******************************************************************************** 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/CG15710.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2L:11307212-11307332 1.0000 120 chr2L:5288336-5288456 1.0000 120 chr2L:612925-613045 1.0000 120 chr3L:10757093-10757213 1.0000 120 chr2L:7923762-7923882 1.0000 120 chr2R:18746920-18747040 1.0000 120 chr3L:17926732-17926852 1.0000 120 chr2L:15909411-15909531 1.0000 120 chr2L:17430755-17430875 1.0000 120 chr3L:12099748-12099868 1.0000 120 chr3R:27199492-27199612 1.0000 120 chr3L:10942603-10942723 1.0000 120 chr3L:16174906-16175026 1.0000 120 chr2L:2432989-2433109 1.0000 120 chr3L:10247694-10247814 1.0000 120 chr2R:18195529-18195649 1.0000 120 chr2L:13482374-13482494 1.0000 120 chr3L:16268461-16268581 1.0000 120 chr2L:5479299-5479419 1.0000 120 chr2R:8318254-8318374 1.0000 120 chr3R:5053013-5053133 1.0000 120 chr2R:19987184-19987304 1.0000 120 chr3L:8822371-8822491 1.0000 120 chr3L:6391493-6391613 1.0000 120 chr3L:1064510-1064630 1.0000 120 chrX:7222250-7222370 1.0000 120 chr2R:8995125-8995245 1.0000 120 chr2R:18207596-18207716 1.0000 120 chr2R:17831939-17832059 1.0000 120 chr3R:13916675-13916795 1.0000 120 chr3L:5864020-5864140 1.0000 120 chrX:19485174-19485294 1.0000 120 chr3L:11382751-11382871 1.0000 120 chrX:12511411-12511531 1.0000 120 chr2R:13473924-13474044 1.0000 120 chr2L:20146350-20146470 1.0000 120 chrX:379640-379760 1.0000 120 chr3R:21940307-21940427 1.0000 120 chr2R:19968849-19968969 1.0000 120 chr3L:3106290-3106410 1.0000 120 chr3L:2830132-2830252 1.0000 120 chr2R:8595972-8596092 1.0000 120 chr3R:10829896-10830016 1.0000 120 chr3L:15220494-15220614 1.0000 120 chr2L:3351962-3352082 1.0000 120 chr2L:13146382-13146502 1.0000 120 chr3L:15013441-15013561 1.0000 120 chr3R:27222097-27222217 1.0000 120 chr3L:10923085-10923205 1.0000 120 chr3L:2849056-2849176 1.0000 120 chrX:7540932-7541052 1.0000 120 chr3L:18057902-18058022 1.0000 120 chr2L:3582835-3582955 1.0000 120 chr2R:18343079-18343199 1.0000 120 chr3L:3338140-3338260 1.0000 120 chr2L:16590901-16591021 1.0000 120 chr3L:13288332-13288452 1.0000 120 chr3L:20582498-20582618 1.0000 120 chr2R:14923070-14923190 1.0000 120 chr2L:5751601-5751721 1.0000 120 chr3R:7025361-7025481 1.0000 120 chr3L:13178366-13178486 1.0000 120 chrX:17537421-17537541 1.0000 120 chr2R:7848697-7848817 1.0000 120 chr2R:7243033-7243153 1.0000 120 chr2R:18194882-18195002 1.0000 120 chr3R:21649600-21649720 1.0000 120 chr3L:12455196-12455316 1.0000 120 chr2R:11551170-11551290 1.0000 120 chr3L:16259672-16259792 1.0000 120 chr2R:15000553-15000673 1.0000 120 chr3L:16211968-16212088 1.0000 120 chr3L:12915579-12915699 1.0000 120 chr3L:6371521-6371641 1.0000 120 chr3L:14350958-14351078 1.0000 120 chr2R:14520478-14520598 1.0000 120 chr3R:14421961-14422081 1.0000 120 chr2L:7911490-7911610 1.0000 120 chr3L:747144-747264 1.0000 120 chr2R:18926583-18926703 1.0000 120 chr3L:5941666-5941786 1.0000 120 chr2L:5372682-5372802 1.0000 120 chr2R:11083852-11083972 1.0000 120 chr2R:19149873-19149993 1.0000 120 chrX:9987818-9987938 1.0000 120 chr2R:12536352-12536472 1.0000 120 chrX:1897516-1897636 1.0000 120 chr2L:15388414-15388534 1.0000 120 chr2R:9498832-9498952 1.0000 120 chr2L:5290023-5290143 1.0000 120 chr3R:30864582-30864702 1.0000 120 chr3R:30259719-30259839 1.0000 120 chr3R:14691613-14691733 1.0000 120 chrX:9656467-9656587 1.0000 120 chr3L:484938-485058 1.0000 120 chrX:6003956-6004076 