******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://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 ******************************************************************************** DATAFILE= /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/seqs-sampled ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrII:266212-266717 1.0000 100 chrVIII:134123-134737 1.0000 100 chrXIV:662900-663849 1.0000 100 chrVI:226352-227320 1.0000 100 chrXI:259142-260002 1.0000 100 chrI:166177-166632 1.0000 100 chrIV:1256749-1257282 1.0000 100 chrXVI:810583-811323 1.0000 100 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1.0000 100 chrXVI:153657-154458 1.0000 100 chrXIII:320942-321316 1.0000 100 chrXV:899802-901242 1.0000 100 chrXII:707913-710139 1.0000 100 chrXIII:625835-627296 1.0000 100 chrVIII:237117-238708 1.0000 100 chrVI:180640-181232 1.0000 100 chrV:438263-438988 1.0000 100 chrII:614460-614996 1.0000 100 chrVIII:62473-63084 1.0000 100 chrXII:764373-764595 1.0000 100 chrXIII:352082-353541 1.0000 100 chrIV:802549-802986 1.0000 100 chrIV:1461449-1461837 1.0000 100 chrVIII:505871-506171 1.0000 100 chrVI:53222-54797 1.0000 100 chrXII:951040-953803 1.0000 100 chrXII:1012441-1013301 1.0000 100 chrXIII:667238-668157 1.0000 100 chrVI:63987-65346 1.0000 100 chrVII:824063-826895 1.0000 100 chrIV:1268558-1269442 1.0000 100 chrIX:68636-69567 1.0000 100 chrXIII:287858-289998 1.0000 100 chrV:492199-492556 1.0000 100 chrVIII:296963-297149 1.0000 100 chrXVI:432499-434396 1.0000 100 chrXII:167704-168238 1.0000 100 chrII:347412-347950 1.0000 100 chrIII:150961-151506 1.0000 100 chrIV:1449813-1451101 1.0000 100 chrIX:25038-25285 1.0000 100 chrX:523497-523597 1.0000 100 chrXVI:75270-77315 1.0000 100 chrXV:881287-882142 1.0000 100 chrI:182223-183146 1.0000 100 chrXIII:161502-162693 1.0000 100 chrIX:83320-84878 1.0000 100 chrXIV:498788-500754 1.0000 100 chrV:396703-398071 1.0000 100 chrIX:197322-197731 1.0000 100 chrV:322107-323347 1.0000 100 chrIV:927529-930345 1.0000 100 chrVI:224296-225116 1.0000 100 chrII:306278-307327 1.0000 100 chrV:85162-87457 1.0000 100 chrXII:281923-282482 1.0000 100 chrXVI:678496-678779 1.0000 100 chrXII:826879-827872 1.0000 100 chrVII:185373-185890 1.0000 100 chrIX:315994-316564 1.0000 100 chrI:181137-181490 1.0000 100 chrIII:851-1025 1.0000 100 chrX:90647-90747 1.0000 100 chrIV:1165529-1166440 1.0000 100 chrXII:368635-369451 1.0000 100 chrXV:909301-911619 1.0000 100 chrX:59016-59116 1.0000 100 chrXII:448503-448983 1.0000 100 chrVII:478969-482849 1.0000 100 chrII:478941-479554 1.0000 100 chrXIV:187069-187556 1.0000 100 chrXIV:282093-283814 1.0000 100 chrIV:884272-885407 1.0000 100 chrXIV:585498-586845 1.0000 100 chrXIII:499032-500777 1.0000 100 chrX:453345-453445 1.0000 100 chrIII:163508-163845 1.0000 100 chrIV:1162035-1164671 1.0000 100 chrVIII:54905-56049 1.0000 100 chrVI:225465-225989 1.0000 100 chrXIII:220035-220947 1.0000 100 chrXVI:133004-135464 1.0000 100 chrXII:636689-640196 1.0000 100 chrXV:407545-408232 1.0000 100 chrII:556247-558465 1.0000 100 chrXI:578631-579391 1.0000 100 chrIV:568702-569372 1.0000 100 chrV:165703-167652 1.0000 100 chrII:162967-164060 1.0000 100 chrXIV:241457-241993 1.0000 100 chrVII:970717-973999 1.0000 100 chrXIII:627525-627839 1.0000 100 chrXII:1028799-1030303 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 30 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 600 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 60000 N= 600 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.300 C 0.200 G 0.200 T 0.300 Background letter frequencies (from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--IES2/background): A 0.304 C 0.196 G 0.196 T 0.304 ******************************************************************************** ******************************************************************************** MOTIF GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 width = 30 sites = 51 llr = 1018 E-value = 6.0e-181 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2::::3a1::::2:3121313432211121 pos.-specific C ::::a::35a76424222116:1:1:::11 probability G 7a:::7:2:::344:54655:511::::11 matrix T ::aa:::45:31:34231131168798878 bits 2.3 * * * 2.1 * * * 1.9 * * * 1.6 **** * * Relative 1.4 ****** * Entropy 1.2 ******* ** * (28.8 bits) 0.9 ******* **** * *** 0.7 ******* ***** ** * *** * 0.5 ******* ******* ** ** ******* 0.2 ****************************** 0.0 ------------------------------ Multilevel GGTTCGATTCCCGGCGGGGGCGTTTTTTTT consensus A A CC TGCTTTTCATAAA sequence CAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------ chrX:204550-204650 + 15 7.46e-13 GCCAGATCGG GGTTCAATTCCCCGTCGCGGAGATTTTTTT TGGCCCTTGA chrXIII:463324-463891 + 47 7.46e-13 GCCAGATCGG GGTTCAATTCCCCGTCGCGGAGATTTTTTT ATCAGACCAG chrII:405691-406400 + 15 7.46e-13 GCCAGATCGG