******************************************************************************** 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/esn.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3L:13488259-13488379 1.0000 120 chrM:4794-4914 1.0000 120 chr2L:634243-634363 1.0000 120 chr3L:13410274-13410394 1.0000 120 chr2L:3341680-3341800 1.0000 120 chr3R:8968955-8969075 1.0000 120 chr3R:27593333-27593453 1.0000 120 chrX:17545694-17545814 1.0000 120 chr2R:18610453-18610573 1.0000 120 chr2R:10772064-10772184 1.0000 120 chrM:12082-12202 1.0000 120 chr2L:17782101-17782221 1.0000 120 chr2R:19615990-19616110 1.0000 120 chr3R:31308970-31309090 1.0000 120 chr3R:15588728-15588848 1.0000 120 chr3L:21099090-21099210 1.0000 120 chr2R:7093006-7093126 1.0000 120 chr3R:13793420-13793540 1.0000 120 chr3L:6471948-6472068 1.0000 120 chr3R:17202479-17202599 1.0000 120 chrX:14750557-14750677 1.0000 120 chr3L:18198874-18198994 1.0000 120 chr3R:22424110-22424230 1.0000 120 chr2L:5429202-5429322 1.0000 120 chr2R:12646949-12647069 1.0000 120 chr2L:651007-651127 1.0000 120 chr2L:11966128-11966248 1.0000 120 chr2L:15275960-15276080 1.0000 120 chr2L:7574389-7574509 1.0000 120 chr2R:19187341-19187461 1.0000 120 chr2L:3004781-3004901 1.0000 120 chr2R:15842690-15842810 1.0000 120 chr3L:15188849-15188969 1.0000 120 chrM:3477-3597 1.0000 120 chr3R:9913578-9913698 1.0000 120 chr3R:22628067-22628187 1.0000 120 chr3R:27171247-27171367 1.0000 120 chr2L:4069719-4069839 1.0000 120 chr3R:31956412-31956532 1.0000 120 chr2L:7973978-7974098 1.0000 120 chr2R:10237756-10237876 1.0000 120 chr3L:21099289-21099409 1.0000 120 chr3R:31505323-31505443 1.0000 120 chrX:20509651-20509771 1.0000 120 chr2L:17421485-17421605 1.0000 120 chr3L:1457341-1457461 1.0000 120 chr3L:17010656-17010776 1.0000 120 chr3R:30843902-30844022 1.0000 120 chr2L:11399616-11399736 1.0000 120 chr2R:23014849-23014969 1.0000 120 chr2L:18466344-18466464 1.0000 120 chr3R:13372094-13372214 1.0000 120 chr3L:21108629-21108749 1.0000 120 chr3L:3612741-3612861 1.0000 120 chr3L:18276077-18276197 1.0000 120 chrX:13541332-13541452 1.0000 120 chr2L:16498199-16498319 1.0000 120 chr3R:21648618-21648738 1.0000 120 chrM:13247-13367 1.0000 120 chr2L:18678400-18678520 1.0000 120 chrX:17760675-17760795 1.0000 120 chr2R:22144341-22144461 1.0000 120 chr2R:7147274-7147394 1.0000 120 chrX:5025374-5025494 1.0000 120 chrM:2747-2867 1.0000 120 chr3L:15180962-15181082 1.0000 120 chr3R:21827561-21827681 1.0000 120 chr3L:12915613-12915733 1.0000 120 chr3R:26192392-26192512 1.0000 120 chrM:7461-7581 1.0000 120 chr2L:1486419-1486539 1.0000 120 chr3L:13406978-13407098 1.0000 120 chr3L:10359556-10359676 1.0000 120 chr3R:16985688-16985808 1.0000 120 chr3R:20283327-20283447 1.0000 120 chr3R:18157561-18157681 1.0000 120 chr2R:14923049-14923169 1.0000 120 chr3R:8029785-8029905 1.0000 120 chr2R:10599169-10599289 1.0000 120 chr3R:29778283-29778403 1.0000 120 chr3L:14453369-14453489 1.0000 120 chr3L:18193750-18193870 1.0000 120 chrM:1716-1836 1.0000 120 chr2R:10600501-10600621 1.0000 120 chr3L:4395664-4395784 1.0000 120 chr3L:15641595-15641715 1.0000 120 chr3R:23496634-23496754 1.0000 120 chr2L:15304455-15304575 1.0000 120 chr3R:22194810-22194930 1.0000 120 chr3R:17825921-17826041 1.0000 120 chr3L:15258523-15258643 1.0000 120 chr2R:13478507-13478627 1.0000 120 chr3L:3513154-3513274 1.0000 120 chr2L:11395810-11395930 1.0000 120 chr3R:16501568-16501688 1.0000 120 chr2L:3554080-3554200 1.0000 120 chr2L:11222219-11222339 1.0000 120 chr3L:21253071-21253191 1.0000 120 chr2R:19913833-19913953 1.0000 