One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/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/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift4 ; 16 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_shift4 (oligos_7nt_mkv5_m2)																		; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=16; ----rrTGACTCAbm- ; Alignment reference a 0 0 0 0 236 279 0 2 812 0 0 2 805 92 215 0 c 0 0 0 0 164 183 4 1 0 812 0 812 1 220 217 0 g 0 0 0 0 229 255 0 811 2 2 2 0 8 245 181 0 t 0 0 0 0 185 97 810 0 0 0 812 0 0 257 201 0
MA0478.1_shift3 (FOSL2)		0.954	0.795	11.120	0.795	0.951	0.478	0.976	9	5	6	5	7	11	6	7.000	1	; oligos_7nt_mkv5_m2 versus MA0478.1 (FOSL2); m=1/15; ncol2=11; w=10; offset=-1; strand=D; shift=3; score= 7; ---krrTGAsTCAb-- ; cor=0.954; Ncor=0.795; logoDP=11.120; NIcor=0.795; NsEucl=0.951; SSD=0.478; NSW=0.976; rcor=9; rNcor=5; rlogoDP=6; rNIcor=5; rNsEucl=7; rSSD=11; rNSW=6; rank_mean=7.000; match_rank=1 a 0 0 0 833 1525 2861 0 0 5075 0 0 205 5318 0 0 0 c 0 0 0 994 592 55 0 0 51 3286 0 5113 0 1399 0 0 g 0 0 0 2086 2707 2328 0 5318 192 1838 0 0 0 1933 0 0 t 0 0 0 1405 494 74 5318 0 0 194 5318 0 0 1986 0 0
MA0477.1_shift4 (FOSL1)		0.943	0.943	11.500	0.945	0.951	0.593	0.973	15	1	2	1	8	18	9	7.714	2	; oligos_7nt_mkv5_m2 versus MA0477.1 (FOSL1); m=2/15; ncol2=11; w=11; offset=0; strand=D; shift=4; score= 7.7143; ----rrTGAsTCAks- ; cor=0.943; Ncor=0.943; logoDP=11.500; NIcor=0.945; NsEucl=0.951; SSD=0.593; NSW=0.973; rcor=15; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=8; rSSD=18; rNSW=9; rank_mean=7.714; match_rank=2 a 0 0 0 0 1791 1568 0 0 5272 124 0 177 5272 37 1184 0 c 0 0 0 0 119 437 0 0 0 3120 0 5095 0 811 1684 0 g 0 0 0 0 2384 3109 0 5272 0 2028 0 0 0 1734 1875 0 t 0 0 0 0 978 158 5272 0 0 0 5272 0 0 2690 529 0
MA0490.1_shift3 (JUNB)		0.949	0.791	11.221	0.790	0.949	0.522	0.974	10	6	4	6	9	14	7	8.000	3	; oligos_7nt_mkv5_m2 versus MA0490.1 (JUNB); m=3/15; ncol2=11; w=10; offset=-1; strand=D; shift=3; score= 8; ---grrTGAsTCAk-- ; cor=0.949; Ncor=0.791; logoDP=11.221; NIcor=0.790; NsEucl=0.949; SSD=0.522; NSW=0.974; rcor=10; rNcor=6; rlogoDP=4; rNIcor=6; rNsEucl=9; rSSD=14; rNSW=7; rank_mean=8.000; match_rank=3 a 0 0 0 3605 5055 8384 0 0 16992 0 0 1256 16992 736 0 0 c 0 0 0 3366 1057 582 0 0 0 9859 0 15736 0 2962 0 0 g 0 0 0 5983 8427 8026 0 16992 0 6281 0 0 0 6117 0 0 t 0 0 0 4038 2453 0 16992 0 0 852 16992 0 0 7177 0 0
MA0491.1_shift4 (JUND)		0.926	0.926	11.425	0.920	0.943	0.783	0.964	17	2	3	2	11	21	17	10.429	4	; oligos_7nt_mkv5_m2 versus MA0491.1 (JUND); m=4/15; ncol2=11; w=11; offset=0; strand=D; shift=4; score=10.4286; ----drTGAsTCATs- ; cor=0.926; Ncor=0.926; logoDP=11.425; NIcor=0.920; NsEucl=0.943; SSD=0.783; NSW=0.964; rcor=17; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=11; rSSD=21; rNSW=17; rank_mean=10.429; match_rank=4 a 0 0 0 0 12389 15163 0 0 38710 0 0 1547 38710 0 5786 0 c 0 0 0 0 759 4824 0 0 0 22857 0 37163 0 5136 14956 0 g 0 0 0 0 13640 18723 0 38710 0 14078 0 0 0 2301 12429 0 t 0 0 0 0 11922 0 38710 0 0 1775 38710 0 0 31273 5539 0
MA0476.1_shift4 (FOS)		0.921	0.921	10.973	0.913	0.942	0.809	0.963	21	3	7	3	12	22	18	12.286	6	; oligos_7nt_mkv5_m2 versus MA0476.1 (FOS); m=5/15; ncol2=11; w=11; offset=0; strand=D; shift=4; score=12.2857; ----dvTGAsTCATb- ; cor=0.921; Ncor=0.921; logoDP=10.973; NIcor=0.913; NsEucl=0.942; SSD=0.809; NSW=0.963; rcor=21; rNcor=3; rlogoDP=7; rNIcor=3; rNsEucl=12; rSSD=22; rNSW=18; rank_mean=12.286; match_rank=6 a 0 0 0 0 7879 7475 0 0 29396 998 0 0 29396 258 4006 0 c 0 0 0 0 712 10177 0 0 0 14079 0 29396 0 5823 8236 0 g 0 0 0 0 9686 10841 0 27108 0 11206 0 0 0 1538 7897 0 t 0 0 0 0 11119 903 29396 2288 0 3113 29396 0 0 21777 9257 0
MA0489.1_shift0 (JUN_(var.2))		0.947	0.631	10.826	0.626	0.948	0.547	0.973	14	24	8	19	10	15	10	14.286	8	; oligos_7nt_mkv5_m2 versus MA0489.1 (JUN_(var.2)); m=6/15; ncol2=14; w=10; offset=-4; strand=D; shift=0; score=14.2857; rrrrrrTGAsTCAt-- ; cor=0.947; Ncor=0.631; logoDP=10.826; NIcor=0.626; NsEucl=0.948; SSD=0.547; NSW=0.973; rcor=14; rNcor=24; rlogoDP=8; rNIcor=19; rNsEucl=10; rSSD=15; rNSW=10; rank_mean=14.286; match_rank=8 a 4852 3927 3726 4396 4146 5930 0 0 10953 382 199 956 10956 376 0 0 c 1250 1324 1127 1122 593 993 0 0 0 5704 0 10000 0 2509 0 0 g 2818 4110 4330 3461 4213 4033 0 10956 0 4090 0 0 0 2645 0 0 t 2036 1595 1773 1977 2004 0 10956 0 3 780 10757 0 0 5426 0 0
MA0099.2_shift6 (JUN::FOS)		0.974	0.620	7.313	0.622	0.934	0.422	0.970	4	28	66	20	22	8	13	23.000	15	; oligos_7nt_mkv5_m2 versus MA0099.2 (JUN::FOS); m=7/15; ncol2=7; w=7; offset=2; strand=D; shift=6; score= 23; ------TGAmTCA--- ; cor=0.974; Ncor=0.620; logoDP=7.313; NIcor=0.622; NsEucl=0.934; SSD=0.422; NSW=0.970; rcor=4; rNcor=28; rlogoDP=66; rNIcor=20; rNsEucl=22; rSSD=8; rNSW=13; rank_mean=23.000; match_rank=15 a 0 0 0 0 0 0 0 0 16 5 3 0 16 0 0 0 c 0 0 0 0 0 0 1 0 2 12 0 15 0 0 0 0 g 0 0 0 0 0 0 0 15 0 1 1 3 1 0 0 0 t 0 0 0 0 0 0 17 3 0 0 14 0 1 0 0 0
MA0462.1_shift2 (BATF::JUN)		0.909	0.630	10.268	0.620	0.925	0.916	0.949	25	26	13	21	38	28	31	26.000	18	; oligos_7nt_mkv5_m2 versus MA0462.1 (BATF::JUN); m=8/15; ncol2=11; w=9; offset=-2; strand=D; shift=2; score= 26; --rrwATGAsTCA--- ; cor=0.909; Ncor=0.630; logoDP=10.268; NIcor=0.620; NsEucl=0.925; SSD=0.916; NSW=0.949; rcor=25; rNcor=26; rlogoDP=13; rNIcor=21; rNsEucl=38; rSSD=28; rNSW=31; rank_mean=26.000; match_rank=18 a 0 0 3082 4782 4519 8258 0 0 10522 586 0 1291 10264 0 0 0 c 0 0 481 553 170 1478 0 0 0 5026 0 8590 0 0 0 0 g 0 0 5136 2889 2219 0 0 10374 0 4910 0 641 0 0 0 0 t 0 0 1823 2298 3614 786 10522 148 0 0 10522 0 258 0 0 0
MA0591.1_shift2 (Bach1::Mafk)		0.859	0.630	10.367	0.606	0.917	1.656	0.925	55	25	11	25	58	83	68	46.429	35	; oligos_7nt_mkv5_m2 versus MA0591.1 (Bach1::Mafk); m=9/15; ncol2=15; w=11; offset=-2; strand=D; shift=2; score=46.4286; --rssrTGACTCAGCA ; cor=0.859; Ncor=0.630; logoDP=10.367; NIcor=0.606; NsEucl=0.917; SSD=1.656; NSW=0.925; rcor=55; rNcor=25; rlogoDP=11; rNIcor=25; rNsEucl=58; rSSD=83; rNSW=68; rank_mean=46.429; match_rank=35 a 0 0 45 14 15 66 2 0 113 0 1 5 108 0 0 98 c 0 0 14 36 41 16 1 0 0 94 0 107 1 1 114 4 g 0 0 41 46 54 32 0 107 0 20 4 2 3 113 0 6 t 0 0 14 18 4 0 111 7 1 0 109 0 2 0 0 6
MA0089.1_shift4 (NFE2L1::MafG)		0.922	0.503	5.953	0.490	0.919	0.471	0.961	20	85	94	70	51	10	19	49.857	44	; oligos_7nt_mkv5_m2 versus MA0089.1 (NFE2L1::MafG); m=10/15; ncol2=6; w=6; offset=0; strand=D; shift=4; score=49.8571; ----sATGAC------ ; cor=0.922; Ncor=0.503; logoDP=5.953; NIcor=0.490; NsEucl=0.919; SSD=0.471; NSW=0.961; rcor=20; rNcor=85; rlogoDP=94; rNIcor=70; rNsEucl=51; rSSD=10; rNSW=19; rank_mean=49.857; match_rank=44 a 0 0 0 0 7 29 0 1 34 0 0 0 0 0 0 0 c 0 0 0 0 11 2 0 0 0 26 0 0 0 0 0 0 g 0 0 0 0 10 3 0 32 0 2 0 0 0 0 0 0 t 0 0 0 0 6 0 34 1 0 6 0 0 0 0 0 0