GGTTCAATTCCCCGTCGCGGAGATTTTTTT GGCTACTCCT chrV:550829-551781 - 22 1.02e-12 GGGGATCAGC GGTTCGATCCCGCTAGAGACCATTTTTTTT GAAAATCGTA chrV:435433-436014 - 71 2.87e-12 . GGTTCGAGCCCCCTACAGGGCTTTCTTTTT AACTTTTTGC chrII:644965-645428 + 71 4.38e-12 TGGAGACCGG GGTTCGACTCCCCGTATCGGAGTTATTTTT chrIV:1256749-1257282 - 35 5.03e-12 ATGGGGCCCG GGTTCGATTCCCGGCTTCCGCATTTTTTGT GCAATTTTTT chrIV:568702-569372 + 27 6.61e-12 GCCAGATCGG GGTTCAATTCCCCGTCGCGGAGAATTTTTT TTAATTGATA chrXIV:569633-570082 - 52 6.61e-12 GGGGATCAGC GGTTCGATCCCGCTAGAGACCATTCTTTTT TTTTGCATTG chrXII:1051920-1052210 - 48 7.56e-12 GGGGATCAGC GGTTCGATCCCGCTAGAGACCATTATTTTT TTTACTTTAA chrXIV:632443-632943 + 8 8.64e-12 GATCGTG AGTTCAACCCTCACTGGGGTCGTTTTTTTT CTTATTTCAG chrIV:1351856-1353057 - 52 9.87e-12 TAAGGTTAGG GGTTCGAGCCCCCTACAGGGCTATCTTTTT TTTAAACAAC chrIV:1016950-1017483 - 33 1.13e-11 TGGAGACCGG GGTTCGACTCCCCGCTTCGGAGTTTCTTTT TTATTTTCTA chrXII:374212-374675 + 13 1.46e-11 GAAGATTCCA GGTTCAAGTCCTGGCGGGGAAGATTTTTTT GCTCCGACAA chrXVI:209956-210497 - 8 2.13e-11 TGGAGACCGG GGTTCGACTCCCCGTATCGGAGTTTTCTTT TTGCTTC chrV:354674-355388 + 3 2.73e-11 GG GGTTCGACTCCCCGTATCGGAGTACTTTTT TGACATCATA chrXV:438434-439054 + 23 3.48e-11 AAATGTCAGG GGTTCGAGCCCCCTATGAGGAGTTCTTTAT TTTTGTCAGT chrV:288132-288743 - 48 3.48e-11 TGCCCGCGCT GGTTCAAATCCTGCTGGTGTCGTTTTTTTT ATTGTTAGAG chrXII:167704-168238 - 15 4.98e-11 TGCCCGCGCA GGTTCGAGTCCTGCAGTTGTCGTTATTTTT TCTTTTTCTT chrXV:228090-228645 + 66 4.98e-11 CAAGATCGTG AGTTCAACCCTCACTGGGGTCGTTATTTTT GAATA chrII:226982-227351 + 19 4.98e-11 TGCCCGCGCA GGTTCGAGTCCTGCAGTTGTCGTTATTTTT TGGACAGTAA chrXIV:96025-96459 - 41 1.24e-10 TGGGGACACG GGTTCGATTCTCGTACCGCTCAAATTTTTT GATGACATTG chrXVI:860178-860704 + 37 1.38e-10 TTGGGCCCCC GGTTCGATTCCGGGCTTGCGCAGATTTTAT TTTTTGCTCC chrXIII:747632-748144 - 46 1.54e-10 GAAGATTATG GGTTCGACCCCCATCGTGAGTGTTTTTTAG TATTGTTTTT chrXII:975749-976162 - 70 1.54e-10 G AGTTCAACCCTCACTGGGGTCGTTTATTTT TTTTGCATTA chrXVI:768881-769480 - 69 2.13e-10 GG GGTTCGAGCCCCCTATGAGGAGTTCTTTAC TTTTTTGCAC chrX:414800-414900 + 24 2.13e-10 TAAGGTTAGG GGTTCGAGCCCCCTACAGGGCTAATATTTT TTTCTTGCCC chrVII:541717-542174 + 5 2.36e-10 CCGG GGTTCGACTCCCCGTATCGGAGTGTTCTTT TTCTTACCTC chrXIII:572644-573134 - 36 2.36e-10 GAAGGTCGAG AGTTCGAACCTCCCCTGGAGCACATTTTTT TTCAAAACTT chrIV:619725-620195 - 51 2.62e-10 GAAGATTCCA GGTTCAAGTCCTGGCGGGGAAGATTTTTTA TACATTTTTC chrX:374178-374278 - 32 2.91e-10 GAAGATTATG GGTTCGACCCCCATCGTGAGTGCTTTGTTT CTTCCGTGAT chrXIII:131558-132104 - 36 2.91e-10 GAAGATTATG GGTTCGACCCCCATCGTGAGTGCTTTGTTT CTTCTTTTTT chrXIII:320942-321316 - 60 4.82e-10 AGAGGTCTCC GGTTCGATTCCGGACTCGTCCATTTTTTAT TTTTTTGGCT chrVII:730959-731422 + 49 5.87e-10 CAAGATCGTG AGTTCAACCCTCACTGGGGTCGTTTTTTGC TTGAAATGAG chrIV:83347-83847 + 50 5.87e-10 TTGGGCCCCC GGTTCGATTCCGGGCTTGCGCAAGTTTAAT TTTTTTTCTT chrII:266212-266717 + 15 5.87e-10 GGAGATCATC GGTTCAAATCCGATTGGAAGCATTTTTTTG AATACTGAAA chrIV:802549-802986 - 6 9.47e-10 GGACAACCCC GGTTCGAATCCGGGTAGGACCTCTTTTTAT TTTTA chrVII:287070-287640 - 37 1.04e-09 AAGGGTTGCA GGTTCAATTCCTGTCCGTTTCATTTTTTAT ACTGCAAGTG chrX:378232-378332 + 59 1.50e-09 GAACGTCCCC AGTTCGATCCTGGGCGAAATCAATTTTTTG TTTTTTTAAT chrII:642828-643244 - 13 1.79e-09 GTTGGTCCTT AGTTCGATCCTGAGTGCGAGCTTCTTTTTT TTTTTGCAAT chrXIII:420293-420855 - 56 2.14e-09 GAACGTCCCC AGTTCGATCCTGGGCGAAATCATTTTTATC TCAGCCGTTA chrV:492199-492556 - 17 2.33e-09 GAAGATTCCA GGTTCAAGTCCTGGCGGGGAAGGATTATTT TTCTTTTAAT chrX:617690-617790 + 66 3.57e-09 CGGATGCAAG GGTTCGAATCCCTTAGCTCTCATTATTTTT TGTAT chrXVI:856739-857125 + 71 4.95e-09 AGAGGTCTCC GGTTCGATTCCGGACTCGTCCATTTTAATT chrVII:823346-823722 + 50 5.81e-09 GAACGTCCCC AGTTCGATCCTGGGCGAAATCATTTTTTGA AGATTACATT chrIV:1175750-1176099 + 6 7.95e-09 TCGAG AGTTCGAACCTCCCCTGGAGCATTTTTGCC GAGCACGGTA chrVII:779409-779952 + 36 2.20e-08 TGGGGACACG GGTTCGATTCTCGTACCGCTCAAGATTACT TTTTTAATTT chrXIII:837764-838254 + 36 3.30e-08 TGAGATCGGG CGTTCGACTCGCCCCCGGGAGATATTTTTT TACTTTTGAT chrVIII:475490-475900 - 53 4.55e-08 AAAGGTCCCG AGTTCGATCCTCGGTTGGAACATTTTAACA TCGATTTTTT chrV:311692-312332 - 53 1.62e-07 AGAGGTCATC GGTTCGATTCCGGTTGCGTCCAATGAAATC TTTTTGTACC chrII:347412-347950 + 34 1.89e-07 TGTCCGCGCG AGTTCGAACCTCGCATCCTTCAGTAATATT TTTTTAATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:204550-204650 7.5e-13 14_[+1]_56 chrXIII:463324-463891 7.5e-13 46_[+1]_24 chrII:405691-406400 7.5e-13 14_[+1]_56 chrV:550829-551781 1e-12 21_[-1]_49 chrV:435433-436014 2.9e-12 70_[-1] chrII:644965-645428 4.4e-12 70_[+1] chrIV:1256749-1257282 5e-12 34_[-1]_36 chrIV:568702-569372 6.6e-12 26_[+1]_44 chrXIV:569633-570082 6.6e-12 51_[-1]_19 chrXII:1051920-1052210 7.6e-12 47_[-1]_23 chrXIV:632443-632943 8.6e-12 7_[+1]_63 chrIV:1351856-1353057 9.9e-12 51_[-1]_19 chrIV:1016950-1017483 1.1e-11 32_[-1]_38 chrXII:374212-374675 1.5e-11 12_[+1]_58 chrXVI:209956-210497 2.1e-11 7_[-1]_63 chrV:354674-355388 