120 chr3R:16210829-16210949 1.0000 120 chr3L:729481-729601 1.0000 120 chr3L:19035642-19035762 1.0000 120 chr2R:8322844-8322964 1.0000 120 chrX:6030157-6030277 1.0000 120 chr2R:6969482-6969602 1.0000 120 chrX:10325089-10325209 1.0000 120 chr2R:7141877-7141997 1.0000 120 chr3R:13934747-13934867 1.0000 120 chr2R:24237477-24237597 1.0000 120 chr2L:423283-423403 1.0000 120 chr2R:6556960-6557080 1.0000 120 chr3L:8368814-8368934 1.0000 120 chr3R:13941545-13941665 1.0000 120 chrX:14897754-14897874 1.0000 120 chr3L:11297675-11297795 1.0000 120 chr3L:18241109-18241229 1.0000 120 chr3R:4961561-4961681 1.0000 120 chr3L:3423176-3423296 1.0000 120 chr3R:8142251-8142371 1.0000 120 chr3R:10530731-10530851 1.0000 120 chr3R:10476122-10476242 1.0000 120 chr3L:5630270-5630390 1.0000 120 chr3R:31505527-31505647 1.0000 120 chr2R:15513543-15513663 1.0000 120 chr3L:10786026-10786146 1.0000 120 chr2L:9496770-9496890 1.0000 120 chr3R:29538560-29538680 1.0000 120 chr3L:21738824-21738944 1.0000 120 chrX:22479462-22479582 1.0000 120 chr3R:4667422-4667542 1.0000 120 chr3R:29762432-29762552 1.0000 120 chr3R:23297645-23297765 1.0000 120 chr2L:10791429-10791549 1.0000 120 chr2R:23022626-23022746 1.0000 120 chr2R:19969861-19969981 1.0000 120 chr2L:7992082-7992202 1.0000 120 chr3L:7792325-7792445 1.0000 120 chr2R:7241732-7241852 1.0000 120 chrX:2452876-2452996 1.0000 120 chr3L:3246816-3246936 1.0000 120 chrX:17814950-17815070 1.0000 120 chr2L:11394258-11394378 1.0000 120 chr2R:16156389-16156509 1.0000 120 chr3L:21594537-21594657 1.0000 120 chr3L:14253578-14253698 1.0000 120 chr3R:25634006-25634126 1.0000 120 chr3L:3343436-3343556 1.0000 120 chrM:5016-5136 1.0000 120 chr3L:761833-761953 1.0000 120 chr2L:9438405-9438525 1.0000 120 chr3L:21060537-21060657 1.0000 120 chr2R:19849231-19849351 1.0000 120 chr2L:9447907-9448027 1.0000 120 chr3R:4667628-4667748 1.0000 120 chr2R:20136844-20136964 1.0000 120 chr3R:28633891-28634011 1.0000 120 chr3R:30689845-30689965 1.0000 120 chr3R:5103716-5103836 1.0000 120 chr2R:19153413-19153533 1.0000 120 chr3R:10579706-10579826 1.0000 120 chr2R:12532789-12532909 1.0000 120 chr2R:11183226-11183346 1.0000 120 chr3L:20403688-20403808 1.0000 120 chr3L:5365281-5365401 1.0000 120 chr3L:14055331-14055451 1.0000 120 chrM:14236-14356 1.0000 120 chr2R:19420614-19420734 1.0000 120 chrX:19164886-19165006 1.0000 120 chrX:12015173-12015293 1.0000 120 chr3L:12090467-12090587 1.0000 120 chr3L:11322612-11322732 1.0000 120 chr3R:5100467-5100587 1.0000 120 chr3L:8157194-8157314 1.0000 120 chr2L:19142639-19142759 1.0000 120 chrX:10104606-10104726 1.0000 120 chr2L:19162918-19163038 1.0000 120 chrX:17571083-17571203 1.0000 120 chr2L:3781555-3781675 1.0000 120 chr3L:14239439-14239559 1.0000 120 chr3R:23486890-23487010 1.0000 120 chr2L:18648372-18648492 1.0000 120 chr2L:11968584-11968704 1.0000 120 chr3L:785844-785964 1.0000 120 chr3L:16024773-16024893 1.0000 120 chr3R:29199866-29199986 1.0000 120 chr2L:10615963-10616083 1.0000 120 chr3L:758676-758796 1.0000 120 chrX:7892595-7892715 1.0000 120 chr2R:21569764-21569884 1.0000 120 chrX:17551180-17551300 1.0000 120 chr3L:17502344-17502464 1.0000 120 chr3L:15762936-15763056 1.0000 120 chr2R:14783006-14783126 1.0000 120 chr2L:7423026-7423146 1.0000 120 chrX:3381101-3381221 1.0000 120 chr3R:31225147-31225267 1.0000 120 chr3R:15596011-15596131 1.0000 120 chr2R:8650574-8650694 1.0000 120 chr2L:7909347-7909467 1.0000 120 chr2R:6994739-6994859 1.0000 120 chr3L:17608680-17608800 1.0000 120 chrX:5026154-5026274 1.0000 120 chr2L:9448800-9448920 1.0000 120 chrX:6339201-6339321 