20830507 49 7.54e-05 GTTGGTGGCG CTGGCAGA CATTTCCCCG chr2R:11453808-11453928 99 7.54e-05 CGTTAACCAG CTGGCAGA GCAGCCACAG chr3L:19687340-19687460 75 9.04e-05 GGAACATCTG GTGGCCAC CGACCTGGTC chr2L:11829426-11829546 15 9.04e-05 ATTGCGCAGC GTGGCCAC CTGGTCACGA chrX:20257387-20257507 46 9.04e-05 CACTGATTAG CTGGCCAA CGTGCCGCAT chr3L:3411742-3411862 36 9.97e-05 GTGCGTGACT TTGGCAGC AAACTTTTCT chr2L:21156230-21156350 19 1.13e-04 ACTGCGCAGT GTGGCAAA GCGACGCTGC chr3L:16004917-16005037 49 1.41e-04 GCAATTTGGG CTGCCAAC TGTGGTCAAG chr2L:18152395-18152515 14 1.41e-04 TCCAGTGTGA CTGCCAAC GGAATCGCCA chr3R:13683821-13683941 94 1.41e-04 GCTGTACTCT CTGGCCGA GTATCGATAC chr2R:21076394-21076514 19 1.60e-04 CTCATCTGTC TTGGCAAA TTCTATCAAA chrX:5084921-5085041 107 1.60e-04 ACAATTGACG TTGGCAAA AATGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:19505683-19505803 8.8e-06 107_[+3]_5 chr2R:20994820-20994940 8.8e-06 91_[+3]_21 chr2L:6479775-6479895 8.8e-06 94_[+3]_18 chr3L:1865311-1865431 1.5e-05 105_[+3]_7 chr3R:30601824-30601944 1.5e-05 82_[+3]_30 chr3L:18870134-18870254 1.5e-05 110_[+3]_2 chrX:1322374-1322494 1.5e-05 56_[+3]_56 chr3R:10109968-10110088 2.1e-05 54_[+3]_58 chr3R:12961601-12961721 2.1e-05 97_[+3]_15 chrX:2094160-2094280 2.1e-05 85_[+3]_27 chr3R:8660409-8660529 4.3e-05 105_[+3]_7 chr3L:21347340-21347460 4.3e-05 62_[+3]_50 chr3R:28887960-28888080 4.3e-05 1_[+3]_111 chr3L:21954609-21954729 4.3e-05 106_[+3]_6 chr3R:5063502-5063622 4.3e-05 112_[+3] chr2L:17470764-17470884 6e-05 108_[+3]_4 chr2L:2883099-2883219 6e-05 83_[+3]_29 chr2L:18443232-18443352 6e-05 65_[+3]_47 chr3R:6368176-6368296 7.5e-05 49_[+3]_63 chr3R:20830387-20830507 7.5e-05 48_[+3]_64 chr2R:11453808-11453928 7.5e-05 98_[+3]_14 chr3L:19687340-19687460 9e-05 74_[+3]_38 chr2L:11829426-11829546 9e-05 14_[+3]_98 chrX:20257387-20257507 9e-05 45_[+3]_67 chr3L:3411742-3411862 0.0001 35_[+3]_77 chr2L:21156230-21156350 0.00011 18_[+3]_94 chr3L:16004917-16005037 0.00014 48_[+3]_64 chr2L:18152395-18152515 0.00014 13_[+3]_99 chr3R:13683821-13683941 0.00014 93_[+3]_19 chr2R:21076394-21076514 0.00016 18_[+3]_94 chrX:5084921-5085041 0.00016 106_[+3]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGGCAAC width=8 seqs=31 chrX:19505683-19505803 ( 108) CTGGCAAC 1 chr2R:20994820-20994940 ( 92) CTGGCAAC 1 chr2L:6479775-6479895 ( 95) CTGGCAAC 1 chr3L:1865311-1865431 ( 106) CTGGCAGC 1 chr3R:30601824-30601944 ( 83) CTGGCAGC 1 chr3L:18870134-18870254 ( 111) CTGGCAGC 1 chrX:1322374-1322494 ( 57) CTGGCAGC 1 chr3R:10109968-10110088 ( 55) CTGGCCAC 1 chr3R:12961601-12961721 ( 98) CTGGCCAC 1 chrX:2094160-2094280 ( 86) CTGGCCAC 1 chr3R:8660409-8660529 ( 106) CTGGCAAA 1 chr3L:21347340-21347460 ( 63) CTGGCAAA 1 chr3R:28887960-28888080 ( 2) GTGGCAAC 1 chr3L:21954609-21954729 ( 107) GTGGCAAC 1 chr3R:5063502-5063622 ( 113) CTGGCAAA 1 chr2L:17470764-17470884 ( 