MA0150.2_shift1 (Nfe2l2)		0.839	0.615	8.330	0.579	0.916	1.716	0.922	71	31	36	34	65	92	75	57.714	50	; oligos_7nt_mkv5_m2 versus MA0150.2 (Nfe2l2); m=11/15; ncol2=15; w=11; offset=-3; strand=D; shift=1; score=57.7143; -casmrTGACTCAGCA ; cor=0.839; Ncor=0.615; logoDP=8.330; NIcor=0.579; NsEucl=0.916; SSD=1.716; NSW=0.922; rcor=71; rNcor=31; rlogoDP=36; rNIcor=34; rNsEucl=65; rSSD=92; rNSW=75; rank_mean=57.714; match_rank=50 a 0 166 401 118 203 488 0 0 726 20 84 65 577 10 4 623 c 0 338 78 239 247 28 0 0 0 533 20 549 3 11 699 26 g 0 109 159 275 152 205 0 711 0 118 16 46 90 698 19 31 t 0 113 88 94 124 5 726 15 0 55 606 66 56 7 4 46
MA0501.1_shift5 (NFE2::MAF)		0.863	0.539	9.764	0.513	0.912	1.545	0.923	51	61	18	59	77	74	73	59.000	52	; oligos_7nt_mkv5_m2 versus MA0501.1 (NFE2::MAF); m=12/15; ncol2=15; w=10; offset=1; strand=D; shift=5; score= 59; -----rTGACTCAGCA ; cor=0.863; Ncor=0.539; logoDP=9.764; NIcor=0.513; NsEucl=0.912; SSD=1.545; NSW=0.923; rcor=51; rNcor=61; rlogoDP=18; rNIcor=59; rNsEucl=77; rSSD=74; rNSW=73; rank_mean=59.000; match_rank=52 a 0 0 0 0 0 726 0 0 1090 16 110 80 978 8 0 931 c 0 0 0 0 0 26 0 0 0 871 1 937 0 4 1063 17 g 0 0 0 0 0 334 0 1082 0 166 12 22 51 1041 22 73 t 0 0 0 0 0 4 1090 8 0 37 967 51 61 37 5 69
MA0099.1_rc_shift6 (JUN::FOS_rc)		0.920	0.669	0.532	-0.216	0.920	0.813	0.949	22	18	141	149	49	23	30	61.714	54	; oligos_7nt_mkv5_m2 versus MA0099.1_rc (JUN::FOS_rc); m=13/15; ncol2=8; w=8; offset=2; strand=R; shift=6; score=61.7143; ------TKAsTCAy-- ; cor=0.920; Ncor=0.669; logoDP=0.532; NIcor=-0.216; NsEucl=0.920; SSD=0.813; NSW=0.949; rcor=22; rNcor=18; rlogoDP=141; rNIcor=149; rNsEucl=49; rSSD=23; rNSW=30; rank_mean=61.714; match_rank=54 a 0 0 0 0 0 0 1 0 17 3 0 0 19 0 0 0 c 0 0 0 0 0 0 0 0 0 9 0 18 0 12 0 0 g 0 0 0 0 0 0 0 13 1 6 1 1 0 2 0 0 t 0 0 0 0 0 0 18 6 1 1 18 0 0 5 0 0
MA0150.1_shift5 (NFE2L2)		0.783	0.653	7.508	0.588	0.894	2.227	0.889	124	20	62	29	124	133	137	89.857	93	; oligos_7nt_mkv5_m2 versus MA0150.1 (NFE2L2); m=14/15; ncol2=11; w=10; offset=1; strand=D; shift=5; score=89.8571; -----rTGACwmAGCA ; cor=0.783; Ncor=0.653; logoDP=7.508; NIcor=0.588; NsEucl=0.894; SSD=2.227; NSW=0.889; rcor=124; rNcor=20; rlogoDP=62; rNIcor=29; rNsEucl=124; rSSD=133; rNSW=137; rank_mean=89.857; match_rank=93 a 0 0 0 0 0 10 0 0 20 0 6 5 16 0 0 15 c 0 0 0 0 0 1 0 0 0 17 2 10 0 0 20 2 g 0 0 0 0 0 9 0 19 0 1 1 1 2 20 0 2 t 0 0 0 0 0 0 20 1 0 2 11 4 2 0 0 1
MA0067.1_rc_shift3 (Pax2_rc)		0.821	0.479	0.313	-0.162	0.888	1.233	0.912	84	100	147	145	131	48	99	107.714	117	; oligos_7nt_mkv5_m2 versus MA0067.1_rc (Pax2_rc); m=15/15; ncol2=8; w=7; offset=-1; strand=R; shift=3; score=107.714; ---vmrTGAcw----- ; cor=0.821; Ncor=0.479; logoDP=0.313; NIcor=-0.162; NsEucl=0.888; SSD=1.233; NSW=0.912; rcor=84; rNcor=100; rlogoDP=147; rNIcor=145; rNsEucl=131; rSSD=48; rNSW=99; rank_mean=107.714; match_rank=117 a 0 0 0 8 10 11 1 2 26 2 9 0 0 0 0 0 c 0 0 0 11 19 1 3 1 0 21 5 0 0 0 0 0 g 0 0 0 11 0 17 1 28 2 1 7 0 0 0 0 0 t 0 0 0 1 2 2 26 0 3 7 10 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift9 ; 18 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_shift9 (oligos_6nt_mkv4_m4)																		; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=9; ncol=20; ---------cvAGGTCAGsg ; Alignment reference a 0 0 0 0 0 0 0 0 0 226 281 963 0 0 0 0 961 15 236 236 c 0 0 0 0 0 0 0 0 0 281 294 9 10 0 1 977 3 93 253 211 g 0 0 0 0 0 0 0 0 0 231 275 4 967 977 1 0 12 821 340 327 t 0 0 0 0 0 0 0 0 0 239 127 1 0 0 975 0 1 48 148 203
MA0071.1_shift7 (RORA_1)		0.977	0.601	10.345	0.606	0.960	0.206	0.987	3	36	12	26	3	3	3	12.286	5	; oligos_6nt_mkv4_m4 versus MA0071.1 (RORA_1); m=1/17; ncol2=10; w=8; offset=-2; strand=D; shift=7; score=12.2857; -------wwcwAGGTCA--- ; cor=0.977; Ncor=0.601; logoDP=10.345; NIcor=0.606; NsEucl=0.960; SSD=0.206; NSW=0.987; rcor=3; rNcor=36; rlogoDP=12; rNIcor=26; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=12.286; match_rank=5 a 0 0 0 0 0 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 c 0 0 0 0 0 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 g 0 0 0 0 0 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 t 0 0 0 0 0 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0
MA0512.1_shift8 (Rxra)		0.887	0.739	8.345	0.734	0.927	1.060	0.947	38	10	34	8	33	35	34	27.429	19	; oligos_6nt_mkv4_m4 versus MA0512.1 (Rxra); m=2/17; ncol2=11; w=10; offset=-1; strand=D; shift=8; score=27.4286; --------CArAGKTCAgd- ; cor=0.887; Ncor=0.739; logoDP=8.345; NIcor=0.734; NsEucl=0.927; SSD=1.060; NSW=0.947; rcor=38; rNcor=10; rlogoDP=34; rNIcor=8; rNsEucl=33; rSSD=35; rNSW=34; rank_mean=27.429; match_rank=19 a 0 0 0 0 0 0 0 0 278 4154 2623 4877 0 0 0 0 5348 1150 1640 0 c 0 0 0 0 0 0 0 0 4521 418 252 0 0 0 583 5348 0 1070 742 0 g 0 0 0 0 0 0 0 0 305 9 2473 471 5348 3882 643 0 0 2336 1569 0 t 0 0 0 0 0 0 0 0 244 767 0 0 0 1466 4122 0 0 792 1397 0
MA0258.1_shift9 (ESR2)		0.885	0.541	6.407	0.539	0.932	1.105	0.950	39	60	76	48	24	39	29	45.000	31	; oligos_6nt_mkv4_m4 versus MA0258.1 (ESR2); m=3/17; ncol2=18; w=11; offset=0; strand=D; shift=9; score= 45; ---------cwrGGTCAsgk ; cor=0.885; Ncor=0.541; logoDP=6.407; NIcor=0.539; NsEucl=0.932; SSD=1.105; NSW=0.950; rcor=39; rNcor=60; rlogoDP=76; rNIcor=48; rNsEucl=24; rSSD=39; rNSW=29; rank_mean=45.000; match_rank=31 a 0 0 0 0 0 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 c 0 0 0 0 0 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 g 0 0 0 0 0 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 t 0 0 0 0 0 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97
MA0258.2_shift11 (ESR2)		0.923	0.489	7.461	0.484	0.932	0.759	0.958	19	92	65	75	25	20	21	45.286	32	; oligos_6nt_mkv4_m4 versus MA0258.2 (ESR2); m=4/17; ncol2=15; w=9; offset=2; strand=D; shift=11; score=45.2857; -----------rGGTCAsms ; cor=0.923; Ncor=0.489; logoDP=7.461; NIcor=0.484; NsEucl=0.932; SSD=0.759; NSW=0.958; rcor=19; rNcor=92; rlogoDP=65; rNIcor=75; rNsEucl=25; rSSD=20; rNSW=21; rank_mean=45.286; match_rank=32 a 0 0 0 0 0 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 c 0 0 0 0 0 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 g 0 0 0 0 0 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 t 0 0 0 0 0 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752
