******************************************************************************** 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/lola.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2R:18963300-18963420 1.0000 120 chr2L:10351320-10351440 1.0000 120 chr3L:15174977-15175097 1.0000 120 chr3L:13032659-13032779 1.0000 120 chr3L:18229103-18229223 1.0000 120 chrX:18910951-18911071 1.0000 120 chr2R:11559270-11559390 1.0000 120 chrX:18208621-18208741 1.0000 120 chr3L:6162144-6162264 1.0000 120 chr3L:15777468-15777588 1.0000 120 chr2L:3855666-3855786 1.0000 120 chrX:18207603-18207723 1.0000 120 chr3R:6672371-6672491 1.0000 120 chr3L:5017612-5017732 1.0000 120 chr3L:15203219-15203339 1.0000 120 chrX:18523325-18523445 1.0000 120 chr3L:21727186-21727306 1.0000 120 chr2L:3439639-3439759 1.0000 120 chr3L:16017110-16017230 1.0000 120 chr3L:21462992-21463112 1.0000 120 chr3R:14586575-14586695 1.0000 120 chr2L:18871852-18871972 1.0000 120 chrX:8671786-8671906 1.0000 120 chr3L:15844695-15844815 1.0000 120 chr2R:12020615-12020735 1.0000 120 chr2L:9586071-9586191 1.0000 120 chr3L:18225081-18225201 1.0000 120 chr2L:4359284-4359404 1.0000 120 chr2L:11470082-11470202 1.0000 120 chrX:12617882-12618002 1.0000 120 chr3L:14961168-14961288 1.0000 120 chr2L:12415868-12415988 1.0000 120 chr3L:15670560-15670680 1.0000 120 chr3R:19935353-19935473 1.0000 120 chr3L:12062347-12062467 1.0000 120 chrX:14846493-14846613 1.0000 120 chr3L:6160029-6160149 1.0000 120 chr3L:11413793-11413913 1.0000 120 chrX:16205289-16205409 1.0000 120 chr2L:7624316-7624436 1.0000 120 chr3R:21566927-21567047 1.0000 120 chr2R:8242215-8242335 1.0000 120 chr2L:18896944-18897064 1.0000 120 chr3L:20687490-20687610 1.0000 120 chr2L:5378982-5379102 1.0000 120 chrX:3344772-3344892 1.0000 120 chr3R:10370586-10370706 1.0000 120 chr3L:14611508-14611628 1.0000 120 chr3R:29547695-29547815 1.0000 120 chr3L:16635935-16636055 1.0000 120 chr3R:19935151-19935271 1.0000 120 chr2L:9990238-9990358 1.0000 120 chrX:17357562-17357682 1.0000 120 chr3R:7135244-7135364 1.0000 120 chr2L:11980182-11980302 1.0000 120 chr3L:15775587-15775707 1.0000 120 chr3R:6674685-6674805 1.0000 120 chr3R:15580817-15580937 1.0000 120 chr3L:7962187-7962307 1.0000 120 chrX:17712614-17712734 1.0000 120 chr3L:10962141-10962261 1.0000 120 chr3L:5994156-5994276 1.0000 120 chr2R:14810436-14810556 1.0000 120 chr3R:6816693-6816813 1.0000 120 chr3R:24580576-24580696 1.0000 120 chr3R:29372774-29372894 1.0000 120 chr3R:10651126-10651246 1.0000 120 chr3L:18227495-18227615 1.0000 120 chr2L:10689501-10689621 1.0000 120 chrX:16171536-16171656 1.0000 120 chr3R:16630660-16630780 1.0000 120 chr3L:16746106-16746226 1.0000 120 chr3L:11309854-11309974 1.0000 120 chr2L:19373896-19374016 1.0000 120 chr2R:22402936-22403056 1.0000 120 chr2L:4185789-4185909 1.0000 120 chr3R:16886944-16887064 1.0000 120 chr3L:13068463-13068583 1.0000 120 chr3L:12444143-12444263 1.0000 120 chr2L:3675911-3676031 1.0000 120 chrX:20756597-20756717 1.0000 120 chr3L:15253686-15253806 1.0000 120 chrX:17799218-17799338 1.0000 120 chr3L:15672956-15673076 1.0000 120 chr2R:8659073-8659193 1.0000 120 chr3L:3873176-3873296 1.0000 120 chr3L:22130325-22130445 1.0000 120 chr3R:8336250-8336370 1.0000 120 chr3L:15353886-15354006 1.0000 120 chrX:17582002-17582122 1.0000 120 chr2L:3555776-3555896 1.0000 120 chr3L:15330246-15330366 1.0000 120 chrX:15364628-15364748 