1.0000 120 chr3L:2835882-2836002 1.0000 120 chr3L:20592728-20592848 1.0000 120 chr2L:3482822-3482942 1.0000 120 chr3L:19055225-19055345 1.0000 120 chr2R:18923620-18923740 1.0000 120 chr2L:20989643-20989763 1.0000 120 chr2R:11544141-11544261 1.0000 120 chr3L:12096900-12097020 1.0000 120 chr3L:21043996-21044116 1.0000 120 chr2L:11069596-11069716 1.0000 120 chrX:5020150-5020270 1.0000 120 chr3L:6458861-6458981 1.0000 120 chr3R:22184230-22184350 1.0000 120 chr2L:16537239-16537359 1.0000 120 chr3R:30843228-30843348 1.0000 120 chr3L:15174243-15174363 1.0000 120 chr3L:10562370-10562490 1.0000 120 chrX:14098415-14098535 1.0000 120 chr3L:20990400-20990520 1.0000 120 chr2L:3557582-3557702 1.0000 120 chrX:17807116-17807236 1.0000 120 chr3L:5851754-5851874 1.0000 120 chr2L:11052515-11052635 1.0000 120 chr2L:3562509-3562629 1.0000 120 chr2R:18271172-18271292 1.0000 120 chr2R:21847826-21847946 1.0000 120 chrX:5301011-5301131 1.0000 120 chr3L:6447821-6447941 1.0000 120 chr2L:13545891-13546011 1.0000 120 chr2L:4069679-4069799 1.0000 120 chr2L:646662-646782 1.0000 120 chrX:7534978-7535098 1.0000 120 chrX:18273313-18273433 1.0000 120 chrX:2358353-2358473 1.0000 120 chr3R:17202462-17202582 1.0000 120 chr3L:11373895-11374015 1.0000 120 chr3L:4731829-4731949 1.0000 120 chr2L:11399647-11399767 1.0000 120 chr2R:18215418-18215538 1.0000 120 chr3R:23878423-23878543 1.0000 120 chr3R:10177049-10177169 1.0000 120 chr2R:14929620-14929740 1.0000 120 chr2L:15390588-15390708 1.0000 120 chr3L:7262629-7262749 1.0000 120 chr2R:20580849-20580969 1.0000 120 chr2R:16836459-16836579 1.0000 120 chr2L:17421490-17421610 1.0000 120 chr2L:16503068-16503188 1.0000 120 chr2R:21225007-21225127 1.0000 120 chr3L:20952228-20952348 1.0000 120 chrX:6028001-6028121 1.0000 120 chr3L:15005882-15006002 1.0000 120 chrX:4435085-4435205 1.0000 120 chr2L:16591492-16591612 1.0000 120 chr2R:11033714-11033834 1.0000 120 chr3R:29847267-29847387 1.0000 120 chr3L:14610624-14610744 1.0000 120 chrX:14017549-14017669 1.0000 120 chr3R:30843865-30843985 1.0000 120 chr2R:18907133-18907253 1.0000 120 chr3R:28848002-28848122 1.0000 120 chrX:21127410-21127530 1.0000 120 chr3L:5128376-5128496 1.0000 120 chr3R:27179139-27179259 1.0000 120 chrX:18929528-18929648 1.0000 120 chr2L:18523142-18523262 1.0000 120 chr3L:13109423-13109543 1.0000 120 chr2R:13478476-13478596 1.0000 120 chr3R:29570407-29570527 1.0000 120 chr3R:9966255-9966375 1.0000 120 chr3L:14463944-14464064 1.0000 120 chr3L:18406116-18406236 1.0000 120 chr3L:7113154-7113274 1.0000 120 chr2R:21569768-21569888 1.0000 120 chr3R:15650423-15650543 1.0000 120 chr3R:19255381-19255501 1.0000 120 chr3R:15556602-15556722 1.0000 120 chrX:17488526-17488646 1.0000 120 chr2L:7899293-7899413 1.0000 120 chr3R:24549875-24549995 1.0000 120 chr3R:21826207-21826327 1.0000 120 chrX:8215586-8215706 1.0000 120 chr3L:2873217-2873337 1.0000 120 chr3L:16762302-16762422 1.0000 120 chr2L:7541471-7541591 1.0000 120 chr3R:30461756-30461876 1.0000 120 chr3L:21042689-21042809 1.0000 120 chr3L:4383227-4383347 1.0000 120 chr2L:11386532-11386652 1.0000 120 chr2L:18003148-18003268 1.0000 120 chr3L:3442222-3442342 1.0000 120 chr3L:22910030-22910150 1.0000 120 chr3R:7171830-7171950 1.0000 120 chr3R:21948789-21948909 1.0000 120 chr3R:30256364-30256484 1.0000 120 chr3R:24970812-24970932 1.0000 120 chr2R:18566140-18566260 1.0000 120 chr2R:18879228-18879348 1.0000 120 chr2L:19156087-19156207 1.0000 120 chr3R:14673095-14673215 1.0000 120 