******************************************************************************** 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/tai.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2L:9227695-9227815 1.0000 120 chr3L:15833907-15834027 1.0000 120 chr2L:9195948-9196068 1.0000 120 chr3L:22774405-22774525 1.0000 120 chr2L:9223936-9224056 1.0000 120 chr3R:21853440-21853560 1.0000 120 chr2L:9173488-9173608 1.0000 120 chr3L:3415240-3415360 1.0000 120 chr3L:69027-69147 1.0000 120 chr2L:21215680-21215800 1.0000 120 chr2L:9165321-9165441 1.0000 120 chr2L:5290580-5290700 1.0000 120 chr2R:16688416-16688536 1.0000 120 chr2L:9193287-9193407 1.0000 120 chr3L:19066848-19066968 1.0000 120 chr2L:7976495-7976615 1.0000 120 chr2L:9192234-9192354 1.0000 120 chr3R:5014331-5014451 1.0000 120 chr3L:17594119-17594239 1.0000 120 chr3R:8942330-8942450 1.0000 120 chr2L:5370085-5370205 1.0000 120 chr2R:14984931-14985051 1.0000 120 chr3L:14206379-14206499 1.0000 120 chr3R:4949532-4949652 1.0000 120 chr2L:8733396-8733516 1.0000 120 chr2L:21752324-21752444 1.0000 120 chr2L:488860-488980 1.0000 120 chr2R:19461046-19461166 1.0000 120 chr2L:9163759-9163879 1.0000 120 chr4:331338-331458 1.0000 120 chr3R:7068291-7068411 1.0000 120 chr3R:24262707-24262827 1.0000 120 chr2L:2195158-2195278 1.0000 120 chr2L:7218533-7218653 1.0000 120 chr3R:4974364-4974484 1.0000 120 chr2R:7088710-7088830 1.0000 120 chr4:1034593-1034713 1.0000 120 chr3R:11566456-11566576 1.0000 120 chr3L:20492108-20492228 1.0000 120 chr3R:10583308-10583428 1.0000 120 chr3L:1574541-1574661 1.0000 120 chr2R:11437741-11437861 1.0000 120 chr2L:9180513-9180633 1.0000 120 chr3L:7990747-7990867 1.0000 120 chr3L:8844851-8844971 1.0000 120 chr3R:10088724-10088844 1.0000 120 chr2L:16592856-16592976 1.0000 120 chr2R:6038780-6038900 1.0000 120 chr3L:22832628-22832748 1.0000 120 chr3L:10736598-10736718 1.0000 120 chr2L:122801-122921 1.0000 120 chrX:115131-115251 1.0000 120 chr2R:1265087-1265207 1.0000 120 chr3L:16197113-16197233 1.0000 120 chr2L:9143863-9143983 1.0000 120 chr2L:17387305-17387425 1.0000 120 chr3L:19300372-19300492 1.0000 120 chr2R:16825321-16825441 1.0000 120 chr3L:20732253-20732373 1.0000 120 chr2L:8269974-8270094 1.0000 120 chr2R:19408903-19409023 1.0000 120 chr3L:7373915-7374035 1.0000 120 chrX:1660035-1660155 1.0000 120 chr3L:11553845-11553965 1.0000 120 chr2L:21763411-21763531 1.0000 120 chr3L:9425104-9425224 1.0000 120 chr2L:8151290-8151410 1.0000 120 chr2L:9201455-9201575 1.0000 120 chr3L:16801107-16801227 1.0000 120 chr2L:8417296-8417416 1.0000 120 chr3L:7991649-7991769 1.0000 120 chr3R:23215326-23215446 1.0000 120 chr3L:8156049-8156169 1.0000 120 chr3L:17918137-17918257 1.0000 120 chr2L:3345021-3345141 1.0000 120 chr3L:19195750-19195870 1.0000 120 chr4:827055-827175 1.0000 120 chr2L:8697537-8697657 1.0000 120 chr3L:19568186-19568306 1.0000 120 chr3R:27550478-27550598 1.0000 120 chr4:464359-464479 1.0000 120 chr3R:32064091-32064211 1.0000 120 chr2L:9180270-9180390 1.0000 120 chr2L:14520250-14520370 1.0000 120 chr2L:8360748-8360868 1.0000 120 chrX:19962419-19962539 1.0000 120 chr3L:21061433-21061553 1.0000 120 chr2R:19472418-19472538 1.0000 120 chr3L:10369936-10370056 1.0000 120 chr3L:502238-502358 1.0000 120 chr2L:5074720-5074840 1.0000 120 chrX:1950506-1950626 1.0000 120 chr2L:9233612-9233732 1.0000 120 chr3L:17481205-17481325 1.0000 120 chr3L:11351885-11352005 1.0000 120 chr2R:5670833-5670953 1.0000 120 chr2L:9204220-9204340 