1.0000 120 chr3L:3978096-3978216 1.0000 120 chr3R:20291736-20291856 1.0000 120 chr3L:7953046-7953166 1.0000 120 chr2L:19481094-19481214 1.0000 120 chrX:9689243-9689363 1.0000 120 chrX:7978152-7978272 1.0000 120 chr2L:13876785-13876905 1.0000 120 chr3R:21834396-21834516 1.0000 120 chr3L:18225281-18225401 1.0000 120 chr3R:16801163-16801283 1.0000 120 chr2L:3844976-3845096 1.0000 120 chr3L:17658849-17658969 1.0000 120 chr3R:6949457-6949577 1.0000 120 chr3R:14716675-14716795 1.0000 120 chrX:19842998-19843118 1.0000 120 chr3L:18273261-18273381 1.0000 120 chr3R:30733236-30733356 1.0000 120 chrX:18914225-18914345 1.0000 120 chr3L:13403300-13403420 1.0000 120 chr2L:18930933-18931053 1.0000 120 chrX:6982241-6982361 1.0000 120 chr2L:14539984-14540104 1.0000 120 chrX:12090260-12090380 1.0000 120 chr3R:10354076-10354196 1.0000 120 chrX:17471733-17471853 1.0000 120 chr3R:9159928-9160048 1.0000 120 chrX:18523530-18523650 1.0000 120 chr3L:380951-381071 1.0000 120 chr3R:30865630-30865750 1.0000 120 chr2R:9660233-9660353 1.0000 120 chr3R:15650474-15650594 1.0000 120 chr3L:6834665-6834785 1.0000 120 chr3L:18404506-18404626 1.0000 120 chr3L:18290474-18290594 1.0000 120 chr3L:21585482-21585602 1.0000 120 chr3R:27826329-27826449 1.0000 120 chr3L:6885742-6885862 1.0000 120 chr3L:20919050-20919170 1.0000 120 chr2L:3805362-3805482 1.0000 120 chr3R:19339330-19339450 1.0000 120 chr3L:12590248-12590368 1.0000 120 chrX:7166444-7166564 1.0000 120 chr3R:13404999-13405119 1.0000 120 chr3L:716357-716477 1.0000 120 chrX:9295672-9295792 1.0000 120 chr2L:5042225-5042345 1.0000 120 chrX:3073717-3073837 1.0000 120 chr3L:12453658-12453778 1.0000 120 chr3R:31696800-31696920 1.0000 120 chrX:457960-458080 1.0000 120 chr3L:16013283-16013403 1.0000 120 chr3L:6797569-6797689 1.0000 120 chr2R:20126733-20126853 1.0000 120 chr3R:14386206-14386326 1.0000 120 chr3R:21835469-21835589 1.0000 120 chr3R:8683423-8683543 1.0000 120 chr2L:7616949-7617069 1.0000 120 chr2L:8080832-8080952 1.0000 120 chr2L:18895131-18895251 1.0000 120 chrX:9615615-9615735 1.0000 120 chr2L:11341084-11341204 1.0000 120 chr2L:7293589-7293709 1.0000 120 chr2R:22384456-22384576 1.0000 120 chr3R:13469405-13469525 1.0000 120 chr3R:31689896-31690016 1.0000 120 chr3L:18297498-18297618 1.0000 120 chr3R:19343711-19343831 1.0000 120 chr3L:18406067-18406187 1.0000 120 chr3R:9246700-9246820 1.0000 120 chr2L:2461712-2461832 1.0000 120 chr2L:3600980-3601100 1.0000 120 chrX:18946973-18947093 1.0000 120 chr2L:1557105-1557225 1.0000 120 chrX:5966086-5966206 1.0000 120 chr3R:7646301-7646421 1.0000 120 chr3L:22130537-22130657 1.0000 120 chr3L:716139-716259 1.0000 120 chr3L:15794462-15794582 1.0000 120 chr2L:20823285-20823405 1.0000 120 chr3L:15199350-15199470 1.0000 120 chr3L:10849654-10849774 1.0000 120 chr3R:30734734-30734854 1.0000 120 chr3L:18102217-18102337 1.0000 120 chrX:8671520-8671640 1.0000 120 chr2L:14691014-14691134 1.0000 120 chrX:4581902-4582022 1.0000 120 chr3R:24580778-24580898 1.0000 120 chrX:17780415-17780535 1.0000 120 chr3L:10391093-10391213 1.0000 120 chr2R:16091886-16092006 1.0000 120 chr2L:14537567-14537687 1.0000 120 chr3R:21826396-21826516 1.0000 120 chr3L:10514961-10515081 1.0000 120 chr3L:19179539-19179659 1.0000 120 chrX:5696143-5696263 1.0000 120 chr2R:14312259-14312379 1.0000 120 chr3L:15253892-15254012 1.0000 120 chr3L:15847761-15847881 1.0000 120 chr3R:29541474-29541594 