109) TTGGCAAC 1 chr2L:2883099-2883219 ( 84) TTGGCAAC 1 chr2L:18443232-18443352 ( 66) TTGGCAAC 1 chr3R:6368176-6368296 ( 50) GTGGCAGC 1 chr3R:20830387-20830507 ( 49) CTGGCAGA 1 chr2R:11453808-11453928 ( 99) CTGGCAGA 1 chr3L:19687340-19687460 ( 75) GTGGCCAC 1 chr2L:11829426-11829546 ( 15) GTGGCCAC 1 chrX:20257387-20257507 ( 46) CTGGCCAA 1 chr3L:3411742-3411862 ( 36) TTGGCAGC 1 chr2L:21156230-21156350 ( 19) GTGGCAAA 1 chr3L:16004917-16005037 ( 49) CTGCCAAC 1 chr2L:18152395-18152515 ( 14) CTGCCAAC 1 chr3R:13683821-13683941 ( 94) CTGGCCGA 1 chr2R:21076394-21076514 ( 19) TTGGCAAA 1 chrX:5084921-5085041 ( 107) TTGGCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 9.79338 E= 5.0e+002 -1160 161 -8 -64 -1160 -1160 -1160 173 -1160 -1160 229 -1160 -1160 -164 219 -1160 -1160 231 -1160 -1160 141 17 -1160 -1160 128 -1160 50 -1160 15 175 -1160 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 5.0e+002 0.000000 0.612903 0.193548 0.193548 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.064516 0.935484 0.000000 0.000000 1.000000 0.000000 0.000000 0.774194 0.225806 0.000000 0.000000 0.709677 0.000000 0.290323 0.000000 0.322581 0.677419 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGGCAAC MEME-3 regular expression -------------------------------------------------------------------------------- CTGGC[AC][AG][CA] -------------------------------------------------------------------------------- Time 20.23 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGCRG MEME-4 width = 8 sites = 12 llr = 122 E-value = 3.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 3:::::6: pos.-specific C ::a:1a:: probability G 8a:89:3a matrix T :::2::1: bits 2.3 ** * * 2.1 ** * * 1.9 ** ** * 1.6 ***** * Relative 1.4 ****** * Entropy 1.2 ****** * (14.6 bits) 0.9 ****** * 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGCGGCAG consensus A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:1861931-1862051 99 4.27e-06 CCGCATGTCG GGCGGCAG GGCAACTCTG chr2L:19155111-19155231 50 4.27e-06 GGAAACATCT GGCGGCAg tagttgttgt chr3R:8660409-8660529 95 7.27e-06 CTGGGCTCTC GGCGGCGG TTACTGGCAA chrX:6346958-6347078 48 7.27e-06 AGTGCCGATA GGCGGCGG TCATCGGGAA chr2L:5946102-5946222 101 7.27e-06 CAAGGCCGAG GGCGGCGG CATCGATCTG chr3R:5300742-5300862 83 1.34e-05 TCGCCCGTGG AGCGGCAG CAACGGTATA chrX:20257387-20257507 28 1.34e-05 TAGCTAATTA AGCGGCAG CACTGATTAG chr3R:14473750-14473870 112 1.76e-05 CTCTCAGTGC AGCGGCGG A chr2R:17215947-17216067 21 2.83e-05 TATGGAAACA GGCGGCTG AACATAAGAT chr3R:7907468-7907588 98 2.83e-05 CTGCAGATGC GGCTGCAG TGTGAACCAT chr3R:24333314-24333434 67 2.83e-05 TGACCATTGC GGCTGCAG TGTGAACAGG chrX:20525091-20525211 103 3.69e-05 TCCGATAGAT GGCGCCAG TACATCCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:1861931-1862051 4.3e-06 98_[+4]_14 chr2L:19155111-19155231 4.3e-06 49_[+4]_63 chr3R:8660409-8660529 