1.0000 120 chr2R:16812241-16812361 1.0000 120 chr3R:19283702-19283822 1.0000 120 chr2L:5493044-5493164 1.0000 120 chr2L:18645601-18645721 1.0000 120 chr3L:8913596-8913716 1.0000 120 chr3R:30281386-30281506 1.0000 120 chr3R:22175840-22175960 1.0000 120 chr3L:1388245-1388365 1.0000 120 chr2R:9674771-9674891 1.0000 120 chr2L:1412831-1412951 1.0000 120 chr2L:7611675-7611795 1.0000 120 chr2L:18003186-18003306 1.0000 120 chr2L:7419533-7419653 1.0000 120 chr2L:9235581-9235701 1.0000 120 chr3R:8154094-8154214 1.0000 120 chr2R:14975296-14975416 1.0000 120 chr2L:5249916-5250036 1.0000 120 chr2R:21569027-21569147 1.0000 120 chr3L:13021879-13021999 1.0000 120 chr3R:6950277-6950397 1.0000 120 chrX:1826231-1826351 1.0000 120 chr3L:19046525-19046645 1.0000 120 chr2R:19647732-19647852 1.0000 120 chr3R:18990613-18990733 1.0000 120 chr3L:728016-728136 1.0000 120 chr3L:660433-660553 1.0000 120 chr2R:17836146-17836266 1.0000 120 chrX:9251419-9251539 1.0000 120 chrX:2365495-2365615 1.0000 120 chr2L:15385426-15385546 1.0000 120 chr3R:17117681-17117801 1.0000 120 chr2L:15743714-15743834 1.0000 120 chr3R:27140089-27140209 1.0000 120 chr3R:9935010-9935130 1.0000 120 chr3L:10777482-10777602 1.0000 120 chr3R:4873900-4874020 1.0000 120 chrM:10867-10987 1.0000 120 chr3R:29096071-29096191 1.0000 120 chr2R:11515864-11515984 1.0000 120 chr3L:1374599-1374719 1.0000 120 chr3R:30811350-30811470 1.0000 120 chr2R:18209792-18209912 1.0000 120 chrX:12663042-12663162 1.0000 120 chrX:13312319-13312439 1.0000 120 chr3L:10794024-10794144 1.0000 120 chr3L:16016022-16016142 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_esn/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/esn.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 0.348 C 0.149 G 0.146 T 0.356 Background letter frequencies (from file dataset with add-one prior applied): A 0.348 C 0.15 G 0.146 T 0.356 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF STGCGGCC MEME-1 width = 8 sites = 6 llr = 72 E-value = 9.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::2::: pos.-specific C 322a:2aa probability G 7:8:88:: matrix T :8:::::: bits 2.8 * ** 2.5 * ** 2.2 ** *** 1.9 * ****** Relative 1.7 * ****** Entropy 1.4 * ****** (17.3 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GTGCGGCC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:9251419-9251539 15 1.11e-06 GGAAATGCAG CTGCGGCC ACAATAATAG chrM:13247-13367 68 1.11e-06 AGTCAAAATA CTGCGGCC ATTTAAAATT chr3R:30689845-30689965 107 1.34e-06 GGCCGCTTTC GCGCGGCC ATCGTA chr3R:16985688-16985808 100 2.69e-06 AAATAAGTCA GTGCGCCC CGCTGTTAAG chr2L:7574389-7574509 112 2.69e-06 CCATATCTAA GTCCGGCC A chr2L:15275960-15276080 112 5.62e-06 ATTTGCGATG GTGCAGCC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:9251419-9251539 1.1e-06 14_[+1]_98 chrM:13247-13367 1.1e-06 67_[+1]_45 chr3R:30689845-30689965 1.3e-06 106_[+1]_6 chr3R:16985688-16985808 2.7e-06 99_[+1]_13 chr2L:7574389-7574509 2.7e-06 111_[+1]_1 chr2L:15275960-15276080 5.6e-06 111_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STGCGGCC width=8 seqs=6 chrX:9251419-9251539 ( 15) CTGCGGCC 1 chrM:13247-13367 ( 68) CTGCGGCC 1 chr3R:30689845-30689965 ( 107) GCGCGGCC 1 chr3R:16985688-16985808 ( 100) GTGCGCCC 1 chr2L:7574389-7574509 ( 112) GTCCGGCC 1 chr2L:15275960-15276080 ( 112) GTGCAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.3004 E= 9.9e+002 -923 116 219 -923 -923 16 -923 123 -923 16 251 -923 -923 274 -923 -923 -106 -923 251 -923 -923 16 251 -923 -923 274 -923 -923 -923 274 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 