******************************************************************************** XSTREME - Motif Discovery and Enrichment Analysis ******************************************************************************** MEME version 5.4.0 (Mon Aug 16 16:18:19 2021 -0700) 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: Charles E. Grant and Timothy L. Bailey, "XSTREME: comprehensive motif analysis of biological sequence datasets", BioRxiv, 2021. ******************************************************************************** ALPHABET "DNA with covalent modifications" DNA-LIKE A "Adenine" 8510A8 ~ T "Thymine" A89610 C "Cytosine" A50026 ~ G "Guanine" 313695 c "5-Carboxylcytosine" FEE090 ~ 4 "Guanine:5-Carboxylcytosine" E0F3F8 f "5-Formylcytosine" FDAE61 ~ 3 "Guanine:5-Formylcytosine" ABD9E9 h "5-Hydroxymethylcytosine" F46D43 ~ 2 "Guanine:5-Hydroxymethylcytosine" 74ADD1 m "5-Methylcytosine" D73027 ~ 1 "Guanine:5-Methylcytosine" 4575B4 ? = ACGTcfhm1234 z = Ccfhm 9 = G1234 N = ACGT V = ACG H = ACT D = AGT B = CGT y = Ccf 8 = G34 M = AC R = AG W = AT S = CG Y = CT K = GT x = hm 7 = 12 END ALPHABET strands: + - Background letter frequencies (from file `results/xstreme4/dna_with_covalent.bg'): A 0.20700 C 0.27130 G 0.27130 T 0.20700 c 0.00000 f 0.00000 h 0.00024 m 0.02146 1 0.02146 2 0.00024 3 0.00000 4 0.00000 MOTIF 1-Sm1BCMWS STREME-1 letter-probability matrix: alength= 12 w= 8 nsites= 1148 E= 2.8e-031 0.187890 0.389197 0.223252 0.157967 0.000000 0.000000 0.000000 0.000003 0.041691 0.000000 0.000000 0.000000 0.000030 0.000039 0.000039 0.000030 0.000000 0.000000 0.000000 0.999860 0.000003 0.000000 0.000000 0.000000 0.000030 0.000039 0.000039 0.000030 0.000000 0.000000 0.000000 0.000003 0.999860 0.000000 0.000000 0.000000 0.101752 0.309668 0.385436 0.203137 0.000000 0.000000 0.000000 0.000003 0.000003 0.000000 0.000000 0.000000 0.164107 0.554160 0.212790 0.068937 0.000000 0.000000 0.000000 0.000003 0.000003 0.000000 0.000000 0.000000 0.414204 0.375006 0.016936 0.193848 0.000000 0.000000 0.000000 0.000003 0.000003 0.000000 0.000000 0.000000 0.411990 0.090206 0.193898 0.303899 0.000000 0.000000 0.000000 0.000003 0.000003 0.000000 0.000000 0.000000 0.114201 0.364815 0.388962 0.095300 0.000000 0.000000 0.000000 0.036720 0.000003 0.000000 0.000000 0.000000 MOTIF 2-KCWGCWGM STREME-2 letter-probability matrix: alength= 12 w= 8 nsites= 1171 E= 1.5e-017 0.056738 0.211426 0.429815 0.300472 0.000000 0.000000 0.000000 0.001544 0.000005 0.000000 0.000000 0.000000 0.060541 0.762924 0.171863 0.000046 0.000000 0.000000 0.000000 0.000005 0.000005 0.004617 0.000000 0.000000 0.403301 0.000060 0.000060 0.596569 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000046 0.052159 0.946970 0.000815 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000815 0.946970 0.052159 0.000046 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.596569 0.000060 0.000060 0.403301 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000046 0.171863 0.762924 0.060541 0.000000 0.000000 0.004617 0.000005 0.000005 0.000000 0.000000 0.000000 0.300472 0.429815 0.211426 0.056738 0.000000 0.000000 0.000000 0.000005 0.001544 0.000000 0.000000 0.000000 MOTIF Gm7GCA TGCx1C letter-probability matrix: alength= 12 w= 6 nsites= 357 E= 2.95e-090 0.000103 0.000136 0.999636 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.000136 0.000136 0.000103 0.000000 0.000000 0.000000 0.999511 0.000011 0.000000 0.000000 0.000000 0.000103 0.000136 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.499761 0.499750 0.000000 0.000000 0.000103 0.000136 0.999636 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.999604 0.000136 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 MOTIF GCAm7C Gx1TGC letter-probability matrix: alength= 12 w= 6 nsites= 325 E= 6.98e-083 0.000103 0.000136 0.999636 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.999604 0.000136 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.000136 0.000136 0.000103 0.000000 0.000000 0.000000 0.999511 0.000011 0.000000 0.000000 0.000000 0.000103 0.000136 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.499761 0.499750 0.000000 0.000000 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 MOTIF MA0079.2 SP1 letter-probability matrix: alength= 12 w= 10 nsites= 1363 E= 1.68e-031 0.000059 0.914102 0.028640 0.057186 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.000059 0.856976 0.028640 0.114312 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.000059 0.999792 0.000077 0.000059 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.114312 0.771285 0.000077 0.114312 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.057186 0.142894 0.428526 0.371382 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.000059 0.799849 0.028640 0.171439 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.028622 0.885539 