2.7e-11 2_[+1]_68 chrXV:438434-439054 3.5e-11 22_[+1]_48 chrV:288132-288743 3.5e-11 47_[-1]_23 chrXII:167704-168238 5e-11 14_[-1]_56 chrXV:228090-228645 5e-11 65_[+1]_5 chrII:226982-227351 5e-11 18_[+1]_52 chrXIV:96025-96459 1.2e-10 40_[-1]_30 chrXVI:860178-860704 1.4e-10 36_[+1]_34 chrXIII:747632-748144 1.5e-10 45_[-1]_25 chrXII:975749-976162 1.5e-10 69_[-1]_1 chrXVI:768881-769480 2.1e-10 68_[-1]_2 chrX:414800-414900 2.1e-10 23_[+1]_47 chrVII:541717-542174 2.4e-10 4_[+1]_66 chrXIII:572644-573134 2.4e-10 35_[-1]_35 chrIV:619725-620195 2.6e-10 50_[-1]_20 chrX:374178-374278 2.9e-10 31_[-1]_39 chrXIII:131558-132104 2.9e-10 35_[-1]_35 chrXIII:320942-321316 4.8e-10 59_[-1]_11 chrVII:730959-731422 5.9e-10 48_[+1]_22 chrIV:83347-83847 5.9e-10 49_[+1]_21 chrII:266212-266717 5.9e-10 14_[+1]_56 chrIV:802549-802986 9.5e-10 5_[-1]_65 chrVII:287070-287640 1e-09 36_[-1]_34 chrX:378232-378332 1.5e-09 58_[+1]_12 chrII:642828-643244 1.8e-09 12_[-1]_58 chrXIII:420293-420855 2.1e-09 55_[-1]_15 chrV:492199-492556 2.3e-09 16_[-1]_54 chrX:617690-617790 3.6e-09 65_[+1]_5 chrXVI:856739-857125 5e-09 70_[+1] chrVII:823346-823722 5.8e-09 49_[+1]_21 chrIV:1175750-1176099 7.9e-09 5_[+1]_65 chrVII:779409-779952 2.2e-08 35_[+1]_35 chrXIII:837764-838254 3.3e-08 35_[+1]_35 chrVIII:475490-475900 4.5e-08 52_[-1]_18 chrV:311692-312332 1.6e-07 52_[-1]_18 chrII:347412-347950 1.9e-07 33_[+1]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT width=30 seqs=51 chrX:204550-204650 ( 15) GGTTCAATTCCCCGTCGCGGAGATTTTTTT 1 chrXIII:463324-463891 ( 47) GGTTCAATTCCCCGTCGCGGAGATTTTTTT 1 chrII:405691-406400 ( 15) GGTTCAATTCCCCGTCGCGGAGATTTTTTT 1 chrV:550829-551781 ( 22) GGTTCGATCCCGCTAGAGACCATTTTTTTT 1 chrV:435433-436014 ( 71) GGTTCGAGCCCCCTACAGGGCTTTCTTTTT 1 chrII:644965-645428 ( 71) GGTTCGACTCCCCGTATCGGAGTTATTTTT 1 chrIV:1256749-1257282 ( 35) GGTTCGATTCCCGGCTTCCGCATTTTTTGT 1 chrIV:568702-569372 ( 27) GGTTCAATTCCCCGTCGCGGAGAATTTTTT 1 chrXIV:569633-570082 ( 52) GGTTCGATCCCGCTAGAGACCATTCTTTTT 1 chrXII:1051920-1052210 ( 48) GGTTCGATCCCGCTAGAGACCATTATTTTT 1 chrXIV:632443-632943 ( 8) AGTTCAACCCTCACTGGGGTCGTTTTTTTT 1 chrIV:1351856-1353057 ( 52) GGTTCGAGCCCCCTACAGGGCTATCTTTTT 1 chrIV:1016950-1017483 ( 33) GGTTCGACTCCCCGCTTCGGAGTTTCTTTT 1 chrXII:374212-374675 ( 13) GGTTCAAGTCCTGGCGGGGAAGATTTTTTT 1 chrXVI:209956-210497 ( 8) GGTTCGACTCCCCGTATCGGAGTTTTCTTT 1 chrV:354674-355388 ( 3) GGTTCGACTCCCCGTATCGGAGTACTTTTT 1 chrXV:438434-439054 ( 23) GGTTCGAGCCCCCTATGAGGAGTTCTTTAT 1 chrV:288132-288743 ( 48) GGTTCAAATCCTGCTGGTGTCGTTTTTTTT 1 chrXII:167704-168238 ( 15) GGTTCGAGTCCTGCAGTTGTCGTTATTTTT 1 chrXV:228090-228645 ( 66) AGTTCAACCCTCACTGGGGTCGTTATTTTT 1 chrII:226982-227351 ( 19) GGTTCGAGTCCTGCAGTTGTCGTTATTTTT 1 chrXIV:96025-96459 ( 41) GGTTCGATTCTCGTACCGCTCAAATTTTTT 1 chrXVI:860178-860704 ( 37) GGTTCGATTCCGGGCTTGCGCAGATTTTAT 1 chrXIII:747632-748144 ( 46) GGTTCGACCCCCATCGTGAGTGTTTTTTAG 1 chrXII:975749-976162 ( 70) AGTTCAACCCTCACTGGGGTCGTTTATTTT 1 chrXVI:768881-769480 ( 69) GGTTCGAGCCCCCTATGAGGAGTTCTTTAC 1 chrX:414800-414900 ( 24) GGTTCGAGCCCCCTACAGGGCTAATATTTT 1 chrVII:541717-542174 ( 5) GGTTCGACTCCCCGTATCGGAGTGTTCTTT 1 chrXIII:572644-573134 ( 36) AGTTCGAACCTCCCCTGGAGCACATTTTTT 1 chrIV:619725-620195 ( 51) GGTTCAAGTCCTGGCGGGGAAGATTTTTTA 1 chrX:374178-374278 ( 32) GGTTCGACCCCCATCGTGAGTGCTTTGTTT 1 chrXIII:131558-132104 ( 36) GGTTCGACCCCCATCGTGAGTGCTTTGTTT 1 chrXIII:320942-321316 ( 60) GGTTCGATTCCGGACTCGTCCATTTTTTAT 1 chrVII:730959-731422 ( 49) AGTTCAACCCTCACTGGGGTCGTTTTTTGC 1 chrIV:83347-83847 ( 50) GGTTCGATTCCGGGCTTGCGCAAGTTTAAT 1 chrII:266212-266717 ( 15) GGTTCAAATCCGATTGGAAGCATTTTTTTG 1 chrIV:802549-802986 ( 6) GGTTCGAATCCGGGTAGGACCTCTTTTTAT 1 chrVII:287070-287640 ( 37) GGTTCAATTCCTGTCCGTTTCATTTTTTAT 1 chrX:378232-378332 ( 59) AGTTCGATCCTGGGCGAAATCAATTTTTTG 1 chrII:642828-643244 ( 13) AGTTCGATCCTGAGTGCGAGCTTCTTTTTT 1 chrXIII:420293-420855 ( 56) AGTTCGATCCTGGGCGAAATCATTTTTATC 1 chrV:492199-492556 ( 17) GGTTCAAGTCCTGGCGGGGAAGGATTATTT 1 chrX:617690-617790 ( 66) GGTTCGAATCCCTTAGCTCTCATTATTTTT 1 chrXVI:856739-857125 ( 71) GGTTCGATTCCGGACTCGTCCATTTTAATT 1 chrVII:823346-823722 ( 50) AGTTCGATCCTGGGCGAAATCATTTTTTGA 1 chrIV:1175750-1176099 ( 6) AGTTCGAACCTCCCCTGGAGCATTTTTGCC 1 chrVII:779409-779952 ( 36) GGTTCGATTCTCGTACCGCTCAAGATTACT 1 chrXIII:837764-838254 ( 36) CGTTCGACTCGCCCCCGGGAGATATTTTTT 1 chrVIII:475490-475900 ( 53) AGTTCGATCCTCGGTTGGAACATTTTAACA 1 chrV:311692-312332 ( 53) GGTTCGATTCCGGTTGCGTCCAATGAAATC 1 chrII:347412-347950 ( 34) AGTTCGAACCTCGCATCCTTCAGTAATATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 30 n= 42600 bayes= 10.2155 E= 6.0e-181 -37 -332 192 -1232 -1232 -1232 235 -1232 -1232 -1232 -1232 172 -1232 -1232 -1232 172 -1232 235 -1232 -1232 -15 -1232 189 -1232 172 -1232 -1232 -1232 -115 38 0 44 -1232 120 -1232 85 -1232 235 -1232 -1232 -1232 185 -332 -15 -1232 158 48 -115 -78 100 107 -395 -295 14 107 13 -15 92 -1232 22 -163 14 120 -37 -78 -32 107 -25 -137 14 153 -163 -5 -74 132 -163 -163 -52 126 -5 -15 172 -332 -237 51 -1232 126 -163 -25 -132 -174 100 -95 -332 -174 133 -95 -74 -332 122 -195 -332 -1232 157 -195 -232 -232 147 -115 -1232 -332 147 -95 -174 -174 126 -237 -100 -174 137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 30 nsites= 51 E= 6.0e-181 0.235294 0.019608 0.745098 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 0.274510 0.000000 0.725490 0.000000 1.000000 0.000000 0.000000 0.000000 0.137255 0.254902 0.196078 0.411765 0.000000 0.450980 0.000000 0.549020 0.000000 1.000000 0.000000 0.000000 0.000000 0.705882 0.019608 0.274510 0.000000 0.588235 0.274510 0.137255 0.176471 0.392157 0.411765 0.019608 0.039216 0.215686 0.411765 0.333333 0.274510 0.372549 0.000000 0.352941 0.098039 0.215686 0.450980 0.235294 0.176471 0.156863 0.411765 0.254902 0.117647 0.215686 0.568627 0.098039 0.294118 0.117647 0.490196 0.098039 0.098039 0.137255 0.470588 0.294118 0.274510 0.647059 0.019608 0.058824 0.431373 0.000000 0.470588 0.098039 0.254902 0.078431 0.058824 0.607843 0.156863 0.019608 0.058824 0.764706 0.156863 0.117647 0.019608 0.705882 0.078431 0.019608 0.000000 0.901961 0.078431 0.039216 0.039216 0.843137 0.137255 0.000000 0.019608 0.843137 0.156863 0.058824 0.058824 0.725490 0.058824 0.098039 0.058824 0.784314 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCGAYYCCCSBHKKGRKCRTTTTTTTT MEME-1 regular expression -------------------------------------------------------------------------------- [GA]GTTC[GA]A[TC][TC]C[CT][CG][GC][GTC][CTA][GTC][GT][GC][GA][GT][CA][GA][TA]TTTTTTT -------------------------------------------------------------------------------- Time 353.16 secs. ******************************************************************************** ******************************************************************************** MOTIF BKTGGCCSAGTKGGTWRAGSS MEME-2 width = 21 sites = 31 llr = 529 E-value = 1.3e-063 ******************************************************************************** -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 Description -------------------------------------------------------------------------------- Simplified A 11:3:::2a1:1::15561:: pos.-specific C 4::::964:::2::2:11:54 probability G 34:7a:13:9:3a71:32956 matrix T 35a::121::a5:36511::: bits 2.3 * * 2.1 * * 1.9 ** * * * 1.6 * ** *** * * Relative 1.4 * ** *** ** *** Entropy 1.2 **** *** ** *** (24.6 bits) 0.9 ***** *** ** *** 0.7 ***** *** ** * *** 0.5 ****** *** ********* 0.2 ********************* 0.0 --------------------- Multilevel CTTGGCCCAGTTGGTTAAGGG consensus GG A TG G T AG CC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- chrXIV:602059-602588 + 44 2.37e-12 ACAATGGTCT CTTGGCCCAGTTGGTTAAGGC ACCGTGCTAA chrV:550829-551781 - 78 2.37e-12 CT CTTGGCCCAGTTGGTTAAGGC ACCGTGCTAA chrXII:734623-734985 + 53 2.37e-12 AGTTTGGTCT CTTGGCCCAGTTGGTTAAGGC ACCGTGCTAA chrXV:228090-228645 + 19 4.30e-10 TATTAGACTC CATGGCCAAGTTGGTTAAGGC GTGCGACTGT chrIII:127493-127893 + 78 4.30e-10 AAAATGACTC CATGGCCAAGTTGGTTAAGGC GT chrVII:730959-731422 + 2 4.30e-10 C CATGGCCAAGTTGGTTAAGGC GTGCGACTGT chrXII:592308-592821 - 80 4.97e-10 . TTTGGCCGAGTGGTTTAAGGC GTCAGATTTA chrXII:167704-168238 - 79 5.73e-10 A CTTGGCCGAGTGGTTAAGGCG AAAGATTAGA chrX:424275-424375 - 47 7.54e-10 AAGATGGAGG GTTGGCCGAGTGGTCTAAGGC GGCAGACTTA chrXII:962805-963332 - 12 7.54e-10 TCGACGGAGG GTTGGCCGAGTGGTCTAAGGC GGCAGACTTA chrXI:578631-579391 + 9 8.67e-10 TCATCCTT GTTAGCTCAGTTGGTAGAGCG TTCGGCTTTT chrVII:115335-115723 + 14 8.67e-10 ACTCATCCTT GTTAGCTCAGTTGGTAGAGCG TTCGGCTTTT chrXIV:374666-375109 + 37 2.91e-09 AATAAGCGGA CTTAGCTCAGTTGGGAGAGCG CCAGACTGAA chrIV:433523-435102 - 49 3.63e-09 CAGAAGCTTC TATGGCCAAGTTGGTAAGGCG CCACACTAGT chrIV:1150709-1151178 - 23 4.04e-09 TTTCAGTCCC AGTGGCCGAGTGGTTAAGGCG ATGCCTGCTA chrVIII:237117-238708 - 52 6.78e-09 AGTAAGCGGA TTTAGCTCAGTTGGGAGAGCG CCAGACTGAA chrVIII:358264-358784 - 70 6.78e-09 AGTAAGCGGA TTTAGCTCAGTTGGGAGAGCG CCAGACTGAA chrVII:700124-701262 + 37 1.31e-08 GAATTGGTAC TCTGGCCGAGTGGTCTAAGGC GTCAGGTCGA chrXVI:856739-857125 + 25 1.85e-08 GATTCGGGCG TGTGGCGTAGTCGGTAGCGCG CTCCCTTAGC chrXI:219624-220126 + 75 1.85e-08 AAATAGGGCG TGTGGCGTAGTCGGTAGCGCG CTCCC chrVII:205324-205817 + 6 2.58e-08 GGTTG TTTGGCCGAGCGGTCTAAGGC GCCTGATTCA chrVII:823346-823722 + 3 3.80e-08 TT CGTGGTCTAGTCGGTTATGGC ATCTGCTTAA chrX:378232-378332 + 12 3.80e-08 TAATAGGTTT CGTGGTCTAGTCGGTTATGGC ATCTGCTTAA chrIV:1201526-1202031 + 27 4.09e-08 AAATAGCCTT GTTGGCGCAATCGGTAGCGCG TATGACTCTT chrV:492199-492556 - 72 4.74e-08 CTATTCCT CGTGGCCCAATGGTCACGGCG TCTGGCTACG chrX:233667-233767 + 47 4.74e-08 TCTTGTTCCT CGTGGCCCAATGGTCACGGCG TCTGGCTACG chrX:354028-354128 + 51 6.72e-08 TATCACTCTC GGTAGCCAAGTTGGTTTAAGG CGCAAGACTG