1.0000 120 chr3L:17564239-17564359 1.0000 120 chr2R:19428893-19429013 1.0000 120 chr4:568033-568153 1.0000 120 chr2L:16636824-16636944 1.0000 120 chr3R:24589902-24590022 1.0000 120 chr4:1026055-1026175 1.0000 120 chr2R:8647165-8647285 1.0000 120 chr3L:3413805-3413925 1.0000 120 chr2R:6104805-6104925 1.0000 120 chr3L:1005065-1005185 1.0000 120 chrX:19163223-19163343 1.0000 120 chr3R:15468484-15468604 1.0000 120 chr3L:18084998-18085118 1.0000 120 chr3L:13011701-13011821 1.0000 120 chr3R:21801381-21801501 1.0000 120 chr2L:12476198-12476318 1.0000 120 chr2L:14514761-14514881 1.0000 120 chr2L:9187473-9187593 1.0000 120 chr3R:10378898-10379018 1.0000 120 chr3L:10644525-10644645 1.0000 120 chr3L:15836425-15836545 1.0000 120 chr2L:7203287-7203407 1.0000 120 chr3R:7126475-7126595 1.0000 120 chr2R:10771152-10771272 1.0000 120 chr3R:31978437-31978557 1.0000 120 chr3L:728717-728837 1.0000 120 chr3L:11287920-11288040 1.0000 120 chr3R:16238213-16238333 1.0000 120 chr2L:9214369-9214489 1.0000 120 chr3L:19563606-19563726 1.0000 120 chr2L:3479602-3479722 1.0000 120 chr2R:1513637-1513757 1.0000 120 chr2R:22396808-22396928 1.0000 120 chr2L:21297743-21297863 1.0000 120 chr2L:10395226-10395346 1.0000 120 chr3R:9221643-9221763 1.0000 120 chr3L:8750717-8750837 1.0000 120 chr2L:10311138-10311258 1.0000 120 chr2L:3634078-3634198 1.0000 120 chr3L:8000539-8000659 1.0000 120 chrX:17294948-17295068 1.0000 120 chr3L:18142979-18143099 1.0000 120 chr3L:12260460-12260580 1.0000 120 chr3L:8710850-8710970 1.0000 120 chr2L:18553377-18553497 1.0000 120 chr2L:21659525-21659645 1.0000 120 chr3L:11242384-11242504 1.0000 120 chr2L:11175994-11176114 1.0000 120 chr3L:3244431-3244551 1.0000 120 chr2R:19480919-19481039 1.0000 120 chr3R:14429639-14429759 1.0000 120 chr2L:10295823-10295943 1.0000 120 chr2L:9186159-9186279 1.0000 120 chr2L:11951915-11952035 1.0000 120 chr2L:14433105-14433225 1.0000 120 chr3L:12750976-12751096 1.0000 120 chr3R:16286846-16286966 1.0000 120 chr2R:12384964-12385084 1.0000 120 chrX:16908455-16908575 1.0000 120 chr2L:16499394-16499514 1.0000 120 chr2L:8103719-8103839 1.0000 120 chr3R:13015141-13015261 1.0000 120 chrX:13320128-13320248 1.0000 120 chr2L:21208114-21208234 1.0000 120 chrX:1610269-1610389 1.0000 120 chr3R:19571961-19572081 1.0000 120 chr3L:7530605-7530725 1.0000 120 chr3L:18816972-18817092 1.0000 120 chr2R:10030801-10030921 1.0000 120 chr2L:10242220-10242340 1.0000 120 chr2L:16322312-16322432 1.0000 120 chr2R:10040713-10040833 1.0000 120 chr3L:12753381-12753501 1.0000 120 chr3L:8288426-8288546 1.0000 120 chr3L:3262786-3262906 1.0000 120 chr2L:18983498-18983618 1.0000 120 chr2R:6139627-6139747 1.0000 120 chr3R:14030029-14030149 1.0000 120 chr2L:9197858-9197978 1.0000 120 chr2L:9178877-9178997 1.0000 120 chr3L:21256081-21256201 1.0000 120 chr4:328481-328601 1.0000 120 chr2L:8425397-8425517 1.0000 120 chr3R:16204013-16204133 1.0000 120 chr2R:10526123-10526243 1.0000 120 chr3L:17921630-17921750 1.0000 120 chrX:12651154-12651274 1.0000 120 chr2L:2361741-2361861 1.0000 120 chr3R:21836356-21836476 1.0000 120 chr2R:25250572-25250692 1.0000 120 chr2L:7533855-7533975 1.0000 120 chr2R:13409852-13409972 1.0000 120 chr2L:16635923-16636043 1.0000 120 chr2R:16834901-16835021 1.0000 120 chr3R:9330585-9330705 1.0000 120 chr3L:21895323-21895443 1.0000 120 chr3L:3442921-3443041 1.0000 120 chr2L:7536985-7537105 1.0000 120 chr3L:16663857-16663977 1.0000 120 chr3L:17666728-17666848 1.0000 120 