1.0000 120 chr3R:13448511-13448631 1.0000 120 chr2L:6819562-6819682 1.0000 120 chrX:7552298-7552418 1.0000 120 chr3L:16744118-16744238 1.0000 120 chrX:20644087-20644207 1.0000 120 chr3L:19056959-19057079 1.0000 120 chr2L:7295128-7295248 1.0000 120 chr3R:16241915-16242035 1.0000 120 chr3R:13972216-13972336 1.0000 120 chr2R:9711946-9712066 1.0000 120 chr2L:14235155-14235275 1.0000 120 chr3R:29581609-29581729 1.0000 120 chr3L:14146535-14146655 1.0000 120 chr2L:14212811-14212931 1.0000 120 chr3L:19557371-19557491 1.0000 120 chr3R:8197262-8197382 1.0000 120 chr3R:22886914-22887034 1.0000 120 chrX:17782156-17782276 1.0000 120 chr2R:22135067-22135187 1.0000 120 chr3L:7861939-7862059 1.0000 120 chrX:8122968-8123088 1.0000 120 chr3R:6723934-6724054 1.0000 120 chr3R:26801570-26801690 1.0000 120 chr3R:21826176-21826296 1.0000 120 chr3R:21830316-21830436 1.0000 120 chr3R:10449131-10449251 1.0000 120 chr2R:10553674-10553794 1.0000 120 chrX:18533375-18533495 1.0000 120 chr3R:21134062-21134182 1.0000 120 chr3L:804680-804800 1.0000 120 chr3R:23303368-23303488 1.0000 120 chr3R:10626126-10626246 1.0000 120 chr2R:11183163-11183283 1.0000 120 chr2R:18677920-18678040 1.0000 120 chr3L:15693209-15693329 1.0000 120 chrX:12724779-12724899 1.0000 120 chr3L:17404847-17404967 1.0000 120 chr2L:9595016-9595136 1.0000 120 chr2L:3851470-3851590 1.0000 120 chr3R:16907944-16908064 1.0000 120 chr3L:15693411-15693531 1.0000 120 chr3L:905140-905260 1.0000 120 chr3R:31704673-31704793 1.0000 120 chr3R:6425856-6425976 1.0000 120 chr3L:14166412-14166532 1.0000 120 chr3L:16452456-16452576 1.0000 120 chr3L:10951173-10951293 1.0000 120 chr3L:14611711-14611831 1.0000 120 chr2L:17747264-17747384 1.0000 120 chrX:17229931-17230051 1.0000 120 chr2L:16281690-16281810 1.0000 120 chr2R:14803429-14803549 1.0000 120 chr2R:20091289-20091409 1.0000 120 chr3L:13049801-13049921 1.0000 120 chrX:15618058-15618178 1.0000 120 chr2L:19370215-19370335 1.0000 120 chr2R:14969712-14969832 1.0000 120 chr3L:14978249-14978369 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_lola/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/lola.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 0.373 C 0.13 G 0.131 T 0.367 Background letter frequencies (from file dataset with add-one prior applied): A 0.373 C 0.13 G 0.131 T 0.367 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TSSCCRCC MEME-1 width = 8 sites = 5 llr = 61 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::6:: pos.-specific C :66aa:a8 probability G :44::4:2 matrix T a::::::: bits 2.9 ** * 2.7 ** * 2.4 ** ** 2.1 **** ** Relative 1.8 **** ** Entropy 1.5 ***** ** (17.5 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TCCCCACC consensus GG G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:20091289-20091409 87 2.32e-07 CATAAGTTAA TCCCCGCC CTTAGCGCGT chrX:5696143-5696263 107 2.93e-06 ATACATTTTG TGCCCACC TCTAGT chr2L:18930933-18931053 63 2.93e-06 TAAATACATT TCGCCACC ATTAGCTTAA chr2R:22384456-22384576 74 3.16e-06 TTTAGATAAT TCCCCGCG TGGCTTTCAT chr3R:27826329-27826449 14 3.83e-06 AGTCTATTAC TGGCCACC TAAGATAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:20091289-20091409 2.3e-07 86_[+1]_26 chrX:5696143-5696263 2.9e-06 106_[+1]_6 chr2L:18930933-18931053 2.9e-06 62_[+1]_50 chr2R:22384456-22384576 3.2e-06 73_[+1]_39 chr3R:27826329-27826449 3.8e-06 13_[+1]_99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TSSCCRCC