chrVI:167193-167701 + 45 6.72e-08 AATGACTCTC GGTAGCCAAGTTGGTTTAAGG CGCAAGACTG chrX:390827-390927 - 26 9.96e-08 ATAGTGCTTC AGTAGCTCAGTAGGAAGAGCG TCAGTCTCAT chrX:422688-422788 + 36 9.96e-08 TGTATGCTTC AGTAGCTCAGTAGGAAGAGCG TCAGTCTCAT chrX:745104-745204 + 75 2.34e-07 GTAGGGTAAT GGTAGTGGAGTTGGATATGGG TAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrXIV:602059-602588 2.4e-12 43_[+2]_36 chrV:550829-551781 2.4e-12 77_[-2]_2 chrXII:734623-734985 2.4e-12 52_[+2]_27 chrXV:228090-228645 4.3e-10 18_[+2]_61 chrIII:127493-127893 4.3e-10 77_[+2]_2 chrVII:730959-731422 4.3e-10 1_[+2]_78 chrXII:592308-592821 5e-10 79_[-2] chrXII:167704-168238 5.7e-10 78_[-2]_1 chrX:424275-424375 7.5e-10 46_[-2]_33 chrXII:962805-963332 7.5e-10 11_[-2]_68 chrXI:578631-579391 8.7e-10 8_[+2]_71 chrVII:115335-115723 8.7e-10 13_[+2]_66 chrXIV:374666-375109 2.9e-09 36_[+2]_43 chrIV:433523-435102 3.6e-09 48_[-2]_31 chrIV:1150709-1151178 4e-09 22_[-2]_57 chrVIII:237117-238708 6.8e-09 51_[-2]_28 chrVIII:358264-358784 6.8e-09 69_[-2]_10 chrVII:700124-701262 1.3e-08 36_[+2]_43 chrXVI:856739-857125 1.9e-08 24_[+2]_55 chrXI:219624-220126 1.9e-08 74_[+2]_5 chrVII:205324-205817 2.6e-08 5_[+2]_74 chrVII:823346-823722 3.8e-08 2_[+2]_77 chrX:378232-378332 3.8e-08 11_[+2]_68 chrIV:1201526-1202031 4.1e-08 26_[+2]_53 chrV:492199-492556 4.7e-08 71_[-2]_8 chrX:233667-233767 4.7e-08 46_[+2]_33 chrX:354028-354128 6.7e-08 50_[+2]_29 chrVI:167193-167701 6.7e-08 44_[+2]_35 chrX:390827-390927 1e-07 25_[-2]_54 chrX:422688-422788 1e-07 35_[+2]_44 chrX:745104-745204 2.3e-07 74_[+2]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF BKTGGCCSAGTKGGTWRAGSS width=21 seqs=31 chrXIV:602059-602588 ( 44) CTTGGCCCAGTTGGTTAAGGC 1 chrV:550829-551781 ( 78) CTTGGCCCAGTTGGTTAAGGC 1 chrXII:734623-734985 ( 53) CTTGGCCCAGTTGGTTAAGGC 1 chrXV:228090-228645 ( 19) CATGGCCAAGTTGGTTAAGGC 1 chrIII:127493-127893 ( 78) CATGGCCAAGTTGGTTAAGGC 1 chrVII:730959-731422 ( 2) CATGGCCAAGTTGGTTAAGGC 1 chrXII:592308-592821 ( 80) TTTGGCCGAGTGGTTTAAGGC 1 chrXII:167704-168238 ( 79) CTTGGCCGAGTGGTTAAGGCG 1 chrX:424275-424375 ( 47) GTTGGCCGAGTGGTCTAAGGC 1 chrXII:962805-963332 ( 12) GTTGGCCGAGTGGTCTAAGGC 1 chrXI:578631-579391 ( 9) GTTAGCTCAGTTGGTAGAGCG 1 chrVII:115335-115723 ( 14) GTTAGCTCAGTTGGTAGAGCG 1 chrXIV:374666-375109 ( 37) CTTAGCTCAGTTGGGAGAGCG 1 chrIV:433523-435102 ( 49) TATGGCCAAGTTGGTAAGGCG 1 chrIV:1150709-1151178 ( 23) AGTGGCCGAGTGGTTAAGGCG 1 chrVIII:237117-238708 ( 52) TTTAGCTCAGTTGGGAGAGCG 1 chrVIII:358264-358784 ( 70) TTTAGCTCAGTTGGGAGAGCG 1 chrVII:700124-701262 ( 37) TCTGGCCGAGTGGTCTAAGGC 1 chrXVI:856739-857125 ( 25) TGTGGCGTAGTCGGTAGCGCG 1 chrXI:219624-220126 ( 75) TGTGGCGTAGTCGGTAGCGCG 1 chrVII:205324-205817 ( 6) TTTGGCCGAGCGGTCTAAGGC 1 chrVII:823346-823722 ( 3) CGTGGTCTAGTCGGTTATGGC 1 chrX:378232-378332 ( 12) CGTGGTCTAGTCGGTTATGGC 1 chrIV:1201526-1202031 ( 27) GTTGGCGCAATCGGTAGCGCG 1 chrV:492199-492556 ( 72) CGTGGCCCAATGGTCACGGCG 1 chrX:233667-233767 ( 47) CGTGGCCCAATGGTCACGGCG 1 chrX:354028-354128 ( 51) GGTAGCCAAGTTGGTTTAAGG 1 chrVI:167193-167701 ( 45) GGTAGCCAAGTTGGTTTAAGG 1 chrX:390827-390927 ( 26) AGTAGCTCAGTAGGAAGAGCG 1 chrX:422688-422788 ( 36) AGTAGCTCAGTAGGAAGAGCG 1 chrX:745104-745204 ( 75) GGTAGTGGAGTTGGATATGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 48000 bayes= 10.5588 E= 1.3e-063 -165 98 39 -23 -123 -260 98 57 -1160 -1160 -1160 172 9 -1160 179 -1160 -1160 -1160 235 -1160 -1160 220 -1160 -165 -1160 172 -61 -43 -65 109 39 -123 172 -1160 -1160 -1160 -165 -1160 220 -1160 -1160 -260 -1160 167 -223 -28 56 67 -1160 -1160 235 -1160 -1160 -1160 185 -6 -165 -2 -102 101 67 -1160 -1160 76 85 -160 72 -223 109 -102 -28 -165 -223 -1160 225 -1160 -1160 130 139 -1160 -1160 109 156 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 1.3e-063 0.096774 0.387097 0.258065 0.258065 0.129032 0.032258 0.387097 0.451613 0.000000 0.000000 0.000000 1.000000 0.322581 0.000000 0.677419 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.903226 0.000000 0.096774 0.000000 0.645161 0.129032 0.225806 0.193548 0.419355 0.258065 0.129032 1.000000 0.000000 0.000000 0.000000 0.096774 0.000000 0.903226 0.000000 0.000000 0.032258 0.000000 0.967742 0.064516 0.161290 0.290323 0.483871 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.709677 0.290323 0.096774 0.193548 0.096774 0.612903 0.483871 0.000000 0.000000 0.516129 0.548387 0.064516 0.322581 0.064516 0.645161 0.096774 0.161290 0.096774 0.064516 0.000000 0.935484 0.000000 0.000000 0.483871 0.516129 0.000000 0.000000 0.419355 0.580645 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BKTGGCCSAGTKGGTWRAGSS MEME-2 regular expression -------------------------------------------------------------------------------- [CGT][TG]T[GA]GC[CT][CG]AGT[TG]G[GT]T[TA][AG]AG[GC][GC] -------------------------------------------------------------------------------- Time 674.07 secs. ******************************************************************************** ******************************************************************************** MOTIF RAWGTGATARCCRYTACACTATAKSRSM MEME-3 width = 28 sites = 11 llr = 281 E-value = 3.2e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 Description -------------------------------------------------------------------------------- Simplified A 5a51::a:a5::5:18:a::a:911615 pos.