One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)																		; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; atGATTGCACAACwy ; Alignment reference a 1049 667 145 2154 1 1 73 7 2557 96 2699 2698 42 1156 679 c 475 241 158 56 4 1 6 2710 51 2532 26 10 2218 617 807 g 582 485 2173 474 4 10 2440 2 31 16 2 11 95 167 542 t 622 1335 252 44 2719 2716 209 9 89 84 1 9 373 788 700
MA0102.3_shift3 (CEBPA)		0.936	0.687	9.841	0.673	0.942	0.820	0.963	2	10	9	10	2	4	2	5.571	1	; oligos_6nt_mkv4_m5 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 5.5714; ---aTTGCAyAAym- ; cor=0.936; Ncor=0.687; logoDP=9.841; NIcor=0.673; NsEucl=0.942; SSD=0.820; NSW=0.963; rcor=2; rNcor=10; rlogoDP=9; rNIcor=10; rNsEucl=2; rSSD=4; rNSW=2; rank_mean=5.571; match_rank=1 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift2 (CEBPB)		0.887	0.650	9.684	0.629	0.923	1.445	0.934	8	23	14	18	10	20	13	15.143	4	; oligos_6nt_mkv4_m5 versus MA0466.1 (CEBPB); m=2/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score=15.1429; --kATTGCAymAy-- ; cor=0.887; Ncor=0.650; logoDP=9.684; NIcor=0.629; NsEucl=0.923; SSD=1.445; NSW=0.934; rcor=8; rNcor=23; rlogoDP=14; rNIcor=18; rNsEucl=10; rSSD=20; rNSW=13; rank_mean=15.143; match_rank=4 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0133.1_shift8 (BRCA1)		0.871	0.406	3.107	0.410	0.910	0.791	0.943	17	113	75	58	33	2	6	43.429	34	; oligos_6nt_mkv4_m5 versus MA0133.1 (BRCA1); m=3/5; ncol2=7; w=7; offset=8; strand=D; shift=8; score=43.4286; --------mCAAcms ; cor=0.871; Ncor=0.406; logoDP=3.107; NIcor=0.410; NsEucl=0.910; SSD=0.791; NSW=0.943; rcor=17; rNcor=113; rlogoDP=75; rNIcor=58; rNsEucl=33; rSSD=2; rNSW=6; rank_mean=43.429; match_rank=34 a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0102.2_rc_shift3 (CEBPA_rc)		0.843	0.506	2.640	0.048	0.895	1.771	0.902	34	81	85	86	78	42	56	66.000	68	; oligos_6nt_mkv4_m5 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=3; strand=R; shift=3; score= 66; ---rTTGcrmaA--- ; cor=0.843; Ncor=0.506; logoDP=2.640; NIcor=0.048; NsEucl=0.895; SSD=1.771; NSW=0.902; rcor=34; rNcor=81; rlogoDP=85; rNIcor=86; rNsEucl=78; rSSD=42; rNSW=56; rank_mean=66.000; match_rank=68 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.802	0.641	0.297	-0.164	0.910	2.328	0.903	74	29	113	108	35	85	53	71.000	79	; oligos_6nt_mkv4_m5 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score= 71; vrbrTTGcrmaA--- ; cor=0.802; Ncor=0.641; logoDP=0.297; NIcor=-0.164; NsEucl=0.910; SSD=2.328; NSW=0.903; rcor=74; rNcor=29; rlogoDP=113; rNIcor=108; rNsEucl=35; rSSD=85; rNSW=53; rank_mean=71.000; match_rank=79 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 7 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)																		; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -wkATTGCACAATcwy ; Alignment reference a 0 881 596 2604 4 6 132 4 2769 41 2931 2943 37 506 1027 722 c 0 545 555 127 12 0 10 2960 44 2728 35 5 195 1897 703 784 g 0 620 810 181 8 12 2652 3 37 10 2 12 67 243 299 499 t 0 926 1011 60 2948 2954 178 5 122 193 4 12 2673 326 943 967
MA0102.3_shift3 (CEBPA)		0.935	0.685	9.923	0.674	0.939	0.907	0.959	3	11	5	9	4	7	4	6.143	2	; oligos_7nt_mkv5_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 6.1429; ---aTTGCAyAAym-- ; cor=0.935; Ncor=0.685; logoDP=9.923; NIcor=0.674; NsEucl=0.939; SSD=0.907; NSW=0.959; rcor=3; rNcor=11; rlogoDP=5; rNIcor=9; rNsEucl=4; rSSD=7; rNSW=4; rank_mean=6.143; match_rank=2 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift2 (CEBPB)		0.934	0.685	9.857	0.677	0.940	0.865	0.961	4	12	8	8	3	6	3	6.286	3	; oligos_7nt_mkv5_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 6.2857; --kATTGCAymAy--- ; cor=0.934; Ncor=0.685; logoDP=9.857; NIcor=0.677; NsEucl=0.940; SSD=0.865; NSW=0.961; rcor=4; rNcor=12; rlogoDP=8; rNIcor=8; rNsEucl=3; rSSD=6; rNSW=3; rank_mean=6.286; match_rank=3 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.1_shift4 (Cebpa)		0.797	0.637	6.191	0.620	0.910	2.314	0.904	78	30	53	21	32	83	51	49.714	44	; oligos_7nt_mkv5_m1 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=12; offset=3; strand=D; shift=4; score=49.7143; ----TtkygCAAyvyb ; cor=0.797; Ncor=0.637; logoDP=6.191; NIcor=0.620; NsEucl=0.910; SSD=2.314; NSW=0.904; rcor=78; rNcor=30; rlogoDP=53; rNIcor=21; rNsEucl=32; rSSD=83; rNSW=51; rank_mean=49.714; match_rank=44 a 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0078.1_rc_shift7 (Sox17_rc)		0.816	0.490	3.080	0.177	0.904	1.499	0.917	57	89	76	67	51	23	35	56.857	55	; oligos_7nt_mkv5_m1 versus MA0078.1_rc (Sox17_rc); m=4/6; ncol2=9; w=9; offset=6; strand=R; shift=7; score=56.8571; -------sACAATrdr ; cor=0.816; Ncor=0.490; logoDP=3.080; NIcor=0.177; NsEucl=0.904; SSD=1.499; NSW=0.917; rcor=57; rNcor=89; rlogoDP=76; rNIcor=67; rNsEucl=51; rSSD=23; rNSW=35; rank_mean=56.857; match_rank=55 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7
MA0102.2_rc_shift3 (CEBPA_rc)		0.838	0.503	2.596	0.048	0.893	1.848	0.897	40	85	88	87	86	51	68	72.143	80	; oligos_7nt_mkv5_m1 versus MA0102.2_rc (CEBPA_rc); m=5/6; ncol2=9; w=9; offset=2; strand=R; shift=3; score=72.1429; ---rTTGcrmaA---- ; cor=0.838; Ncor=0.503; logoDP=2.596; NIcor=0.048; NsEucl=0.893; SSD=1.848; NSW=0.897; rcor=40; rNcor=85; rlogoDP=88; rNIcor=87; rNsEucl=86; rSSD=51; rNSW=68; rank_mean=72.143; match_rank=80 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0
MA0019.1_rc_shift0 (Ddit3::Cebpa_rc)		0.756	0.520	0.428	-0.161	0.896	2.597	0.882	109	77	103	107	72	102	93	94.714	112	; oligos_7nt_mkv5_m1 versus MA0019.1_rc (Ddit3::Cebpa_rc); m=6/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=94.7143; ggkATTGCAyyy---- ; cor=0.756; Ncor=0.520; logoDP=0.428; NIcor=-0.161; NsEucl=0.896; SSD=2.597; NSW=0.882; rcor=109; rNcor=77; rlogoDP=103; rNIcor=107; rNsEucl=72; rSSD=102; rNSW=93; rank_mean=94.714; match_rank=112 a 7 3 3 33 0 0 2 1 38 3 7 6 0 0 0 0 c 6 9 5 0 1 0 0 38 0 15 14 12 0 0 0 0 g 26 23 17 6 2 1 33 0 1 3 7 7 0 0 0 0 t 0 4 14 0 36 38 4 0 0 18 11 14 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m1_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m1_shift0 (oligos_8nt_mkv6_m1)																		; oligos_8nt_mkv6_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; atGGTTGCACAACwh ; Alignment reference a 991 446 177 354 1 2 76 3 2057 59 2210 2207 18 1073 570 c 349 252 30 55 10 0 3 2211 43 2086 12 4 1847 418 624 g 470 340 1759 1769 1 4 2107 4 72 10 1 6 50 136 460 t 414 1186 258 46 2212 2218 38 6 52 69 1 7 309 597 570
MA0102.3_shift3 (CEBPA)		0.882	0.647	9.868	0.623	0.922	1.461	0.934	10	26	6	20	11	21	15	15.571	5	; oligos_8nt_mkv6_m1 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score=15.5714; ---aTTGCAyAAym- ; cor=0.882; Ncor=0.647; logoDP=9.868; NIcor=0.623; NsEucl=0.922; SSD=1.461; NSW=0.934; rcor=10; rNcor=26; rlogoDP=6; rNIcor=20; rNsEucl=11; rSSD=21; rNSW=15; rank_mean=15.571; match_rank=5 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0133.1_shift8 (BRCA1)		0.874	0.408	3.200	0.412	0.910	0.795	0.943	15	112	72	57	36	3	7	43.143	32	; oligos_8nt_mkv6_m1 versus MA0133.1 (BRCA1); m=2/5; ncol2=7; w=7; offset=8; strand=D; shift=8; score=43.1429; --------mCAAcms ; cor=0.874; Ncor=0.408; logoDP=3.200; NIcor=0.412; NsEucl=0.910; SSD=0.795; NSW=0.943; rcor=15; rNcor=112; rlogoDP=72; rNIcor=57; rNsEucl=36; rSSD=3; rNSW=7; rank_mean=43.143; match_rank=32 a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0466.1_shift2 (CEBPB)		0.823	0.604	9.656	0.567	0.904	2.211	0.900	52	45	16	29	50	74	61	46.714	40	; oligos_8nt_mkv6_m1 versus MA0466.1 (CEBPB); m=3/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score=46.7143; --kATTGCAymAy-- ; cor=0.823; Ncor=0.604; logoDP=9.656; NIcor=0.567; NsEucl=0.904; SSD=2.211; NSW=0.900; rcor=52; rNcor=45; rlogoDP=16; rNIcor=29; rNsEucl=50; rSSD=74; rNSW=61; rank_mean=46.714; match_rank=40 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.814	0.488	2.586	0.051	0.887	2.067	0.885	60	90	89	84	100	62	86	81.571	95	; oligos_8nt_mkv6_m1 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=3; strand=R; shift=3; score=81.5714; ---rTTGcrmaA--- ; cor=0.814; Ncor=0.488; logoDP=2.586; NIcor=0.051; NsEucl=0.887; SSD=2.067; NSW=0.885; rcor=60; rNcor=90; rlogoDP=89; rNIcor=84; rNsEucl=100; rSSD=62; rNSW=86; rank_mean=81.571; match_rank=95 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.770	0.616	0.329	-0.164	0.903	2.689	0.888	98	40	110	109	54	109	84	86.286	102	; oligos_8nt_mkv6_m1 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score=86.2857; vrbrTTGcrmaA--- ; cor=0.770; Ncor=0.616; logoDP=0.329; NIcor=-0.164; NsEucl=0.903; SSD=2.689; NSW=0.888; rcor=98; rNcor=40; rlogoDP=110; rNIcor=109; rNsEucl=54; rSSD=109; rNSW=84; rank_mean=86.286; match_rank=102 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m4_shift1 ; 8 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m4_shift1 (oligos_8nt_mkv6_m4)																		; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wrTTACACAATah ; Alignment reference a 0 714 1247 9 3 2479 2 1960 1 2463 2478 125 915 663 c 0 367 375 3 0 0 2486 7 2449 4 2 391 571 645 g 0 555 662 8 10 10 2 516 0 21 8 175 399 404 t 0 862 214 2478 2485 9 8 15 48 10 10 1807 613 786