0.000077 0.085749 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.000059 0.685596 0.085767 0.228565 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.171439 0.714159 0.000077 0.114312 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 0.085749 0.742723 0.085767 0.085749 0.000000 0.000000 0.000000 0.000006 0.000006 0.000000 0.000000 0.000000 URL http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?ID=MA0079.2&rm=present&collection=CORE MOTIF MA0091.1 TAL1::TCF3 letter-probability matrix: alength= 12 w= 12 nsites= 238 E= 5.61e-027 0.295435 0.318171 0.181838 0.204546 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.204546 0.227283 0.454504 0.113657 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.886209 0.000062 0.068228 0.045492 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.454489 0.545393 0.000062 0.000047 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000047 0.977113 0.022784 0.000047 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.999820 0.000062 0.000062 0.000047 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000047 0.022784 0.250005 0.727155 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.272712 0.727169 0.000062 0.000047 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000047 0.000062 0.000062 0.999820 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000047 0.000062 0.977113 0.022769 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.000047 0.068228 0.454503 0.477212 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 0.090935 0.090950 0.045506 0.772598 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000 URL http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?ID=MA0091.1&rm=present&collection=CORE MOTIF MA0140.1 Tal1::Gata1 letter-probability matrix: alength= 12 w= 18 nsites= 943 E= 1.51e-011 0.135962 0.451733 0.210061 0.202243 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.088715 0.150918 0.176751 0.583615 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.044498 0.061822 0.652513 0.241168 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.089983 0.253311 0.416978 0.239728 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.227165 0.215620 0.263158 0.294057 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.238031 0.233277 0.306621 0.222071 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.225390 0.252885 0.318398 0.203327 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.241941 0.237190 0.302341 0.218527 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.248898 0.224483 0.292302 0.234317 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.338086 0.138153 0.319077 0.204684 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.178947 0.397963 0.305942 0.117148 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.664742 0.010520 0.012556 0.312182 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.001019 0.002377 0.996604 0.000001 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.993550 0.002376 0.000680 0.003394 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.005434 0.008830 0.010188 0.975548 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.941214 0.002040 0.007816 0.048931 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.809376 0.017330 0.127761 0.045532 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.186054 0.187075 0.544557 0.082313 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 URL http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?ID=MA0140.1&rm=present&collection=CORE MOTIF CCTTCC GGAAGG letter-probability matrix: alength= 12 w= 6 nsites= 127 E= 6.55e-004 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.000136 0.000136 0.999604 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.000136 0.000136 0.999604 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 0.000103 0.999636 0.000136 0.000103 0.000000 0.000000 0.000000 0.000011 0.000011 0.000000 0.000000 0.000000 MOTIF MA0270.1 AFT2 letter-probability matrix: alength= 12 w= 8 nsites= 36 E= 7.66e-004 0.080013 0.449982 0.270000 0.200001 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.699951 0.000027 0.299997 0.000021 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.000021 0.999927 0.000027 0.000021 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.999921 0.000027 0.000027 0.000021 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.000021 0.999927 0.000027 0.000021 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.000021 0.999927 0.000027 0.000021 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.000021 0.999927 0.000027 0.000021 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 0.090921 0.424227 0.272727 0.212121 0.000000 0.000000 0.000000 0.000002 0.000002 0.000000 0.000000 0.000000 URL http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?ID=MA0270.1&rm=present&collection=CORE