-specific C 1:1:21::::8a:4:29:a::::25:55 probability G 4::9:9:2:5::51:::::1:3:3444: matrix T ::5:8::8::2::59:1::9:715:::: bits 2.3 * * 2.1 * * 1.9 * * * * * 1.6 * * ** * ** *** * Relative 1.4 * * ** * ** ***** Entropy 1.2 * ****** ** ******* * (36.8 bits) 0.9 * ********** ********* **** 0.7 ** ******************** **** 0.5 *********************** **** 0.2 **************************** 0.0 ---------------------------- Multilevel AAAGTGATAACCATTACACTATATCACA consensus G T G GC G GGGGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------------------- chrXVI:209956-210497 + 60 1.14e-14 GTGAAAGCGT GATGTGATAGCCGTTACACTATATCGGA CAATAATTGG chrXI:140704-141487 + 17 1.14e-14 GTGAAAGCGT GATGTGATAGCCGTTACACTATATCGGA TTACAAAGGA chrII:644965-645428 - 21 1.14e-14 GTGAAAGCGT GATGTGATAGCCGTTACACTATATCGGA TAATAACTCA chrXIII:290473-291175 - 27 1.14e-14 GTGAAAGCGT GATGTGATAGCCGTTACACTATATCGGA TTATATTTCA chrXII:448503-448983 + 1 1.87e-14 . AAAGTGATAACCACTACACTATAGGACC GGAACTTCTT chrIV:802549-802986 + 58 1.87e-14 ATCAAAACCG AAAGTGATAACCACTACACTATAGGACC GACAATTCAT chrII:350566-351061 - 64 1.56e-12 TCAAAACCG AAAGTGATAACCACTACACTATAAAACC CTTTTATTGA chrIV:1075276-1075755 + 52 7.94e-12 GTGTGAAGGC AACGTGATAGCCGCTACACTATTGGAAC AATATTACGG chrXV:980121-981239 - 58 1.46e-11 GGGATCGCCC AAAGCGAGAATCATTCCACTAGACCACA CGCCCATACA chrXII:92336-92724 - 73 5.78e-11 . AAAGCGAGAATCATACCACTAGACCACA CGCCCTTATT chrXVI:576499-581197 + 50 5.17e-10 TTGCATCATC CATATCATAACCAGTATACGAGATGACC GCAACAACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrXVI:209956-210497 1.1e-14 59_[+3]_13 chrXI:140704-141487 1.1e-14 16_[+3]_56 chrII:644965-645428 1.1e-14 20_[-3]_52 chrXIII:290473-291175 1.1e-14 26_[-3]_46 chrXII:448503-448983 1.9e-14 [+3]_72 chrIV:802549-802986 1.9e-14 57_[+3]_15 chrII:350566-351061 1.6e-12 63_[-3]_9 chrIV:1075276-1075755 7.9e-12 51_[+3]_21 chrXV:980121-981239 1.5e-11 57_[-3]_15 chrXII:92336-92724 5.8e-11 72_[-3] chrXVI:576499-581197 5.2e-10 49_[+3]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAWGTGATARCCRYTACACTATAKSRSM width=28 seqs=11 chrXVI:209956-210497 ( 60) GATGTGATAGCCGTTACACTATATCGGA 1 chrXI:140704-141487 ( 17) GATGTGATAGCCGTTACACTATATCGGA 1 chrII:644965-645428 ( 21) GATGTGATAGCCGTTACACTATATCGGA 1 chrXIII:290473-291175 ( 27) GATGTGATAGCCGTTACACTATATCGGA 1 chrXII:448503-448983 ( 1) AAAGTGATAACCACTACACTATAGGACC 1 chrIV:802549-802986 ( 58) AAAGTGATAACCACTACACTATAGGACC 1 chrII:350566-351061 ( 64) AAAGTGATAACCACTACACTATAAAACC 1 chrIV:1075276-1075755 ( 52) AACGTGATAGCCGCTACACTATTGGAAC 1 chrXV:980121-981239 ( 58) AAAGCGAGAATCATTCCACTAGACCACA 1 chrXII:92336-92724 ( 73) AAAGCGAGAATCATACCACTAGACCACA 1 chrXVI:576499-581197 ( 50) CATATCATAACCAGTATACGAGATGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 43800 bayes= 11.5113 E= 3.2e-025 84 -111 89 -1010 172 -1010 -1010 -1010 58 -111 -1010 58 -174 -1010 221 -1010 -1010 -11 -1010 143 -1010 -111 221 -1010 172 -1010 -1010 -1010 -1010 -1010 -11 143 172 -1010 -1010 -1010 84 -1010 121 -1010 -1010 206 -1010 -74 -1010 235 -1010 -1010 84 -1010 121 -1010 -1010 89 -111 84 -174 -1010 -1010 158 143 -11 -1010 -1010 -1010 221 -1010 -174 172 -1010 -1010 -1010 -1010 235 -1010 -1010 -1010 -1010 -111 158 172 -1010 -1010 -1010 -1010 -1010 47 126 158 -1010 -1010 -174 -174 -11 47 58 -174 147 89 -1010 107 -1010 89 -1010 -174 147 89 -1010 84 121 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 11 E= 3.2e-025 0.545455 0.090909 0.363636 0.000000 1.000000 0.000000 0.000000 0.000000 0.454545 0.090909 0.000000 0.454545 0.090909 0.000000 0.909091 0.000000 0.000000 0.181818 0.000000 0.818182 0.000000 0.090909 0.909091 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.818182 1.000000 0.000000 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 0.000000 0.818182 0.000000 0.181818 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 0.000000 0.363636 0.090909 0.545455 0.090909 0.000000 0.000000 0.909091 0.818182 0.181818 0.000000 0.000000 0.000000 0.909091 0.000000 0.090909 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.909091 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.727273 0.909091 0.000000 0.000000 0.090909 0.090909 0.181818 0.272727 0.454545 0.090909 0.545455 0.363636 0.000000 0.636364 0.000000 0.363636 0.000000 0.090909 0.545455 0.363636 0.000000 0.545455 0.454545 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAWGTGATARCCRYTACACTATAKSRSM