MA0141.1_shift5 (Esrrb)		0.910	0.485	8.828	0.476	0.919	0.839	0.948	23	94	27	78	52	24	32	47.143	36	; oligos_6nt_mkv4_m4 versus MA0141.1 (Esrrb); m=5/17; ncol2=12; w=8; offset=-4; strand=D; shift=5; score=47.1429; -----rgsyCAAGGTCA--- ; cor=0.910; Ncor=0.485; logoDP=8.828; NIcor=0.476; NsEucl=0.919; SSD=0.839; NSW=0.948; rcor=23; rNcor=94; rlogoDP=27; rNIcor=78; rNsEucl=52; rSSD=24; rNSW=32; rank_mean=47.143; match_rank=36 a 0 0 0 0 0 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 c 0 0 0 0 0 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 g 0 0 0 0 0 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 t 0 0 0 0 0 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0
MA0141.2_shift5 (Esrrb)		0.910	0.485	8.936	0.475	0.919	0.845	0.947	24	95	25	80	53	25	33	47.857	39	; oligos_6nt_mkv4_m4 versus MA0141.2 (Esrrb); m=6/17; ncol2=12; w=8; offset=-4; strand=D; shift=5; score=47.8571; -----rgsyCAAGGTCA--- ; cor=0.910; Ncor=0.485; logoDP=8.936; NIcor=0.475; NsEucl=0.919; SSD=0.845; NSW=0.947; rcor=24; rNcor=95; rlogoDP=25; rNIcor=80; rNsEucl=53; rSSD=25; rNSW=33; rank_mean=47.857; match_rank=39 a 0 0 0 0 0 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 c 0 0 0 0 0 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 g 0 0 0 0 0 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 t 0 0 0 0 0 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0
MA0160.1_shift10 (NR4A2)		0.870	0.633	7.532	0.627	0.903	1.194	0.925	44	23	61	18	111	45	65	52.429	46	; oligos_6nt_mkv4_m4 versus MA0160.1 (NR4A2); m=7/17; ncol2=8; w=8; offset=1; strand=D; shift=10; score=52.4286; ----------aAGGTCAc-- ; cor=0.870; Ncor=0.633; logoDP=7.532; NIcor=0.627; NsEucl=0.903; SSD=1.194; NSW=0.925; rcor=44; rNcor=23; rlogoDP=61; rNIcor=18; rNsEucl=111; rSSD=45; rNSW=65; rank_mean=52.429; match_rank=46 a 0 0 0 0 0 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 c 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 g 0 0 0 0 0 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 t 0 0 0 0 0 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0
MA0592.1_shift8 (ESRRA)		0.833	0.695	9.293	0.672	0.908	1.696	0.915	76	15	23	13	94	90	89	57.143	49	; oligos_6nt_mkv4_m4 versus MA0592.1 (ESRRA); m=8/17; ncol2=11; w=10; offset=-1; strand=D; shift=8; score=57.1429; --------yCAAGGTCAcm- ; cor=0.833; Ncor=0.695; logoDP=9.293; NIcor=0.672; NsEucl=0.908; SSD=1.696; NSW=0.915; rcor=76; rNcor=15; rlogoDP=23; rNIcor=13; rNsEucl=94; rSSD=90; rNSW=89; rank_mean=57.143; match_rank=49 a 0 0 0 0 0 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 c 0 0 0 0 0 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 g 0 0 0 0 0 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 t 0 0 0 0 0 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0
MA0112.2_shift6 (ESR1)		0.840	0.462	4.366	0.459	0.922	1.484	0.933	70	109	109	89	46	67	50	77.143	68	; oligos_6nt_mkv4_m4 versus MA0112.2 (ESR1); m=9/17; ncol2=20; w=11; offset=-3; strand=D; shift=6; score=77.1429; ------vkscmaGGtCAccc ; cor=0.840; Ncor=0.462; logoDP=4.366; NIcor=0.459; NsEucl=0.922; SSD=1.484; NSW=0.933; rcor=70; rNcor=109; rlogoDP=109; rNIcor=89; rNsEucl=46; rSSD=67; rNSW=50; rank_mean=77.143; match_rank=68 a 0 0 0 0 0 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 c 0 0 0 0 0 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 g 0 0 0 0 0 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 t 0 0 0 0 0 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56
MA0072.1_shift4 (RORA_2)		0.835	0.469	10.206	0.465	0.899	1.640	0.909	74	103	15	85	117	80	105	82.714	79	; oligos_6nt_mkv4_m4 versus MA0072.1 (RORA_2); m=10/17; ncol2=14; w=9; offset=-5; strand=D; shift=4; score=82.7143; ----wwwAwbTAGGTCAr-- ; cor=0.835; Ncor=0.469; logoDP=10.206; NIcor=0.465; NsEucl=0.899; SSD=1.640; NSW=0.909; rcor=74; rNcor=103; rlogoDP=15; rNIcor=85; rNsEucl=117; rSSD=80; rNSW=105; rank_mean=82.714; match_rank=79 a 0 0 0 0 9 17 15 35 23 2 0 28 0 0 0 0 36 15 0 0 c 0 0 0 0 8 2 0 1 0 12 0 0 0 0 0 36 0 6 0 0 g 0 0 0 0 8 7 3 0 0 13 0 8 36 36 0 0 0 10 0 0 t 0 0 0 0 11 10 18 0 13 9 36 0 0 0 36 0 0 5 0 0
MA0112.1_shift9 (ESR1)		0.793	0.485	6.878	0.482	0.912	1.870	0.915	107	97	68	77	78	109	91	89.571	92	; oligos_6nt_mkv4_m4 versus MA0112.1 (ESR1); m=11/17; ncol2=18; w=11; offset=0; strand=D; shift=9; score=89.5714; ---------ccAGGTCaCcr ; cor=0.793; Ncor=0.485; logoDP=6.878; NIcor=0.482; NsEucl=0.912; SSD=1.870; NSW=0.915; rcor=107; rNcor=97; rlogoDP=68; rNIcor=77; rNsEucl=78; rSSD=109; rNSW=91; rank_mean=89.571; match_rank=92 a 0 0 0 0 0 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 c 0 0 0 0 0 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 g 0 0 0 0 0 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 t 0 0 0 0 0 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0
MA0505.1_shift4 (Nr5a2)		0.805	0.503	7.773	0.467	0.902	1.915	0.904	96	84	50	84	113	113	110	92.857	95	; oligos_6nt_mkv4_m4 versus MA0505.1 (Nr5a2); m=12/17; ncol2=15; w=10; offset=-5; strand=D; shift=4; score=92.8571; ----ragtTCAAGGyCAgs- ; cor=0.805; Ncor=0.503; logoDP=7.773; NIcor=0.467; NsEucl=0.902; SSD=1.915; NSW=0.904; rcor=96; rNcor=84; rlogoDP=50; rNIcor=84; rNsEucl=113; rSSD=113; rNSW=110; rank_mean=92.857; match_rank=95 a 0 0 0 0 645 985 276 122 71 8 1685 1679 39 0 169 0 1437 271 249 0 c 0 0 0 0 224 170 198 378 351 1616 14 0 0 0 584 1568 20 345 693 0 g 0 0 0 0 634 336 990 366 23 74 0 23 1663 1702 61 12 90 740 454 0 t 0 0 0 0 199 211 238 836 1257 4 3 0 0 0 888 122 155 346 306 0
MA0504.1_shift9 (NR2C2)		0.771	0.565	5.902	0.534	0.906	2.135	0.903	135	48	95	50	103	126	112	95.571	99	; oligos_6nt_mkv4_m4 versus MA0504.1 (NR2C2); m=13/17; ncol2=15; w=11; offset=0; strand=D; shift=9; score=95.5714; ---------mgrGGTCArAG ; cor=0.771; Ncor=0.565; logoDP=5.902; NIcor=0.534; NsEucl=0.906; SSD=2.135; NSW=0.903; rcor=135; rNcor=48; rlogoDP=95; rNIcor=50; rNsEucl=103; rSSD=126; rNSW=112; rank_mean=95.571; match_rank=99 a 0 0 0 0 0 0 0 0 0 129 82 193 0 10 3 6 343 187 324 10 c 0 0 0 0 0 0 0 0 0 126 70 6 8 3 0 309 0 0 0 0 g 0 0 0 0 0 0 0 0 0 90 221 195 366 355 79 54 48 208 71 385 t 0 0 0 0 0 0 0 0 0 50 22 1 21 27 313 26 4 0 0 0
MA0066.1_shift9 (PPARG)		0.776	0.427	6.761	0.428	0.908	2.052	0.907	129	127	70	94	95	121	108	106.286	114	; oligos_6nt_mkv4_m4 versus MA0066.1 (PPARG); m=14/17; ncol2=20; w=11; offset=0; strand=D; shift=9; score=106.286; ---------sTrGGTCAcsg ; cor=0.776; Ncor=0.427; logoDP=6.761; NIcor=0.428; NsEucl=0.908; SSD=2.052; NSW=0.907; rcor=129; rNcor=127; rlogoDP=70; rNIcor=94; rNsEucl=95; rSSD=121; rNSW=108; rank_mean=106.286; match_rank=114 a 0 0 0 0 0 0 0 0 0 3 3 19 0 1 0 2 26 5 5 4 c 0 0 0 0 0 0 0 0 0 8 0 0 1 0 1 23 1 15 7 2 g 0 0 0 0 0 0 0 0 0 14 0 9 27 26 4 3 0 4 10 18 t 0 0 0 0 0 0 0 0 0 3 25 0 0 1 23 0 1 4 6 4