7.3e-06 94_[+4]_18 chrX:6346958-6347078 7.3e-06 47_[+4]_65 chr2L:5946102-5946222 7.3e-06 100_[+4]_12 chr3R:5300742-5300862 1.3e-05 82_[+4]_30 chrX:20257387-20257507 1.3e-05 27_[+4]_85 chr3R:14473750-14473870 1.8e-05 111_[+4]_1 chr2R:17215947-17216067 2.8e-05 20_[+4]_92 chr3R:7907468-7907588 2.8e-05 97_[+4]_15 chr3R:24333314-24333434 2.8e-05 66_[+4]_46 chrX:20525091-20525211 3.7e-05 102_[+4]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGGCRG width=8 seqs=12 chr3L:1861931-1862051 ( 99) GGCGGCAG 1 chr2L:19155111-19155231 ( 50) GGCGGCAG 1 chr3R:8660409-8660529 ( 95) GGCGGCGG 1 chrX:6346958-6347078 ( 48) GGCGGCGG 1 chr2L:5946102-5946222 ( 101) GGCGGCGG 1 chr3R:5300742-5300862 ( 83) AGCGGCAG 1 chrX:20257387-20257507 ( 28) AGCGGCAG 1 chr3R:14473750-14473870 ( 112) AGCGGCGG 1 chr2R:17215947-17216067 ( 21) GGCGGCTG 1 chr3R:7907468-7907588 ( 98) GGCTGCAG 1 chr3R:24333314-24333434 ( 67) GGCTGCAG 1 chrX:20525091-20525211 ( 103) GGCGCCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.3003 E= 3.1e+004 -22 -1023 187 -1023 -1023 -1023 229 -1023 -1023 231 -1023 -1023 -1023 -1023 202 -86 -1023 -127 216 -1023 -1023 231 -1023 -1023 100 -1023 70 -186 -1023 -1023 229 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 3.1e+004 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.083333 0.916667 0.000000 0.000000 1.000000 0.000000 0.000000 0.583333 0.000000 0.333333 0.083333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCRG MEME-4 regular expression -------------------------------------------------------------------------------- [GA]GCGGC[AG]G -------------------------------------------------------------------------------- Time 26.44 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCACCGC MEME-5 width = 8 sites = 2 llr = 25 E-value = 3.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCACCGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a:::: pos.-specific C aaa:aa:a probability G ::::::a: matrix T :::::::: bits 2.3 *** **** 2.1 *** **** 1.9 ******** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.9 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCACCGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:26188837-26188957 37 3.95e-06 GGCTGCTATG CCCACCGC GGAGTGTGTA chrX:1478437-1478557 78 3.95e-06 AAAGTGCGTT CCCACCGC CACGGGGAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:26188837-26188957 3.9e-06 36_[+5]_76 chrX:1478437-1478557 3.9e-06 77_[+5]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCACCGC width=8 seqs=2 chr3R:26188837-26188957 ( 37) CCCACCGC 1 chrX:1478437-1478557 ( 78) CCCACCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 3.0e+004 -765 231 -765 -765 -765 231 -765 -765 -765 231 -765 -765 177 -765 -765 -765 -765 231 -765 -765 -765 231 -765 -765 -765 -765 228 -765 -765 231 