MA0043.1_shift1 (HLF)		0.859	0.793	6.302	0.770	0.926	1.585	0.934	25	1	44	1	6	27	14	16.857	6	; oligos_8nt_mkv6_m4 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score=16.8571; -krTTACryAAth- ; cor=0.859; Ncor=0.793; logoDP=6.302; NIcor=0.770; NsEucl=0.926; SSD=1.585; NSW=0.934; rcor=25; rNcor=1; rlogoDP=44; rNIcor=1; rNsEucl=6; rSSD=27; rNSW=14; rank_mean=16.857; match_rank=6 a 0 1 6 1 0 13 0 6 0 13 15 2 5 0 c 0 4 0 0 0 1 15 0 9 4 0 3 5 0 g 0 8 12 0 3 2 1 12 0 1 1 1 3 0 t 0 5 0 17 15 2 2 0 9 0 2 12 5 0
MA0102.3_shift2 (CEBPA)		0.809	0.685	9.041	0.680	0.907	2.099	0.905	67	13	26	7	42	63	49	38.143	21	; oligos_8nt_mkv6_m4 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score=38.1429; --aTTGCAyAAym- ; cor=0.809; Ncor=0.685; logoDP=9.041; NIcor=0.680; NsEucl=0.907; SSD=2.099; NSW=0.905; rcor=67; rNcor=13; rlogoDP=26; rNIcor=7; rNsEucl=42; rSSD=63; rNSW=49; rank_mean=38.143; match_rank=21 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0102.1_shift3 (Cebpa)		0.808	0.634	6.273	0.611	0.908	2.063	0.906	69	32	45	22	41	61	47	45.286	35	; oligos_8nt_mkv6_m4 versus MA0102.1 (Cebpa); m=3/7; ncol2=12; w=11; offset=2; strand=D; shift=3; score=45.2857; ---TtkygCAAyvy ; cor=0.808; Ncor=0.634; logoDP=6.273; NIcor=0.611; NsEucl=0.908; SSD=2.063; NSW=0.906; rcor=69; rNcor=32; rlogoDP=45; rNIcor=22; rNsEucl=41; rSSD=61; rNSW=47; rank_mean=45.286; match_rank=35 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0466.1_shift1 (CEBPB)		0.784	0.664	8.817	0.654	0.901	2.375	0.892	85	18	28	14	61	89	76	53.000	47	; oligos_8nt_mkv6_m4 versus MA0466.1 (CEBPB); m=4/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 53; -kATTGCAymAy-- ; cor=0.784; Ncor=0.664; logoDP=8.817; NIcor=0.654; NsEucl=0.901; SSD=2.375; NSW=0.892; rcor=85; rNcor=18; rlogoDP=28; rNIcor=14; rNsEucl=61; rSSD=89; rNSW=76; rank_mean=53.000; match_rank=47 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0078.1_rc_shift6 (Sox17_rc)		0.840	0.480	2.389	0.159	0.903	1.211	0.924	38	95	93	69	56	14	23	55.429	53	; oligos_8nt_mkv6_m4 versus MA0078.1_rc (Sox17_rc); m=5/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score=55.4286; ------sACAATrd ; cor=0.840; Ncor=0.480; logoDP=2.389; NIcor=0.159; NsEucl=0.903; SSD=1.211; NSW=0.924; rcor=38; rNcor=95; rlogoDP=93; rNIcor=69; rNsEucl=56; rSSD=14; rNSW=23; rank_mean=55.429; match_rank=53 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8
MA0102.2_shift3 (CEBPA)		0.818	0.566	6.271	0.538	0.890	1.971	0.890	56	57	46	35	96	56	80	60.857	63	; oligos_8nt_mkv6_m4 versus MA0102.2 (CEBPA); m=6/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score=60.8571; ---TtkygCAAy-- ; cor=0.818; Ncor=0.566; logoDP=6.271; NIcor=0.538; NsEucl=0.890; SSD=1.971; NSW=0.890; rcor=56; rNcor=57; rlogoDP=46; rNIcor=35; rNsEucl=96; rSSD=56; rNSW=80; rank_mean=60.857; match_rank=63 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0
MA0025.1_rc_shift0 (NFIL3_rc)		0.813	0.581	1.794	0.055	0.899	2.027	0.899	62	52	99	83	67	59	63	69.286	76	; oligos_8nt_mkv6_m4 versus MA0025.1_rc (NFIL3_rc); m=7/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score=69.2857; ayrTTACrTAA--- ; cor=0.813; Ncor=0.581; logoDP=1.794; NIcor=0.055; NsEucl=0.899; SSD=2.027; NSW=0.899; rcor=62; rNcor=52; rlogoDP=99; rNIcor=83; rNsEucl=67; rSSD=59; rNSW=63; rank_mean=69.286; match_rank=76 a 10 4 8 0 0 23 0 15 1 21 22 0 0 0 c 3 7 4 1 0 0 21 0 0 2 0 0 0 0 g 5 5 11 0 0 0 0 8 0 0 0 0 0 0 t 5 7 0 22 23 0 2 0 22 0 1 0 0 0

One-to-n matrix alignment; reference matrix: positions_8nt_m1_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m1_shift0 (positions_8nt_m1)																		; positions_8nt_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; amAGATTGCAAAACww ; Alignment reference a 173 182 485 53 502 2 2 12 3 522 456 527 540 8 217 164 c 113 162 5 27 15 3 0 2 544 6 70 25 3 483 124 121 g 134 133 23 442 22 2 2 523 5 15 2 2 7 23 44 128 t 134 77 41 32 15 547 550 17 2 11 26 0 4 40 169 141
MA0102.3_shift4 (CEBPA)		0.888	0.610	9.450	0.600	0.925	1.362	0.938	7	41	20	27	7	16	10	18.286	7	; positions_8nt_m1 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=18.2857; ----aTTGCAyAAym- ; cor=0.888; Ncor=0.610; logoDP=9.450; NIcor=0.600; NsEucl=0.925; SSD=1.362; NSW=0.938; rcor=7; rNcor=41; rlogoDP=20; rNIcor=27; rNsEucl=7; rSSD=16; rNSW=10; rank_mean=18.286; match_rank=7 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift3 (CEBPB)		0.828	0.569	9.334	0.559	0.906	2.130	0.903	48	55	22	30	44	66	52	45.286	36	; positions_8nt_m1 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score=45.2857; ---kATTGCAymAy-- ; cor=0.828; Ncor=0.569; logoDP=9.334; NIcor=0.559; NsEucl=0.906; SSD=2.130; NSW=0.903; rcor=48; rNcor=55; rlogoDP=22; rNIcor=30; rNsEucl=44; rSSD=66; rNSW=52; rank_mean=45.286; match_rank=36 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0102.2_rc_shift4 (CEBPA_rc)		0.861	0.484	3.275	0.135	0.901	1.600	0.911	23	92	70	75	62	29	37	55.429	52	; positions_8nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score=55.4286; ----rTTGcrmaA--- ; cor=0.861; Ncor=0.484; logoDP=3.275; NIcor=0.135; NsEucl=0.901; SSD=1.600; NSW=0.911; rcor=23; rNcor=92; rlogoDP=70; rNIcor=75; rNsEucl=62; rSSD=29; rNSW=37; rank_mean=55.429; match_rank=52 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.833	0.624	0.300	-0.198	0.913	2.201	0.908	44	36	112	113	30	71	43	64.143	66	; positions_8nt_m1 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score=64.1429; -vrbrTTGcrmaA--- ; cor=0.833; Ncor=0.624; logoDP=0.300; NIcor=-0.198; NsEucl=0.913; SSD=2.201; NSW=0.908; rcor=44; rNcor=36; rlogoDP=112; rNIcor=113; rNsEucl=30; rSSD=71; rNSW=43; rank_mean=64.143; match_rank=66 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)																		; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; rmAGATTGCACAACTyt ; Alignment reference a 94 132 262 16 316 0 0 10 2 313 7 332 335 6 35 67 74 c 72 86 4 10 5 0 0 0 332 11 320 3 0 297 15 106 77 g 95 78 9 279 13 1 2 311 1 1 1 1 0 7 2 77 54 t 75 40 61 31 2 335 334 15 1 11 8 0 1 26 284 86 131
MA0102.3_shift4 (CEBPA)		0.886	0.573	10.142	0.557	0.919	1.588	0.928	9	53	2	31	15	28	20	22.571	8	; positions_7nt_m2 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=22.5714; ----aTTGCAyAAym-- ; cor=0.886; Ncor=0.573; logoDP=10.142; NIcor=0.557; NsEucl=0.919; SSD=1.588; NSW=0.928; rcor=9; rNcor=53; rlogoDP=2; rNIcor=31; rNsEucl=15; rSSD=28; rNSW=20; rank_mean=22.571; match_rank=8 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.875	0.566	10.055	0.546	0.916	1.708	0.922	14	56	3	33	19	35	25	26.429	12	; positions_7nt_m2 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score=26.4286; ---kATTGCAymAy--- ; cor=0.875; Ncor=0.566; logoDP=10.055; NIcor=0.546; NsEucl=0.916; SSD=1.708; NSW=0.922; rcor=14; rNcor=56; rlogoDP=3; rNIcor=33; rNsEucl=19; rSSD=35; rNSW=25; rank_mean=26.429; match_rank=12 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.2_rc_shift4 (CEBPA_rc)		0.835	0.442	2.684	0.035	0.890	1.972	0.890	42	100	83	91	97	57	81	78.714	89	; positions_7nt_m2 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score=78.7143; ----rTTGcrmaA---- ; cor=0.835; Ncor=0.442; logoDP=2.684; NIcor=0.035; NsEucl=0.890; SSD=1.972; NSW=0.890; rcor=42; rNcor=100; rlogoDP=83; rNIcor=91; rNsEucl=97; rSSD=57; rNSW=81; rank_mean=78.714; match_rank=89 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.811	0.572	0.356	-0.184	0.906	2.541	0.894	65	54	107	111	45	98	73	79.000	91	; positions_7nt_m2 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 79; -vrbrTTGcrmaA---- ; cor=0.811; Ncor=0.572; logoDP=0.356; NIcor=-0.184; NsEucl=0.906; SSD=2.541; NSW=0.894; rcor=65; rNcor=54; rlogoDP=107; rNIcor=111; rNsEucl=45; rSSD=98; rNSW=73; rank_mean=79.000; match_rank=91 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift1 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)																		; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -dkATTGTGCAATCwt ; Alignment reference a 0 1020 725 2836 11 6 122 129 5 244 3304 3306 61 474 1385 763 c 0 526 533 95 7 0 18 37 1 2943 18 4 304 2273 689 753 g 0 848 851 351 11 35 3080 63 3310 7 1 6 79 297 338 629 t 0 930 1215 42 3295 3283 104 3095 8 130 1 8 2880 280 912 1179