chr2R:16670412-16670532 1.0000 120 chr2R:6039823-6039943 1.0000 120 chr2L:71569-71689 1.0000 120 chr3L:15861551-15861671 1.0000 120 chr2L:2011056-2011176 1.0000 120 chr2L:10240007-10240127 1.0000 120 chr3L:14648800-14648920 1.0000 120 chr3R:21631636-21631756 1.0000 120 chr3R:17393235-17393355 1.0000 120 chr2L:13463048-13463168 1.0000 120 chr2R:11649319-11649439 1.0000 120 chr3R:10086806-10086926 1.0000 120 chrX:13394538-13394658 1.0000 120 chr3R:23151135-23151255 1.0000 120 chr4:974324-974444 1.0000 120 chr2R:12390081-12390201 1.0000 120 chr3R:27092352-27092472 1.0000 120 chr2L:13101612-13101732 1.0000 120 chr3R:20803750-20803870 1.0000 120 chr2L:93865-93985 1.0000 120 chr3R:4130758-4130878 1.0000 120 chr2L:18655807-18655927 1.0000 120 chr2R:7480419-7480539 1.0000 120 chr3R:30262562-30262682 1.0000 120 chr2L:3858218-3858338 1.0000 120 chr2L:8145134-8145254 1.0000 120 chr3L:16637747-16637867 1.0000 120 chr2L:478324-478444 1.0000 120 chr3R:10391683-10391803 1.0000 120 chrX:1578321-1578441 1.0000 120 chr2L:4812342-4812462 1.0000 120 chr3L:21928629-21928749 1.0000 120 chrX:14214476-14214596 1.0000 120 chr2R:4674151-4674271 1.0000 120 chr2R:6190516-6190636 1.0000 120 chr3R:27070576-27070696 1.0000 120 chr3L:11535519-11535639 1.0000 120 chr3R:21949757-21949877 1.0000 120 chr2R:10531575-10531695 1.0000 120 chr2L:20884784-20884904 1.0000 120 chr2L:115204-115324 1.0000 120 chr4:669864-669984 1.0000 120 chr3R:13402036-13402156 1.0000 120 chr2L:5393464-5393584 1.0000 120 chr3L:230748-230868 1.0000 120 chr3L:17536279-17536399 1.0000 120 chr3R:21628511-21628631 1.0000 120 chrX:11431003-11431123 1.0000 120 chr2L:16526791-16526911 1.0000 120 chr4:1028390-1028510 1.0000 120 chr2R:11509755-11509875 1.0000 120 chr2R:25007688-25007808 1.0000 120 chr2R:1512882-1513002 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_tai/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/tai.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 0.333 C 0.169 G 0.16 T 0.338 Background letter frequencies (from file dataset with add-one prior applied): A 0.333 C 0.169 G 0.16 T 0.338 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CGAGCAGS MEME-1 width = 8 sites = 6 llr = 72 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::a::a:: pos.-specific C 8:::a::7 probability G 2a:a::a3 matrix T :::::::: bits 2.6 * ** * 2.4 * ** * 2.1 * ** * 1.9 ** ** * Relative 1.6 ******** Entropy 1.3 ******** (17.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGAGCAGC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:7536985-7537105 113 2.19e-06 TCGAACATCT CGAGCAGC chr3R:16204013-16204133 93 2.19e-06 AAAAGGAGTT CGAGCAGC TTTATAACGA chr3L:21061433-21061553 39 2.19e-06 gtaaactttg cgagcagc gggAACGTTT chr3L:21256081-21256201 6 4.27e-06 TTATT CGAGCAGG TTCAAAATAC chrX:1660035-1660155 34 4.27e-06 AGCTGCTGCA CGAGCAGG CCAATACCac chr2L:21752324-21752444 53 6.34e-06 TCTATGTTAT GGAGCAGC TCACTAATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:7536985-7537105 2.2e-06 112_[+1] chr3R:16204013-16204133 2.2e-06 92_[+1]_20 chr3L:21061433-21061553 2.2e-06 38_[+1]_74 chr3L:21256081-21256201 4.3e-06 5_[+1]_107 chrX:1660035-1660155 4.3e-06 33_[+1]_79 chr2L:21752324-21752444 6.3e-06 52_[+1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGAGCAGS width=8 seqs=6 chr2L:7536985-7537105 ( 113) CGAGCAGC 1 chr3R:16204013-16204133 ( 93) CGAGCAGC 1 chr3L:21061433-21061553 ( 39) CGAGCAGC 1 chr3L:21256081-21256201 ( 6) CGAGCAGG 1 chrX:1660035-1660155 ( 34) CGAGCAGG 1 chr2L:21752324-21752444 ( 53) GGAGCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.8596 E= 1.5e+003 -923 230 6 -923 -923 -923 264 -923 158 -923 -923 -923 -923 -923 264 -923 -923 256 -923 -923 158 -923 -923 -923 -923 -923 264 -923 -923 198 106 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 1.5e+003 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.666667 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCAGS MEME-1 regular expression -------------------------------------------------------------------------------- CGAGCAG[CG] -------------------------------------------------------------------------------- Time 7.50 secs. ******************************************************************************** ******************************************************************************** MOTIF GYGGCGSC MEME-2 width = 8 sites = 4 llr = 49 E-value = 1.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 35::a:5a probability G 8:aa:a5: matrix T :5:::::: bits 2.6 **** * 2.4 **** * 2.1 **** * 1.9 * **** * Relative 1.6 * ****** Entropy 1.3 * ****** (17.5 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCGGCGCC consensus CT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:69027-69147 101 1.04e-06 ATGGCGTTCG GCGGCGCC TGAGTCACAT chr2R:19428893-19429013 28 2.05e-06 TATAAAAAGG GTGGCGGC AGCAACATAG chr2L:2361741-2361861 19 3.12e-06 AGATGATTGT GTGGCGCC TTTGTTTGTT chr2L:478324-478444 35 3.66e-06 GCTAATTACG CCGGCGGC TGACAAGGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:69027-69147 1e-06 100_[+2]_12 chr2R:19428893-19429013 2.1e-06 27_[+2]_85 chr2L:2361741-2361861 3.1e-06 18_[+2]_94 chr2L:478324-478444 3.7e-06 34_[+2]_78 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GYGGCGSC width=8 seqs=4 chr3L:69027-69147 ( 101) GCGGCGCC 1 chr2R:19428893-19429013 ( 28) GTGGCGGC 1 chr2L:2361741-2361861 ( 19) GTGGCGCC 1 chr2L:478324-478444 ( 35) CCGGCGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.5228 E= 1.1e+004 -865 56 223 -865 -865 156 -865 57 -865 -865 264 -865 -865 -865 264 -865 -865 256 -865 -865 -865 -865 264 -865 -865 156 164 -865 -865 256 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.1e+004 0.000000 0.250000 0.750000 0.000000 0.000000 0.500000 0.000000 0.500000 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 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGGCGSC MEME-2 regular expression -------------------------------------------------------------------------------- [GC][CT]GGCG[CG]C -------------------------------------------------------------------------------- Time 13.80 secs. ******************************************************************************** ******************************************************************************** MOTIF CGCGSGCM MEME-3 width = 8 sites = 3 llr = 38 E-value = 2.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::7 pos.-specific C a:a:3:a3 probability G :a:a7a:: matrix T :::::::: bits 2.6 **** ** 2.4 **** ** 2.1 **** ** 1.9 **** ** Relative 1.6 ******* Entropy 1.3 ******* (18.