width=8 seqs=5 chr2R:20091289-20091409 ( 87) TCCCCGCC 1 chrX:5696143-5696263 ( 107) TGCCCACC 1 chr2L:18930933-18931053 ( 63) TCGCCACC 1 chr2R:22384456-22384576 ( 74) TCCCCGCG 1 chr3R:27826329-27826449 ( 14) TGGCCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.4073 E= 1.3e+003 -897 -897 -897 144 -897 221 161 -897 -897 221 161 -897 -897 295 -897 -897 -897 295 -897 -897 69 -897 161 -897 -897 295 -897 -897 -897 262 61 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.3e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSSCCRCC MEME-1 regular expression -------------------------------------------------------------------------------- T[CG][CG]CC[AG]C[CG] -------------------------------------------------------------------------------- Time 7.86 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCKGCGG MEME-2 width = 8 sites = 2 llr = 30 E-value = 2.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a::a:: probability G aa:5a:aa matrix T :::5:::: bits 2.9 *** **** 2.7 *** **** 2.4 *** **** 2.1 *** **** Relative 1.8 *** **** Entropy 1.5 *** **** (21.8 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGCGGCGG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:19370215-19370335 42 8.54e-08 GTGTGAAAAG GGCGGCGG CGGGGTGACG chr3L:6834665-6834785 6 3.25e-07 TATGA GGCTGCGG GAACGAAGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:19370215-19370335 8.5e-08 41_[+2]_71 chr3L:6834665-6834785 3.2e-07 5_[+2]_107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCKGCGG width=8 seqs=2 chr2L:19370215-19370335 ( 42) GGCGGCGG 1 chr3L:6834665-6834785 ( 6) GGCTGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.0e+003 -765 -765 293 -765 -765 -765 293 -765 -765 294 -765 -765 -765 -765 193 44 -765 -765 293 -765 -765 294 -765 -765 -765 -765 293 -765 -765 -765 293 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.0e+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 0.000000 0.000000 0.500000 0.500000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCKGCGG MEME-2 regular expression -------------------------------------------------------------------------------- GGC[GT]GCGG -------------------------------------------------------------------------------- Time 14.17 secs. ******************************************************************************** ******************************************************************************** MOTIF GKKAMCCC MEME-3 width = 8 sites = 6 llr = 73 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::a3::: pos.-specific C ::::7aaa probability G a57::::: matrix T :53::::: bits 2.9 * *** 2.7 * *** 2.4 * *** 2.1 * *** Relative 1.8 * *** Entropy 1.5 * ****** (17.4 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGACCCC consensus TT A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:18914225-18914345 12 9.10e-07 TTTAGGTTTG GTGACCCC AATCCattat chr2R:14810436-14810556 112 9.10e-07 CAGGTGTTTC GTGACCCC T chr3L:380951-381071 59 1.58e-06 AATATTAATA GGTACCCC CTATTTCAAG chr3L:16744118-16744238 113 2.27e-06 CATTCAGTTT GGGAACCC chr3R:27826329-27826449 55 2.27e-06 GTGCTTATAA GGGAACCC AATTTATTTT chr3R:24580576-24580696 112 4.15e-06 attttatgat gttacccc t -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:18914225-18914345 9.1e-07 11_[+3]_101 chr2R:14810436-14810556 9.1e-07 111_[+3]_1 chr3L:380951-381071 1.6e-06 58_[+3]_54 chr3L:16744118-16744238 