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACCGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.0e+004 0.000000 1.000000 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 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 CCCACCGC MEME-5 regular expression -------------------------------------------------------------------------------- CCCACCGC -------------------------------------------------------------------------------- Time 32.62 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:6406447-6406567 9.99e-01 120 chr3L:10866738-10866858 8.60e-01 120 chrX:10473695-10473815 4.24e-02 71_[+2(8.01e-05)]_41 chr2R:17161069-17161189 7.42e-01 120 chr2R:13586384-13586504 8.39e-02 120 chrX:5084921-5085041 3.63e-01 120 chr3L:11258572-11258692 4.42e-01 120 chr3L:7861172-7861292 9.12e-01 120 chrX:3399482-3399602 8.61e-01 120 chr4:1181842-1181962 9.83e-01 120 chr2R:14488542-14488662 9.95e-01 120 chr3L:4186822-4186942 8.53e-03 59_[+4(8.86e-05)]_53 chr3L:20395360-20395480 3.69e-01 120 chr2R:23554569-23554689 9.85e-01 120 chr2L:5946102-5946222 1.29e-03 100_[+4(7.27e-06)]_12 chr2R:24748886-24749006 4.19e-01 120 chr2L:20078984-20079104 4.53e-01 120 chr3R:9055249-9055369 9.12e-01 120 chrX:6310527-6310647 1.41e-01 120 chr2L:18666064-18666184 8.97e-02 120 chr2L:6479775-6479895 1.49e-03 94_[+3(8.79e-06)]_1_[+3(7.54e-05)]_\ 9 chr3R:20555136-20555256 9.02e-01 120 chr2L:8610926-8611046 4.53e-01 120 chr3L:8440862-8440982 9.93e-01 120 chr2R:20994820-20994940 1.12e-03 52_[+1(8.50e-05)]_31_[+3(8.79e-06)]_\ 21 chr2R:12757519-12757639 4.67e-03 7_[+1(5.13e-05)]_105 chr3L:20276746-20276866 1.00e+00 120 chr2R:21721032-21721152 2.05e-03 60_[+4(6.14e-05)]_52 chr3R:28429716-28429836 8.49e-01 120 chr2R:18172396-18172516 9.39e-01 120 chr3L:1139530-1139650 7.99e-01 120 chr2L:5980994-5981114 7.88e-02 120 chr3L:4413160-4413280 4.77e-01 120 chr2L:10061478-10061598 3.40e-01 120 chr2R:7052513-7052633 9.83e-01 120 chr3R:11671888-11672008 1.85e-01 120 chr2L:6339630-6339750 8.29e-01 120 chrX:11137704-11137824 8.32e-02 104_[+2(2.83e-05)]_8 chr3R:13683821-13683941 5.19e-04 44_[+2(2.83e-05)]_50_[+2(2.83e-05)]_\ 10 chr3L:9972602-9972722 6.36e-01 120 chr3L:2265820-2265940 1.90e-02 120 chr3R:5063502-5063622 3.21e-02 112_[+3(4.27e-05)] chr2R:11453808-11453928 2.60e-02 98_[+3(7.54e-05)]_14 chrX:13391257-13391377 4.07e-02 120 chr3R:25215268-25215388 1.00e+00 120 chr3L:3411742-3411862 1.97e-01 35_[+3(9.97e-05)]_77 chrX:3390038-3390158 9.59e-01 120 chrX:10488013-10488133 4.27e-01 120 chr2R:7492691-7492811 2.26e-01 120 chrX:14839838-14839958 5.31e-01 120 chr2R:20832469-20832589 2.32e-02 96_[+1(5.13e-05)]_16 chr3L:13923487-13923607 9.78e-01 120 chr2L:7037929-7038049 8.61e-04 65_[+1(8.50e-05)]_47 chr2L:12467926-12468046 7.71e-01 120 chr2R:19129532-19129652 1.00e-03 17_[+2(4.81e-05)]_35_[+1(8.50e-05)]_\ 52 chrX:20257387-20257507 5.70e-05 27_[+4(1.34e-05)]_10_[+3(9.04e-05)]_\ 