9.9e+002 0.000000 0.333333 0.666667 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STGCGGCC MEME-1 regular expression -------------------------------------------------------------------------------- [GC]TGCGGCC -------------------------------------------------------------------------------- Time 7.47 secs. ******************************************************************************** ******************************************************************************** MOTIF GCACTGGG MEME-2 width = 8 sites = 12 llr = 123 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2:a:::2: pos.-specific C :a:8:113 probability G 8::2:968 matrix T ::::a:2: bits 2.8 * 2.5 * 2.2 * * * 1.9 ** * * * Relative 1.7 ** * * * Entropy 1.4 ****** * (14.8 bits) 1.1 ****** * 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCACTGGG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:10777482-10777602 40 1.27e-06 GAGAGGCAGT GCACTGGG AGAAAATGTA chr2L:5249916-5250036 9 2.57e-06 GTCAGGAT GCACTGGC AGAAATTGTA chr2L:19162918-19163038 110 3.80e-06 ACCACTGTTG GCAGTGGG TGT chr3L:20403688-20403808 47 3.80e-06 ACTGCAGTTT GCAGTGGG AAGATTATAC chr3L:660433-660553 19 8.12e-06 TACCAATAAA GCACTGAG AGAAATGTTA chr3L:15641595-15641715 75 8.12e-06 TCGCATGGAT GCACTGAG AAAAATGTAT chr2R:7147274-7147394 28 1.12e-05 ACATAAACAT GCACTGTG TTTTTATTAT chr3L:729481-729601 11 1.55e-05 AGGATCAGCA ACACTGGG AAAAAAAACG chrX:5025374-5025494 27 1.55e-05 TGCAACAGCT GCACTCGG CGAAAGTCAG chr2L:3004781-3004901 6 1.55e-05 AAGGA ACACTGGG GGAAATTTGA chrX:10325089-10325209 97 1.81e-05 ATGACTTTTG GCACTGCC TTTAAAATTA chr3L:21594537-21594657 21 2.44e-05 AATAAGCGGT GCACTGTC CCGCTCAGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:10777482-10777602 1.3e-06 39_[+2]_73 chr2L:5249916-5250036 2.6e-06 8_[+2]_104 chr2L:19162918-19163038 3.8e-06 109_[+2]_3 chr3L:20403688-20403808 3.8e-06 46_[+2]_66 chr3L:660433-660553 8.1e-06 18_[+2]_94 chr3L:15641595-15641715 8.1e-06 74_[+2]_38 chr2R:7147274-7147394 1.1e-05 27_[+2]_85 chr3L:729481-729601 1.6e-05 10_[+2]_102 chrX:5025374-5025494 1.6e-05 26_[+2]_86 chr2L:3004781-3004901 1.6e-05 5_[+2]_107 chrX:10325089-10325209 1.8e-05 96_[+2]_16 chr3L:21594537-21594657 2.4e-05 20_[+2]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCACTGGG width=8 seqs=12 chr3L:10777482-10777602 ( 40) GCACTGGG 1 chr2L:5249916-5250036 ( 9) GCACTGGC 1 chr2L:19162918-19163038 ( 110) GCAGTGGG 1 chr3L:20403688-20403808 ( 47) GCAGTGGG 1 chr3L:660433-660553 ( 19) GCACTGAG 1 chr3L:15641595-15641715 ( 75) GCACTGAG 1 chr2R:7147274-7147394 ( 28) GCACTGTG 1 chr3L:729481-729601 ( 11) ACACTGGG 1 chrX:5025374-5025494 ( 27) GCACTCGG 1 chr2L:3004781-3004901 ( 6) ACACTGGG 1 chrX:10325089-10325209 ( 97) GCACTGCC 1 chr3L:21594537-21594657 ( 21) GCACTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.648 E= 1.2e+003 -106 -1023 251 -1023 -1023 274 -1023 -1023 152 -1023 -1023 -1023 -1023 248 19 -1023 -1023 -1023 -1023 149 -1023 -84 265 -1023 -106 -84 200 -109 -1023 74 236 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 1.2e+003 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.083333 0.916667 0.000000 0.166667 0.083333 0.583333 0.166667 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 regular expression -------------------------------------------------------------------------------- GCACTGG[GC] -------------------------------------------------------------------------------- Time 13.79 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGSGGCG MEME-3 width = 8 sites = 2 llr = 28 E-value = 3.