chr2L:7323078-7323198 1.0000 120 chr3L:20632469-20632589 1.0000 120 chr3R:14373946-14374066 1.0000 120 chr3R:10455043-10455163 1.0000 120 chr2R:15100630-15100750 1.0000 120 chr2L:19454494-19454614 1.0000 120 chr3L:6364353-6364473 1.0000 120 chr3L:13212978-13213098 1.0000 120 chr2R:19985090-19985210 1.0000 120 chr3L:10928833-10928953 1.0000 120 chr2R:10057960-10058080 1.0000 120 chr3R:13934746-13934866 1.0000 120 chr3R:18485403-18485523 1.0000 120 chr2R:14126268-14126388 1.0000 120 chr2L:608289-608409 1.0000 120 chrX:8212204-8212324 1.0000 120 chr3L:10365053-10365173 1.0000 120 chrX:342553-342673 1.0000 120 chrX:18256617-18256737 1.0000 120 chr3R:15596114-15596234 1.0000 120 chr2L:15385490-15385610 1.0000 120 chrX:17542886-17543006 1.0000 120 chr2L:1456983-1457103 1.0000 120 chr3L:15264747-15264867 1.0000 120 chr2R:17499291-17499411 1.0000 120 chr2R:14313678-14313798 1.0000 120 chr2R:8655402-8655522 1.0000 120 chr3L:18078727-18078847 1.0000 120 chrX:18544818-18544938 1.0000 120 chr2L:1409812-1409932 1.0000 120 chr2R:22529804-22529924 1.0000 120 chr3L:2866990-2867110 1.0000 120 chr3L:2553232-2553352 1.0000 120 chr3R:7651146-7651266 1.0000 120 chr3R:8847405-8847525 1.0000 120 chr3R:14389404-14389524 1.0000 120 chr2L:12823744-12823864 1.0000 120 chr3R:22140187-22140307 1.0000 120 chr3R:6102475-6102595 1.0000 120 chr2L:15392472-15392592 1.0000 120 chr2L:8919802-8919922 1.0000 120 chr3R:22194844-22194964 1.0000 120 chr3L:16286422-16286542 1.0000 120 chr3R:31312433-31312553 1.0000 120 chr2R:15745308-15745428 1.0000 120 chr3L:531310-531430 1.0000 120 chrX:17558855-17558975 1.0000 120 chr2L:14236272-14236392 1.0000 120 chr3R:9594045-9594165 1.0000 120 chr3L:3444353-3444473 1.0000 120 chr2L:12602324-12602444 1.0000 120 chrX:4442630-4442750 1.0000 120 chr2L:20381453-20381573 1.0000 120 chr2L:7199679-7199799 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_CG15710/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG15710.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 0.365 C 0.135 G 0.14 T 0.36 Background letter frequencies (from file dataset with add-one prior applied): A 0.365 C 0.135 G 0.14 T 0.36 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCSCSASG MEME-1 width = 8 sites = 5 llr = 63 E-value = 5.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::8:: pos.-specific C :a4a6:4: probability G a:6:426a matrix T :::::::: bits 2.9 ** * * 2.6 ** * * 2.3 ** * * 2.0 ***** ** Relative 1.7 ***** ** Entropy 1.4 ***** ** (18.1 bits) 1.2 ***** ** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCGCCAGG consensus C GGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:11083852-11083972 72 1.01e-06 CTTGCTAAAG GCGCCACG TAAAACTTTG chr2L:7911490-7911610 49 1.01e-06 TTTTTATGAT GCCCCAGG GCCAATAGAA chr2R:10057960-10058080 88 1.50e-06 AAGAAAAAGA GCGCGAGG AGCTGCAAAA chr2L:3562509-3562629 26 1.82e-06 TATGTACTTG GCCCCACG TTGGGCGCTA chr2R:8655402-8655522 19 2.90e-06 TCTGCAGCTG GCGCGGGG AACTGGAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:11083852-11083972 1e-06 71_[+1]_41 chr2L:7911490-7911610 1e-06 48_[+1]_64 chr2R:10057960-10058080 1.5e-06 87_[+1]_25 chr2L:3562509-3562629 1.8e-06 25_[+1]_87 chr2R:8655402-8655522 2.9e-06 18_[+1]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCSCSASG width=8 seqs=5 chr2R:11083852-11083972 ( 72) GCGCCACG 1 chr2L:7911490-7911610 ( 49) GCCCCAGG 1 chr2R:10057960-10058080 ( 88) GCGCGAGG 1 chr2L:3562509-3562629 ( 26) GCCCCACG 1 chr2R:8655402-8655522 ( 19) GCGCGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.4073 E= 5.9e+002 -897 -897 283 -897 -897 288 -897 -897 -897 156 210 -897 -897 288 -897 -897 -897 215 151 -897 113 -897 51 -897 -897 156 210 -897 -897 -897 283 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 5.9e+002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCSCSASG MEME-1 regular expression -------------------------------------------------------------------------------- GC[GC]C[CG][AG][GC]G -------------------------------------------------------------------------------- Time 7.53 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCACACS MEME-2 width = 8 sites = 5 llr = 63 E-value = 3.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::a:8:: pos.-specific C aaa:a286 probability G ::::::24 matrix T :::::::: bits 2.9 *** * 2.6 *** * 2.3 *** * 2.0 *** * ** Relative 1.7 *** * ** Entropy 1.4 ***** ** (18.1 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCCACACC consensus CGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:1456983-1457103 97 8.06e-07 TTCTCAGTGC CCCACACC CATAGACCGA chr2R:10057960-10058080 8 8.06e-07 CTTCAAT CCCACACC TTGATTTTTG chr3R:10455043-10455163 26 1.94e-06 CACAATGTAA CCCACACG ATGTTAATGG chr3L:2553232-2553352 109 2.25e-06 CTTACTCATT CCCACCCG ATCG chrX:1897516-1897636 99 3.09e-06 AATGGTTTAG CCCACAGC TGATGAATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:1456983-1457103 8.1e-07 96_[+2]_16 chr2R:10057960-10058080 8.1e-07 7_[+2]_105 chr3R:10455043-10455163 1.9e-06 25_[+2]_87 chr3L:2553232-2553352 2.3e-06 108_[+2]_4 chrX:1897516-1897636 3.1e-06 98_[+2]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCACACS width=8 seqs=5 chr2L:1456983-1457103 ( 97) CCCACACC 1 chr2R:10057960-10058080 ( 8) CCCACACC 1 chr3R:10455043-10455163 ( 26) CCCACACG 1 chr3L:2553232-2553352 ( 109) CCCACCCG 1 chrX:1897516-1897636 ( 99) CCCACAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.4073 E= 3.1e+002 -897 288 -897 -897 -897 288 -897 -897 -897 288 -897 -897 145 -897 -897 -897 -897 288 -897 -897 113 56 -897 -897 -897 256 51 -897 -897 215 151 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 3.1e+002 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 0.800000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.600000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCACACS MEME-2 regular expression -------------------------------------------------------------------------------- CCCAC[AC][CG][CG] -------------------------------------------------------------------------------- Time 13.79 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCTGGGC MEME-3 width = 8 sites = 4 llr = 52 E-value = 4.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::3::3: pos.-specific C ::a::3:a probability G aa::a88: matrix T :::8:::: bits 2.9 *** * * 2.6 *** * * 2.3 *** * * 2.0 *** ** * Relative 1.7 *** **** Entropy 1.4 *** **** (18.7 bits) 1.2 *** **** 0.9 *** **** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGCTGGGC consensus A CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:19485174-19485294 14 3.53e-07 CTCAAGTGAA GGCTGGGC TATTGCTCGG chrX:5301011-5301131 49 6.93e-07 TTGCAACAGA GGCTGCGC ACAGTGTTGC chr3L:21042689-21042809 111 1.05e-06 TAGAATAAAA GGCAGGGC AT chr2R:20580849-20580969 48 1.97e-06 TTATCTTGTT GGCTGGAC TGTGCtttgt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:19485174-19485294 3.5e-07 13_[+3]_99 chrX:5301011-5301131 6.9e-07 48_[+3]_64 chr3L:21042689-21042809 1.1e-06 