MA0102.3_rc_shift2 (CEBPA_rc)		0.948	0.695	4.203	0.060	0.946	0.706	0.968	1	7	66	82	1	1	1	22.714	9	; oligos_6nt_mkv4_m1 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=1; strand=R; shift=2; score=22.7143; --krTTrTGCAAt--- ; cor=0.948; Ncor=0.695; logoDP=4.203; NIcor=0.060; NsEucl=0.946; SSD=0.706; NSW=0.968; rcor=1; rNcor=7; rlogoDP=66; rNIcor=82; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=22.714; match_rank=9 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0
MA0466.1_rc_shift3 (CEBPB_rc)		0.924	0.678	2.820	-0.039	0.935	1.012	0.954	5	15	81	97	5	8	5	30.857	17	; oligos_6nt_mkv4_m1 versus MA0466.1_rc (CEBPB_rc); m=2/5; ncol2=11; w=11; offset=2; strand=R; shift=3; score=30.8571; ---rTkrTGCAATm-- ; cor=0.924; Ncor=0.678; logoDP=2.820; NIcor=-0.039; NsEucl=0.935; SSD=1.012; NSW=0.954; rcor=5; rNcor=15; rlogoDP=81; rNIcor=97; rNsEucl=5; rSSD=8; rNSW=5; rank_mean=30.857; match_rank=17 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0
MA0078.1_shift0 (Sox17)		0.861	0.431	6.882	0.426	0.908	1.089	0.932	22	102	35	53	40	10	17	39.857	25	; oligos_6nt_mkv4_m1 versus MA0078.1 (Sox17); m=3/5; ncol2=9; w=8; offset=-1; strand=D; shift=0; score=39.8571; yhyATTGTs------- ; cor=0.861; Ncor=0.431; logoDP=6.882; NIcor=0.426; NsEucl=0.908; SSD=1.089; NSW=0.932; rcor=22; rNcor=102; rlogoDP=35; rNIcor=53; rNsEucl=40; rSSD=10; rNSW=17; rank_mean=39.857; match_rank=25 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0
MA0102.1_shift4 (Cebpa)		0.811	0.649	6.234	0.631	0.913	2.195	0.909	64	25	50	17	29	70	42	42.429	30	; oligos_6nt_mkv4_m1 versus MA0102.1 (Cebpa); m=4/5; ncol2=12; w=12; offset=3; strand=D; shift=4; score=42.4286; ----TtkygCAAyvyb ; cor=0.811; Ncor=0.649; logoDP=6.234; NIcor=0.631; NsEucl=0.913; SSD=2.195; NSW=0.909; rcor=64; rNcor=25; rlogoDP=50; rNIcor=17; rNsEucl=29; rSSD=70; rNSW=42; rank_mean=42.429; match_rank=30 a 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift4 (CEBPA)		0.839	0.503	6.221	0.480	0.894	1.836	0.898	39	84	52	49	84	50	66	60.571	62	; oligos_6nt_mkv4_m1 versus MA0102.2 (CEBPA); m=5/5; ncol2=9; w=9; offset=3; strand=D; shift=4; score=60.5714; ----TtkygCAAy--- ; cor=0.839; Ncor=0.503; logoDP=6.221; NIcor=0.480; NsEucl=0.894; SSD=1.836; NSW=0.898; rcor=39; rNcor=84; rlogoDP=52; rNIcor=49; rNsEucl=84; rSSD=50; rNSW=66; rank_mean=60.571; match_rank=62 a 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)																		; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wtATTTCACAATCwh ; Alignment reference a 394 220 1355 8 10 132 6 1292 18 1376 1397 18 238 485 355 c 279 243 17 9 7 9 1403 26 1344 34 4 64 1058 302 372 g 318 341 33 4 46 167 3 48 6 1 7 13 45 157 229 t 423 610 9 1393 1351 1106 2 48 46 3 6 1319 73 470 458
MA0466.1_shift1 (CEBPB)		0.862	0.632	9.270	0.609	0.917	1.673	0.924	20	33	25	23	18	32	24	25.000	10	; positions_7nt_m1 versus MA0466.1 (CEBPB); m=1/5; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 25; -kATTGCAymAy--- ; cor=0.862; Ncor=0.632; logoDP=9.270; NIcor=0.609; NsEucl=0.917; SSD=1.673; NSW=0.924; rcor=20; rNcor=33; rlogoDP=25; rNIcor=23; rNsEucl=18; rSSD=32; rNSW=24; rank_mean=25.000; match_rank=10 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.3_shift2 (CEBPA)		0.858	0.629	9.274	0.601	0.914	1.801	0.918	26	35	24	26	25	45	31	30.286	16	; positions_7nt_m1 versus MA0102.3 (CEBPA); m=2/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score=30.2857; --aTTGCAyAAym-- ; cor=0.858; Ncor=0.629; logoDP=9.274; NIcor=0.601; NsEucl=0.914; SSD=1.801; NSW=0.918; rcor=26; rNcor=35; rlogoDP=24; rNIcor=26; rNsEucl=25; rSSD=45; rNSW=31; rank_mean=30.286; match_rank=16 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0102.1_shift3 (Cebpa)		0.813	0.650	6.080	0.632	0.914	2.140	0.911	61	22	55	16	24	67	39	40.571	26	; positions_7nt_m1 versus MA0102.1 (Cebpa); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=40.5714; ---TtkygCAAyvyb ; cor=0.813; Ncor=0.650; logoDP=6.080; NIcor=0.632; NsEucl=0.914; SSD=2.140; NSW=0.911; rcor=61; rNcor=22; rlogoDP=55; rNIcor=16; rNsEucl=24; rSSD=67; rNSW=39; rank_mean=40.571; match_rank=26 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift3 (CEBPA)		0.840	0.504	6.064	0.482	0.896	1.761	0.902	36	83	56	48	75	41	55	56.286	54	; positions_7nt_m1 versus MA0102.2 (CEBPA); m=4/5; ncol2=9; w=9; offset=3; strand=D; shift=3; score=56.2857; ---TtkygCAAy--- ; cor=0.840; Ncor=0.504; logoDP=6.064; NIcor=0.482; NsEucl=0.896; SSD=1.761; NSW=0.902; rcor=36; rNcor=83; rlogoDP=56; rNIcor=48; rNsEucl=75; rSSD=41; rNSW=55; rank_mean=56.286; match_rank=54 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0078.1_rc_shift6 (Sox17_rc)		0.800	0.480	3.194	0.182	0.898	1.675	0.907	75	94	73	65	69	33	46	65.000	67	; positions_7nt_m1 versus MA0078.1_rc (Sox17_rc); m=5/5; ncol2=9; w=9; offset=6; strand=R; shift=6; score= 65; ------sACAATrdr ; cor=0.800; Ncor=0.480; logoDP=3.194; NIcor=0.182; NsEucl=0.898; SSD=1.675; NSW=0.907; rcor=75; rNcor=94; rlogoDP=73; rNIcor=65; rNsEucl=69; rSSD=33; rNSW=46; rank_mean=65.000; match_rank=67 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

One-to-n matrix alignment; reference matrix: positions_8nt_m4_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m4_shift1 (positions_8nt_m4)																		; positions_8nt_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -wtATTGCCCAATaw ; Alignment reference a 0 336 249 850 1 1 12 2 35 5 1120 1128 51 410 290 c 0 230 213 94 0 1 0 1126 936 1106 4 0 179 261 274 g 0 245 259 141 0 1 1114 0 148 5 3 0 78 192 202 t 0 317 407 43 1127 1125 2 0 9 12 1 0 820 265 362
MA0102.3_shift3 (CEBPA)		0.844	0.663	9.784	0.657	0.913	1.811	0.918	33	19	10	12	26	46	32	25.429	11	; positions_8nt_m4 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=2; strand=D; shift=3; score=25.4286; ---aTTGCAyAAym- ; cor=0.844; Ncor=0.663; logoDP=9.784; NIcor=0.657; NsEucl=0.913; SSD=1.811; NSW=0.918; rcor=33; rNcor=19; rlogoDP=10; rNIcor=12; rNsEucl=26; rSSD=46; rNSW=32; rank_mean=25.429; match_rank=11 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift2 (CEBPB)		0.829	0.652	9.665	0.650	0.910	1.979	0.910	46	21	15	15	37	58	40	33.143	18	; positions_8nt_m4 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=1; strand=D; shift=2; score=33.1429; --kATTGCAymAy-- ; cor=0.829; Ncor=0.652; logoDP=9.665; NIcor=0.650; NsEucl=0.910; SSD=1.979; NSW=0.910; rcor=46; rNcor=21; rlogoDP=15; rNIcor=15; rNsEucl=37; rSSD=58; rNSW=40; rank_mean=33.143; match_rank=18 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.816	0.598	0.308	-0.155	0.908	2.039	0.907	58	48	111	105	39	60	45	66.571	69	; positions_8nt_m4 versus MA0102.1_rc (Cebpa_rc); m=3/4; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=66.5714; vrbrTTGcrmaA--- ; cor=0.816; Ncor=0.598; logoDP=0.308; NIcor=-0.155; NsEucl=0.908; SSD=2.039; NSW=0.907; rcor=58; rNcor=48; rlogoDP=111; rNIcor=105; rNsEucl=39; rSSD=60; rNSW=45; rank_mean=66.571; match_rank=69 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.827	0.531	2.978	0.142	0.890	1.946	0.892	49	71	79	73	93	54	77	70.857	78	; positions_8nt_m4 versus MA0102.2_rc (CEBPA_rc); m=4/4; ncol2=9; w=9; offset=2; strand=R; shift=3; score=70.8571; ---rTTGcrmaA--- ; cor=0.827; Ncor=0.531; logoDP=2.978; NIcor=0.142; NsEucl=0.890; SSD=1.946; NSW=0.892; rcor=49; rNcor=71; rlogoDP=79; rNIcor=73; rNsEucl=93; rSSD=54; rNSW=77; rank_mean=70.857; match_rank=78 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m2_shift1 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m2_shift1 (oligos_8nt_mkv6_m2)																		; oligos_8nt_mkv6_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGTGAAATaw ; Alignment reference a 0 1314 898 3074 24 26 71 73 20 3257 3961 4033 93 1624 1211 c 0 660 557 241 11 10 15 263 2 360 61 7 335 985 878 g 0 993 1040 571 8 33 3952 36 4011 11 6 7 248 674 788 t 0 1090 1562 171 4014 3988 19 3685 24 429 29 10 3381 774 1180