67 chrX:18405086-18405206 5.14e-01 120 chrX:1478437-1478557 5.73e-03 77_[+5(3.95e-06)]_35 chr3L:21349040-21349160 1.64e-01 120 chr3L:14190116-14190236 5.61e-01 120 chr3R:5300742-5300862 2.72e-03 82_[+4(1.34e-05)]_30 chr2R:17062633-17062753 1.86e-02 76_[+2(4.81e-05)]_36 chr3L:18621226-18621346 4.30e-01 120 chr2L:20807761-20807881 9.41e-02 120 chrX:19505683-19505803 1.64e-02 107_[+3(8.79e-06)]_5 chr3R:4220907-4221027 3.08e-04 21_[+2(4.81e-05)]_6_[+1(3.74e-05)]_\ 62_[+1(8.50e-05)]_7 chrX:15653643-15653763 7.28e-01 120 chr3L:4239602-4239722 8.57e-01 120 chrX:9137300-9137420 9.43e-01 120 chr2L:21156230-21156350 3.10e-03 120 chr3R:20948097-20948217 8.31e-01 120 chrX:1392915-1393035 7.68e-02 120 chr2R:6652963-6653083 5.26e-01 120 chr2L:21309984-21310104 2.48e-02 48_[+1(1.57e-05)]_64 chr2L:19155111-19155231 1.21e-03 49_[+4(4.27e-06)]_63 chr2L:283222-283342 1.77e-01 120 chr3R:26172131-26172251 9.79e-01 120 chr3L:21954609-21954729 4.87e-04 6_[+2(6.69e-05)]_92_[+3(4.27e-05)]_\ 6 chr3R:23028651-23028771 6.28e-01 120 chr2L:9938795-9938915 2.22e-01 72_[+1(5.13e-05)]_40 chr2L:18377352-18377472 3.25e-01 120 chr2R:15114510-15114630 5.05e-01 120 chrX:5082970-5083090 6.49e-02 59_[+1(1.57e-05)]_11_[+1(5.13e-05)]_\ 34 chr2R:23818412-23818532 1.00e-01 120 chr2L:7219987-7220107 6.77e-01 120 chr3R:24333314-24333434 4.25e-02 66_[+4(2.83e-05)]_46 chr3L:6189706-6189826 2.57e-01 120 chr3L:7912038-7912158 4.01e-01 120 chr3R:5758972-5759092 1.05e-01 18_[+1(6.98e-05)]_94 chr3R:5588282-5588402 4.23e-01 120 chr3L:21130975-21131095 8.94e-01 120 chr3L:11449028-11449148 6.97e-01 120 chrX:1322374-1322494 7.42e-03 56_[+3(1.50e-05)]_56 chr2R:10117575-10117695 8.48e-02 95_[+2(8.01e-05)]_17 chr2L:3042208-3042328 3.64e-01 120 chr3R:28887960-28888080 9.84e-03 1_[+3(4.27e-05)]_55_[+2(6.69e-05)]_\ 9_[+2(6.69e-05)]_31 chr2R:8900150-8900270 1.16e-03 84_[+2(2.83e-05)]_28 chr3R:30796845-30796965 8.03e-01 120 chrX:6741217-6741337 1.12e-01 47_[+2(2.83e-05)]_65 chr2L:18567757-18567877 2.86e-01 80_[+3(9.04e-05)]_32 chr2L:11829426-11829546 6.95e-03 14_[+3(9.04e-05)]_19_[+1(5.13e-05)]_\ 71 chr3L:22163770-22163890 3.56e-01 120 chrX:5285935-5286055 9.08e-01 120 chr3R:15472869-15472989 9.58e-01 120 chr2R:23856927-23857047 1.14e-02 [+2(2.83e-05)]_112 chr3L:15626166-15626286 1.96e-01 120 chr3L:20309920-20310040 8.86e-01 120 chr2R:19669808-19669928 1.82e-01 120 chrX:10768250-10768370 4.47e-02 28_[+2(2.83e-05)]_84 chr2R:15848058-15848178 9.79e-02 120 chr3L:9128129-9128249 4.39e-01 120 chr3R:10350839-10350959 9.66e-02 120 chr2R:9440437-9440557 9.64e-01 120 chr3R:20312985-20313105 1.29e-01 120 chr3R:27131488-27131608 6.03e-01 120 chr3R:13676274-13676394 8.96e-02 120 chrX:8113560-8113680 9.83e-01 120 chr3R:5474683-5474803 9.60e-01 120 chr2L:18443232-18443352 2.69e-03 65_[+3(6.02e-05)]_[+1(6.29e-06)]_39 chr3R:7813941-7814061 9.62e-01 