110_[+3]_2 chr2R:20580849-20580969 2e-06 47_[+3]_65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCTGGGC width=8 seqs=4 chrX:19485174-19485294 ( 14) GGCTGGGC 1 chrX:5301011-5301131 ( 49) GGCTGCGC 1 chr3L:21042689-21042809 ( 111) GGCAGGGC 1 chr2R:20580849-20580969 ( 48) GGCTGGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.7858 E= 4.5e+003 -865 -865 283 -865 -865 -865 283 -865 -865 288 -865 -865 -54 -865 -865 106 -865 -865 283 -865 -865 88 242 -865 -54 -865 242 -865 -865 288 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 4.5e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTGGGC MEME-3 regular expression -------------------------------------------------------------------------------- GGC[TA]G[GC][GA]C -------------------------------------------------------------------------------- Time 20.07 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCCTCKC MEME-4 width = 8 sites = 2 llr = 28 E-value = 4.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C aaaa:a:a probability G ::::::5: matrix T ::::a:5: bits 2.9 **** * * 2.6 **** * * 2.3 **** * * 2.0 **** * * Relative 1.7 **** * * Entropy 1.4 ****** * (19.9 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCCCTCGC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:18271172-18271292 59 3.05e-07 TAGCTTTAAA CCCCTCGC TTCAAATGCA chr3L:2553232-2553352 81 1.09e-06 GCTCTCGCTC CCCCTCTC TCCCGCTTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:18271172-18271292 3.1e-07 58_[+4]_54 chr3L:2553232-2553352 1.1e-06 80_[+4]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCCTCKC width=8 seqs=2 chr2R:18271172-18271292 ( 59) CCCCTCGC 1 chr3L:2553232-2553352 ( 81) CCCCTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 4.6e+003 -765 288 -765 -765 -765 288 -765 -765 -765 288 -765 -765 -765 288 -765 -765 -765 -765 -765 147 -765 288 -765 -765 -765 -765 183 47 -765 288 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.6e+003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCCTCKC MEME-4 regular expression -------------------------------------------------------------------------------- CCCCTC[GT]C -------------------------------------------------------------------------------- Time 26.35 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGCTGGC MEME-5 width = 8 sites = 4 llr = 51 E-value = 3.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::3::: pos.-specific C 3::a:33a probability G 8aa::88: matrix T ::::8::: bits 2.9 *** * 2.6 *** * 2.3 *** * 2.0 **** *** Relative 1.7 **** *** Entropy 1.4 **** *** (18.2 bits) 1.2 **** *** 0.9 **** *** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGCTGGC consensus C ACC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:19156087-19156207 50 3.53e-07 TGCCATTGGC GGGCTGGC AGTTTTTTTT chr2L:13545891-13546011 88 1.37e-06 TTTTTTCAAT GGGCTCGC GACCAAAACC chr2L:3351962-3352082 56 1.73e-06 TGAAATTCTA GGGCAGGC TAAAACTGCT chr3R:21948789-21948909 74 2.72e-06 CTTTTTTTAC CGGCTGCC ATGAATGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:19156087-19156207 3.5e-07 49_[+5]_63 chr2L:13545891-13546011 1.4e-06 87_[+5]_25 chr2L:3351962-3352082 1.7e-06 55_[+5]_57 chr3R:21948789-21948909 2.7e-06 73_[+5]_39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGCTGGC width=8 seqs=4 chr2L:19156087-19156207 ( 50) GGGCTGGC 1 chr2L:13545891-13546011 ( 88) GGGCTCGC 1 chr2L:3351962-3352082 ( 56) GGGCAGGC 1 chr3R:21948789-21948909 ( 74) CGGCTGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.5228 