MA0102.3_rc_shift2 (CEBPA_rc)		0.879	0.691	4.259	0.146	0.924	1.396	0.937	11	8	64	71	8	17	11	27.143	13	; oligos_8nt_mkv6_m2 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=1; strand=R; shift=2; score=27.1429; --krTTrTGCAAt-- ; cor=0.879; Ncor=0.691; logoDP=4.259; NIcor=0.146; NsEucl=0.924; SSD=1.396; NSW=0.937; rcor=11; rNcor=8; rlogoDP=64; rNIcor=71; rNsEucl=8; rSSD=17; rNSW=11; rank_mean=27.143; match_rank=13 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0
MA0466.1_rc_shift3 (CEBPB_rc)		0.860	0.676	2.835	0.043	0.918	1.608	0.927	24	16	80	89	16	30	22	39.571	24	; oligos_8nt_mkv6_m2 versus MA0466.1_rc (CEBPB_rc); m=2/5; ncol2=11; w=11; offset=2; strand=R; shift=3; score=39.5714; ---rTkrTGCAATm- ; cor=0.860; Ncor=0.676; logoDP=2.835; NIcor=0.043; NsEucl=0.918; SSD=1.608; NSW=0.927; rcor=24; rNcor=16; rlogoDP=80; rNIcor=89; rNsEucl=16; rSSD=30; rNSW=22; rank_mean=39.571; match_rank=24 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
MA0078.1_shift0 (Sox17)		0.852	0.454	6.713	0.449	0.905	1.143	0.929	28	99	36	52	47	12	19	41.857	29	; oligos_8nt_mkv6_m2 versus MA0078.1 (Sox17); m=3/5; ncol2=9; w=8; offset=-1; strand=D; shift=0; score=41.8571; yhyATTGTs------ ; cor=0.852; Ncor=0.454; logoDP=6.713; NIcor=0.449; NsEucl=0.905; SSD=1.143; NSW=0.929; rcor=28; rNcor=99; rlogoDP=36; rNIcor=52; rNsEucl=47; rSSD=12; rNSW=19; rank_mean=41.857; match_rank=29 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.850	0.547	3.151	0.175	0.900	1.627	0.910	29	64	74	68	66	31	41	53.286	48	; oligos_8nt_mkv6_m2 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=2; strand=R; shift=3; score=53.2857; ---rTTGcrmaA--- ; cor=0.850; Ncor=0.547; logoDP=3.151; NIcor=0.175; NsEucl=0.900; SSD=1.627; NSW=0.910; rcor=29; rNcor=64; rlogoDP=74; rNIcor=68; rNsEucl=66; rSSD=31; rNSW=41; rank_mean=53.286; match_rank=48 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.840	0.616	0.283	-0.189	0.916	1.717	0.922	37	39	114	112	20	36	26	54.857	49	; oligos_8nt_mkv6_m2 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=54.8571; vrbrTTGcrmaA--- ; cor=0.840; Ncor=0.616; logoDP=0.283; NIcor=-0.189; NsEucl=0.916; SSD=1.717; NSW=0.922; rcor=37; rNcor=39; rlogoDP=114; rNIcor=112; rNsEucl=20; rSSD=36; rNSW=26; rank_mean=54.857; match_rank=49 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: positions_8nt_m5_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m5_shift0 (positions_8nt_m5)																		; positions_8nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; raTGGTTGCACAAyAwt ; Alignment reference a 176 350 18 19 56 1 1 11 1 634 4 645 644 6 547 174 92 c 61 82 6 1 8 0 0 2 642 3 634 1 0 239 29 148 111 g 351 112 19 612 576 0 0 627 0 4 1 0 0 12 34 147 48 t 58 102 603 14 6 645 645 6 3 5 7 0 2 389 36 177 395
MA0102.3_shift4 (CEBPA)		0.872	0.564	10.265	0.542	0.916	1.721	0.922	16	58	1	34	21	37	27	27.714	14	; positions_8nt_m5 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=4; strand=D; shift=4; score=27.7143; ----aTTGCAyAAym-- ; cor=0.872; Ncor=0.564; logoDP=10.265; NIcor=0.542; NsEucl=0.916; SSD=1.721; NSW=0.922; rcor=16; rNcor=58; rlogoDP=1; rNIcor=34; rNsEucl=21; rSSD=37; rNSW=27; rank_mean=27.714; match_rank=14 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.825	0.534	10.036	0.501	0.902	2.332	0.894	51	69	4	42	58	86	75	55.000	50	; positions_8nt_m5 versus MA0466.1 (CEBPB); m=2/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 55; ---kATTGCAymAy--- ; cor=0.825; Ncor=0.534; logoDP=10.036; NIcor=0.501; NsEucl=0.902; SSD=2.332; NSW=0.894; rcor=51; rNcor=69; rlogoDP=4; rNIcor=42; rNsEucl=58; rSSD=86; rNSW=75; rank_mean=55.000; match_rank=50 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.1_shift5 (Cebpa)		0.770	0.544	6.562	0.521	0.902	2.778	0.884	97	65	37	37	59	111	88	70.571	77	; positions_8nt_m5 versus MA0102.1 (Cebpa); m=3/5; ncol2=12; w=12; offset=5; strand=D; shift=5; score=70.5714; -----TtkygCAAyvyb ; cor=0.770; Ncor=0.544; logoDP=6.562; NIcor=0.521; NsEucl=0.902; SSD=2.778; NSW=0.884; rcor=97; rNcor=65; rlogoDP=37; rNIcor=37; rNsEucl=59; rSSD=111; rNSW=88; rank_mean=70.571; match_rank=77 a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift5 (CEBPA)		0.814	0.431	6.536	0.408	0.886	2.105	0.883	59	101	38	59	102	64	90	73.286	83	; positions_8nt_m5 versus MA0102.2 (CEBPA); m=4/5; ncol2=9; w=9; offset=5; strand=D; shift=5; score=73.2857; -----TtkygCAAy--- ; cor=0.814; Ncor=0.431; logoDP=6.536; NIcor=0.408; NsEucl=0.886; SSD=2.105; NSW=0.883; rcor=59; rNcor=101; rlogoDP=38; rNIcor=59; rNsEucl=102; rSSD=64; rNSW=90; rank_mean=73.286; match_rank=83 a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0078.1_rc_shift8 (Sox17_rc)		0.781	0.413	2.538	0.088	0.892	1.874	0.896	88	108	92	78	89	52	71	82.571	98	; positions_8nt_m5 versus MA0078.1_rc (Sox17_rc); m=5/5; ncol2=9; w=9; offset=8; strand=R; shift=8; score=82.5714; --------sACAATrdr ; cor=0.781; Ncor=0.413; logoDP=2.538; NIcor=0.088; NsEucl=0.892; SSD=1.874; NSW=0.896; rcor=88; rNcor=108; rlogoDP=92; rNIcor=78; rNsEucl=89; rSSD=52; rNSW=71; rank_mean=82.571; match_rank=98 a 0 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m3_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m3_shift0 (oligos_8nt_mkv6_m3)																		; oligos_8nt_mkv6_m3; m=0 (reference); ncol1=14; shift=0; ncol=15; wtATTGAGCAATaw- ; Alignment reference a 1047 667 2712 14 18 176 2365 4 73 3285 3285 91 1402 945 0 c 570 504 181 5 5 8 210 9 3122 9 9 294 644 732 0 g 771 667 330 10 17 3025 85 3279 5 4 4 215 531 674 0 t 918 1468 83 3277 3266 97 646 14 106 8 8 2706 729 955 0
MA0102.3_rc_shift1 (CEBPA_rc)		0.875	0.687	4.343	0.142	0.923	1.437	0.935	13	9	62	74	9	19	12	28.286	15	; oligos_8nt_mkv6_m3 versus MA0102.3_rc (CEBPA_rc); m=1/4; ncol2=11; w=11; offset=1; strand=R; shift=1; score=28.2857; -krTTrTGCAAt--- ; cor=0.875; Ncor=0.687; logoDP=4.343; NIcor=0.142; NsEucl=0.923; SSD=1.437; NSW=0.935; rcor=13; rNcor=9; rlogoDP=62; rNIcor=74; rNsEucl=9; rSSD=19; rNSW=12; rank_mean=28.286; match_rank=15 a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0
MA0466.1_rc_shift2 (CEBPB_rc)		0.870	0.683	2.614	-0.034	0.921	1.491	0.932	19	14	86	95	13	22	16	37.857	20	; oligos_8nt_mkv6_m3 versus MA0466.1_rc (CEBPB_rc); m=2/4; ncol2=11; w=11; offset=2; strand=R; shift=2; score=37.8571; --rTkrTGCAATm-- ; cor=0.870; Ncor=0.683; logoDP=2.614; NIcor=-0.034; NsEucl=0.921; SSD=1.491; NSW=0.932; rcor=19; rNcor=14; rlogoDP=86; rNIcor=95; rNsEucl=13; rSSD=22; rNSW=16; rank_mean=37.857; match_rank=20 a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0
MA0102.1_shift3 (Cebpa)		0.828	0.607	6.269	0.604	0.913	1.816	0.917	47	43	47	25	27	47	33	38.429	22	; oligos_8nt_mkv6_m3 versus MA0102.1 (Cebpa); m=3/4; ncol2=12; w=11; offset=3; strand=D; shift=3; score=38.4286; ---TtkygCAAyvyb ; cor=0.828; Ncor=0.607; logoDP=6.269; NIcor=0.604; NsEucl=0.913; SSD=1.816; NSW=0.917; rcor=47; rNcor=43; rlogoDP=47; rNIcor=25; rNsEucl=27; rSSD=47; rNSW=33; rank_mean=38.429; match_rank=22 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift3 (CEBPA)		0.842	0.541	6.267	0.532	0.898	1.691	0.906	35	66	48	36	70	34	48	48.143	42	; oligos_8nt_mkv6_m3 versus MA0102.2 (CEBPA); m=4/4; ncol2=9; w=9; offset=3; strand=D; shift=3; score=48.1429; ---TtkygCAAy--- ; cor=0.842; Ncor=0.541; logoDP=6.267; NIcor=0.532; NsEucl=0.898; SSD=1.691; NSW=0.906; rcor=35; rNcor=66; rlogoDP=48; rNIcor=36; rNsEucl=70; rSSD=34; rNSW=48; rank_mean=48.143; match_rank=42 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)																		; positions_7nt_m3; m=0 (reference); ncol1=16; shift=0; ncol=16; arAGATTGCGAAATrw ; Alignment reference a 162 113 402 15 414 0 0 7 36 40 397 424 433 2 127 151 c 77 108 4 27 6 0 0 0 303 14 17 10 0 15 102 90 g 99 129 9 351 11 0 1 423 24 366 2 0 1 7 112 76 t 96 84 19 41 3 434 433 4 71 14 18 0 0 410 93 117