MEME-3 regular expression -------------------------------------------------------------------------------- [AG]A[AT]GTGATA[AG]CC[AG][TC]TACACTA[TG]A[TG][CG][AG][CG][AC] -------------------------------------------------------------------------------- Time 991.79 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:266212-266717 1.17e-05 14_[+1(5.87e-10)]_56 chrVIII:134123-134737 2.22e-01 100 chrXIV:662900-663849 1.29e-01 100 chrVI:226352-227320 4.98e-01 100 chrXI:259142-260002 8.06e-01 100 chrI:166177-166632 6.93e-01 100 chrIV:1256749-1257282 6.84e-08 34_[-1(5.03e-12)]_36 chrXVI:810583-811323 1.78e-01 100 chrXIII:572644-573134 2.50e-06 35_[-1(2.36e-10)]_35 chrVII:422886-423593 8.05e-01 100 chrVII:319231-320140 4.88e-01 100 chrXI:382719-384727 9.34e-01 100 chrIV:520692-521169 2.95e-01 100 chrIII:47149-48027 1.90e-01 100 chrXVI:339830-340730 2.09e-01 100 chrIV:915055-916284 3.04e-01 100 chrXI:558655-559477 6.56e-01 100 chrIX:257486-258350 3.63e-01 100 chrXIV:493702-495045 7.92e-01 100 chrIV:769506-770118 5.56e-02 100 chrXII:371157-371336 6.68e-01 100 chrIX:255013-257142 1.23e-01 100 chrII:236491-237450 7.99e-01 100 chrXI:458001-458976 7.45e-01 100 chrXVI:131564-132217 1.45e-01 100 chrVII:328391-329114 3.83e-01 100 chrXV:663439-664113 7.60e-01 100 chrXII:149860-150706 7.99e-01 100 chrVII:798477-800254 1.82e-01 100 chrXV:778571-779498 9.88e-01 100 chrXIII:67416-68056 4.23e-01 100 chrV:117186-118297 8.13e-01 100 chrXVI:559677-560504 8.19e-01 100 chrII:373500-374923 2.45e-01 100 chrIV:555400-556634 4.32e-01 100 chrXV:571651-572142 8.35e-01 100 chrIV:644881-645356 1.67e-01 100 chrXIII:699761-701167 5.45e-01 100 chrVI:190983-191776 8.70e-01 100 chrXII:734623-734985 3.20e-08 52_[+2(2.37e-12)]_27 chrVIII:144059-146457 9.29e-02 18_[-2(6.42e-05)]_61 chrX:540888-540988 7.92e-01 100 chrVII:255175-255768 4.85e-01 100 chrVIII:385229-386507 2.23e-01 100 chrXII:855794-857652 8.30e-01 100 chrXIII:170349-171328 4.54e-01 100 chrXIV:88933-89927 1.00e+00 100 chrXIV:569633-570082 5.78e-08 51_[-1(6.61e-12)]_19 chrII:226982-227351 6.73e-08 18_[+1(4.98e-11)]_52 chrXVI:730880-731346 8.62e-01 100 chrXII:1051920-1052210 1.05e-07 47_[-1(7.56e-12)]_23 chrIV:1401330-1403450 6.46e-01 100 chrXV:493360-494960 1.82e-01 100 chrXIII:168233-169042 9.77e-01 100 chrVII:827108-827262 3.22e-01 100 chrXI:612617-613611 2.55e-01 100 chrX:396551-396651 9.59e-01 100 chrVI:157898-158206 8.39e-01 100 chrXVI:280500-281801 3.14e-01 100 chrV:550829-551781 5.42e-17 21_[-1(1.02e-12)]_26_[-2(2.37e-12)]_\ 2 chrXI:325825-327636 9.10e-01 100 chrXII:818514-819073 9.34e-01 100 chrXII:96117-96278 7.28e-01 100 chrXI:46723-47011 6.04e-01 100 chrV:176895-177513 5.99e-01 100 chrIV:835749-836211 5.86e-01 100 chrVII:110270-110780 8.52e-01 100 chrXIII:290473-291175 1.46e-11 26_[-3(1.14e-14)]_46 chrXIII:886991-889448 3.77e-01 100 chrII:591613-591803 9.12e-01 100 chrXII:514045-514814 6.88e-01 100 chrVII:938938-939754 9.96e-01 100 chrXI:107118-109033 2.14e-01 100 chrII:87915-88591 3.37e-01 100 chrXII:975749-976162 2.43e-06 69_[-1(1.54e-10)]_1 chrII:739864-741150 1.76e-01 100 chrV:222646-225261 5.07e-01 100 chrXII:374212-374675 3.70e-07 12_[+1(1.46e-11)]_58 chrIV:980666-981150 9.39e-02 43_[-3(4.15e-05)]_29 chrXII:214635-215058 6.43e-01 100 chrVII:115335-115723 3.79e-07 13_[+2(8.67e-10)]_28_[-1(9.84e-05)]_\ 8 chrXVI:435270-436210 1.91e-01 100 chrV:483311-484211 1.52e-01 100 chrXIV:568062-568613 4.40e-01 100 chrVII:774124-774780 2.58e-01 100 chrXII:369635-370295 7.93e-01 100 chrII:59525-61218 7.02e-01 100 chrXII:919374-924458 5.83e-01 100 chrXV:896736-898286 1.06e-01 100 chrVII:1059022-1059634 7.12e-01 100 chrVI:167193-167701 1.88e-04 44_[+2(6.72e-08)]_35 chrIII:48228-48444 2.76e-01 100 chrXV:980121-981239 1.49e-08 57_[-3(1.46e-11)]_15 chrVII:738883-739633 3.19e-01 100 chrXV:79757-80088 5.75e-01 100 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50_[+2(6.72e-08)]_29 chrVII:823346-823722 1.21e-10 2_[+2(3.80e-08)]_26_[+1(5.81e-09)]_\ 21 chrXII:592308-592821 3.49e-07 79_[-2(4.97e-10)] chrIII:122731-123823 2.90e-01 100 chrIV:992727-993517 6.74e-01 100 chrVIII:173416-175401 7.45e-01 100 chrIV:1301555-1302541 6.02e-01 100 chrX:374178-374278 7.69e-09 3_[-2(6.95e-05)]_7_[-1(2.91e-10)]_\ 39 chrXIV:104590-105582 3.12e-01 100 chrII:350566-351061 5.20e-10 63_[-3(1.56e-12)]_9 chrXV:841448-842245 9.83e-01 100 chrXIV:229059-230759 9.01e-01 100 chrXII:97087-97521 6.14e-01 100 chrXI:109206-110648 3.38e-02 100 chrXV:722863-724730 7.53e-01 100 chrVII:779409-779952 8.84e-05 35_[+1(2.20e-08)]_35 chrIV:410176-410804 2.26e-01 100 chrXII:47326-49526 8.17e-01 100 chrIII:127493-127893 6.12e-06 77_[+2(4.30e-10)]_2 chrV:462535-462871 1.42e-02 100 chrXVI:209956-210497 1.90e-18 7_[-1(2.13e-11)]_22_[+3(1.14e-14)]_\ 13 chrV:354674-355388 1.28e-08 2_[+1(2.73e-11)]_68 