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 Description -------------------------------------------------------------------------------- Simplified A a::::::: pos.-specific C :::5::a: probability G :aa5aa:a matrix T :::::::: bits 2.8 ** **** 2.5 ** **** 2.2 ** **** 1.9 ** **** Relative 1.7 ******* Entropy 1.4 ******** (19.9 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel AGGCGGCG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6030157-6030277 24 1.03e-06 AAATCGAATA AGGCGGCG CGTCAATGAT chr3R:30843902-30844022 112 1.03e-06 TCTCGCATTT AGGGGGCG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6030157-6030277 1e-06 23_[+3]_89 chr3R:30843902-30844022 1e-06 111_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGGSGGCG width=8 seqs=2 chrX:6030157-6030277 ( 24) AGGCGGCG 1 chr3R:30843902-30844022 ( 112) AGGGGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 3.2e+003 152 -765 -765 -765 -765 -765 277 -765 -765 -765 277 -765 -765 174 177 -765 -765 -765 277 -765 -765 -765 277 -765 -765 274 -765 -765 -765 -765 277 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.2e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGSGGCG MEME-3 regular expression -------------------------------------------------------------------------------- AGG[CG]GGCG -------------------------------------------------------------------------------- Time 20.04 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGAGCAG MEME-4 width = 8 sites = 2 llr = 26 E-value = 3.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :a:a::a: pos.-specific C :::::a:: probability G a:a:a::a matrix T :::::::: bits 2.8 * * ** * 2.5 * * ** * 2.2 * * ** * 1.9 * * ** * Relative 1.7 * * ** * Entropy 1.4 ******** (18.4 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GAGAGCAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:18193750-18193870 32 2.87e-06 TTATAAAGTC GAGAGCAG AATTAAACTA chr3L:1457341-1457461 58 2.87e-06 ATGGTATTTA GAGAGCAG AAGCTCAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:18193750-18193870 2.9e-06 31_[+4]_81 chr3L:1457341-1457461 2.9e-06 57_[+4]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGAGCAG width=8 seqs=2 chr3L:18193750-18193870 ( 32) GAGAGCAG 1 chr3L:1457341-1457461 ( 58) GAGAGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.0201 E= 3.1e+004 -765 -765 277 -765 152 -765 -765 -765 -765 -765 277 -765 152 -765 -765 -765 -765 -765 277 -765 -765 274 -765 -765 152 -765 -765 -765 -765 -765 277 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.1e+004 0.000000 0.000000 1.000000 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 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGAGCAG MEME-4 regular expression -------------------------------------------------------------------------------- GAGAGCAG -------------------------------------------------------------------------------- Time 26.32 secs. ******************************************************************************** ******************************************************************************** MOTIF GCACGGAW MEME-5 width = 8 sites = 2 llr = 24 E-value = 1.6e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::a:::a5 pos.