MA0102.2_rc_shift4 (CEBPA_rc)		0.914	0.514	3.782	0.178	0.918	1.083	0.940	6	78	68	66	17	9	8	36.000	19	; positions_7nt_m3 versus MA0102.2_rc (CEBPA_rc); m=1/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 36; ----rTTGcrmaA--- ; cor=0.914; Ncor=0.514; logoDP=3.782; NIcor=0.178; NsEucl=0.918; SSD=1.083; NSW=0.940; rcor=6; rNcor=78; rlogoDP=68; rNIcor=66; rNsEucl=17; rSSD=9; rNSW=8; rank_mean=36.000; match_rank=19 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.876	0.657	0.379	-0.212	0.922	1.749	0.927	12	20	105	114	12	39	21	46.143	38	; positions_7nt_m3 versus MA0102.1_rc (Cebpa_rc); m=2/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score=46.1429; -vrbrTTGcrmaA--- ; cor=0.876; Ncor=0.657; logoDP=0.379; NIcor=-0.212; NsEucl=0.922; SSD=1.749; NSW=0.927; rcor=12; rNcor=20; rlogoDP=105; rNIcor=114; rNsEucl=12; rSSD=39; rNSW=21; rank_mean=46.143; match_rank=38 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.3_shift4 (CEBPA)		0.763	0.524	8.481	0.502	0.894	2.706	0.877	102	74	31	41	82	110	101	77.286	87	; positions_7nt_m3 versus MA0102.3 (CEBPA); m=3/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=77.2857; ----aTTGCAyAAym- ; cor=0.763; Ncor=0.524; logoDP=8.481; NIcor=0.502; NsEucl=0.894; SSD=2.706; NSW=0.877; rcor=102; rNcor=74; rlogoDP=31; rNIcor=41; rNsEucl=82; rSSD=110; rNSW=101; rank_mean=77.286; match_rank=87 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_rc_shift4 (CEBPB_rc)		0.757	0.520	3.051	0.047	0.893	2.783	0.873	108	76	77	88	87	112	103	93.000	111	; positions_7nt_m3 versus MA0466.1_rc (CEBPB_rc); m=4/4; ncol2=11; w=11; offset=4; strand=R; shift=4; score= 93; ----rTkrTGCAATm- ; cor=0.757; Ncor=0.520; logoDP=3.051; NIcor=0.047; NsEucl=0.893; SSD=2.783; NSW=0.873; rcor=108; rNcor=76; rlogoDP=77; rNIcor=88; rNsEucl=87; rSSD=112; rNSW=103; rank_mean=93.000; match_rank=111 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift2 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)																		; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wrTTGCTCAAya ; Alignment reference a 0 0 798 1165 0 0 0 0 5 0 2811 2811 291 989 c 0 0 484 563 0 1 0 2811 0 2811 0 0 857 675 g 0 0 602 755 0 0 2811 0 6 0 0 0 492 465 t 0 0 927 328 2811 2810 0 0 2800 0 0 0 1171 682
MA0102.3_shift3 (CEBPA)		0.803	0.736	9.717	0.722	0.904	2.210	0.900	72	2	12	2	49	73	60	38.571	23	; oligos_7nt_mkv5_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=1; strand=D; shift=3; score=38.5714; ---aTTGCAyAAym ; cor=0.803; Ncor=0.736; logoDP=9.717; NIcor=0.722; NsEucl=0.904; SSD=2.210; NSW=0.900; rcor=72; rNcor=2; rlogoDP=12; rNIcor=2; rNsEucl=49; rSSD=73; rNSW=60; rank_mean=38.571; match_rank=23 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift2 (CEBPB)		0.779	0.714	9.501	0.691	0.899	2.478	0.887	91	5	19	5	68	97	85	52.857	46	; oligos_7nt_mkv5_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=2; score=52.8571; --kATTGCAymAy- ; cor=0.779; Ncor=0.714; logoDP=9.501; NIcor=0.691; NsEucl=0.899; SSD=2.478; NSW=0.887; rcor=91; rNcor=5; rlogoDP=19; rNIcor=5; rNsEucl=68; rSSD=97; rNSW=85; rank_mean=52.857; match_rank=46 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.784	0.588	2.577	0.065	0.880	2.350	0.869	86	50	90	81	108	87	109	87.286	104	; oligos_7nt_mkv5_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=1; strand=R; shift=3; score=87.2857; ---rTTGcrmaA-- ; cor=0.784; Ncor=0.588; logoDP=2.577; NIcor=0.065; NsEucl=0.880; SSD=2.350; NSW=0.869; rcor=86; rNcor=50; rlogoDP=90; rNIcor=81; rNsEucl=108; rSSD=87; rNSW=109; rank_mean=87.286; match_rank=104 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.778	0.556	0.504	-0.105	0.890	2.408	0.880	94	61	102	101	95	92	97	91.714	110	; oligos_7nt_mkv5_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=10; offset=-2; strand=R; shift=0; score=91.7143; vrbrTTGcrmaA-- ; cor=0.778; Ncor=0.556; logoDP=0.504; NIcor=-0.105; NsEucl=0.890; SSD=2.408; NSW=0.880; rcor=94; rNcor=61; rlogoDP=102; rNIcor=101; rNsEucl=95; rSSD=92; rNSW=97; rank_mean=91.714; match_rank=110 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0

One-to-n matrix alignment; reference matrix: positions_8nt_m2_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m2_shift0 (positions_8nt_m2)																		; positions_8nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=15; mtGTTGAGCAATmw- ; Alignment reference a 161 151 9 2 5 14 446 0 13 605 606 7 162 169 0 c 154 107 1 2 1 0 95 0 584 2 1 23 195 134 0 g 149 141 600 3 4 591 14 607 0 2 3 5 130 140 0 t 146 211 0 603 600 5 55 3 13 1 0 575 123 167 0
MA0102.1_shift3 (Cebpa)		0.825	0.605	6.398	0.593	0.910	1.956	0.911	50	44	39	28	34	55	38	41.143	27	; positions_8nt_m2 versus MA0102.1 (Cebpa); m=1/5; ncol2=12; w=11; offset=3; strand=D; shift=3; score=41.1429; ---TtkygCAAyvyb ; cor=0.825; Ncor=0.605; logoDP=6.398; NIcor=0.593; NsEucl=0.910; SSD=1.956; NSW=0.911; rcor=50; rNcor=44; rlogoDP=39; rNIcor=28; rNsEucl=34; rSSD=55; rNSW=38; rank_mean=41.143; match_rank=27 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.3_rc_shift1 (CEBPA_rc)		0.820	0.644	4.290	0.128	0.905	2.204	0.900	54	28	63	76	48	72	58	57.000	56	; positions_8nt_m2 versus MA0102.3_rc (CEBPA_rc); m=2/5; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 57; -krTTrTGCAAt--- ; cor=0.820; Ncor=0.644; logoDP=4.290; NIcor=0.128; NsEucl=0.905; SSD=2.204; NSW=0.900; rcor=54; rNcor=28; rlogoDP=63; rNIcor=76; rNsEucl=48; rSSD=72; rNSW=58; rank_mean=57.000; match_rank=56 a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0
MA0102.2_shift3 (CEBPA)		0.835	0.537	6.397	0.520	0.892	1.879	0.896	43	68	40	38	90	53	72	57.714	57	; positions_8nt_m2 versus MA0102.2 (CEBPA); m=3/5; ncol2=9; w=9; offset=3; strand=D; shift=3; score=57.7143; ---TtkygCAAy--- ; cor=0.835; Ncor=0.537; logoDP=6.397; NIcor=0.520; NsEucl=0.892; SSD=1.879; NSW=0.896; rcor=43; rNcor=68; rlogoDP=40; rNIcor=38; rNsEucl=90; rSSD=53; rNSW=72; rank_mean=57.714; match_rank=57 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0133.1_rc_shift0 (BRCA1_rc)		0.857	0.428	0.165	-0.127	0.906	0.857	0.939	27	103	115	102	43	5	9	57.714	58	; positions_8nt_m2 versus MA0133.1_rc (BRCA1_rc); m=4/5; ncol2=7; w=7; offset=0; strand=R; shift=0; score=57.7143; skgTTGk-------- ; cor=0.857; Ncor=0.428; logoDP=0.165; NIcor=-0.127; NsEucl=0.906; SSD=0.857; NSW=0.939; rcor=27; rNcor=103; rlogoDP=115; rNIcor=102; rNsEucl=43; rSSD=5; rNSW=9; rank_mean=57.714; match_rank=58 a 3 3 1 1 0 2 7 0 0 0 0 0 0 0 0 c 15 7 6 4 1 2 10 0 0 0 0 0 0 0 0 g 22 14 29 2 1 35 11 0 0 0 0 0 0 0 0 t 3 19 7 36 41 4 15 0 0 0 0 0 0 0 0
MA0466.1_rc_shift2 (CEBPB_rc)		0.802	0.630	2.569	-0.025	0.900	2.408	0.891	73	34	91	94	64	91	79	75.143	85	; positions_8nt_m2 versus MA0466.1_rc (CEBPB_rc); m=5/5; ncol2=11; w=11; offset=2; strand=R; shift=2; score=75.1429; --rTkrTGCAATm-- ; cor=0.802; Ncor=0.630; logoDP=2.569; NIcor=-0.025; NsEucl=0.900; SSD=2.408; NSW=0.891; rcor=73; rNcor=34; rlogoDP=91; rNIcor=94; rNsEucl=64; rSSD=91; rNSW=79; rank_mean=75.143; match_rank=85 a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m5_shift2 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m5_shift2 (oligos_8nt_mkv6_m5)																		; oligos_8nt_mkv6_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wmTTGCCCAAya ; Alignment reference a 0 0 526 686 0 0 0 0 5 0 1906 1908 237 612 c 0 0 413 478 0 0 0 1909 1852 1908 0 1 578 399 g 0 0 403 462 0 0 1907 0 50 0 3 0 440 462 t 0 0 567 283 1909 1909 2 0 2 1 0 0 654 436
MA0102.3_shift3 (CEBPA)		0.797	0.730	9.685	0.721	0.904	2.242	0.898	77	3	13	3	52	76	65	41.286	28	; oligos_8nt_mkv6_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=1; strand=D; shift=3; score=41.2857; ---aTTGCAyAAym ; cor=0.797; Ncor=0.730; logoDP=9.685; NIcor=0.721; NsEucl=0.904; SSD=2.242; NSW=0.898; rcor=77; rNcor=3; rlogoDP=13; rNIcor=3; rNsEucl=52; rSSD=76; rNSW=65; rank_mean=41.286; match_rank=28 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift2 (CEBPB)		0.761	0.698	9.424	0.689	0.896	2.634	0.880	103	6	21	6	76	106	96	59.143	59	; oligos_8nt_mkv6_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=2; score=59.1429; --kATTGCAymAy- ; cor=0.761; Ncor=0.698; logoDP=9.424; NIcor=0.689; NsEucl=0.896; SSD=2.634; NSW=0.880; rcor=103; rNcor=6; rlogoDP=21; rNIcor=6; rNsEucl=76; rSSD=106; rNSW=96; rank_mean=59.143; match_rank=59 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.783	0.587	3.319	0.198	0.880	2.321	0.871	87	51	69	64	106	84	107	81.143	94	; oligos_8nt_mkv6_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=1; strand=R; shift=3; score=81.1429; ---rTTGcrmaA-- ; cor=0.783; Ncor=0.587; logoDP=3.319; NIcor=0.198; NsEucl=0.880; SSD=2.321; NSW=0.871; rcor=87; rNcor=51; rlogoDP=69; rNIcor=64; rNsEucl=106; rSSD=84; rNSW=107; rank_mean=81.143; match_rank=94 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.778	0.556	0.345	-0.146	0.891	2.367	0.882	93	60	109	104	92	88	94	91.429	109	; oligos_8nt_mkv6_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=10; offset=-2; strand=R; shift=0; score=91.4286; vrbrTTGcrmaA-- ; cor=0.778; Ncor=0.556; logoDP=0.345; NIcor=-0.146; NsEucl=0.891; SSD=2.367; NSW=0.882; rcor=93; rNcor=60; rlogoDP=109; rNIcor=104; rNsEucl=92; rSSD=88; rNSW=94; rank_mean=91.429; match_rank=109 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift1 ; 8 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)																		; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=13; shift=1; ncol=14; -wrTTACACAAtww ; Alignment reference a 0 858 1227 211 1 2938 0 2923 0 2923 2926 729 1021 848 c 0 454 523 61 1 0 2937 0 2935 0 3 720 718 708 g 0 669 744 112 0 0 0 15 0 13 3 388 442 590 t 0 957 444 2554 2936 0 1 0 3 2 6 1101 757 792