MA0065.1_shift0 (PPARG::RXRA)		0.778	0.428	8.775	0.416	0.902	2.316	0.895	128	126	29	103	112	138	128	109.143	120	; oligos_6nt_mkv4_m4 versus MA0065.1 (PPARG::RXRA); m=15/17; ncol2=20; w=11; offset=-9; strand=D; shift=0; score=109.143; yywrrGGTCAAAGGTCAymk ; cor=0.778; Ncor=0.428; logoDP=8.775; NIcor=0.416; NsEucl=0.902; SSD=2.316; NSW=0.895; rcor=128; rNcor=126; rlogoDP=29; rNIcor=103; rNsEucl=112; rSSD=138; rNSW=128; rank_mean=109.143; match_rank=120 a 10 7 19 13 17 0 0 0 2 41 41 39 0 0 0 2 38 10 13 7 c 12 13 4 1 0 0 0 2 37 0 0 0 0 0 2 36 1 12 15 10 g 7 8 6 27 24 41 39 0 2 0 0 2 41 39 0 1 2 4 9 12 t 12 13 12 0 0 0 2 39 0 0 0 0 0 2 39 2 0 15 4 12
MA0115.1_shift2 (NR1H2::RXRA)		0.762	0.424	11.168	0.418	0.882	2.804	0.860	142	129	5	100	140	150	150	116.571	132	; oligos_6nt_mkv4_m4 versus MA0115.1 (NR1H2::RXRA); m=16/17; ncol2=17; w=10; offset=-7; strand=D; shift=2; score=116.571; --AAAGGTCAAAGGTCAAc- ; cor=0.762; Ncor=0.424; logoDP=11.168; NIcor=0.418; NsEucl=0.882; SSD=2.804; NSW=0.860; rcor=142; rNcor=129; rlogoDP=5; rNIcor=100; rNsEucl=140; rSSD=150; rNSW=150; rank_mean=116.571; match_rank=132 a 0 0 17 17 20 0 0 0 0 25 24 25 0 0 0 0 25 20 0 0 c 0 0 5 1 0 0 0 0 25 0 0 0 0 0 0 25 0 1 15 0 g 0 0 0 5 5 25 24 0 0 0 0 0 25 25 0 0 0 2 6 0 t 0 0 3 2 0 0 1 25 0 0 1 0 0 0 25 0 0 2 4 0
MA0089.1_rc_shift13 (NFE2L1::MafG_rc)		0.791	0.431	0.095	-0.131	0.862	1.362	0.887	110	124	150	141	149	57	139	124.286	143	; oligos_6nt_mkv4_m4 versus MA0089.1_rc (NFE2L1::MafG_rc); m=17/17; ncol2=6; w=6; offset=4; strand=R; shift=13; score=124.286; -------------GTCATs- ; cor=0.791; Ncor=0.431; logoDP=0.095; NIcor=-0.131; NsEucl=0.862; SSD=1.362; NSW=0.887; rcor=110; rNcor=124; rlogoDP=150; rNIcor=141; rNsEucl=149; rSSD=57; rNSW=139; rank_mean=124.286; match_rank=143 a 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 1 34 0 6 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 32 0 3 10 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 0 0 2 11 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 1 0 29 7 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift3 ; 12 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_shift3 (positions_7nt_m2)																		; positions_7nt_m2; m=0 (reference); ncol1=15; shift=3; ncol=21; ---byCAAGGTCACCttg--- ; Alignment reference a 0 0 0 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 0 0 0 c 0 0 0 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 0 0 0 g 0 0 0 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 0 0 0 t 0 0 0 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62 0 0 0
MA0592.1_shift4 (ESRRA)		0.949	0.696	8.828	0.687	0.951	0.578	0.974	11	14	26	12	6	17	8	13.429	7	; positions_7nt_m2 versus MA0592.1 (ESRRA); m=1/11; ncol2=11; w=11; offset=1; strand=D; shift=4; score=13.4286; ----yCAAGGTCAcm------ ; cor=0.949; Ncor=0.696; logoDP=8.828; NIcor=0.687; NsEucl=0.951; SSD=0.578; NSW=0.974; rcor=11; rNcor=14; rlogoDP=26; rNIcor=12; rNsEucl=6; rSSD=17; rNSW=8; rank_mean=13.429; match_rank=7 a 0 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 0 c 0 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 0 g 0 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 0 t 0 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0 0
MA0141.1_shift1 (Esrrb)		0.987	0.581	8.051	0.580	0.975	0.127	0.994	1	44	42	32	1	1	1	17.429	9	; positions_7nt_m2 versus MA0141.1 (Esrrb); m=2/11; ncol2=12; w=10; offset=-2; strand=D; shift=1; score=17.4286; -rgsyCAAGGTCA-------- ; cor=0.987; Ncor=0.581; logoDP=8.051; NIcor=0.580; NsEucl=0.975; SSD=0.127; NSW=0.994; rcor=1; rNcor=44; rlogoDP=42; rNIcor=32; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=17.429; match_rank=9 a 0 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 c 0 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 g 0 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 t 0 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0
MA0141.2_shift1 (Esrrb)		0.987	0.580	8.159	0.580	0.974	0.131	0.993	2	45	39	33	2	2	2	17.857	10	; positions_7nt_m2 versus MA0141.2 (Esrrb); m=3/11; ncol2=12; w=10; offset=-2; strand=D; shift=1; score=17.8571; -rgsyCAAGGTCA-------- ; cor=0.987; Ncor=0.580; logoDP=8.159; NIcor=0.580; NsEucl=0.974; SSD=0.131; NSW=0.993; rcor=2; rNcor=45; rlogoDP=39; rNIcor=33; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=17.857; match_rank=10 a 0 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 c 0 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 g 0 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 t 0 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0
MA0071.1_shift3 (RORA_1)		0.887	0.591	8.312	0.590	0.926	1.103	0.945	36	39	37	28	36	38	38	36.000	24	; positions_7nt_m2 versus MA0071.1 (RORA_1); m=4/11; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 36; ---wwcwAGGTCA-------- ; cor=0.887; Ncor=0.591; logoDP=8.312; NIcor=0.590; NsEucl=0.926; SSD=1.103; NSW=0.945; rcor=36; rNcor=39; rlogoDP=37; rNIcor=28; rNsEucl=36; rSSD=38; rNSW=38; rank_mean=36.000; match_rank=24 a 0 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 c 0 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 g 0 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
MA0160.1_shift6 (NR4A2)		0.959	0.511	6.265	0.505	0.941	0.438	0.973	8	76	82	63	13	9	11	37.429	25	; positions_7nt_m2 versus MA0160.1 (NR4A2); m=5/11; ncol2=8; w=8; offset=3; strand=D; shift=6; score=37.4286; ------aAGGTCAc------- ; cor=0.959; Ncor=0.511; logoDP=6.265; NIcor=0.505; NsEucl=0.941; SSD=0.438; NSW=0.973; rcor=8; rNcor=76; rlogoDP=82; rNIcor=63; rNsEucl=13; rSSD=9; rNSW=11; rank_mean=37.429; match_rank=25 a 0 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 g 0 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0
MA0258.2_shift7 (ESR2)		0.898	0.520	6.101	0.511	0.938	0.927	0.958	33	72	90	60	15	29	22	45.857	33	; positions_7nt_m2 versus MA0258.2 (ESR2); m=6/11; ncol2=15; w=11; offset=4; strand=D; shift=7; score=45.8571; -------rGGTCAsmstGaCC ; cor=0.898; Ncor=0.520; logoDP=6.101; NIcor=0.511; NsEucl=0.938; SSD=0.927; NSW=0.958; rcor=33; rNcor=72; rlogoDP=90; rNIcor=60; rNsEucl=15; rSSD=29; rNSW=22; rank_mean=45.857; match_rank=33 a 0 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 c 0 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 g 0 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 t 0 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278
MA0505.1_shift0 (Nr5a2)		0.864	0.576	7.995	0.561	0.927	1.523	0.937	50	46	46	40	32	72	45	47.286	38	; positions_7nt_m2 versus MA0505.1 (Nr5a2); m=7/11; ncol2=15; w=12; offset=-3; strand=D; shift=0; score=47.2857; ragtTCAAGGyCAgs------ ; cor=0.864; Ncor=0.576; logoDP=7.995; NIcor=0.561; NsEucl=0.927; SSD=1.523; NSW=0.937; rcor=50; rNcor=46; rlogoDP=46; rNIcor=40; rNsEucl=32; rSSD=72; rNSW=45; rank_mean=47.286; match_rank=38 a 645 985 276 122 71 8 1685 1679 39 0 169 0 1437 271 249 0 0 0 0 0 0 c 224 170 198 378 351 1616 14 0 0 0 584 1568 20 345 693 0 0 0 0 0 0 g 634 336 990 366 23 74 0 23 1663 1702 61 12 90 740 454 0 0 0 0 0 0 t 199 211 238 836 1257 4 3 0 0 0 888 122 155 346 306 0 0 0 0 0 0