-specific C :a:a:::: probability G a:::aa:: matrix T :::::::5 bits 2.8 ** *** 2.5 ** *** 2.2 ** *** 1.9 ** *** Relative 1.7 ** *** Entropy 1.4 ******* (17.4 bits) 1.1 ******* 0.8 ******* 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCACGGAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:14055331-14055451 69 5.97e-06 ATATCATATT GCACGGAA TTATTCGTAA chr2R:19153413-19153533 94 5.97e-06 AACTAACTGA GCACGGAT TTTCTCGCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:14055331-14055451 6e-06 68_[+5]_44 chr2R:19153413-19153533 6e-06 93_[+5]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCACGGAW width=8 seqs=2 chr3L:14055331-14055451 ( 69) GCACGGAA 1 chr2R:19153413-19153533 ( 94) GCACGGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.0201 E= 1.6e+005 -765 -765 277 -765 -765 274 -765 -765 152 -765 -765 -765 -765 274 -765 -765 -765 -765 277 -765 -765 -765 277 -765 152 -765 -765 -765 52 -765 -765 49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.6e+005 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACGGAW MEME-5 regular expression -------------------------------------------------------------------------------- GCACGGA[AT] -------------------------------------------------------------------------------- Time 32.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:13488259-13488379 8.64e-01 120 chrM:4794-4914 9.90e-01 120 chr2L:634243-634363 5.04e-01 120 chr3L:13410274-13410394 9.98e-01 120 chr2L:3341680-3341800 9.69e-01 120 chr3R:8968955-8969075 1.90e-01 120 chr3R:27593333-27593453 6.02e-02 100_[+2(9.55e-05)]_12 chrX:17545694-17545814 8.81e-01 120 chr2R:18610453-18610573 9.28e-01 120 chr2R:10772064-10772184 2.61e-01 120 chrM:12082-12202 1.00e+00 120 chr2L:17782101-17782221 5.80e-01 120 chr2R:19615990-19616110 1.69e-02 120 chr3R:31308970-31309090 1.59e-02 120 chr3R:15588728-15588848 9.99e-01 120 chr3L:21099090-21099210 5.75e-02 120 chr2R:7093006-7093126 6.47e-01 120 chr3R:13793420-13793540 7.37e-01 120 chr3L:6471948-6472068 9.47e-01 120 chr3R:17202479-17202599 8.63e-01 120 chrX:14750557-14750677 8.08e-01 120 chr3L:18198874-18198994 9.31e-01 120 chr3R:22424110-22424230 1.32e-01 120 chr2L:5429202-5429322 1.37e-02 120 chr2R:12646949-12647069 9.97e-01 120 chr2L:651007-651127 2.91e-01 120 chr2L:11966128-11966248 7.18e-02 120 chr2L:15275960-15276080 2.48e-02 111_[+1(5.62e-06)]_1 chr2L:7574389-7574509 3.40e-02 111_[+1(2.69e-06)]_1 chr2R:19187341-19187461 9.19e-01 120 chr2L:3004781-3004901 2.36e-02 5_[+2(1.55e-05)]_107 chr2R:15842690-15842810 2.71e-01 120 chr3L:15188849-15188969 2.02e-01 120 chrM:3477-3597 8.78e-01 120 chr3R:9913578-9913698 7.09e-01 120 chr3R:22628067-22628187 9.87e-01 120 chr3R:27171247-27171367 9.11e-01 120 chr2L:4069719-4069839 6.12e-01 120 chr3R:31956412-31956532 3.90e-01 120 chr2L:7973978-7974098 7.62e-01 120 chr2R:10237756-10237876 1.00e+00 120 chr3L:21099289-21099409 9.04e-01 120 chr3R:31505323-31505443 8.04e-02 120 chrX:20509651-20509771 4.90e-02 120 chr2L:17421485-17421605 4.86e-01 120 chr3L:1457341-1457461 6.86e-03 57_[+4(2.87e-06)]_55 chr3L:17010656-17010776 1.00e+00 120 chr3R:30843902-30844022 3.75e-03 111_[+3(1.03e-06)]_1 chr2L:11399616-11399736 1.35e-01 120 chr2R:23014849-23014969 9.67e-02 120 chr2L:18466344-18466464 6.98e-01 120 chr3R:13372094-13372214 1.68e-01 120 chr3L:21108629-21108749 8.43e-01 120 chr3L:3612741-3612861 6.25e-01 120 chr3L:18276077-18276197 6.79e-01 120 chrX:13541332-13541452 4.11e-01 120 chr2L:16498199-16498319 9.84e-01 120 chr3R:21648618-21648738 7.78e-01 120 chrM:13247-13367 1.44e-05 67_[+1(1.11e-06)]_45 chr2L:18678400-18678520 6.72e-01 120 chrX:17760675-17760795 2.63e-02 6_[+1(6.51e-05)]_106 chr2R:22144341-22144461 7.74e-02 120 chr2R:7147274-7147394 1.01e-01 27_[+2(1.12e-05)]_85 chrX:5025374-5025494 2.35e-03 26_[+2(1.55e-05)]_86 chrM:2747-2867 9.83e-01 120 chr3L:15180962-15181082 9.83e-01 120 chr3R:21827561-21827681 9.97e-01 120 chr3L:12915613-12915733 7.98e-01 120 chr3R:26192392-26192512 6.61e-01 120 chrM:7461-7581 1.57e-01 