MA0043.1_shift1 (HLF)		0.788	0.727	5.794	0.702	0.912	2.217	0.908	83	4	59	4	31	75	44	42.857	31	; oligos_7nt_mkv5_m3 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score=42.8571; -krTTACryAAth- ; cor=0.788; Ncor=0.727; logoDP=5.794; NIcor=0.702; NsEucl=0.912; SSD=2.217; NSW=0.908; rcor=83; rNcor=4; rlogoDP=59; rNIcor=4; rNsEucl=31; rSSD=75; rNSW=44; rank_mean=42.857; match_rank=31 a 0 1 6 1 0 13 0 6 0 13 15 2 5 0 c 0 4 0 0 0 1 15 0 9 4 0 3 5 0 g 0 8 12 0 3 2 1 12 0 1 1 1 3 0 t 0 5 0 17 15 2 2 0 9 0 2 12 5 0
MA0102.3_shift2 (CEBPA)		0.790	0.669	8.675	0.664	0.903	2.262	0.897	80	17	29	11	55	79	69	48.571	43	; oligos_7nt_mkv5_m3 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score=48.5714; --aTTGCAyAAym- ; cor=0.790; Ncor=0.669; logoDP=8.675; NIcor=0.664; NsEucl=0.903; SSD=2.262; NSW=0.897; rcor=80; rNcor=17; rlogoDP=29; rNIcor=11; rNsEucl=55; rSSD=79; rNSW=69; rank_mean=48.571; match_rank=43 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0133.1_shift7 (BRCA1)		0.779	0.419	3.209	0.421	0.890	1.196	0.915	92	106	71	55	98	13	36	67.286	72	; oligos_7nt_mkv5_m3 versus MA0133.1 (BRCA1); m=3/7; ncol2=7; w=7; offset=6; strand=D; shift=7; score=67.2857; -------mCAAcms ; cor=0.779; Ncor=0.419; logoDP=3.209; NIcor=0.421; NsEucl=0.890; SSD=1.196; NSW=0.915; rcor=92; rNcor=106; rlogoDP=71; rNIcor=55; rNsEucl=98; rSSD=13; rNSW=36; rank_mean=67.286; match_rank=72 a 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0466.1_shift1 (CEBPB)		0.752	0.636	8.314	0.623	0.895	2.680	0.878	111	31	32	19	80	107	99	68.429	75	; oligos_7nt_mkv5_m3 versus MA0466.1 (CEBPB); m=4/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score=68.4286; -kATTGCAymAy-- ; cor=0.752; Ncor=0.636; logoDP=8.314; NIcor=0.623; NsEucl=0.895; SSD=2.680; NSW=0.878; rcor=111; rNcor=31; rlogoDP=32; rNIcor=19; rNsEucl=80; rSSD=107; rNSW=99; rank_mean=68.429; match_rank=75 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0078.1_rc_shift6 (Sox17_rc)		0.799	0.456	1.990	0.086	0.890	1.541	0.904	76	97	98	79	94	26	50	74.286	84	; oligos_7nt_mkv5_m3 versus MA0078.1_rc (Sox17_rc); m=5/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score=74.2857; ------sACAATrd ; cor=0.799; Ncor=0.456; logoDP=1.990; NIcor=0.086; NsEucl=0.890; SSD=1.541; NSW=0.904; rcor=76; rNcor=97; rlogoDP=98; rNIcor=79; rNsEucl=94; rSSD=26; rNSW=50; rank_mean=74.286; match_rank=84 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8
MA0025.1_rc_shift0 (NFIL3_rc)		0.790	0.564	2.256	0.072	0.893	2.310	0.884	81	59	94	80	88	82	87	81.571	96	; oligos_7nt_mkv5_m3 versus MA0025.1_rc (NFIL3_rc); m=6/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score=81.5714; ayrTTACrTAA--- ; cor=0.790; Ncor=0.564; logoDP=2.256; NIcor=0.072; NsEucl=0.893; SSD=2.310; NSW=0.884; rcor=81; rNcor=59; rlogoDP=94; rNIcor=80; rNsEucl=88; rSSD=82; rNSW=87; rank_mean=81.571; match_rank=96 a 10 4 8 0 0 23 0 15 1 21 22 0 0 0 c 3 7 4 1 0 0 21 0 0 2 0 0 0 0 g 5 5 11 0 0 0 0 8 0 0 0 0 0 0 t 5 7 0 22 23 0 2 0 22 0 1 0 0 0
MA0102.2_shift3 (CEBPA)		0.756	0.523	5.976	0.496	0.877	2.470	0.863	110	75	58	43	110	96	112	86.286	103	; oligos_7nt_mkv5_m3 versus MA0102.2 (CEBPA); m=7/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score=86.2857; ---TtkygCAAy-- ; cor=0.756; Ncor=0.523; logoDP=5.976; NIcor=0.496; NsEucl=0.877; SSD=2.470; NSW=0.863; rcor=110; rNcor=75; rlogoDP=58; rNIcor=43; rNsEucl=110; rSSD=96; rNSW=112; rank_mean=86.286; match_rank=103 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0

One-to-n matrix alignment; reference matrix: positions_8nt_m3_shift1 ; 7 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m3_shift1 (positions_8nt_m3)																		; positions_8nt_m3; m=0 (reference); ncol1=16; shift=1; ncol=17; -wrTGATTGTGCAAgad ; Alignment reference a 0 189 178 43 19 598 4 1 25 18 1 25 643 642 19 276 169 c 0 144 133 14 20 13 4 1 4 12 1 594 5 0 72 133 149 g 0 141 180 25 586 24 1 10 600 7 642 3 0 4 416 107 167 t 0 174 157 566 23 13 639 636 19 611 4 26 0 2 141 132 163
MA0466.1_rc_shift5 (CEBPB_rc)		0.870	0.598	2.675	-0.037	0.920	1.539	0.930	18	47	84	96	14	25	18	43.143	33	; positions_8nt_m3 versus MA0466.1_rc (CEBPB_rc); m=1/6; ncol2=11; w=11; offset=4; strand=R; shift=5; score=43.1429; -----rTkrTGCAATm- ; cor=0.870; Ncor=0.598; logoDP=2.675; NIcor=-0.037; NsEucl=0.920; SSD=1.539; NSW=0.930; rcor=18; rNcor=47; rlogoDP=84; rNIcor=96; rNsEucl=14; rSSD=25; rNSW=18; rank_mean=43.143; match_rank=33 a 0 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
MA0102.3_rc_shift4 (CEBPA_rc)		0.861	0.592	4.254	0.040	0.914	1.779	0.919	21	49	65	90	23	43	30	45.857	37	; positions_8nt_m3 versus MA0102.3_rc (CEBPA_rc); m=2/6; ncol2=11; w=11; offset=3; strand=R; shift=4; score=45.8571; ----krTTrTGCAAt-- ; cor=0.861; Ncor=0.592; logoDP=4.254; NIcor=0.040; NsEucl=0.914; SSD=1.779; NSW=0.919; rcor=21; rNcor=49; rlogoDP=65; rNIcor=90; rNsEucl=23; rSSD=43; rNSW=30; rank_mean=45.857; match_rank=37 a 0 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0
MA0102.1_shift6 (Cebpa)		0.780	0.505	6.047	0.491	0.903	2.255	0.898	90	82	57	44	53	77	67	67.143	70	; positions_8nt_m3 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=11; offset=5; strand=D; shift=6; score=67.1429; ------TtkygCAAyvy ; cor=0.780; Ncor=0.505; logoDP=6.047; NIcor=0.491; NsEucl=0.903; SSD=2.255; NSW=0.898; rcor=90; rNcor=82; rlogoDP=57; rNIcor=44; rNsEucl=53; rSSD=77; rNSW=67; rank_mean=67.143; match_rank=70 a 0 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0038.1_rc_shift0 (Gfi1_rc)		0.780	0.413	0.367	-0.138	0.896	1.761	0.902	89	109	106	103	74	40	54	82.143	97	; positions_8nt_m3 versus MA0038.1_rc (Gfi1_rc); m=4/6; ncol2=10; w=9; offset=-1; strand=R; shift=0; score=82.1429; cwgtGATTkr------- ; cor=0.780; Ncor=0.413; logoDP=0.367; NIcor=-0.138; NsEucl=0.896; SSD=1.761; NSW=0.902; rcor=89; rNcor=109; rlogoDP=106; rNIcor=103; rNsEucl=74; rSSD=40; rNSW=54; rank_mean=82.143; match_rank=97 a 5 21 6 13 0 51 0 0 2 15 0 0 0 0 0 0 0 c 28 2 11 2 0 1 0 0 7 9 0 0 0 0 0 0 0 g 13 11 28 7 52 0 0 0 16 20 0 0 0 0 0 0 0 t 7 19 8 31 1 1 53 53 28 9 0 0 0 0 0 0 0
MA0102.2_rc_shift5 (CEBPA_rc)		0.812	0.457	2.596	0.049	0.886	2.121	0.882	63	96	87	85	103	65	92	84.429	100	; positions_8nt_m3 versus MA0102.2_rc (CEBPA_rc); m=5/6; ncol2=9; w=9; offset=4; strand=R; shift=5; score=84.4286; -----rTTGcrmaA--- ; cor=0.812; Ncor=0.457; logoDP=2.596; NIcor=0.049; NsEucl=0.886; SSD=2.121; NSW=0.882; rcor=63; rNcor=96; rlogoDP=87; rNIcor=85; rNsEucl=103; rSSD=65; rNSW=92; rank_mean=84.429; match_rank=100 a 0 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0078.1_shift2 (Sox17)		0.752	0.423	7.135	0.423	0.881	2.299	0.872	113	105	34	54	105	81	105	85.286	101	; positions_8nt_m3 versus MA0078.1 (Sox17); m=6/6; ncol2=9; w=9; offset=1; strand=D; shift=2; score=85.2857; --yhyATTGTs------ ; cor=0.752; Ncor=0.423; logoDP=7.135; NIcor=0.423; NsEucl=0.881; SSD=2.299; NSW=0.872; rcor=113; rNcor=105; rlogoDP=34; rNIcor=54; rNsEucl=105; rSSD=81; rNSW=105; rank_mean=85.286; match_rank=101 a 0 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 0 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 0 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 0 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)																		; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wwAGATTGTGAAAtm ; Alignment reference a 358 258 771 43 867 5 8 37 26 3 721 851 886 58 368 c 124 176 20 25 8 5 2 2 40 1 82 31 1 184 243 g 173 214 31 694 17 3 17 852 7 889 6 5 6 111 102 t 242 249 75 135 5 884 870 6 824 4 88 10 4 544 184