chrXII:713152-713580 9.15e-01 100 chrXIII:353864-354657 4.23e-01 100 chrXV:779775-781460 3.99e-01 100 chrVII:700124-701262 1.98e-05 36_[+2(1.31e-08)]_43 chrXI:39436-39871 8.68e-01 100 chrXI:551562-552836 7.72e-01 100 chrV:302761-303419 4.73e-01 100 chrVIII:475490-475900 2.25e-04 52_[-1(4.55e-08)]_18 chrXVI:642013-643379 1.09e-01 100 chrXIV:784062-784316 1.90e-01 100 chrX:204550-204650 1.40e-08 14_[+1(7.46e-13)]_56 chrXII:669185-669636 9.02e-01 100 chrXIV:413548-417309 9.05e-01 100 chrIV:339695-341719 8.12e-01 100 chrXIV:87729-88738 5.76e-01 100 chrII:332309-334147 6.49e-01 100 chrXIV:518055-519137 2.34e-01 100 chrXVI:404500-407801 5.05e-01 100 chrXV:254228-254718 7.59e-01 100 chrIV:229609-231868 5.50e-01 100 chrXIII:277486-279777 6.89e-01 100 chrV:192256-192652 6.61e-01 100 chrIV:768289-769123 5.01e-01 100 chrXV:110128-110673 8.13e-01 100 chrIV:1269896-1271065 5.86e-02 23_[+2(2.15e-05)]_56 chrV:269051-270237 9.65e-01 100 chrIV:308057-310216 9.46e-01 100 chrXVI:378694-378946 4.62e-01 100 chrV:305827-307754 5.61e-01 100 chrXVI:449315-450326 3.52e-01 100 chrXII:92336-92724 3.42e-08 72_[-3(5.78e-11)] chrXV:228090-228645 2.19e-13 18_[+2(4.30e-10)]_26_[+1(4.98e-11)]_\ 5 chrVII:610452-611497 4.14e-02 34_[+1(7.94e-05)]_36 chrIV:1175750-1176099 1.06e-04 5_[+1(7.95e-09)]_65 chrXII:282813-284042 1.05e-01 62_[-2(7.52e-05)]_17 chrXIII:258834-259372 9.06e-01 100 chrXV:978878-979345 3.50e-01 100 chrX:122157-122257 5.47e-01 100 chrXV:31089-31757 3.31e-01 100 chrVII:531389-532538 2.44e-01 100 chrIV:1241208-1242132 5.56e-01 100 chrXI:69701-70296 1.33e-01 100 chrIV:1236426-1238608 3.33e-01 100 chrVII:599356-601411 4.28e-01 100 chrXVI:153657-154458 7.20e-01 100 chrXIII:320942-321316 2.08e-06 59_[-1(4.82e-10)]_11 chrXV:899802-901242 2.78e-01 100 chrXII:707913-710139 6.02e-01 100 chrXIII:625835-627296 4.00e-01 100 chrVIII:237117-238708 1.43e-05 51_[-2(6.78e-09)]_28 chrVI:180640-181232 8.97e-01 100 chrV:438263-438988 6.18e-01 100 chrII:614460-614996 3.75e-01 100 chrVIII:62473-63084 4.96e-02 100 chrXII:764373-764595 4.10e-01 100 chrXIII:352082-353541 2.36e-01 100 chrIV:802549-802986 5.72e-18 5_[-1(9.47e-10)]_22_[+3(1.87e-14)]_\ 15 chrIV:1461449-1461837 4.93e-01 100 chrVIII:505871-506171 5.25e-01 100 chrVI:53222-54797 2.82e-01 100 chrXII:951040-953803 8.88e-03 68_[+3(8.32e-06)]_4 chrXII:1012441-1013301 9.98e-01 100 chrXIII:667238-668157 2.34e-01 100 chrVI:63987-65346 6.96e-01 100 chrVII:824063-826895 7.41e-01 100 chrIV:1268558-1269442 4.06e-01 100 chrIX:68636-69567 7.81e-01 100 chrXIII:287858-289998 4.69e-01 100 chrV:492199-492556 5.39e-10 16_[-1(2.33e-09)]_25_[-2(4.74e-08)]_\ 8 chrVIII:296963-297149 3.22e-01 100 chrXVI:432499-434396 8.32e-01 100 chrXII:167704-168238 1.37e-13 14_[-1(4.98e-11)]_34_[-2(5.73e-10)]_\ 1 chrII:347412-347950 1.17e-03 33_[+1(1.89e-07)]_37 chrIII:150961-151506 3.39e-01 100 chrIV:1449813-1451101 8.70e-01 100 chrIX:25038-25285 5.24e-01 100 chrX:523497-523597 9.98e-01 100 chrXVI:75270-77315 2.25e-02 13_[-3(4.23e-05)]_59 chrXV:881287-882142 5.12e-01 100 chrI:182223-183146 4.02e-01 100 chrXIII:161502-162693 7.39e-01 100 chrIX:83320-84878 9.50e-02 100 chrXIV:498788-500754 8.85e-01 100 chrV:396703-398071 2.45e-02 12_[-3(9.69e-05)]_60 chrIX:197322-197731 6.51e-01 100 chrV:322107-323347 5.53e-01 100 chrIV:927529-930345 5.22e-01 100 chrVI:224296-225116 8.95e-01 100 chrII:306278-307327 7.98e-01 100 chrV:85162-87457 8.03e-01 100 chrXII:281923-282482 2.77e-01 100 chrXVI:678496-678779 3.27e-01 100 chrXII:826879-827872 1.66e-01 100 chrVII:185373-185890 6.54e-01 100 chrIX:315994-316564 8.95e-01 100 chrI:181137-181490 3.64e-01 100 chrIII:851-1025 2.89e-01 100 chrX:90647-90747 9.95e-01 100 chrIV:1165529-1166440 2.83e-01 100 chrXII:368635-369451 9.53e-03 39_[+3(4.41e-05)]_33 chrXV:909301-911619 2.38e-01 100 chrX:59016-59116 7.69e-01 100 chrXII:448503-448983 3.24e-12 [+3(1.87e-14)]_72 chrVII:478969-482849 9.27e-01 100 chrII:478941-479554 5.87e-01 100 chrXIV:187069-187556 9.65e-01 100 chrXIV:282093-283814 4.92e-01 100 chrIV:884272-885407 5.56e-01 100 chrXIV:585498-586845 9.76e-01 100 chrXIII:499032-500777 2.07e-01 100 chrX:453345-453445 2.38e-01 100 chrIII:163508-163845 9.17e-01 100 chrIV:1162035-1164671 7.80e-01 100 chrVIII:54905-56049 5.38e-01 100 chrVI:225465-225989 8.04e-01 100 chrXIII:220035-220947 9.76e-01 100 chrXVI:133004-135464 1.97e-01 100 chrXII:636689-640196 1.98e-01 100 chrXV:407545-408232 7.03e-01 100 chrII:556247-558465 4.99e-01 100 chrXI:578631-579391 3.79e-07 8_[+2(8.67e-10)]_28_[-1(9.84e-05)]_\ 13 chrIV:568702-569372 8.03e-08 26_[+1(6.61e-12)]_44 chrV:165703-167652 8.86e-02 100 chrII:162967-164060 5.59e-01 100 chrXIV:241457-241993 7.64e-01 100 chrVII:970717-973999 4.86e-01 100 chrXIII:627525-627839 3.21e-01 100 chrXII:1028799-1030303 3.01e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************