120 chr3L:18870134-18870254 3.73e-02 110_[+3(1.50e-05)]_2 chr2R:16608350-16608470 9.46e-01 120 chr3R:20835096-20835216 4.43e-01 120 chrX:2588747-2588867 6.84e-02 120 chr3R:12718269-12718389 9.31e-01 120 chr3R:20327987-20328107 5.43e-04 34_[+1(6.29e-06)]_78 chr3L:16165784-16165904 9.78e-01 120 chr3R:5264746-5264866 9.36e-01 120 chrX:17881265-17881385 8.47e-01 120 chrX:1907876-1907996 3.06e-01 120 chr3R:4387636-4387756 4.10e-01 120 chr3L:11350992-11351112 2.59e-03 20_[+1(6.29e-06)]_92 chr3L:16011783-16011903 9.86e-02 120 chr2R:11636052-11636172 9.64e-01 120 chr2R:18151498-18151618 6.69e-01 120 chr3R:31252708-31252828 8.15e-01 120 chr3R:23332758-23332878 5.22e-01 120 chr2L:7262175-7262295 2.60e-01 120 chrX:15599734-15599854 1.49e-01 120 chr2L:21657531-21657651 5.23e-02 120 chr2R:12605799-12605919 7.47e-01 120 chr3L:14762334-14762454 3.94e-01 120 chr3L:11483288-11483408 9.90e-01 120 chr3R:22356566-22356686 5.54e-02 98_[+2(6.69e-05)]_14 chr3L:12572500-12572620 2.59e-01 120 chr2R:15991251-15991371 1.63e-01 120 chr2R:7466748-7466868 6.93e-04 78_[+1(3.74e-05)]_34 chr2R:23067129-23067249 2.36e-02 120 chrX:8517358-8517478 1.00e-02 120 chr2L:2883099-2883219 1.30e-06 27_[+1(6.29e-06)]_14_[+2(6.69e-05)]_\ 8_[+1(1.57e-05)]_10_[+3(6.02e-05)]_29 chr2R:18411946-18412066 3.75e-02 120 chrX:2094160-2094280 7.38e-04 85_[+3(2.10e-05)]_27 chrX:20525091-20525211 8.89e-02 102_[+4(3.69e-05)]_10 chr3R:23240388-23240508 8.43e-01 120 chr3R:7907468-7907588 2.21e-02 97_[+4(2.83e-05)]_15 chr3R:12961601-12961721 1.08e-03 62_[+2(2.83e-05)]_27_[+3(2.10e-05)]_\ 15 chr2R:17892982-17893102 4.15e-01 120 chr3R:20830387-20830507 6.70e-02 48_[+3(7.54e-05)]_64 chr3R:29148206-29148326 2.99e-01 120 chr2R:19205331-19205451 6.09e-01 120 chr2R:17871989-17872109 2.58e-01 120 chr3R:26188837-26188957 1.03e-02 36_[+5(3.95e-06)]_76 chr3R:15794521-15794641 2.13e-01 120 chr3L:18786810-18786930 9.42e-01 120 chr3R:19623760-19623880 4.87e-01 120 chr2L:13549216-13549336 1.08e-01 120 chr3R:31215918-31216038 8.31e-03 17_[+2(2.83e-05)]_95 chr2L:2885183-2885303 1.59e-01 120 chr2R:10874719-10874839 3.46e-01 120 chr2R:7278199-7278319 9.82e-01 120 chrX:3363827-3363947 2.35e-01 120 chr3L:22868228-22868348 1.85e-02 77_[+2(2.83e-05)]_35 chr2L:17470764-17470884 2.65e-01 108_[+3(6.02e-05)]_4 chr3R:4970825-4970945 1.79e-03 10_[+1(6.29e-06)]_102 chr3L:21177030-21177150 9.49e-01 120 chr3L:1861931-1862051 4.15e-03 98_[+4(4.27e-06)]_14 chr3R:13999716-13999836 8.27e-01 120 chr3R:30601824-30601944 1.98e-02 82_[+3(1.50e-05)]_30 chr2L:18152395-18152515 1.71e-02 120 chr3R:8670665-8670785 9.98e-01 120 chr3L:17016222-17016342 1.00e+00 120 chr3R:14036101-14036221 1.30e-02 81_[+1(6.98e-05)]_31 chrX:20656794-20656914 9.30e-01 120 chr3R:14707057-14707177 9.90e-01 120 chrX:245795-245915 5.07e-03 40_[+1(2.50e-05)]_72 chr3R:10109968-10110088 5.50e-03 