MA0102.3_rc_shift3 (CEBPA_rc)		0.847	0.621	4.050	0.121	0.913	1.820	0.917	32	38	67	77	28	48	34	46.286	39	; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=3; strand=R; shift=3; score=46.2857; ---krTTrTGCAAt- ; cor=0.847; Ncor=0.621; logoDP=4.050; NIcor=0.121; NsEucl=0.913; SSD=1.820; NSW=0.917; rcor=32; rNcor=38; rlogoDP=67; rNIcor=77; rNsEucl=28; rSSD=48; rNSW=34; rank_mean=46.286; match_rank=39 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0
MA0466.1_rc_shift4 (CEBPB_rc)		0.848	0.622	2.740	0.033	0.915	1.730	0.921	31	37	82	92	22	38	28	47.143	41	; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/5; ncol2=11; w=11; offset=4; strand=R; shift=4; score=47.1429; ----rTkrTGCAATm ; cor=0.848; Ncor=0.622; logoDP=2.740; NIcor=0.033; NsEucl=0.915; SSD=1.730; NSW=0.921; rcor=31; rNcor=37; rlogoDP=82; rNIcor=92; rNsEucl=22; rSSD=38; rNSW=28; rank_mean=47.143; match_rank=41 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006
MA0102.2_rc_shift4 (CEBPA_rc)		0.836	0.502	3.028	0.151	0.894	1.826	0.899	41	86	78	70	83	49	64	67.286	71	; positions_6nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/5; ncol2=9; w=9; offset=4; strand=R; shift=4; score=67.2857; ----rTTGcrmaA-- ; cor=0.836; Ncor=0.502; logoDP=3.028; NIcor=0.151; NsEucl=0.894; SSD=1.826; NSW=0.899; rcor=41; rNcor=86; rlogoDP=78; rNIcor=70; rNsEucl=83; rSSD=49; rNSW=64; rank_mean=67.286; match_rank=71 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.808	0.646	0.416	-0.221	0.908	2.422	0.899	68	27	104	115	38	93	62	72.429	81	; positions_6nt_m1 versus MA0102.1_rc (Cebpa_rc); m=4/5; ncol2=12; w=12; offset=1; strand=R; shift=1; score=72.4286; -vrbrTTGcrmaA-- ; cor=0.808; Ncor=0.646; logoDP=0.416; NIcor=-0.221; NsEucl=0.908; SSD=2.422; NSW=0.899; rcor=68; rNcor=27; rlogoDP=104; rNIcor=115; rNsEucl=38; rSSD=93; rNSW=62; rank_mean=72.429; match_rank=81 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0
MA0078.1_shift1 (Sox17)		0.761	0.456	7.347	0.462	0.884	2.168	0.880	104	98	33	50	104	69	98	79.429	92	; positions_6nt_m1 versus MA0078.1 (Sox17); m=5/5; ncol2=9; w=9; offset=1; strand=D; shift=1; score=79.4286; -yhyATTGTs----- ; cor=0.761; Ncor=0.456; logoDP=7.347; NIcor=0.462; NsEucl=0.884; SSD=2.168; NSW=0.880; rcor=104; rNcor=98; rlogoDP=33; rNIcor=50; rNsEucl=104; rSSD=69; rNSW=98; rank_mean=79.429; match_rank=92 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift2 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)																		; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --aaACAAAAACaa ; Alignment reference a 0 0 619 628 1156 0 1178 1183 1184 1184 1184 0 645 505 c 0 0 153 188 6 1184 0 0 0 0 0 1184 232 207 g 0 0 169 157 9 0 6 0 0 0 0 0 79 221 t 0 0 243 211 13 0 0 1 0 0 0 0 228 251
MA0084.1_shift0 (SRY)		0.848	0.424	6.358	0.414	0.893	1.116	0.920	30	104	41	56	85	11	29	50.857	45	; oligos_7nt_mkv5_m4 versus MA0084.1 (SRY); m=1/1; ncol2=9; w=7; offset=-2; strand=D; shift=0; score=50.8571; kwwaACAAw----- ; cor=0.848; Ncor=0.424; logoDP=6.358; NIcor=0.414; NsEucl=0.893; SSD=1.116; NSW=0.920; rcor=30; rNcor=104; rlogoDP=41; rNIcor=56; rNsEucl=85; rSSD=11; rNSW=29; rank_mean=50.857; match_rank=45 a 5 8 15 18 25 0 28 27 7 0 0 0 0 0 c 5 3 0 3 0 26 0 0 0 0 0 0 0 0 g 10 4 3 3 0 0 0 1 2 0 0 0 0 0 t 8 13 10 4 3 2 0 0 19 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)																		; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wvATGTTGCACAACAGtr ; Alignment reference a 39 30 88 5 6 0 1 4 2 116 3 119 118 2 107 5 21 32 c 22 32 17 2 4 0 0 0 115 0 111 0 0 111 2 8 26 29 g 28 31 7 0 107 0 0 111 1 0 1 0 0 3 2 100 25 34 t 30 26 7 112 2 119 118 4 1 3 4 0 1 3 8 6 47 24
MA0102.3_shift4 (CEBPA)		0.830	0.507	9.858	0.484	0.903	2.290	0.896	45	80	7	47	57	80	70	55.143	51	; positions_6nt_m4 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=55.1429; ----aTTGCAyAAym--- ; cor=0.830; Ncor=0.507; logoDP=9.858; NIcor=0.484; NsEucl=0.903; SSD=2.290; NSW=0.896; rcor=45; rNcor=80; rlogoDP=7; rNIcor=47; rNsEucl=57; rSSD=80; rNSW=70; rank_mean=55.143; match_rank=51 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
MA0466.1_shift3 (CEBPB)		0.788	0.482	9.601	0.453	0.892	2.813	0.872	82	93	17	51	91	113	106	79.000	90	; positions_6nt_m4 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 79; ---kATTGCAymAy---- ; cor=0.788; Ncor=0.482; logoDP=9.601; NIcor=0.453; NsEucl=0.892; SSD=2.813; NSW=0.872; rcor=82; rNcor=93; rlogoDP=17; rNIcor=51; rNsEucl=91; rSSD=113; rNSW=106; rank_mean=79.000; match_rank=90 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.751	0.501	0.356	-0.161	0.896	3.135	0.869	114	87	108	106	77	115	110	102.429	114	; positions_6nt_m4 versus MA0102.1_rc (Cebpa_rc); m=3/3; ncol2=12; w=12; offset=1; strand=R; shift=1; score=102.429; -vrbrTTGcrmaA----- ; cor=0.751; Ncor=0.501; logoDP=0.356; NIcor=-0.161; NsEucl=0.896; SSD=3.135; NSW=0.869; rcor=114; rNcor=87; rlogoDP=108; rNIcor=106; rNsEucl=77; rSSD=115; rNSW=110; rank_mean=102.429; match_rank=114 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)																		; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; dkATTACGCAAGArw ; Alignment reference a 203 157 612 2 1 589 32 68 11 677 677 9 629 179 202 c 108 117 23 2 2 3 539 20 645 1 0 57 15 148 142 g 175 199 33 1 11 48 27 575 2 0 1 540 14 185 144 t 192 205 10 673 664 38 80 15 20 0 0 72 20 166 190
MA0102.2_shift3 (CEBPA)		0.819	0.491	6.232	0.484	0.895	1.793	0.900	55	88	51	46	79	44	57	60.000	60	; positions_6nt_m2 versus MA0102.2 (CEBPA); m=1/2; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 60; ---TtkygCAAy--- ; cor=0.819; Ncor=0.491; logoDP=6.232; NIcor=0.484; NsEucl=0.895; SSD=1.793; NSW=0.900; rcor=55; rNcor=88; rlogoDP=51; rNIcor=46; rNsEucl=79; rSSD=44; rNSW=57; rank_mean=60.000; match_rank=60 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0102.1_shift3 (Cebpa)		0.760	0.608	6.251	0.605	0.906	2.544	0.894	105	42	49	24	46	99	74	62.714	65	; positions_6nt_m2 versus MA0102.1 (Cebpa); m=2/2; ncol2=12; w=12; offset=3; strand=D; shift=3; score=62.7143; ---TtkygCAAyvyb ; cor=0.760; Ncor=0.608; logoDP=6.251; NIcor=0.605; NsEucl=0.906; SSD=2.544; NSW=0.894; rcor=105; rNcor=42; rlogoDP=49; rNIcor=24; rNsEucl=46; rSSD=99; rNSW=74; rank_mean=62.714; match_rank=65 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)																		; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wyCTCTTGCACAACTbh ; Alignment reference a 53 47 13 1 20 0 1 2 0 181 11 196 198 3 6 36 50 c 42 60 160 8 161 0 0 0 199 8 186 2 1 179 15 54 54 g 46 38 9 0 18 0 1 190 1 3 1 1 0 3 4 54 25 t 59 55 18 191 1 200 198 8 0 8 2 1 1 15 175 56 71
MA0102.3_shift4 (CEBPA)		0.811	0.525	9.745	0.510	0.900	2.402	0.891	66	73	11	40	63	90	78	60.143	61	; positions_7nt_m5 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=60.1429; ----aTTGCAyAAym-- ; cor=0.811; Ncor=0.525; logoDP=9.745; NIcor=0.510; NsEucl=0.900; SSD=2.402; NSW=0.891; rcor=66; rNcor=73; rlogoDP=11; rNIcor=40; rNsEucl=63; rSSD=90; rNSW=78; rank_mean=60.143; match_rank=61 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.791	0.512	9.578	0.490	0.895	2.681	0.878	79	79	18	45	81	108	100	72.857	82	; positions_7nt_m5 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score=72.8571; ---kATTGCAymAy--- ; cor=0.791; Ncor=0.512; logoDP=9.578; NIcor=0.490; NsEucl=0.895; SSD=2.681; NSW=0.878; rcor=79; rNcor=79; rlogoDP=18; rNIcor=45; rNsEucl=81; rSSD=108; rNSW=100; rank_mean=72.857; match_rank=82 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.2_shift5 (CEBPA)		0.774	0.410	6.119	0.384	0.877	2.449	0.864	96	111	54	60	109	95	111	90.857	107	; positions_7nt_m5 versus MA0102.2 (CEBPA); m=3/3; ncol2=9; w=9; offset=5; strand=D; shift=5; score=90.8571; -----TtkygCAAy--- ; cor=0.774; Ncor=0.410; logoDP=6.119; NIcor=0.384; NsEucl=0.877; SSD=2.449; NSW=0.864; rcor=96; rNcor=111; rlogoDP=54; rNIcor=60; rNsEucl=109; rSSD=95; rNSW=111; rank_mean=90.857; match_rank=107 a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)																		; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=0; ncol=14; ttTTCTTTTCTtt- ; Alignment reference a 277 295 138 193 3 0 6 8 2 1 7 292 280 0 c 246 196 49 43 1346 1 0 0 1 1348 16 261 295 0 g 214 181 39 30 0 11 1 0 0 0 46 240 172 0 t 612 677 1123 1083 0 1337 1342 1341 1346 0 1280 556 602 0