2.3e-06 112_[+3] chr3R:27826329-27826449 2.3e-06 54_[+3]_58 chr3R:24580576-24580696 4.1e-06 111_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GKKAMCCC width=8 seqs=6 chrX:18914225-18914345 ( 12) GTGACCCC 1 chr2R:14810436-14810556 ( 112) GTGACCCC 1 chr3L:380951-381071 ( 59) GGTACCCC 1 chr3L:16744118-16744238 ( 113) GGGAACCC 1 chr3R:27826329-27826449 ( 55) GGGAACCC 1 chr3R:24580576-24580696 ( 112) GTTACCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.3004 E= 1.1e+003 -923 -923 293 -923 -923 -923 193 45 -923 -923 235 -14 142 -923 -923 -923 -16 236 -923 -923 -923 295 -923 -923 -923 295 -923 -923 -923 295 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 1.1e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.666667 0.333333 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKKAMCCC MEME-3 regular expression -------------------------------------------------------------------------------- G[GT][GT]A[CA]CCC -------------------------------------------------------------------------------- Time 20.64 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGCSCC MEME-4 width = 8 sites = 2 llr = 29 E-value = 2.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C ::::a5aa probability G aa:a:5:: matrix T :::::::: bits 2.9 ** ** ** 2.7 ** ** ** 2.4 ** ** ** 2.1 ** ***** Relative 1.8 ** ***** Entropy 1.5 ******** (21.0 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGAGCCCC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:14537567-14537687 34 2.39e-07 GAAAATAAAA GGAGCCCC AATTGAAATT chrX:17780415-17780535 108 4.81e-07 TCATGGAAAT GGAGCGCC TAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:14537567-14537687 2.4e-07 33_[+4]_79 chrX:17780415-17780535 4.8e-07 107_[+4]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGCSCC width=8 seqs=2 chr2L:14537567-14537687 ( 34) GGAGCCCC 1 chrX:17780415-17780535 ( 108) GGAGCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.0e+003 -765 -765 293 -765 -765 -765 293 -765 142 -765 -765 -765 -765 -765 293 -765 -765 294 -765 -765 -765 194 193 -765 -765 294 -765 -765 -765 294 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.0e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCSCC MEME-4 regular expression -------------------------------------------------------------------------------- GGAGC[CG]CC -------------------------------------------------------------------------------- Time 26.94 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGWGCG MEME-5 width = 8 sites = 2 llr = 29 E-value = 2.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::5::: pos.-specific C ::a:::a: probability G aa:a:a:a matrix T ::::5::: bits 2.9 **** *** 2.7 **** *** 2.4 **** *** 2.1 **** *** Relative 1.8 **** *** Entropy 1.5 **** *** (21.0 bits) 1.2 **** *** 0.9 **** *** 0.6 **** *** 0.3 ******** 0.0 -------- Multilevel GGCGAGCG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:16744118-16744238 68 4.82e-07 CATGATTAGT GGCGTGCG CTACTGTACC chr3R:20291736-20291856 21 4.82e-07 TTTCACAAAA GGCGAGCG GACTTGGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:16744118-16744238 4.8e-07 67_[+5]_45 chr3R:20291736-20291856 4.8e-07 20_[+5]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGWGCG width=8 seqs=2 chr3L:16744118-16744238 ( 68) GGCGTGCG 1 chr3R:20291736-20291856 ( 21) GGCGAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.8e+003 -765 -765 293 -765 -765 -765 293 -765 -765 294 -765 -765 -765 -765 293 -765 42 -765 -765 44 -765 -765 293 -765 -765 294 -765 -765 -765 -765 293 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.8e+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 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGWGCG MEME-5 regular expression -------------------------------------------------------------------------------- GGCG[AT]GCG -------------------------------------------------------------------------------- Time 33.