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGCGGGCA consensus C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:16197113-16197233 82 1.59e-06 TCATCTCTTC CGCGGGCA CATTTATTTA chr2R:1265087-1265207 104 1.59e-06 CAAAATTCTA CGCGGGCC ACGACGAAC chr2L:8697537-8697657 20 3.27e-06 CGCCCGTTGC CGCGCGCA CAAACAATGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:16197113-16197233 1.6e-06 81_[+3]_31 chr2R:1265087-1265207 1.6e-06 103_[+3]_9 chr2L:8697537-8697657 3.3e-06 19_[+3]_93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGCGSGCM width=8 seqs=3 chr3L:16197113-16197233 ( 82) CGCGGGCA 1 chr2R:1265087-1265207 ( 104) CGCGGGCC 1 chr2L:8697537-8697657 ( 20) CGCGCGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.6483 E= 2.2e+004 -823 256 -823 -823 -823 -823 264 -823 -823 256 -823 -823 -823 -823 264 -823 -823 98 206 -823 -823 -823 264 -823 -823 256 -823 -823 100 98 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 2.2e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCGSGCM MEME-3 regular expression -------------------------------------------------------------------------------- CGCG[GC]GC[AC] -------------------------------------------------------------------------------- Time 20.13 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGCTGWG MEME-4 width = 8 sites = 4 llr = 49 E-value = 4.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::5: pos.-specific C aa:a:::: probability G ::a::a:a matrix T ::::a:5: bits 2.6 **** * * 2.4 **** * * 2.1 **** * * 1.9 **** * * Relative 1.6 ****** * Entropy 1.3 ****** * (17.8 bits) 1.1 ****** * 0.8 ****** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CCGCTGAG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:7533855-7533975 113 4.48e-06 GCTTAATTAG CCGCTGAG chr3L:21256081-21256201 43 4.48e-06 TGTGGTAATT CCGCTGAG ACCACACCGC chr3L:18142979-18143099 86 4.48e-06 GGCTTATTCA CCGCTGTG CACTCGAAAA chr2R:22396808-22396928 76 4.48e-06 GTTCAATGAA CCGCTGTG TACGAAAGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:7533855-7533975 4.5e-06 112_[+4] chr3L:21256081-21256201 4.5e-06 42_[+4]_70 chr3L:18142979-18143099 4.5e-06 85_[+4]_27 chr2R:22396808-22396928 4.5e-06 75_[+4]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGCTGWG width=8 seqs=4 chr2L:7533855-7533975 ( 113) CCGCTGAG 1 chr3L:21256081-21256201 ( 43) CCGCTGAG 1 chr3L:18142979-18143099 ( 86) CCGCTGTG 1 chr2R:22396808-22396928 ( 76) CCGCTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.7858 E= 4.5e+004 -865 256 -865 -865 -865 256 -865 -865 -865 -865 264 -865 -865 256 -865 -865 -865 -865 -865 156 -865 -865 264 -865 58 -865 -865 57 -865 -865 264 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 4.5e+004 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCTGWG MEME-4 regular expression -------------------------------------------------------------------------------- CCGCTG[AT]G -------------------------------------------------------------------------------- Time 26.46 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGMGTG MEME-5 width = 8 sites = 3 llr = 38 E-value = 2.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::7::: pos.-specific C ::a:3::: probability G aa:a:a:a matrix T ::::::a: bits 2.6 **** * * 2.4 **** * * 2.1 **** * * 1.9 **** * * Relative 1.6 **** *** Entropy 1.3 **** *** (18.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GGCGAGTG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:32064091-32064211 71 3.01e-06 TCATTACTTG GGCGCGTG AACATGTTTG chr2L:8151290-8151410 110 3.01e-06 AACAACAAAT GGCGAGTG CAA chr2L:488860-488980 99 3.01e-06 CAGGCCTCCA GGCGAGTG TATTGCACTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:32064091-32064211 3e-06 70_[+5]_42 chr2L:8151290-8151410 3e-06 109_[+5]_3 chr2L:488860-488980 3e-06 98_[+5]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGMGTG width=8 seqs=3 chr3R:32064091-32064211 ( 