E= 3.2e+003 -865 88 242 -865 -865 -865 283 -865 -865 -865 283 -865 -865 288 -865 -865 -54 -865 -865 106 -865 88 242 -865 -865 88 242 -865 -865 288 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 3.2e+003 0.000000 0.250000 0.750000 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 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCTGGC MEME-5 regular expression -------------------------------------------------------------------------------- [GC]GGC[TA][GC][GC]C -------------------------------------------------------------------------------- Time 32.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:11307212-11307332 5.48e-01 120 chr2L:5288336-5288456 1.28e-01 120 chr2L:612925-613045 4.02e-01 120 chr3L:10757093-10757213 6.59e-01 120 chr2L:7923762-7923882 9.86e-01 120 chr2R:18746920-18747040 2.34e-02 27_[+5(2.08e-05)]_85 chr3L:17926732-17926852 1.00e+00 120 chr2L:15909411-15909531 1.93e-01 120 chr2L:17430755-17430875 9.71e-02 120 chr3L:12099748-12099868 1.22e-01 120 chr3R:27199492-27199612 6.44e-01 120 chr3L:10942603-10942723 8.87e-01 120 chr3L:16174906-16175026 9.01e-01 120 chr2L:2432989-2433109 3.42e-01 120 chr3L:10247694-10247814 3.12e-01 120 chr2R:18195529-18195649 4.94e-01 120 chr2L:13482374-13482494 6.14e-01 120 chr3L:16268461-16268581 6.57e-01 120 chr2L:5479299-5479419 5.16e-01 120 chr2R:8318254-8318374 7.79e-01 120 chr3R:5053013-5053133 1.05e-01 120 chr2R:19987184-19987304 3.05e-01 120 chr3L:8822371-8822491 2.13e-04 108_[+3(4.65e-05)]_4 chr3L:6391493-6391613 5.21e-01 120 chr3L:1064510-1064630 9.78e-01 120 chrX:7222250-7222370 6.68e-01 120 chr2R:8995125-8995245 5.23e-01 120 chr2R:18207596-18207716 9.55e-01 120 chr2R:17831939-17832059 8.63e-01 120 chr3R:13916675-13916795 7.45e-01 120 chr3L:5864020-5864140 6.39e-01 120 chrX:19485174-19485294 8.64e-06 13_[+3(3.53e-07)]_4_[+1(8.28e-05)]_\ 87 chr3L:11382751-11382871 8.23e-01 120 chrX:12511411-12511531 5.95e-01 120 chr2R:13473924-13474044 9.53e-01 120 chr2L:20146350-20146470 1.41e-02 102_[+2(9.68e-05)]_10 chrX:379640-379760 9.53e-01 120 chr3R:21940307-21940427 6.79e-01 120 chr2R:19968849-19968969 7.13e-01 120 chr3L:3106290-3106410 1.39e-01 120 chr3L:2830132-2830252 9.79e-01 120 chr2R:8595972-8596092 2.51e-01 120 chr3R:10829896-10830016 9.64e-01 120 chr3L:15220494-15220614 8.97e-01 120 chr2L:3351962-3352082 4.00e-03 55_[+5(1.73e-06)]_57 chr2L:13146382-13146502 9.79e-01 120 chr3L:15013441-15013561 8.80e-01 120 chr3R:27222097-27222217 6.39e-01 120 chr3L:10923085-10923205 1.00e+00 120 chr3L:2849056-2849176 8.64e-01 120 chrX:7540932-7541052 8.39e-01 120 chr3L:18057902-18058022 7.39e-01 120 chr2L:3582835-3582955 2.15e-01 120 chr2R:18343079-18343199 3.08e-01 120 chr3L:3338140-3338260 8.15e-01 120 chr2L:16590901-16591021 1.00e+00 120 chr3L:13288332-13288452 3.01e-02 120 chr3L:20582498-20582618 2.71e-01 120 chr2R:14923070-14923190 8.79e-01 120 chr2L:5751601-5751721 8.02e-01 120 chr3R:7025361-7025481 3.02e-02 47_[+5(6.33e-05)]_65 chr3L:13178366-13178486 6.67e-01 120 chrX:17537421-17537541 2.00e-01 120 chr2R:7848697-7848817 8.42e-02 19_[+2(1.89e-05)]_93 chr2R:7243033-7243153 2.21e-01 120 chr2R:18194882-18195002 1.71e-01 120 chr3R:21649600-21649720 2.40e-01 120 chr3L:12455196-12455316 2.80e-01 120 chr2R:11551170-11551290 9.72e-01 120 chr3L:16259672-16259792 5.30e-01 120 chr2R:15000553-15000673 8.99e-01 120 chr3L:16211968-16212088 9.90e-01 120 chr3L:12915579-12915699 1.95e-01 120 chr3L:6371521-6371641 1.00e+00 120 chr3L:14350958-14351078 