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:18963300-18963420 2.56e-01 120 chr2L:10351320-10351440 8.10e-01 120 chr3L:15174977-15175097 9.92e-01 120 chr3L:13032659-13032779 1.00e+00 120 chr3L:18229103-18229223 1.00e+00 120 chrX:18910951-18911071 1.06e-01 120 chr2R:11559270-11559390 1.00e+00 120 chrX:18208621-18208741 9.10e-01 120 chr3L:6162144-6162264 1.00e+00 120 chr3L:15777468-15777588 9.99e-01 120 chr2L:3855666-3855786 5.57e-01 120 chrX:18207603-18207723 9.79e-01 120 chr3R:6672371-6672491 7.49e-01 120 chr3L:5017612-5017732 9.08e-01 120 chr3L:15203219-15203339 3.41e-01 120 chrX:18523325-18523445 9.96e-01 120 chr3L:21727186-21727306 6.00e-01 120 chr2L:3439639-3439759 9.51e-01 120 chr3L:16017110-16017230 4.76e-01 120 chr3L:21462992-21463112 9.98e-01 120 chr3R:14586575-14586695 3.08e-01 120 chr2L:18871852-18871972 8.85e-01 120 chrX:8671786-8671906 7.62e-01 120 chr3L:15844695-15844815 8.15e-01 120 chr2R:12020615-12020735 5.58e-01 120 chr2L:9586071-9586191 9.99e-01 120 chr3L:18225081-18225201 8.27e-01 120 chr2L:4359284-4359404 6.66e-01 120 chr2L:11470082-11470202 9.99e-01 120 chrX:12617882-12618002 1.00e+00 120 chr3L:14961168-14961288 1.00e+00 120 chr2L:12415868-12415988 1.00e+00 120 chr3L:15670560-15670680 4.41e-01 120 chr3R:19935353-19935473 5.49e-01 120 chr3L:12062347-12062467 9.55e-01 120 chrX:14846493-14846613 7.33e-01 120 chr3L:6160029-6160149 9.86e-01 120 chr3L:11413793-11413913 2.45e-01 120 chrX:16205289-16205409 9.95e-01 120 chr2L:7624316-7624436 8.57e-01 120 chr3R:21566927-21567047 7.30e-01 120 chr2R:8242215-8242335 4.30e-02 120 chr2L:18896944-18897064 6.99e-01 120 chr3L:20687490-20687610 7.82e-01 120 chr2L:5378982-5379102 1.31e-01 120 chrX:3344772-3344892 9.92e-01 120 chr3R:10370586-10370706 3.30e-01 120 chr3L:14611508-14611628 1.00e+00 120 chr3R:29547695-29547815 9.91e-01 120 chr3L:16635935-16636055 3.82e-01 120 chr3R:19935151-19935271 5.38e-01 120 chr2L:9990238-9990358 4.46e-01 120 chrX:17357562-17357682 3.46e-01 120 chr3R:7135244-7135364 8.83e-01 120 chr2L:11980182-11980302 9.92e-01 120 chr3L:15775587-15775707 8.52e-01 120 chr3R:6674685-6674805 2.15e-02 120 chr3R:15580817-15580937 3.82e-01 120 chr3L:7962187-7962307 2.35e-01 120 chrX:17712614-17712734 3.56e-01 120 chr3L:10962141-10962261 9.24e-01 120 chr3L:5994156-5994276 6.44e-01 120 chr2R:14810436-14810556 1.41e-03 111_[+3(9.10e-07)]_1 chr3R:6816693-6816813 7.55e-02 120 chr3R:24580576-24580696 1.04e-02 111_[+3(4.15e-06)]_1 chr3R:29372774-29372894 9.37e-01 120 chr3R:10651126-10651246 5.06e-01 120 chr3L:18227495-18227615 9.83e-01 120 chr2L:10689501-10689621 9.96e-01 120 chrX:16171536-16171656 3.49e-01 120 chr3R:16630660-16630780 9.59e-02 120 chr3L:16746106-16746226 4.46e-01 120 chr3L:11309854-11309974 6.56e-01 120 chr2L:19373896-19374016 9.88e-01 120 chr2R:22402936-22403056 8.73e-01 120 chr2L:4185789-4185909 1.00e+00 120 chr3R:16886944-16887064 9.77e-01 