MA0035.3_shift2 (Gata1)		0.767	0.649	9.322	0.657	0.896	2.625	0.881	100	24	23	13	73	104	95	61.714	64	; oligos_6nt_mkv4_m4 versus MA0035.3 (Gata1); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score=61.7143; --tyCTTATCTsy- ; cor=0.767; Ncor=0.649; logoDP=9.322; NIcor=0.657; NsEucl=0.896; SSD=2.625; NSW=0.881; rcor=100; rNcor=24; rlogoDP=23; rNIcor=13; rNsEucl=73; rSSD=104; rNSW=95; rank_mean=61.714; match_rank=64 a 0 0 2035 506 0 0 0 17955 0 0 2166 2502 1886 0 c 0 0 4321 6406 14869 697 0 0 0 17955 0 6166 5072 0 g 0 0 2530 2792 437 0 0 0 0 0 0 6687 1598 0 t 0 0 9069 8251 2649 17258 17955 0 17955 0 15789 2600 9399 0
MA0482.1_shift3 (Gata4)		0.757	0.541	8.941	0.551	0.887	2.550	0.872	107	67	27	32	99	100	104	76.571	86	; oligos_6nt_mkv4_m4 versus MA0482.1 (Gata4); m=2/3; ncol2=11; w=10; offset=3; strand=D; shift=3; score=76.5714; ---yCTTATCTsyy ; cor=0.757; Ncor=0.541; logoDP=8.941; NIcor=0.551; NsEucl=0.887; SSD=2.550; NSW=0.872; rcor=107; rNcor=67; rlogoDP=27; rNIcor=32; rNsEucl=99; rSSD=100; rNSW=104; rank_mean=76.571; match_rank=86 a 0 0 0 10 0 0 0 2707 0 0 547 0 601 386 c 0 0 0 1039 2165 89 0 39 0 2746 0 1240 1004 929 g 0 0 0 374 306 0 0 0 0 0 0 940 157 682 t 0 0 0 1323 275 2657 2746 0 2746 0 2199 566 984 749
MA0037.2_rc_shift3 (GATA3_rc)		0.787	0.484	2.031	-0.076	0.867	2.256	0.859	84	91	96	100	112	78	113	96.286	113	; oligos_6nt_mkv4_m4 versus MA0037.2_rc (GATA3_rc); m=3/3; ncol2=8; w=8; offset=3; strand=R; shift=3; score=96.2857; ---tYTTATCT--- ; cor=0.787; Ncor=0.484; logoDP=2.031; NIcor=-0.076; NsEucl=0.867; SSD=2.256; NSW=0.859; rcor=84; rNcor=91; rlogoDP=96; rNIcor=100; rNsEucl=112; rSSD=78; rNSW=113; rank_mean=96.286; match_rank=113 a 0 0 0 0 0 0 0 4628 0 0 0 0 0 0 c 0 0 0 1120 3338 0 0 0 0 4628 0 0 0 0 g 0 0 0 712 0 0 0 0 0 0 0 0 0 0 t 0 0 0 2796 1290 4628 4628 0 4628 0 4628 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)																		; positions_6nt_m3; m=0 (reference); ncol1=13; shift=1; ncol=14; -rmAGTTGCAAAay ; Alignment reference a 0 120 119 350 0 0 0 0 0 351 350 352 225 70 c 0 77 101 2 0 0 1 0 352 0 0 0 30 93 g 0 92 72 0 352 0 0 352 0 1 0 0 52 71 t 0 63 60 0 0 352 351 0 0 0 2 0 45 118
MA0100.1_shift0 (Myb)		0.807	0.403	6.308	0.382	0.880	1.405	0.900	70	115	43	61	107	18	59	67.571	73	; positions_6nt_m3 versus MA0100.1 (Myb); m=1/4; ncol2=8; w=7; offset=-1; strand=D; shift=0; score=67.5714; grCvGTTG------ ; cor=0.807; Ncor=0.403; logoDP=6.308; NIcor=0.382; NsEucl=0.880; SSD=1.405; NSW=0.900; rcor=70; rNcor=115; rlogoDP=43; rNIcor=61; rNsEucl=107; rSSD=18; rNSW=59; rank_mean=67.571; match_rank=73 a 8 22 2 16 1 2 0 6 0 0 0 0 0 0 c 4 1 48 17 0 1 0 0 0 0 0 0 0 0 g 34 25 1 16 50 0 0 44 0 0 0 0 0 0 t 5 3 0 2 0 48 51 1 0 0 0 0 0 0
MA0102.3_shift4 (CEBPA)		0.769	0.549	8.658	0.519	0.886	2.598	0.870	99	63	30	39	101	103	108	77.571	88	; positions_6nt_m3 versus MA0102.3 (CEBPA); m=2/4; ncol2=11; w=10; offset=3; strand=D; shift=4; score=77.5714; ----aTTGCAyAAy ; cor=0.769; Ncor=0.549; logoDP=8.658; NIcor=0.519; NsEucl=0.886; SSD=2.598; NSW=0.870; rcor=99; rNcor=63; rlogoDP=30; rNIcor=39; rNsEucl=101; rSSD=103; rNSW=108; rank_mean=77.571; match_rank=88 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826
MA0102.2_rc_shift4 (CEBPA_rc)		0.759	0.525	4.504	0.217	0.873	2.632	0.854	106	72	61	63	111	105	114	90.286	106	; positions_6nt_m3 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=3; strand=R; shift=4; score=90.2857; ----rTTGcrmaA- ; cor=0.759; Ncor=0.525; logoDP=4.504; NIcor=0.217; NsEucl=0.873; SSD=2.632; NSW=0.854; rcor=106; rNcor=72; rlogoDP=61; rNIcor=63; rNsEucl=111; rSSD=105; rNSW=114; rank_mean=90.286; match_rank=106 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0
MA0152.1_rc_shift6 (NFATC2_rc)		0.752	0.405	0.914	-0.051	0.852	2.144	0.847	112	114	101	98	115	68	115	103.286	115	; positions_6nt_m3 versus MA0152.1_rc (NFATC2_rc); m=4/4; ncol2=7; w=7; offset=5; strand=R; shift=6; score=103.286; ------TGGAAAA- ; cor=0.752; Ncor=0.405; logoDP=0.914; NIcor=-0.051; NsEucl=0.852; SSD=2.144; NSW=0.847; rcor=112; rNcor=114; rlogoDP=101; rNIcor=98; rNsEucl=115; rSSD=68; rNSW=115; rank_mean=103.286; match_rank=115 a 0 0 0 0 0 0 4 0 0 26 24 21 20 0 c 0 0 0 0 0 0 1 0 0 0 0 2 2 0 g 0 0 0 0 0 0 3 26 25 0 1 2 1 0 t 0 0 0 0 0 0 18 0 1 0 1 1 3 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift2 ; 3 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m2_shift2 (oligos_7nt_mkv5_m2)																		; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=2; ncol=15; --wwATTTTTAAaw- ; Alignment reference a 0 0 733 697 2692 0 0 0 0 0 2692 2691 1303 989 0 c 0 0 574 667 0 0 0 0 0 0 0 1 332 343 0 g 0 0 419 398 0 0 0 0 0 0 0 0 578 427 0 t 0 0 966 930 0 2692 2692 2692 2692 2692 0 0 479 933 0
MA0151.1_rc_shift7 (ARID3A_rc)		0.820	0.410	6.330	0.335	0.864	1.339	0.888	53	110	42	62	113	15	83	68.286	74	; oligos_7nt_mkv5_m2 versus MA0151.1_rc (ARID3A_rc); m=1/2; ncol2=6; w=6; offset=5; strand=R; shift=7; score=68.2857; -------TTTrAT-- ; cor=0.820; Ncor=0.410; logoDP=6.330; NIcor=0.335; NsEucl=0.864; SSD=1.339; NSW=0.888; rcor=53; rNcor=110; rlogoDP=42; rNIcor=62; rNsEucl=113; rSSD=15; rNSW=83; rank_mean=68.286; match_rank=74 a 0 0 0 0 0 0 0 6 0 0 17 27 0 0 0 c 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 t 0 0 0 0 0 0 0 20 27 27 1 0 27 0 0
MA0497.1_rc_shift0 (MEF2C_rc)		0.751	0.601	2.167	-0.067	0.901	2.826	0.882	115	46	95	99	60	114	91	88.571	105	; oligos_7nt_mkv5_m2 versus MA0497.1_rc (MEF2C_rc); m=2/2; ncol2=15; w=12; offset=-2; strand=R; shift=0; score=88.5714; wkCTATTTTTrgmhy ; cor=0.751; Ncor=0.601; logoDP=2.167; NIcor=-0.067; NsEucl=0.901; SSD=2.826; NSW=0.882; rcor=115; rNcor=46; rlogoDP=95; rNIcor=99; rNsEucl=60; rSSD=114; rNSW=91; rank_mean=88.571; match_rank=105 a 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752 507 c 126 148 1671 32 0 4 2 87 241 74 0 78 822 573 676 g 450 836 120 0 62 0 0 0 32 256 985 1412 196 151 321 t 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733 705

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)																		; positions_7nt_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; arATGATGCAACCAkw ; Alignment reference a 134 112 325 0 1 338 15 1 14 362 355 10 36 327 85 104 c 69 68 14 0 2 1 5 1 342 0 1 269 315 12 84 72 g 90 100 20 0 336 10 10 356 0 0 6 10 3 6 99 69 t 69 82 3 362 23 13 332 4 6 0 0 73 8 17 94 117
MA0102.3_rc_shift1 (CEBPA_rc)		0.776	0.534	4.707	0.144	0.897	2.567	0.883	95	70	60	72	71	101	89	79.714	93	; positions_7nt_m4 versus MA0102.3_rc (CEBPA_rc); m=1/2; ncol2=11; w=11; offset=1; strand=R; shift=1; score=79.7143; -krTTrTGCAAt---- ; cor=0.776; Ncor=0.534; logoDP=4.707; NIcor=0.144; NsEucl=0.897; SSD=2.567; NSW=0.883; rcor=95; rNcor=70; rlogoDP=60; rNIcor=72; rNsEucl=71; rSSD=101; rNSW=89; rank_mean=79.714; match_rank=93 a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
MA0466.1_rc_shift2 (CEBPB_rc)		0.804	0.553	1.196	-0.168	0.900	2.425	0.890	71	62	100	110	65	94	82	83.429	99	; positions_7nt_m4 versus MA0466.1_rc (CEBPB_rc); m=2/2; ncol2=11; w=11; offset=2; strand=R; shift=2; score=83.4286; --rTkrTGCAATm--- ; cor=0.804; Ncor=0.553; logoDP=1.196; NIcor=-0.168; NsEucl=0.900; SSD=2.425; NSW=0.890; rcor=71; rNcor=62; rlogoDP=100; rNIcor=110; rNsEucl=65; rSSD=94; rNSW=82; rank_mean=83.429; match_rank=99 a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)																		; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=11; waCAAAACwa- ; Alignment reference a 3789 3782 0 9991 9991 9991 9991 0 4608 3524 0 c 1446 1847 9991 0 0 0 0 9991 2039 2075 0 g 1693 1936 0 0 0 0 0 0 531 1897 0 t 3063 2426 0 0 0 0 0 0 2813 2495 0
MA0087.1_rc_shift4 (Sox5_rc)		0.767	0.418	1.994	0.014	0.855	1.516	0.874	101	107	97	93	114	24	102	91.143	108	; oligos_6nt_mkv4_m2 versus MA0087.1_rc (Sox5_rc); m=1/1; ncol2=7; w=6; offset=4; strand=R; shift=4; score=91.1429; ----wAACAAT ; cor=0.767; Ncor=0.418; logoDP=1.994; NIcor=0.014; NsEucl=0.855; SSD=1.516; NSW=0.874; rcor=101; rNcor=107; rlogoDP=97; rNIcor=93; rNsEucl=114; rSSD=24; rNSW=102; rank_mean=91.143; match_rank=108 a 0 0 0 0 8 21 22 0 23 22 0 c 0 0 0 0 4 0 0 22 0 1 0 g 0 0 0 0 3 1 1 0 0 0 0 t 0 0 0 0 8 1 0 1 0 0 23