71) GGCGCGTG 1 chr2L:8151290-8151410 ( 110) GGCGAGTG 1 chr2L:488860-488980 ( 99) GGCGAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 2.4e+004 -823 -823 264 -823 -823 -823 264 -823 -823 256 -823 -823 -823 -823 264 -823 100 98 -823 -823 -823 -823 264 -823 -823 -823 -823 156 -823 -823 264 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 2.4e+004 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 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGMGTG MEME-5 regular expression -------------------------------------------------------------------------------- GGCG[AC]GTG -------------------------------------------------------------------------------- Time 32.75 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:9227695-9227815 6.81e-02 120 chr3L:15833907-15834027 9.97e-01 120 chr2L:9195948-9196068 8.85e-01 120 chr3L:22774405-22774525 9.95e-01 120 chr2L:9223936-9224056 4.93e-02 87_[+4(8.16e-05)]_25 chr3R:21853440-21853560 9.62e-02 75_[+3(8.63e-05)]_37 chr2L:9173488-9173608 1.03e-01 120 chr3L:3415240-3415360 2.88e-01 120 chr3L:69027-69147 1.56e-05 100_[+2(1.04e-06)]_12 chr2L:21215680-21215800 9.92e-01 120 chr2L:9165321-9165441 6.54e-01 120 chr2L:5290580-5290700 7.76e-02 31_[+4(8.16e-05)]_81 chr2R:16688416-16688536 4.66e-01 120 chr2L:9193287-9193407 1.85e-01 120 chr3L:19066848-19066968 8.83e-01 120 chr2L:7976495-7976615 1.06e-01 120 chr2L:9192234-9192354 2.59e-01 120 chr3R:5014331-5014451 8.50e-01 120 chr3L:17594119-17594239 1.00e+00 120 chr3R:8942330-8942450 8.26e-02 120 chr2L:5370085-5370205 9.75e-01 120 chr2R:14984931-14985051 9.58e-01 120 chr3L:14206379-14206499 7.00e-01 120 chr3R:4949532-4949652 6.01e-01 120 chr2L:8733396-8733516 3.33e-02 120 chr2L:21752324-21752444 5.36e-03 52_[+1(6.34e-06)]_60 chr2L:488860-488980 2.23e-03 98_[+5(3.01e-06)]_14 chr2R:19461046-19461166 9.53e-01 120 chr2L:9163759-9163879 4.64e-01 120 chr4:331338-331458 4.90e-01 120 chr3R:7068291-7068411 3.79e-01 120 chr3R:24262707-24262827 1.00e+00 120 chr2L:2195158-2195278 3.11e-01 120 chr2L:7218533-7218653 1.46e-03 94_[+3(1.32e-05)]_18 chr3R:4974364-4974484 8.26e-01 120 chr2R:7088710-7088830 7.08e-01 120 chr4:1034593-1034713 9.82e-01 120 chr3R:11566456-11566576 2.41e-02 120 chr3L:20492108-20492228 9.83e-01 120 chr3R:10583308-10583428 9.92e-01 120 chr3L:1574541-1574661 7.80e-01 120 chr2R:11437741-11437861 9.59e-01 120 chr2L:9180513-9180633 9.86e-01 120 chr3L:7990747-7990867 6.75e-01 120 chr3L:8844851-8844971 4.42e-01 120 chr3R:10088724-10088844 8.93e-01 120 chr2L:16592856-16592976 6.52e-01 120 chr2R:6038780-6038900 3.28e-01 120 chr3L:22832628-22832748 8.41e-01 120 chr3L:10736598-10736718 6.66e-01 120 chr2L:122801-122921 5.64e-01 120 chrX:115131-115251 4.72e-01 120 chr2R:1265087-1265207 3.95e-03 103_[+3(1.59e-06)]_9 chr3L:16197113-16197233 1.32e-03 81_[+3(1.59e-06)]_31 chr2L:9143863-9143983 5.94e-02 120 chr2L:17387305-17387425 1.00e+00 120 chr3L:19300372-19300492 9.96e-01 120 chr2R:16825321-16825441 9.57e-01 120 chr3L:20732253-20732373 5.58e-01 120 chr2L:8269974-8270094 6.50e-01 120 chr2R:19408903-19409023 9.99e-01 120 chr3L:7373915-7374035 9.00e-01 120 chrX:1660035-1660155 7.75e-04 33_[+1(4.27e-06)]_79 chr3L:11553845-11553965 9.81e-01 120 chr2L:21763411-21763531 9.73e-01 120 chr3L:9425104-9425224 7.97e-01 120 chr2L:8151290-8151410 3.10e-04 109_[+5(3.01e-06)]_3 chr2L:9201455-9201575 4.86e-01 120 chr3L:16801107-16801227 2.85e-01 120 chr2L:8417296-8417416 9.37e-01 120 chr3L:7991649-7991769 4.44e-01 