2.03e-01 120 chr2R:14520478-14520598 3.14e-01 120 chr3R:14421961-14422081 1.93e-01 120 chr2L:7911490-7911610 3.74e-05 48_[+1(1.01e-06)]_64 chr3L:747144-747264 3.31e-01 120 chr2R:18926583-18926703 4.13e-01 120 chr3L:5941666-5941786 8.82e-01 120 chr2L:5372682-5372802 4.14e-01 120 chr2R:11083852-11083972 5.43e-04 71_[+1(1.01e-06)]_41 chr2R:19149873-19149993 7.22e-01 120 chrX:9987818-9987938 3.74e-01 120 chr2R:12536352-12536472 6.69e-01 120 chrX:1897516-1897636 3.71e-04 98_[+2(3.09e-06)]_14 chr2L:15388414-15388534 8.96e-01 120 chr2R:9498832-9498952 7.86e-01 120 chr2L:5290023-5290143 9.43e-01 120 chr3R:30864582-30864702 3.34e-01 120 chr3R:30259719-30259839 3.15e-02 120 chr3R:14691613-14691733 9.95e-01 120 chrX:9656467-9656587 1.13e-01 120 chr3L:484938-485058 6.62e-02 120 chrX:6003956-6004076 1.00e+00 120 chr3L:2835882-2836002 1.51e-01 120 chr3L:20592728-20592848 5.93e-01 120 chr2L:3482822-3482942 9.95e-01 120 chr3L:19055225-19055345 8.06e-01 120 chr2R:18923620-18923740 9.97e-01 120 chr2L:20989643-20989763 4.56e-01 120 chr2R:11544141-11544261 1.00e+00 120 chr3L:12096900-12097020 8.20e-01 120 chr3L:21043996-21044116 2.74e-01 120 chr2L:11069596-11069716 9.95e-01 120 chrX:5020150-5020270 9.96e-01 120 chr3L:6458861-6458981 8.43e-01 120 chr3R:22184230-22184350 6.45e-01 120 chr2L:16537239-16537359 1.00e+00 120 chr3R:30843228-30843348 2.81e-01 120 chr3L:15174243-15174363 9.99e-01 120 chr3L:10562370-10562490 8.99e-01 120 chrX:14098415-14098535 9.95e-01 120 chr3L:20990400-20990520 6.67e-01 120 chr2L:3557582-3557702 3.52e-01 120 chrX:17807116-17807236 9.99e-01 120 chr3L:5851754-5851874 9.95e-01 120 chr2L:11052515-11052635 1.06e-01 120 chr2L:3562509-3562629 8.78e-06 25_[+1(1.82e-06)]_87 chr2R:18271172-18271292 2.60e-05 58_[+4(3.05e-07)]_54 chr2R:21847826-21847946 1.43e-01 120 chrX:5301011-5301131 4.84e-04 48_[+3(6.93e-07)]_64 chr3L:6447821-6447941 1.98e-01 120 chr2L:13545891-13546011 2.66e-05 87_[+5(1.37e-06)]_25 chr2L:4069679-4069799 9.54e-01 120 chr2L:646662-646782 9.79e-01 120 chrX:7534978-7535098 9.62e-01 120 chrX:18273313-18273433 3.31e-02 42_[+5(3.13e-05)]_70 chrX:2358353-2358473 5.62e-02 120 chr3R:17202462-17202582 9.91e-01 120 chr3L:11373895-11374015 4.60e-01 120 chr3L:4731829-4731949 4.03e-01 120 chr2L:11399647-11399767 9.99e-01 120 chr2R:18215418-18215538 9.92e-01 120 chr3R:23878423-23878543 9.90e-01 120 chr3R:10177049-10177169 6.23e-02 120 chr2R:14929620-14929740 4.99e-02 120 chr2L:15390588-15390708 9.99e-01 120 chr3L:7262629-7262749 6.75e-01 120 chr2R:20580849-20580969 2.38e-03 47_[+3(1.97e-06)]_65 chr2R:16836459-16836579 2.88e-01 120 chr2L:17421490-17421610 5.45e-01 120 chr2L:16503068-16503188 9.98e-01 120 chr2R:21225007-21225127 2.08e-03 120 chr3L:20952228-20952348 4.31e-01 120 chrX:6028001-6028121 9.99e-01 120 chr3L:15005882-15006002 8.34e-01 120 chrX:4435085-4435205 9.81e-02 120 chr2L:16591492-16591612 1.24e-02 19_[+4(4.60e-05)]_93 chr2R:11033714-11033834 5.59e-01 120 chr3R:29847267-29847387 4.23e-01 120 chr3L:14610624-14610744 9.74e-01 120 chrX:14017549-14017669 7.09e-01 120 chr3R:30843865-30843985 6.33e-01 120 chr2R:18907133-18907253 7.75e-01 120 chr3R:28848002-28848122 6.52e-01 120 chrX:21127410-21127530 3.98e-01 120 chr3L:5128376-5128496 1.88e-02 60_[+2(8.23e-05)]_52 chr3R:27179139-27179259 9.64e-01 120 chrX:18929528-18929648 4.99e-03 69_[+5(6.33e-05)]_43 chr2L:18523142-18523262 8.79e-01 120 chr3L:13109423-13109543 9.23e-02 9_[+3(8.19e-05)]_103 chr2R:13478476-13478596 