120 chr2L:1486419-1486539 3.21e-01 120 chr3L:13406978-13407098 1.00e+00 120 chr3L:10359556-10359676 6.58e-01 120 chr3R:16985688-16985808 6.34e-03 99_[+1(2.69e-06)]_13 chr3R:20283327-20283447 1.41e-01 120 chr3R:18157561-18157681 2.15e-01 120 chr2R:14923049-14923169 9.41e-01 120 chr3R:8029785-8029905 9.01e-01 120 chr2R:10599169-10599289 2.87e-01 120 chr3R:29778283-29778403 9.44e-01 120 chr3L:14453369-14453489 9.79e-01 120 chr3L:18193750-18193870 6.64e-02 31_[+4(2.87e-06)]_81 chrM:1716-1836 2.27e-01 120 chr2R:10600501-10600621 9.82e-02 120 chr3L:4395664-4395784 9.99e-01 120 chr3L:15641595-15641715 3.89e-04 74_[+2(8.12e-06)]_38 chr3R:23496634-23496754 9.39e-01 120 chr2L:15304455-15304575 9.26e-01 120 chr3R:22194810-22194930 9.87e-01 120 chr3R:17825921-17826041 9.98e-01 120 chr3L:15258523-15258643 8.93e-01 120 chr2R:13478507-13478627 8.24e-02 120 chr3L:3513154-3513274 5.73e-01 120 chr2L:11395810-11395930 7.69e-01 120 chr3R:16501568-16501688 5.59e-01 120 chr2L:3554080-3554200 3.91e-01 120 chr2L:11222219-11222339 1.00e+00 120 chr3L:21253071-21253191 1.00e+00 120 chr2R:19913833-19913953 8.94e-01 120 chr3R:16210829-16210949 9.70e-01 120 chr3L:729481-729601 3.39e-03 10_[+2(1.55e-05)]_102 chr3L:19035642-19035762 7.00e-01 120 chr2R:8322844-8322964 1.28e-01 51_[+1(1.56e-05)]_61 chrX:6030157-6030277 7.69e-04 23_[+3(1.03e-06)]_89 chr2R:6969482-6969602 9.98e-01 120 chrX:10325089-10325209 9.80e-03 96_[+2(1.81e-05)]_16 chr2R:7141877-7141997 8.48e-01 120 chr3R:13934747-13934867 7.31e-01 120 chr2R:24237477-24237597 9.21e-01 120 chr2L:423283-423403 6.35e-01 120 chr2R:6556960-6557080 8.37e-01 120 chr3L:8368814-8368934 7.86e-03 99_[+3(5.38e-06)]_13 chr3R:13941545-13941665 1.78e-01 120 chrX:14897754-14897874 6.28e-01 120 chr3L:11297675-11297795 9.99e-01 120 chr3L:18241109-18241229 5.66e-01 120 chr3R:4961561-4961681 6.63e-01 120 chr3L:3423176-3423296 9.98e-01 120 chr3R:8142251-8142371 2.97e-01 120 chr3R:10530731-10530851 1.97e-01 120 chr3R:10476122-10476242 9.08e-01 120 chr3L:5630270-5630390 5.78e-01 120 chr3R:31505527-31505647 1.01e-01 120 chr2R:15513543-15513663 2.68e-02 120 chr3L:10786026-10786146 9.96e-01 120 chr2L:9496770-9496890 6.35e-01 120 chr3R:29538560-29538680 9.14e-01 120 chr3L:21738824-21738944 4.60e-01 120 chrX:22479462-22479582 2.93e-02 120 chr3R:4667422-4667542 8.66e-01 120 chr3R:29762432-29762552 6.12e-01 120 chr3R:23297645-23297765 9.84e-01 120 chr2L:10791429-10791549 1.00e+00 120 chr2R:23022626-23022746 8.17e-01 120 chr2R:19969861-19969981 7.76e-01 120 chr2L:7992082-7992202 4.89e-03 120 chr3L:7792325-7792445 3.57e-01 120 chr2R:7241732-7241852 5.52e-01 120 chrX:2452876-2452996 1.38e-01 120 chr3L:3246816-3246936 1.79e-02 46_[+5(5.97e-06)]_66 chrX:17814950-17815070 9.99e-01 120 chr2L:11394258-11394378 6.86e-01 120 chr2R:16156389-16156509 3.24e-01 120 chr3L:21594537-21594657 1.03e-02 20_[+2(2.44e-05)]_92 chr3L:14253578-14253698 9.75e-01 120 chr3R:25634006-25634126 6.74e-01 120 chr3L:3343436-3343556 8.74e-01 120 chrM:5016-5136 8.80e-01 120 chr3L:761833-761953 1.26e-01 120 chr2L:9438405-9438525 3.46e-01 120 chr3L:21060537-21060657 4.40e-01 120 chr2R:19849231-19849351 1.82e-01 [+3(4.12e-05)]_112 chr2L:9447907-9448027 6.93e-01 120 chr3R:4667628-4667748 5.90e-01 120 chr2R:20136844-20136964 8.85e-03 83_[+2(6.99e-05)]_29 chr3R:28633891-28634011 5.58e-01 120 chr3R:30689845-30689965 4.54e-03 106_[+1(1.34e-06)]_6 chr3R:5103716-5103836 3.23e-02 120 chr2R:19153413-19153533 2.59e-04 93_[+5(5.97e-06)]_19 chr3R:10579706-10579826 4.60e-01 120 chr2R:12532789-12532909 9.17e-01 120 chr2R:11183226-11183346 