MA0112.2_shift2 (ESR1)		0.787	0.590	3.745	0.553	0.929	2.242	0.925	117	40	113	44	29	134	66	77.571	70	; positions_7nt_m2 versus MA0112.2 (ESR1); m=8/11; ncol2=20; w=15; offset=-1; strand=D; shift=2; score=77.5714; --vkscmaGGtCAcccTGaCC ; cor=0.787; Ncor=0.590; logoDP=3.745; NIcor=0.553; NsEucl=0.929; SSD=2.242; NSW=0.925; rcor=117; rNcor=40; rlogoDP=113; rNIcor=44; rNsEucl=29; rSSD=134; rNSW=66; rank_mean=77.571; match_rank=70 a 0 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 c 0 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 g 0 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 t 0 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61
MA0112.1_shift5 (ESR1)		0.804	0.523	6.118	0.517	0.921	2.104	0.919	97	71	88	56	48	124	76	80.000	76	; positions_7nt_m2 versus MA0112.1 (ESR1); m=9/11; ncol2=18; w=13; offset=2; strand=D; shift=5; score= 80; -----ccAGGTCaCcrtGrCC ; cor=0.804; Ncor=0.523; logoDP=6.118; NIcor=0.517; NsEucl=0.921; SSD=2.104; NSW=0.919; rcor=97; rNcor=71; rlogoDP=88; rNIcor=56; rNsEucl=48; rSSD=124; rNSW=76; rank_mean=80.000; match_rank=76 a 0 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 c 0 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 g 0 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 t 0 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0
MA0258.1_shift5 (ESR2)		0.776	0.504	5.179	0.484	0.917	2.331	0.910	131	80	104	74	59	139	103	98.571	100	; positions_7nt_m2 versus MA0258.1 (ESR2); m=10/11; ncol2=18; w=13; offset=2; strand=D; shift=5; score=98.5714; -----cwrGGTCAsgkTGmCC ; cor=0.776; Ncor=0.504; logoDP=5.179; NIcor=0.484; NsEucl=0.917; SSD=2.331; NSW=0.910; rcor=131; rNcor=80; rlogoDP=104; rNIcor=74; rNsEucl=59; rSSD=139; rNSW=103; rank_mean=98.571; match_rank=100 a 0 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46 c 0 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289 g 0 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0 t 0 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22
MA0159.1_shift7 (RXR::RAR_DR5)		0.786	0.412	5.294	0.410	0.913	1.836	0.917	121	141	102	107	76	105	86	105.429	112	; positions_7nt_m2 versus MA0159.1 (RXR::RAR_DR5); m=11/11; ncol2=17; w=11; offset=4; strand=D; shift=7; score=105.429; -------rGkTCAysgrsAGK ; cor=0.786; Ncor=0.412; logoDP=5.294; NIcor=0.410; NsEucl=0.913; SSD=1.836; NSW=0.917; rcor=121; rNcor=141; rlogoDP=102; rNIcor=107; rNsEucl=76; rSSD=105; rNSW=86; rank_mean=105.429; match_rank=112 a 0 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 c 0 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 g 0 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 t 0 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6

One-to-n matrix alignment; reference matrix: dyads_m4_shift8 ; 17 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
dyads_m4_shift8 (dyads_m4)																		; dyads_m4; m=0 (reference); ncol1=13; shift=8; ncol=21; --------cyAAGGTCACCst ; Alignment reference a 0 0 0 0 0 0 0 0 16 15 64 78 0 0 0 0 76 0 1 19 16 c 0 0 0 0 0 0 0 0 26 32 4 0 1 0 0 78 0 77 75 25 16 g 0 0 0 0 0 0 0 0 19 11 9 0 77 78 0 0 2 1 2 20 19 t 0 0 0 0 0 0 0 0 17 20 1 0 0 0 78 0 0 0 0 14 27
MA0071.1_shift7 (RORA_1)		0.936	0.601	10.432	0.608	0.938	0.618	0.966	16	35	10	24	14	19	16	19.143	11	; dyads_m4 versus MA0071.1 (RORA_1); m=1/16; ncol2=10; w=9; offset=-1; strand=D; shift=7; score=19.1429; -------wwcwAGGTCA---- ; cor=0.936; Ncor=0.601; logoDP=10.432; NIcor=0.608; NsEucl=0.938; SSD=0.618; NSW=0.966; rcor=16; rNcor=35; rlogoDP=10; rNIcor=24; rNsEucl=14; rSSD=19; rNSW=16; rank_mean=19.143; match_rank=11 a 0 0 0 0 0 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 c 0 0 0 0 0 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 g 0 0 0 0 0 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0
MA0141.2_shift5 (Esrrb)		0.968	0.545	9.638	0.544	0.956	0.312	0.983	5	57	19	46	5	5	5	20.286	12	; dyads_m4 versus MA0141.2 (Esrrb); m=2/16; ncol2=12; w=9; offset=-3; strand=D; shift=5; score=20.2857; -----rgsyCAAGGTCA---- ; cor=0.968; Ncor=0.545; logoDP=9.638; NIcor=0.544; NsEucl=0.956; SSD=0.312; NSW=0.983; rcor=5; rNcor=57; rlogoDP=19; rNIcor=46; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=20.286; match_rank=12 a 0 0 0 0 0 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 c 0 0 0 0 0 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 g 0 0 0 0 0 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 t 0 0 0 0 0 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0
MA0141.1_shift5 (Esrrb)		0.968	0.545	9.506	0.544	0.956	0.312	0.983	6	58	20	47	4	4	4	20.429	13	; dyads_m4 versus MA0141.1 (Esrrb); m=3/16; ncol2=12; w=9; offset=-3; strand=D; shift=5; score=20.4286; -----rgsyCAAGGTCA---- ; cor=0.968; Ncor=0.545; logoDP=9.506; NIcor=0.544; NsEucl=0.956; SSD=0.312; NSW=0.983; rcor=6; rNcor=58; rlogoDP=20; rNIcor=47; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=20.429; match_rank=13 a 0 0 0 0 0 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 c 0 0 0 0 0 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 g 0 0 0 0 0 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 t 0 0 0 0 0 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0
MA0160.1_shift10 (NR4A2)		0.964	0.593	8.026	0.586	0.936	0.516	0.968	7	37	44	30	17	13	15	23.286	16	; dyads_m4 versus MA0160.1 (NR4A2); m=4/16; ncol2=8; w=8; offset=2; strand=D; shift=10; score=23.2857; ----------aAGGTCAc--- ; cor=0.964; Ncor=0.593; logoDP=8.026; NIcor=0.586; NsEucl=0.936; SSD=0.516; NSW=0.968; rcor=7; rNcor=37; rlogoDP=44; rNIcor=30; rNsEucl=17; rSSD=13; rNSW=15; rank_mean=23.286; match_rank=16 a 0 0 0 0 0 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 g 0 0 0 0 0 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 t 0 0 0 0 0 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0
MA0592.1_shift8 (ESRRA)		0.883	0.747	10.206	0.719	0.924	1.406	0.936	41	9	14	9	41	61	47	31.714	21	; dyads_m4 versus MA0592.1 (ESRRA); m=5/16; ncol2=11; w=11; offset=0; strand=D; shift=8; score=31.7143; --------yCAAGGTCAcm-- ; cor=0.883; Ncor=0.747; logoDP=10.206; NIcor=0.719; NsEucl=0.924; SSD=1.406; NSW=0.936; rcor=41; rNcor=9; rlogoDP=14; rNIcor=9; rNsEucl=41; rSSD=61; rNSW=47; rank_mean=31.714; match_rank=21 a 0 0 0 0 0 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 c 0 0 0 0 0 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 g 0 0 0 0 0 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 t 0 0 0 0 0 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0