120 chr3R:23215326-23215446 6.39e-02 120 chr3L:8156049-8156169 3.58e-01 120 chr3L:17918137-17918257 3.84e-01 120 chr2L:3345021-3345141 9.70e-01 120 chr3L:19195750-19195870 7.05e-01 120 chr4:827055-827175 4.24e-01 120 chr2L:8697537-8697657 5.22e-04 19_[+3(3.27e-06)]_93 chr3L:19568186-19568306 2.43e-01 120 chr3R:27550478-27550598 1.00e+00 120 chr4:464359-464479 8.52e-01 120 chr3R:32064091-32064211 3.95e-03 70_[+5(3.01e-06)]_42 chr2L:9180270-9180390 2.08e-01 120 chr2L:14520250-14520370 6.01e-01 120 chr2L:8360748-8360868 7.05e-01 120 chrX:19962419-19962539 3.13e-03 112_[+1(5.36e-05)] chr3L:21061433-21061553 5.94e-04 38_[+1(2.19e-06)]_74 chr2R:19472418-19472538 5.27e-01 120 chr3L:10369936-10370056 3.52e-03 24_[+1(4.28e-05)]_88 chr3L:502238-502358 5.26e-01 120 chr2L:5074720-5074840 2.42e-01 120 chrX:1950506-1950626 8.26e-06 54_[+2(7.09e-05)]_58 chr2L:9233612-9233732 7.34e-01 120 chr3L:17481205-17481325 2.82e-01 120 chr3L:11351885-11352005 9.59e-01 120 chr2R:5670833-5670953 4.89e-01 120 chr2L:9204220-9204340 3.69e-01 120 chr3L:17564239-17564359 9.02e-01 120 chr2R:19428893-19429013 5.13e-03 27_[+2(2.05e-06)]_85 chr4:568033-568153 4.99e-01 120 chr2L:16636824-16636944 1.00e+00 120 chr3R:24589902-24590022 7.59e-01 120 chr4:1026055-1026175 9.99e-01 120 chr2R:8647165-8647285 6.83e-01 120 chr3L:3413805-3413925 4.72e-01 120 chr2R:6104805-6104925 8.68e-01 120 chr3L:1005065-1005185 9.58e-01 120 chrX:19163223-19163343 8.27e-01 120 chr3R:15468484-15468604 9.77e-02 120 chr3L:18084998-18085118 8.19e-01 120 chr3L:13011701-13011821 5.42e-02 120 chr3R:21801381-21801501 1.00e+00 120 chr2L:12476198-12476318 9.19e-01 120 chr2L:14514761-14514881 9.99e-01 120 chr2L:9187473-9187593 6.82e-01 120 chr3R:10378898-10379018 1.00e+00 120 chr3L:10644525-10644645 9.94e-01 120 chr3L:15836425-15836545 9.92e-01 120 chr2L:7203287-7203407 9.97e-01 120 chr3R:7126475-7126595 9.61e-01 120 chr2R:10771152-10771272 7.26e-01 120 chr3R:31978437-31978557 1.31e-03 15_[+3(3.66e-05)]_97 chr3L:728717-728837 6.18e-01 120 chr3L:11287920-11288040 3.52e-01 120 chr3R:16238213-16238333 7.04e-01 120 chr2L:9214369-9214489 9.86e-01 120 chr3L:19563606-19563726 6.24e-02 120 chr2L:3479602-3479722 4.57e-01 120 chr2R:1513637-1513757 6.75e-01 120 chr2R:22396808-22396928 2.51e-03 75_[+4(4.48e-06)]_37 chr2L:21297743-21297863 4.70e-02 25_[+4(8.16e-05)]_87 chr2L:10395226-10395346 4.02e-01 120 chr3R:9221643-9221763 6.18e-01 120 chr3L:8750717-8750837 7.69e-01 120 chr2L:10311138-10311258 1.11e-01 120 chr2L:3634078-3634198 7.67e-01 120 chr3L:8000539-8000659 9.96e-01 120 chrX:17294948-17295068 1.00e+00 120 chr3L:18142979-18143099 3.26e-02 85_[+4(4.48e-06)]_27 chr3L:12260460-12260580 8.52e-01 120 chr3L:8710850-8710970 9.29e-01 120 chr2L:18553377-18553497 5.86e-01 120 chr2L:21659525-21659645 6.50e-01 120 chr3L:11242384-11242504 3.13e-01 120 chr2L:11175994-11176114 1.00e+00 120 chr3L:3244431-3244551 9.40e-01 120 chr2R:19480919-19481039 9.99e-01 120 chr3R:14429639-14429759 4.74e-02 120 chr2L:10295823-10295943 1.00e+00 120 chr2L:9186159-9186279 4.50e-01 120 chr2L:11951915-11952035 1.00e+00 120 chr2L:14433105-14433225 6.46e-02 120 chr3L:12750976-12751096 9.23e-01 120 chr3R:16286846-16286966 8.42e-01 120 chr2R:12384964-12385084 2.35e-02 120 chrX:16908455-16908575 3.14e-01 120 chr2L:16499394-16499514 9.86e-01 120 chr2L:8103719-8103839 1.00e+00 120 chr3R:13015141-13015261 9.97e-01 120 chrX:13320128-13320248 8.14e-01 120 chr2L:21208114-21208234 5.76e-01 120 