120 chr3L:13068463-13068583 7.22e-01 120 chr3L:12444143-12444263 9.86e-01 120 chr2L:3675911-3676031 1.66e-01 120 chrX:20756597-20756717 8.65e-01 120 chr3L:15253686-15253806 2.16e-01 120 chrX:17799218-17799338 8.98e-01 120 chr3L:15672956-15673076 2.18e-01 120 chr2R:8659073-8659193 9.66e-01 120 chr3L:3873176-3873296 9.43e-01 120 chr3L:22130325-22130445 1.76e-02 120 chr3R:8336250-8336370 8.08e-01 120 chr3L:15353886-15354006 7.84e-01 120 chrX:17582002-17582122 7.49e-01 120 chr2L:3555776-3555896 5.74e-01 120 chr3L:15330246-15330366 7.47e-01 120 chrX:15364628-15364748 9.36e-01 120 chr3L:3978096-3978216 9.12e-01 120 chr3R:20291736-20291856 8.44e-04 20_[+5(4.82e-07)]_92 chr3L:7953046-7953166 9.16e-01 120 chr2L:19481094-19481214 9.37e-01 120 chrX:9689243-9689363 1.00e+00 120 chrX:7978152-7978272 4.94e-01 120 chr2L:13876785-13876905 1.00e+00 120 chr3R:21834396-21834516 8.09e-01 120 chr3L:18225281-18225401 7.06e-01 120 chr3R:16801163-16801283 3.75e-01 120 chr2L:3844976-3845096 1.00e+00 120 chr3L:17658849-17658969 1.00e+00 120 chr3R:6949457-6949577 5.12e-01 120 chr3R:14716675-14716795 7.33e-01 120 chrX:19842998-19843118 6.97e-01 120 chr3L:18273261-18273381 3.79e-01 120 chr3R:30733236-30733356 9.98e-01 120 chrX:18914225-18914345 1.83e-04 11_[+3(9.10e-07)]_101 chr3L:13403300-13403420 1.00e+00 120 chr2L:18930933-18931053 4.26e-02 62_[+1(2.93e-06)]_50 chrX:6982241-6982361 1.00e+00 120 chr2L:14539984-14540104 6.79e-01 120 chrX:12090260-12090380 9.82e-01 120 chr3R:10354076-10354196 6.63e-01 120 chrX:17471733-17471853 4.70e-01 120 chr3R:9159928-9160048 1.00e+00 120 chrX:18523530-18523650 6.83e-01 120 chr3L:380951-381071 3.53e-04 58_[+3(1.58e-06)]_54 chr3R:30865630-30865750 7.57e-01 120 chr2R:9660233-9660353 9.93e-01 120 chr3R:15650474-15650594 8.72e-01 120 chr3L:6834665-6834785 8.40e-04 5_[+2(3.25e-07)]_107 chr3L:18404506-18404626 8.24e-01 120 chr3L:18290474-18290594 6.74e-01 120 chr3L:21585482-21585602 1.00e+00 120 chr3R:27826329-27826449 8.59e-06 13_[+1(3.83e-06)]_33_[+3(2.27e-06)]_\ 58 chr3L:6885742-6885862 1.00e+00 120 chr3L:20919050-20919170 2.46e-01 120 chr2L:3805362-3805482 9.74e-01 120 chr3R:19339330-19339450 9.64e-01 120 chr3L:12590248-12590368 1.00e+00 120 chrX:7166444-7166564 1.00e+00 120 chr3R:13404999-13405119 8.19e-01 120 chr3L:716357-716477 3.60e-02 120 chrX:9295672-9295792 9.62e-01 120 chr2L:5042225-5042345 9.99e-01 120 chrX:3073717-3073837 3.59e-01 120 chr3L:12453658-12453778 9.61e-02 120 chr3R:31696800-31696920 2.23e-01 120 chrX:457960-458080 1.08e-02 120 chr3L:16013283-16013403 9.94e-01 120 chr3L:6797569-6797689 9.59e-01 120 chr2R:20126733-20126853 7.35e-01 120 chr3R:14386206-14386326 5.69e-01 120 chr3R:21835469-21835589 3.33e-01 120 chr3R:8683423-8683543 9.69e-01 120 chr2L:7616949-7617069 6.32e-01 120 chr2L:8080832-8080952 7.84e-01 120 chr2L:18895131-18895251 9.96e-01 120 chrX:9615615-9615735 2.70e-01 120 chr2L:11341084-11341204 9.92e-01 120 chr2L:7293589-7293709 1.87e-01 120 chr2R:22384456-22384576 2.44e-02 73_[+1(3.16e-06)]_39 chr3R:13469405-13469525 3.35e-01 120 chr3R:31689896-31690016 5.06e-01 120 chr3L:18297498-18297618 4.12e-01 120 chr3R:19343711-19343831 8.85e-01 120 chr3L:18406067-18406187 7.00e-01 120 chr3R:9246700-9246820 2.56e-01 120 chr2L:2461712-2461832 7.25e-01 120 chr2L:3600980-3601100 6.05e-01 120 chrX:18946973-18947093 9.65e-01 120 chr2L:1557105-1557225 8.55e-01 120 chrX:5966086-5966206 