9.51e-01 120 chr3L:20403688-20403808 7.33e-03 46_[+2(3.80e-06)]_66 chr3L:5365281-5365401 1.51e-01 120 chr3L:14055331-14055451 5.13e-02 68_[+5(5.97e-06)]_44 chrM:14236-14356 9.83e-01 120 chr2R:19420614-19420734 8.74e-01 120 chrX:19164886-19165006 8.88e-01 120 chrX:12015173-12015293 6.86e-01 120 chr3L:12090467-12090587 1.94e-01 120 chr3L:11322612-11322732 8.11e-01 120 chr3R:5100467-5100587 6.97e-01 120 chr3L:8157194-8157314 7.34e-01 120 chr2L:19142639-19142759 2.89e-01 120 chrX:10104606-10104726 2.08e-02 120 chr2L:19162918-19163038 2.25e-04 109_[+2(3.80e-06)]_3 chrX:17571083-17571203 2.80e-01 120 chr2L:3781555-3781675 9.92e-01 120 chr3L:14239439-14239559 7.81e-01 120 chr3R:23486890-23487010 8.98e-01 120 chr2L:18648372-18648492 3.55e-01 120 chr2L:11968584-11968704 2.87e-01 120 chr3L:785844-785964 9.40e-01 120 chr3L:16024773-16024893 7.50e-01 120 chr3R:29199866-29199986 1.56e-01 120 chr2L:10615963-10616083 9.61e-01 120 chr3L:758676-758796 4.38e-01 120 chrX:7892595-7892715 7.86e-01 120 chr2R:21569764-21569884 8.08e-01 120 chrX:17551180-17551300 4.64e-01 120 chr3L:17502344-17502464 7.35e-01 120 chr3L:15762936-15763056 7.68e-01 120 chr2R:14783006-14783126 4.63e-01 120 chr2L:7423026-7423146 9.95e-01 120 chrX:3381101-3381221 7.59e-01 120 chr3R:31225147-31225267 1.74e-03 93_[+3(4.12e-05)]_19 chr3R:15596011-15596131 2.15e-01 120 chr2R:8650574-8650694 5.78e-01 120 chr2L:7909347-7909467 9.99e-01 120 chr2R:6994739-6994859 4.05e-01 120 chr3L:17608680-17608800 6.02e-01 120 chrX:5026154-5026274 7.54e-01 120 chr2L:9448800-9448920 9.45e-01 120 chrX:6339201-6339321 7.30e-01 120 chr2R:16812241-16812361 9.71e-01 120 chr3R:19283702-19283822 2.60e-01 120 chr2L:5493044-5493164 6.64e-01 120 chr2L:18645601-18645721 5.05e-01 120 chr3L:8913596-8913716 6.93e-01 120 chr3R:30281386-30281506 2.05e-01 81_[+1(3.32e-05)]_31 chr3R:22175840-22175960 7.09e-01 120 chr3L:1388245-1388365 2.02e-01 120 chr2R:9674771-9674891 8.91e-01 120 chr2L:1412831-1412951 3.63e-01 120 chr2L:7611675-7611795 7.73e-01 120 chr2L:18003186-18003306 9.95e-01 120 chr2L:7419533-7419653 2.98e-01 120 chr2L:9235581-9235701 5.85e-01 120 chr3R:8154094-8154214 2.74e-01 120 chr2R:14975296-14975416 9.90e-01 120 chr2L:5249916-5250036 4.37e-05 8_[+2(2.57e-06)]_74_[+2(3.61e-05)]_\ 7_[+3(4.12e-05)]_7 chr2R:21569027-21569147 7.43e-01 120 chr3L:13021879-13021999 8.83e-01 120 chr3R:6950277-6950397 5.65e-01 120 chrX:1826231-1826351 7.85e-01 120 chr3L:19046525-19046645 9.55e-01 120 chr2R:19647732-19647852 2.25e-01 120 chr3R:18990613-18990733 8.66e-01 120 chr3L:728016-728136 4.09e-01 120 chr3L:660433-660553 5.86e-03 18_[+2(8.12e-06)]_94 chr2R:17836146-17836266 8.87e-01 120 chrX:9251419-9251539 3.20e-03 14_[+1(1.11e-06)]_98 chrX:2365495-2365615 5.94e-01 120 chr2L:15385426-15385546 8.46e-02 30_[+2(9.55e-05)]_82 chr3R:17117681-17117801 6.97e-01 120 chr2L:15743714-15743834 8.63e-01 120 chr3R:27140089-27140209 2.63e-01 120 chr3R:9935010-9935130 1.62e-01 80_[+1(5.09e-05)]_32 chr3L:10777482-10777602 9.83e-04 39_[+2(1.27e-06)]_73 chr3R:4873900-4874020 3.59e-01 120 chrM:10867-10987 8.55e-01 120 chr3R:29096071-29096191 9.03e-01 120 chr2R:11515864-11515984 7.91e-01 120 chr3L:1374599-1374719 1.39e-01 120 chr3R:30811350-30811470 6.24e-01 120 chr2R:18209792-18209912 4.41e-01 120 chrX:12663042-12663162 8.22e-01 120 chrX:13312319-13312439 7.13e-01 120 chr3L:10794024-10794144 9.51e-01 120 chr3L:16016022-16016142 7.61e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n01.farnam.hpc.yale.internal ********************************************************************************