chrX:1610269-1610389 3.84e-03 120 chr3R:19571961-19572081 3.10e-02 120 chr3L:7530605-7530725 7.64e-03 120 chr3L:18816972-18817092 2.33e-01 120 chr2R:10030801-10030921 9.66e-01 120 chr2L:10242220-10242340 1.98e-01 120 chr2L:16322312-16322432 3.99e-01 120 chr2R:10040713-10040833 1.30e-01 94_[+3(8.63e-05)]_18 chr3L:12753381-12753501 4.97e-01 120 chr3L:8288426-8288546 5.54e-01 120 chr3L:3262786-3262906 4.58e-01 120 chr2L:18983498-18983618 9.68e-01 120 chr2R:6139627-6139747 5.58e-01 120 chr3R:14030029-14030149 6.40e-01 120 chr2L:9197858-9197978 2.68e-01 120 chr2L:9178877-9178997 5.47e-02 120 chr3L:21256081-21256201 1.80e-04 5_[+1(4.27e-06)]_29_[+4(4.48e-06)]_\ 70 chr4:328481-328601 1.06e-01 120 chr2L:8425397-8425517 2.84e-02 120 chr3R:16204013-16204133 1.36e-02 92_[+1(2.19e-06)]_20 chr2R:10526123-10526243 9.88e-01 120 chr3L:17921630-17921750 1.34e-01 120 chrX:12651154-12651274 8.08e-01 120 chr2L:2361741-2361861 1.99e-03 18_[+2(3.12e-06)]_94 chr3R:21836356-21836476 7.64e-01 120 chr2R:25250572-25250692 3.30e-01 120 chr2L:7533855-7533975 4.15e-03 112_[+4(4.48e-06)] chr2R:13409852-13409972 1.45e-02 46_[+2(3.84e-05)]_66 chr2L:16635923-16636043 9.89e-01 120 chr2R:16834901-16835021 7.23e-01 120 chr3R:9330585-9330705 1.00e+00 120 chr3L:21895323-21895443 9.03e-01 120 chr3L:3442921-3443041 2.63e-01 120 chr2L:7536985-7537105 7.41e-03 112_[+1(2.19e-06)] chr3L:16663857-16663977 9.86e-01 120 chr3L:17666728-17666848 8.90e-01 120 chr2R:16670412-16670532 4.95e-01 120 chr2R:6039823-6039943 6.84e-01 120 chr2L:71569-71689 5.65e-01 120 chr3L:15861551-15861671 8.33e-01 120 chr2L:2011056-2011176 7.06e-02 120 chr2L:10240007-10240127 4.57e-01 120 chr3L:14648800-14648920 9.11e-01 120 chr3R:21631636-21631756 1.11e-01 120 chr3R:17393235-17393355 9.84e-01 120 chr2L:13463048-13463168 6.30e-01 120 chr2R:11649319-11649439 9.97e-01 120 chr3R:10086806-10086926 9.95e-01 120 chrX:13394538-13394658 2.11e-01 120 chr3R:23151135-23151255 9.07e-01 120 chr4:974324-974444 5.21e-01 120 chr2R:12390081-12390201 4.57e-01 120 chr3R:27092352-27092472 8.26e-01 120 chr2L:13101612-13101732 8.38e-02 120 chr3R:20803750-20803870 4.21e-01 120 chr2L:93865-93985 9.79e-01 120 chr3R:4130758-4130878 3.12e-02 120 chr2L:18655807-18655927 9.14e-01 120 chr2R:7480419-7480539 8.85e-01 120 chr3R:30262562-30262682 9.96e-01 120 chr2L:3858218-3858338 3.70e-01 120 chr2L:8145134-8145254 8.80e-03 58_[+1(8.81e-05)]_54 chr3L:16637747-16637867 3.02e-03 120 chr2L:478324-478444 6.56e-05 34_[+2(3.66e-06)]_78 chr3R:10391683-10391803 1.00e+00 120 chrX:1578321-1578441 2.93e-02 120 chr2L:4812342-4812462 9.15e-01 120 chr3L:21928629-21928749 7.40e-01 120 chrX:14214476-14214596 2.97e-01 120 chr2R:4674151-4674271 3.92e-01 120 chr2R:6190516-6190636 9.73e-01 120 chr3R:27070576-27070696 8.00e-01 120 chr3L:11535519-11535639 9.99e-01 120 chr3R:21949757-21949877 7.36e-01 120 chr2R:10531575-10531695 2.40e-01 120 chr2L:20884784-20884904 2.79e-01 120 chr2L:115204-115324 1.94e-01 120 chr4:669864-669984 7.86e-01 120 chr3R:13402036-13402156 8.92e-01 120 chr2L:5393464-5393584 1.00e+00 120 chr3L:230748-230868 6.80e-02 120 chr3L:17536279-17536399 8.65e-01 120 chr3R:21628511-21628631 1.77e-02 40_[+4(8.16e-05)]_72 chrX:11431003-11431123 3.67e-01 120 chr2L:16526791-16526911 8.76e-01 120 chr4:1028390-1028510 4.40e-02 120 chr2R:11509755-11509875 5.00e-01 120 chr2R:25007688-25007808 4.14e-01 120 chr2R:1512882-1513002 2.49e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************