MA0258.2_shift11 (ESR2)		0.899	0.500	7.603	0.485	0.923	1.183	0.941	31	86	57	73	43	44	41	53.571	47	; dyads_m4 versus MA0258.2 (ESR2); m=6/16; ncol2=15; w=10; offset=3; strand=D; shift=11; score=53.5714; -----------rGGTCAsmst ; cor=0.899; Ncor=0.500; logoDP=7.603; NIcor=0.485; NsEucl=0.923; SSD=1.183; NSW=0.941; rcor=31; rNcor=86; rlogoDP=57; rNIcor=73; rNsEucl=43; rSSD=44; rNSW=41; rank_mean=53.571; match_rank=47 a 0 0 0 0 0 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 c 0 0 0 0 0 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 g 0 0 0 0 0 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 t 0 0 0 0 0 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133
MA0112.1_shift9 (ESR1)		0.851	0.538	7.739	0.537	0.922	1.761	0.927	62	64	51	49	45	98	62	61.571	53	; dyads_m4 versus MA0112.1 (ESR1); m=7/16; ncol2=18; w=12; offset=1; strand=D; shift=9; score=61.5714; ---------ccAGGTCaCcrt ; cor=0.851; Ncor=0.538; logoDP=7.739; NIcor=0.537; NsEucl=0.922; SSD=1.761; NSW=0.927; rcor=62; rNcor=64; rlogoDP=51; rNIcor=49; rNsEucl=45; rSSD=98; rNSW=62; rank_mean=61.571; match_rank=53 a 0 0 0 0 0 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 c 0 0 0 0 0 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 g 0 0 0 0 0 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 t 0 0 0 0 0 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6
MA0112.2_shift6 (ESR1)		0.841	0.547	4.679	0.520	0.925	1.921	0.926	68	56	107	54	40	114	63	71.714	62	; dyads_m4 versus MA0112.2 (ESR1); m=8/16; ncol2=20; w=13; offset=-2; strand=D; shift=6; score=71.7143; ------vkscmaGGtCAcccT ; cor=0.841; Ncor=0.547; logoDP=4.679; NIcor=0.520; NsEucl=0.925; SSD=1.921; NSW=0.926; rcor=68; rNcor=56; rlogoDP=107; rNIcor=54; rNsEucl=40; rSSD=114; rNSW=63; rank_mean=71.714; match_rank=62 a 0 0 0 0 0 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 c 0 0 0 0 0 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 g 0 0 0 0 0 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 t 0 0 0 0 0 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416
MA0505.1_shift4 (Nr5a2)		0.788	0.510	8.750	0.473	0.899	2.483	0.887	113	77	30	81	119	146	138	100.571	103	; dyads_m4 versus MA0505.1 (Nr5a2); m=9/16; ncol2=15; w=11; offset=-4; strand=D; shift=4; score=100.571; ----ragtTCAAGGyCAgs-- ; cor=0.788; Ncor=0.510; logoDP=8.750; NIcor=0.473; NsEucl=0.899; SSD=2.483; NSW=0.887; rcor=113; rNcor=77; rlogoDP=30; rNIcor=81; rNsEucl=119; rSSD=146; rNSW=138; rank_mean=100.571; match_rank=103 a 0 0 0 0 645 985 276 122 71 8 1685 1679 39 0 169 0 1437 271 249 0 0 c 0 0 0 0 224 170 198 378 351 1616 14 0 0 0 584 1568 20 345 693 0 0 g 0 0 0 0 634 336 990 366 23 74 0 23 1663 1702 61 12 90 740 454 0 0 t 0 0 0 0 199 211 238 836 1257 4 3 0 0 0 888 122 155 346 306 0 0
MA0065.1_shift0 (PPARG::RXRA)		0.787	0.450	9.805	0.420	0.904	2.629	0.890	116	115	17	97	109	148	132	104.857	111	; dyads_m4 versus MA0065.1 (PPARG::RXRA); m=10/16; ncol2=20; w=12; offset=-8; strand=D; shift=0; score=104.857; yywrrGGTCAAAGGTCAymk- ; cor=0.787; Ncor=0.450; logoDP=9.805; NIcor=0.420; NsEucl=0.904; SSD=2.629; NSW=0.890; rcor=116; rNcor=115; rlogoDP=17; rNIcor=97; rNsEucl=109; rSSD=148; rNSW=132; rank_mean=104.857; match_rank=111 a 10 7 19 13 17 0 0 0 2 41 41 39 0 0 0 2 38 10 13 7 0 c 12 13 4 1 0 0 0 2 37 0 0 0 0 0 2 36 1 12 15 10 0 g 7 8 6 27 24 41 39 0 2 0 0 2 41 39 0 1 2 4 9 12 0 t 12 13 12 0 0 0 2 39 0 0 0 0 0 2 39 2 0 15 4 12 0
MA0258.1_shift9 (ESR2)		0.774	0.489	6.472	0.471	0.906	2.542	0.894	133	91	74	82	104	147	130	108.714	119	; dyads_m4 versus MA0258.1 (ESR2); m=11/16; ncol2=18; w=12; offset=1; strand=D; shift=9; score=108.714; ---------cwrGGTCAsgkT ; cor=0.774; Ncor=0.489; logoDP=6.472; NIcor=0.471; NsEucl=0.906; SSD=2.542; NSW=0.894; rcor=133; rNcor=91; rlogoDP=74; rNIcor=82; rNsEucl=104; rSSD=147; rNSW=130; rank_mean=108.714; match_rank=119 a 0 0 0 0 0 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 c 0 0 0 0 0 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 g 0 0 0 0 0 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 t 0 0 0 0 0 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279
MA0115.1_shift2 (NR1H2::RXRA)		0.760	0.440	12.314	0.422	0.883	3.288	0.851	145	119	1	96	137	151	151	114.286	127	; dyads_m4 versus MA0115.1 (NR1H2::RXRA); m=12/16; ncol2=17; w=11; offset=-6; strand=D; shift=2; score=114.286; --AAAGGTCAAAGGTCAAc-- ; cor=0.760; Ncor=0.440; logoDP=12.314; NIcor=0.422; NsEucl=0.883; SSD=3.288; NSW=0.851; rcor=145; rNcor=119; rlogoDP=1; rNIcor=96; rNsEucl=137; rSSD=151; rNSW=151; rank_mean=114.286; match_rank=127 a 0 0 17 17 20 0 0 0 0 25 24 25 0 0 0 0 25 20 0 0 0 c 0 0 5 1 0 0 0 0 25 0 0 0 0 0 0 25 0 1 15 0 0 g 0 0 0 5 5 25 24 0 0 0 0 0 25 25 0 0 0 2 6 0 0 t 0 0 3 2 0 0 1 25 0 0 1 0 0 0 25 0 0 2 4 0 0
MA0595.1_shift13 (SREBF1)		0.786	0.419	7.218	0.408	0.882	1.780	0.889	120	130	67	110	138	99	136	114.286	128	; dyads_m4 versus MA0595.1 (SREBF1); m=13/16; ncol2=10; w=8; offset=5; strand=D; shift=13; score=114.286; -------------rTCACcCC ; cor=0.786; Ncor=0.419; logoDP=7.218; NIcor=0.408; NsEucl=0.882; SSD=1.780; NSW=0.889; rcor=120; rNcor=130; rlogoDP=67; rNIcor=110; rNsEucl=138; rSSD=99; rNSW=136; rank_mean=114.286; match_rank=128 a 0 0 0 0 0 0 0 0 0 0 0 0 0 28 0 0 58 0 6 0 2 c 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 58 0 51 38 44 45 g 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0 7 13 0 11 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 0 0 0 1 14 0
MA0017.1_rc_shift3 (NR2F1_rc)		0.821	0.410	0.698	-0.117	0.897	1.725	0.904	86	143	139	139	121	94	111	119.000	136	; dyads_m4 versus MA0017.1_rc (NR2F1_rc); m=14/16; ncol2=14; w=9; offset=-5; strand=R; shift=3; score= 119; ---arGkkCAAAGkTCA---- ; cor=0.821; Ncor=0.410; logoDP=0.698; NIcor=-0.117; NsEucl=0.897; SSD=1.725; NSW=0.904; rcor=86; rNcor=143; rlogoDP=139; rNIcor=139; rNsEucl=121; rSSD=94; rNSW=111; rank_mean=119.000; match_rank=136 a 0 0 0 7 4 1 1 0 0 12 11 10 0 0 0 0 11 0 0 0 0 c 0 0 0 3 0 1 1 3 11 0 0 0 0 0 1 12 2 0 0 0 0 g 0 0 0 3 6 10 5 4 0 0 2 3 13 7 0 0 0 0 0 0 0 t 0 0 0 0 3 1 6 6 2 1 0 0 0 6 12 1 0 0 0 0 0
MA0494.1_rc_shift8 (Nr1h3::Rxra_rc)		0.764	0.523	0.784	-0.068	0.910	2.721	0.895	141	70	137	135	84	149	126	120.286	139	; dyads_m4 versus MA0494.1_rc (Nr1h3::Rxra_rc); m=15/16; ncol2=19; w=13; offset=0; strand=R; shift=8; score=120.286; --------cmrrGGTyACyyb ; cor=0.764; Ncor=0.523; logoDP=0.784; NIcor=-0.068; NsEucl=0.910; SSD=2.721; NSW=0.895; rcor=141; rNcor=70; rlogoDP=137; rNIcor=135; rNsEucl=84; rSSD=149; rNSW=126; rank_mean=120.286; match_rank=139 a 0 0 0 0 0 0 0 0 303 459 430 714 112 32 0 193 1188 69 154 302 250 c 0 0 0 0 0 0 0 0 439 333 196 42 0 20 192 440 4 903 321 336 343 g 0 0 0 0 0 0 0 0 290 196 508 502 1040 962 177 77 0 19 0 257 318 t 0 0 0 0 0 0 0 0 237 281 135 11 117 255 900 559 77 278 794 374 358