54_[+3(2.10e-05)]_58 chr3L:19687340-19687460 4.23e-03 74_[+3(9.04e-05)]_23_[+1(2.50e-05)]_\ 7 chr3R:21487907-21488027 2.85e-01 120 chrX:1953057-1953177 2.26e-02 92_[+4(3.69e-05)]_20 chr3L:6576857-6576977 2.22e-01 120 chrX:2534022-2534142 2.59e-02 120 chr2R:21076394-21076514 2.88e-01 120 chrX:6346958-6347078 5.71e-04 47_[+4(7.27e-06)]_65 chr2R:8082817-8082937 4.92e-01 120 chr3L:7882299-7882419 6.15e-01 120 chr2R:5974466-5974586 3.16e-01 120 chr3L:2501932-2502052 2.86e-01 120 chr3L:21828319-21828439 9.87e-01 120 chr3L:1865311-1865431 5.56e-03 105_[+3(1.50e-05)]_7 chr4:486667-486787 2.89e-01 120 chr2L:18138048-18138168 5.00e-02 43_[+2(6.69e-05)]_69 chr3R:12369474-12369594 1.29e-01 120 chr2R:7565592-7565712 3.78e-01 120 chr3L:16004917-16005037 1.08e-01 120 chr2L:1986802-1986922 7.62e-01 120 chr2R:13577646-13577766 1.98e-01 120 chr3R:11458699-11458819 8.69e-01 120 chr2R:9862729-9862849 8.46e-01 120 chr3R:13779395-13779515 9.71e-01 120 chr3L:21347340-21347460 1.43e-01 62_[+3(4.27e-05)]_50 chr2L:13515070-13515190 8.88e-02 120 chrX:7334185-7334305 9.35e-01 120 chr3R:8660409-8660529 1.39e-07 10_[+1(6.29e-06)]_12_[+2(4.81e-05)]_\ 56_[+4(7.27e-06)]_3_[+3(4.27e-05)]_7 chr3R:5547766-5547886 1.63e-04 36_[+2(4.81e-05)]_9_[+2(4.81e-05)]_\ 11_[+1(6.29e-06)]_40 chr3L:14217822-14217942 6.75e-01 120 chr2L:9759044-9759164 2.51e-01 120 chrX:8114590-8114710 9.20e-01 120 chr3R:31977637-31977757 8.94e-01 120 chr3R:27407208-27407328 1.10e-01 120 chr3L:2733349-2733469 9.67e-01 120 chr2L:9490961-9491081 1.10e-01 120 chr3L:8768012-8768132 2.74e-01 120 chr2L:11269071-11269191 5.20e-03 51_[+1(6.29e-06)]_61 chr2R:9137897-9138017 6.07e-03 18_[+1(1.57e-05)]_94 chrX:2270729-2270849 7.88e-02 20_[+2(8.01e-05)]_34_[+2(4.81e-05)]_\ 50 chr2R:23366586-23366706 8.92e-01 120 chrX:2919868-2919988 6.93e-01 120 chr3R:8663979-8664099 4.80e-02 85_[+2(2.83e-05)]_27 chr2R:17215947-17216067 1.52e-02 20_[+4(2.83e-05)]_92 chr3L:749584-749704 1.88e-01 120 chr3R:24771626-24771746 5.44e-01 120 chr3R:28332496-28332616 6.08e-01 120 chr2R:7489219-7489339 5.97e-01 120 chrX:3025645-3025765 9.88e-01 120 chrX:2070783-2070903 1.46e-01 120 chr3R:18439475-18439595 9.66e-01 120 chr3R:6368176-6368296 8.09e-02 49_[+3(7.54e-05)]_63 chr2R:10158689-10158809 2.41e-01 120 chr3R:14473750-14473870 1.44e-02 111_[+4(1.76e-05)]_1 chrX:19247471-19247591 9.41e-01 120 chr3L:563109-563229 3.82e-01 120 chrX:12217739-12217859 3.20e-01 120 chr2R:12150355-12150475 9.97e-01 120 chr2R:14164902-14165022 9.96e-01 120 chr2L:7434056-7434176 8.25e-01 120 chr3L:347172-347292 4.76e-02 120 chrX:7286223-7286343 3.40e-01 120 chr2L:8000769-8000889 1.63e-01 120 chr2L:6557476-6557596 5.88e-02 120 chr2R:14574973-14575093 6.82e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n07.farnam.hpc.yale.internal ********************************************************************************