9.94e-01 120 chr3R:7646301-7646421 5.50e-01 120 chr3L:22130537-22130657 1.33e-01 120 chr3L:716139-716259 4.56e-01 120 chr3L:15794462-15794582 9.32e-01 120 chr2L:20823285-20823405 9.60e-01 120 chr3L:15199350-15199470 9.43e-01 120 chr3L:10849654-10849774 9.05e-01 120 chr3R:30734734-30734854 9.89e-01 120 chr3L:18102217-18102337 1.00e+00 120 chrX:8671520-8671640 1.24e-02 91_[+1(5.20e-05)]_21 chr2L:14691014-14691134 9.79e-01 120 chrX:4581902-4582022 9.13e-01 120 chr3R:24580778-24580898 1.65e-01 120 chrX:17780415-17780535 1.06e-03 107_[+4(4.81e-07)]_5 chr3L:10391093-10391213 9.68e-01 120 chr2R:16091886-16092006 3.61e-01 120 chr2L:14537567-14537687 8.15e-04 33_[+4(2.39e-07)]_79 chr3R:21826396-21826516 7.48e-01 120 chr3L:10514961-10515081 9.98e-01 120 chr3L:19179539-19179659 9.72e-01 120 chrX:5696143-5696263 3.32e-03 106_[+1(2.93e-06)]_6 chr2R:14312259-14312379 9.67e-01 120 chr3L:15253892-15254012 6.97e-01 120 chr3L:15847761-15847881 6.55e-01 120 chr3R:29541474-29541594 6.81e-01 120 chr3R:13448511-13448631 5.15e-01 120 chr2L:6819562-6819682 5.67e-01 120 chrX:7552298-7552418 9.77e-01 120 chr3L:16744118-16744238 2.80e-07 67_[+5(4.82e-07)]_37_[+3(2.27e-06)] chrX:20644087-20644207 7.87e-02 120 chr3L:19056959-19057079 9.99e-01 120 chr2L:7295128-7295248 4.58e-01 120 chr3R:16241915-16242035 4.51e-01 120 chr3R:13972216-13972336 9.52e-01 120 chr2R:9711946-9712066 9.92e-01 120 chr2L:14235155-14235275 6.86e-01 120 chr3R:29581609-29581729 2.20e-01 120 chr3L:14146535-14146655 9.37e-01 120 chr2L:14212811-14212931 1.29e-03 10_[+5(2.31e-05)]_102 chr3L:19557371-19557491 9.83e-01 120 chr3R:8197262-8197382 2.54e-01 120 chr3R:22886914-22887034 1.00e+00 120 chrX:17782156-17782276 9.17e-01 120 chr2R:22135067-22135187 3.59e-01 120 chr3L:7861939-7862059 1.00e+00 120 chrX:8122968-8123088 7.82e-01 120 chr3R:6723934-6724054 4.83e-01 120 chr3R:26801570-26801690 1.00e+00 120 chr3R:21826176-21826296 9.86e-01 120 chr3R:21830316-21830436 3.78e-01 120 chr3R:10449131-10449251 5.35e-01 120 chr2R:10553674-10553794 9.82e-01 120 chrX:18533375-18533495 1.00e+00 120 chr3R:21134062-21134182 1.00e+00 120 chr3L:804680-804800 7.59e-01 120 chr3R:23303368-23303488 1.00e+00 120 chr3R:10626126-10626246 3.78e-01 120 chr2R:11183163-11183283 7.05e-01 120 chr2R:18677920-18678040 9.42e-01 120 chr3L:15693209-15693329 9.61e-01 120 chrX:12724779-12724899 8.07e-01 120 chr3L:17404847-17404967 6.01e-01 120 chr2L:9595016-9595136 5.51e-01 120 chr2L:3851470-3851590 9.93e-01 120 chr3R:16907944-16908064 6.56e-01 120 chr3L:15693411-15693531 8.97e-01 120 chr3L:905140-905260 3.05e-02 120 chr3R:31704673-31704793 1.00e+00 120 chr3R:6425856-6425976 9.83e-01 120 chr3L:14166412-14166532 1.89e-01 120 chr3L:16452456-16452576 7.79e-01 120 chr3L:10951173-10951293 9.98e-01 120 chr3L:14611711-14611831 7.92e-01 120 chr2L:17747264-17747384 9.82e-01 120 chrX:17229931-17230051 2.19e-01 120 chr2L:16281690-16281810 2.79e-01 120 chr2R:14803429-14803549 9.24e-01 120 chr2R:20091289-20091409 1.41e-04 86_[+1(2.32e-07)]_26 chr3L:13049801-13049921 4.75e-01 120 chrX:15618058-15618178 8.08e-01 120 chr2L:19370215-19370335 5.41e-07 41_[+2(8.54e-08)]_42_[+5(2.31e-05)]_\ 21 chr2R:14969712-14969832 8.62e-01 120 chr3L:14978249-14978369 1.00e+00 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c23n01.farnam.hpc.yale.internal ********************************************************************************