MA0114.1_shift4 (HNF4A)		0.758	0.401	3.463	0.369	0.886	2.096	0.884	147	151	116	116	133	123	141	132.429	150	; dyads_m4 versus MA0114.1 (HNF4A); m=16/16; ncol2=13; w=9; offset=-4; strand=D; shift=4; score=132.429; ----rGgbCAAAGkyCa---- ; cor=0.758; Ncor=0.401; logoDP=3.463; NIcor=0.369; NsEucl=0.886; SSD=2.096; NSW=0.884; rcor=147; rNcor=151; rlogoDP=116; rNIcor=116; rNsEucl=133; rSSD=123; rNSW=141; rank_mean=132.429; match_rank=150 a 0 0 0 0 28 2 12 5 3 59 53 56 4 6 3 4 42 0 0 0 0 c 0 0 0 0 7 2 4 23 51 1 2 1 4 2 22 49 7 0 0 0 0 g 0 0 0 0 27 56 35 20 4 3 10 8 58 33 11 5 10 0 0 0 0 t 0 0 0 0 5 7 16 19 9 4 2 2 1 26 31 9 8 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_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_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)																		; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; cvCCACACCcg ; Alignment reference a 107 133 3 1 463 1 450 0 1 83 110 c 184 124 487 482 4 491 3 495 482 223 112 g 120 154 5 9 25 1 42 0 12 75 152 t 84 84 0 3 3 2 0 0 0 114 121
MA0493.1_shift0 (Klf1)		0.898	0.898	8.244	0.890	0.936	1.005	0.954	32	4	38	4	18	33	24	21.857	14	; oligos_7nt_mkv5_m1 versus MA0493.1 (Klf1); m=1/5; ncol2=11; w=11; offset=0; strand=D; shift=0; score=21.8571; rrCCACACCCw ; cor=0.898; Ncor=0.898; logoDP=8.244; NIcor=0.890; NsEucl=0.936; SSD=1.005; NSW=0.954; rcor=32; rNcor=4; rlogoDP=38; rNIcor=4; rNsEucl=18; rSSD=33; rNSW=24; rank_mean=21.857; match_rank=14 a 150 167 67 13 404 0 400 0 0 0 280 c 76 40 396 461 118 526 0 526 526 508 35 g 202 305 32 0 0 0 97 0 0 0 0 t 98 14 31 52 4 0 29 0 0 18 211
MA0130.1_shift0 (ZNF354C)		0.923	0.504	6.306	0.515	0.918	0.483	0.960	18	82	79	57	55	12	20	46.143	34	; oligos_7nt_mkv5_m1 versus MA0130.1 (ZNF354C); m=2/5; ncol2=6; w=6; offset=0; strand=D; shift=0; score=46.1429; mTCCAC----- ; cor=0.923; Ncor=0.504; logoDP=6.306; NIcor=0.515; NsEucl=0.918; SSD=0.483; NSW=0.960; rcor=18; rNcor=82; rlogoDP=79; rNIcor=57; rNsEucl=55; rSSD=12; rNSW=20; rank_mean=46.143; match_rank=34 a 7 3 0 0 16 0 0 0 0 0 0 c 6 2 16 16 0 15 0 0 0 0 0 g 3 0 0 0 0 1 0 0 0 0 0 t 0 11 0 0 0 0 0 0 0 0 0
MA0599.1_shift1 (KLF5)		0.787	0.716	8.022	0.688	0.899	2.026	0.899	115	12	45	11	118	119	120	77.143	69	; oligos_7nt_mkv5_m1 versus MA0599.1 (KLF5); m=3/5; ncol2=10; w=10; offset=1; strand=D; shift=1; score=77.1429; -gCCMCrCCCh ; cor=0.787; Ncor=0.716; logoDP=8.022; NIcor=0.688; NsEucl=0.899; SSD=2.026; NSW=0.899; rcor=115; rNcor=12; rlogoDP=45; rNIcor=11; rNsEucl=118; rSSD=119; rNSW=120; rank_mean=77.143; match_rank=69 a 0 1429 0 0 3477 0 5051 0 0 0 3915 c 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 g 0 7572 0 0 0 0 5182 0 0 0 0 t 0 2587 1711 1603 565 0 3378 0 0 476 4101
MA0039.2_rc_shift1 (Klf4_rc)		0.848	0.770	0.606	-0.220	0.914	1.463	0.927	64	8	140	150	67	65	60	79.143	74	; oligos_7nt_mkv5_m1 versus MA0039.2_rc (Klf4_rc); m=4/5; ncol2=10; w=10; offset=1; strand=R; shift=1; score=79.1429; -gCCmCrCCCw ; cor=0.848; Ncor=0.770; logoDP=0.606; NIcor=-0.220; NsEucl=0.914; SSD=1.463; NSW=0.927; rcor=64; rNcor=8; rlogoDP=140; rNIcor=150; rNsEucl=67; rSSD=65; rNSW=60; rank_mean=79.143; match_rank=74 a 0 932 289 125 2042 34 2139 16 13 6 1765 c 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 g 0 2858 130 46 80 15 1922 36 13 9 81 t 0 254 123 264 42 22 277 14 14 88 1468
MA0103.1_shift5 (ZEB1)		0.852	0.465	4.866	0.450	0.889	0.895	0.925	61	107	106	91	130	27	64	83.714	81	; oligos_7nt_mkv5_m1 versus MA0103.1 (ZEB1); m=5/5; ncol2=6; w=6; offset=5; strand=D; shift=5; score=83.7143; -----CACCTk ; cor=0.852; Ncor=0.465; logoDP=4.866; NIcor=0.450; NsEucl=0.889; SSD=0.895; NSW=0.925; rcor=61; rNcor=107; rlogoDP=106; rNIcor=91; rNsEucl=130; rSSD=27; rNSW=64; rank_mean=83.714; match_rank=81 a 0 0 0 0 0 1 38 0 0 0 10 c 0 0 0 0 0 34 0 40 38 1 1 g 0 0 0 0 0 1 2 1 3 0 16 t 0 0 0 0 0 5 1 0 0 40 14

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift3 ; 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_m4_shift3 (oligos_7nt_mkv5_m4)																		; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=3; ncol=15; ---rsCCTCAGGsm- ; Alignment reference a 0 0 0 195 115 1 0 1 0 700 0 0 114 214 0 c 0 0 0 160 206 746 744 1 748 20 10 2 274 219 0 g 0 0 0 237 283 1 5 20 1 29 739 746 239 151 0 t 0 0 0 157 145 1 0 727 0 0 0 1 122 165 0
MA0524.1_shift0 (TFAP2C)		0.902	0.661	8.344	0.658	0.937	0.955	0.957	30	19	35	16	16	30	23	24.143	17	; oligos_7nt_mkv5_m4 versus MA0524.1 (TFAP2C); m=1/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score=24.1429; hmydsCCyCAGGsca ; cor=0.902; Ncor=0.661; logoDP=8.344; NIcor=0.658; NsEucl=0.937; SSD=0.955; NSW=0.957; rcor=30; rNcor=19; rlogoDP=35; rNIcor=16; rNsEucl=16; rSSD=30; rNSW=23; rank_mean=24.143; match_rank=17 a 4801 6477 2550 4918 421 0 0 0 1082 16442 191 0 285 4343 8905 c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259 g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536 t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726
MA0003.2_shift0 (TFAP2A)		0.864	0.634	7.633	0.617	0.926	1.314	0.940	49	21	55	23	34	52	42	39.429	29	; oligos_7nt_mkv5_m4 versus MA0003.2 (TFAP2A); m=2/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score=39.4286; maywGCCysAGGsCa ; cor=0.864; Ncor=0.634; logoDP=7.633; NIcor=0.617; NsEucl=0.926; SSD=1.314; NSW=0.940; rcor=49; rNcor=21; rlogoDP=55; rNIcor=23; rNsEucl=34; rSSD=52; rNSW=42; rank_mean=39.429; match_rank=29 a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146 c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690 g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168 t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift1 ; 9 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_shift1 (oligos_7nt_mkv5_m5)																		; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=1; ncol=16; -ckCCCCTCCcs---- ; Alignment reference a 0 122 95 1 1 0 0 4 3 0 98 91 0 0 0 0 c 0 288 176 725 680 704 718 1 734 731 306 278 0 0 0 0 g 0 175 277 12 55 36 20 102 2 10 158 233 0 0 0 0 t 0 156 193 3 5 1 3 634 2 0 179 139 0 0 0 0
MA0079.3_shift2 (SP1)		0.883	0.735	8.087	0.718	0.926	1.097	0.945	42	11	41	10	35	37	37	30.429	20	; oligos_7nt_mkv5_m5 versus MA0079.3 (SP1); m=1/8; ncol2=11; w=10; offset=1; strand=D; shift=2; score=30.4286; --gCCCCkCCCCy--- ; cor=0.883; Ncor=0.735; logoDP=8.087; NIcor=0.718; NsEucl=0.926; SSD=1.097; NSW=0.945; rcor=42; rNcor=11; rlogoDP=41; rNIcor=10; rNsEucl=35; rSSD=37; rNSW=37; rank_mean=30.429; match_rank=20 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0