1.99e-01 120 chr3R:29570407-29570527 9.92e-01 120 chr3R:9966255-9966375 9.58e-01 120 chr3L:14463944-14464064 9.79e-01 120 chr3L:18406116-18406236 7.25e-01 120 chr3L:7113154-7113274 1.04e-01 120 chr2R:21569768-21569888 7.22e-01 120 chr3R:15650423-15650543 7.09e-01 120 chr3R:19255381-19255501 6.06e-01 120 chr3R:15556602-15556722 8.35e-01 120 chrX:17488526-17488646 9.84e-01 120 chr2L:7899293-7899413 5.88e-01 120 chr3R:24549875-24549995 1.11e-01 120 chr3R:21826207-21826327 9.64e-01 120 chrX:8215586-8215706 9.91e-01 120 chr3L:2873217-2873337 3.88e-02 120 chr3L:16762302-16762422 9.98e-01 120 chr2L:7541471-7541591 1.00e+00 120 chr3R:30461756-30461876 9.26e-02 120 chr3L:21042689-21042809 5.27e-03 110_[+3(1.05e-06)]_2 chr3L:4383227-4383347 9.15e-01 120 chr2L:11386532-11386652 5.05e-02 48_[+5(6.33e-05)]_64 chr2L:18003148-18003268 9.04e-01 120 chr3L:3442222-3442342 4.78e-01 120 chr3L:22910030-22910150 3.43e-01 120 chr3R:7171830-7171950 2.16e-01 120 chr3R:21948789-21948909 5.17e-05 73_[+5(2.72e-06)]_39 chr3R:30256364-30256484 9.55e-01 120 chr3R:24970812-24970932 1.49e-01 120 chr2R:18566140-18566260 9.59e-02 120 chr2R:18879228-18879348 7.22e-01 120 chr2L:19156087-19156207 2.60e-04 49_[+5(3.53e-07)]_63 chr3R:14673095-14673215 1.62e-01 120 chr2L:7323078-7323198 3.76e-01 120 chr3L:20632469-20632589 1.69e-01 120 chr3R:14373946-14374066 7.99e-01 120 chr3R:10455043-10455163 3.71e-03 25_[+2(1.94e-06)]_87 chr2R:15100630-15100750 9.13e-01 120 chr2L:19454494-19454614 9.80e-01 120 chr3L:6364353-6364473 9.90e-01 120 chr3L:13212978-13213098 1.34e-02 120 chr2R:19985090-19985210 9.97e-01 120 chr3L:10928833-10928953 9.41e-01 120 chr2R:10057960-10058080 6.54e-07 7_[+2(8.06e-07)]_72_[+1(1.50e-06)]_\ 25 chr3R:13934746-13934866 6.93e-01 120 chr3R:18485403-18485523 1.53e-01 120 chr2R:14126268-14126388 4.60e-02 120 chr2L:608289-608409 4.77e-02 120 chrX:8212204-8212324 5.45e-01 120 chr3L:10365053-10365173 3.79e-01 120 chrX:342553-342673 5.52e-01 120 chrX:18256617-18256737 4.25e-03 107_[+3(4.14e-06)]_5 chr3R:15596114-15596234 7.56e-01 120 chr2L:15385490-15385610 2.47e-01 120 chrX:17542886-17543006 7.79e-02 120 chr2L:1456983-1457103 7.04e-06 96_[+2(8.06e-07)]_16 chr3L:15264747-15264867 1.00e+00 120 chr2R:17499291-17499411 2.84e-01 120 chr2R:14313678-14313798 1.00e+00 120 chr2R:8655402-8655522 3.64e-04 18_[+1(2.90e-06)]_94 chr3L:18078727-18078847 7.73e-02 120 chrX:18544818-18544938 1.51e-02 34_[+5(8.83e-05)]_78 chr2L:1409812-1409932 7.32e-01 120 chr2R:22529804-22529924 6.42e-02 120 chr3L:2866990-2867110 4.76e-01 120 chr3L:2553232-2553352 5.08e-06 80_[+4(1.09e-06)]_20_[+2(2.25e-06)]_\ 4 chr3R:7651146-7651266 4.70e-01 120 chr3R:8847405-8847525 1.52e-01 120 chr3R:14389404-14389524 9.14e-01 120 chr2L:12823744-12823864 9.93e-01 120 chr3R:22140187-22140307 5.62e-03 15_[+5(6.33e-05)]_97 chr3R:6102475-6102595 9.64e-01 120 chr2L:15392472-15392592 6.83e-01 120 chr2L:8919802-8919922 6.88e-01 120 chr3R:22194844-22194964 9.62e-01 120 chr3L:16286422-16286542 1.98e-01 120 chr3R:31312433-31312553 2.11e-01 120 chr2R:15745308-15745428 7.89e-01 120 chr3L:531310-531430 7.73e-01 120 chrX:17558855-17558975 1.85e-02 120 chr2L:14236272-14236392 9.98e-01 120 chr3R:9594045-9594165 1.25e-01 120 chr3L:3444353-3444473 9.91e-01 120 chr2L:12602324-12602444 9.70e-01 120 chrX:4442630-4442750 2.44e-01 120 chr2L:20381453-20381573 2.73e-01 120 chr2L:7199679-7199799 1.28e-01 82_[+4(4.60e-05)]_30 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************