MA0079.2_shift3 (SP1)		0.905	0.679	6.201	0.665	0.928	0.850	0.953	27	17	86	14	31	26	26	32.429	22	; oligos_7nt_mkv5_m5 versus MA0079.2 (SP1); m=2/8; ncol2=10; w=9; offset=2; strand=D; shift=3; score=32.4286; ---CCCCkCCCCC--- ; cor=0.905; Ncor=0.679; logoDP=6.201; NIcor=0.665; NsEucl=0.928; SSD=0.850; NSW=0.953; rcor=27; rNcor=17; rlogoDP=86; rNIcor=14; rNsEucl=31; rSSD=26; rNSW=26; rank_mean=32.429; match_rank=22 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0
MA0599.1_shift2 (KLF5)		0.857	0.779	7.904	0.765	0.918	1.337	0.933	58	7	49	7	54	54	48	39.571	30	; oligos_7nt_mkv5_m5 versus MA0599.1 (KLF5); m=3/8; ncol2=10; w=10; offset=1; strand=D; shift=2; score=39.5714; --gCCMCrCCCh---- ; cor=0.857; Ncor=0.779; logoDP=7.904; NIcor=0.765; NsEucl=0.918; SSD=1.337; NSW=0.933; rcor=58; rNcor=7; rlogoDP=49; rNIcor=7; rNsEucl=54; rSSD=54; rNSW=48; rank_mean=39.571; match_rank=30 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 g 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 t 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0
MA0516.1_shift2 (SP2)		0.812	0.507	7.501	0.488	0.906	1.755	0.912	90	79	63	72	102	97	98	85.857	86	; oligos_7nt_mkv5_m5 versus MA0516.1 (SP2); m=4/8; ncol2=15; w=10; offset=1; strand=D; shift=2; score=85.8571; --gyCCCGCCyCyycc ; cor=0.812; Ncor=0.507; logoDP=7.501; NIcor=0.488; NsEucl=0.906; SSD=1.755; NSW=0.912; rcor=90; rNcor=79; rlogoDP=63; rNIcor=72; rNsEucl=102; rSSD=97; rNSW=98; rank_mean=85.857; match_rank=86 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256
MA0162.2_shift2 (EGR1)		0.801	0.534	5.883	0.509	0.907	1.733	0.913	102	66	96	61	100	95	96	88.000	90	; oligos_7nt_mkv5_m5 versus MA0162.2 (EGR1); m=5/8; ncol2=14; w=10; offset=1; strand=D; shift=2; score= 88; --sccCCgCCCMCkCc ; cor=0.801; Ncor=0.534; logoDP=5.883; NIcor=0.509; NsEucl=0.907; SSD=1.733; NSW=0.913; rcor=102; rNcor=66; rlogoDP=96; rNIcor=61; rNsEucl=100; rSSD=95; rNSW=96; rank_mean=88.000; match_rank=90 a 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 c 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 g 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 t 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722
MA0057.1_rc_shift0 (MZF1_5-13_rc)		0.811	0.609	0.422	-0.223	0.901	1.594	0.911	91	33	142	151	114	76	101	101.143	105	; oligos_7nt_mkv5_m5 versus MA0057.1_rc (MZF1_5-13_rc); m=6/8; ncol2=10; w=9; offset=-1; strand=R; shift=0; score=101.143; yymCCCMTmv------ ; cor=0.811; Ncor=0.609; logoDP=0.422; NIcor=-0.223; NsEucl=0.901; SSD=1.594; NSW=0.911; rcor=91; rNcor=33; rlogoDP=142; rNIcor=151; rNsEucl=114; rSSD=76; rNSW=101; rank_mean=101.143; match_rank=105 a 2 2 4 2 0 1 5 0 7 4 0 0 0 0 0 0 c 4 4 8 14 14 15 11 0 7 7 0 0 0 0 0 0 g 2 0 1 0 2 0 0 1 0 4 0 0 0 0 0 0 t 8 10 3 0 0 0 0 15 2 1 0 0 0 0 0 0
MA0039.2_rc_shift2 (Klf4_rc)		0.766	0.696	0.728	-0.213	0.895	2.203	0.890	137	13	138	148	122	130	134	117.429	133	; oligos_7nt_mkv5_m5 versus MA0039.2_rc (Klf4_rc); m=7/8; ncol2=10; w=10; offset=1; strand=R; shift=2; score=117.429; --gCCmCrCCCw---- ; cor=0.766; Ncor=0.696; logoDP=0.728; NIcor=-0.213; NsEucl=0.895; SSD=2.203; NSW=0.890; rcor=137; rNcor=13; rlogoDP=138; rNIcor=148; rNsEucl=122; rSSD=130; rNSW=134; rank_mean=117.429; match_rank=133 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0
MA0056.1_rc_shift2 (MZF1_1-4_rc)		0.795	0.433	0.230	-0.153	0.865	1.318	0.890	104	121	149	144	148	53	133	121.714	141	; oligos_7nt_mkv5_m5 versus MA0056.1_rc (MZF1_1-4_rc); m=8/8; ncol2=6; w=6; offset=1; strand=R; shift=2; score=121.714; --TCCCCr-------- ; cor=0.795; Ncor=0.433; logoDP=0.230; NIcor=-0.153; NsEucl=0.865; SSD=1.318; NSW=0.890; rcor=104; rNcor=121; rlogoDP=149; rNIcor=144; rNsEucl=148; rSSD=53; rNSW=133; rank_mean=121.714; match_rank=141 a 0 0 0 0 1 0 1 8 0 0 0 0 0 0 0 0 c 0 0 2 20 19 18 19 4 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 t 0 0 18 0 0 2 0 3 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 10 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_shift2 (positions_6nt_m1)																		; positions_6nt_m1; m=0 (reference); ncol1=14; shift=2; ncol=20; --byCCAGGTCACasw---- ; Alignment reference a 0 0 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 0 c 0 0 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 0 g 0 0 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 0 t 0 0 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0 0
MA0071.1_shift2 (RORA_1)		0.877	0.627	10.635	0.649	0.922	1.221	0.939	43	27	9	17	44	46	43	32.714	23	; positions_6nt_m1 versus MA0071.1 (RORA_1); m=1/9; ncol2=10; w=10; offset=0; strand=D; shift=2; score=32.7143; --wwcwAGGTCA-------- ; cor=0.877; Ncor=0.627; logoDP=10.635; NIcor=0.649; NsEucl=0.922; SSD=1.221; NSW=0.939; rcor=43; rNcor=27; rlogoDP=9; rNIcor=17; rNsEucl=44; rSSD=46; rNSW=43; rank_mean=32.714; match_rank=23 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
MA0141.1_shift0 (Esrrb)		0.889	0.555	9.310	0.553	0.925	1.123	0.944	34	51	22	43	37	40	39	38.000	26	; positions_6nt_m1 versus MA0141.1 (Esrrb); m=2/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 38; rgsyCAAGGTCA-------- ; cor=0.889; Ncor=0.555; logoDP=9.310; NIcor=0.553; NsEucl=0.925; SSD=1.123; NSW=0.944; rcor=34; rNcor=51; rlogoDP=22; rNIcor=43; rNsEucl=37; rSSD=40; rNSW=39; rank_mean=38.000; match_rank=26 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)		0.888	0.555	9.423	0.552	0.925	1.134	0.943	35	52	21	45	39	41	40	39.000	27	; positions_6nt_m1 versus MA0141.2 (Esrrb); m=3/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 39; rgsyCAAGGTCA-------- ; cor=0.888; Ncor=0.555; logoDP=9.423; NIcor=0.552; NsEucl=0.925; SSD=1.134; NSW=0.943; rcor=35; rNcor=52; rlogoDP=21; rNIcor=45; rNsEucl=39; rSSD=41; rNSW=40; rank_mean=39.000; match_rank=27 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0
MA0592.1_shift3 (ESRRA)		0.864	0.679	9.939	0.661	0.920	1.542	0.930	47	16	16	15	50	73	56	39.000	28	; positions_6nt_m1 versus MA0592.1 (ESRRA); m=4/9; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 39; ---yCAAGGTCAcm------ ; cor=0.864; Ncor=0.679; logoDP=9.939; NIcor=0.661; NsEucl=0.920; SSD=1.542; NSW=0.930; rcor=47; rNcor=16; rlogoDP=16; rNIcor=15; rNsEucl=50; rSSD=73; rNSW=56; rank_mean=39.000; match_rank=28 a 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 0 c 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 0 g 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 0 t 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0 0
MA0112.1_shift4 (ESR1)		0.883	0.530	7.478	0.533	0.933	1.311	0.945	40	67	64	51	23	51	35	47.286	37	; positions_6nt_m1 versus MA0112.1 (ESR1); m=5/9; ncol2=18; w=12; offset=2; strand=D; shift=4; score=47.2857; ----ccAGGTCaCcrtGrCC ; cor=0.883; Ncor=0.530; logoDP=7.478; NIcor=0.533; NsEucl=0.933; SSD=1.311; NSW=0.945; rcor=40; rNcor=67; rlogoDP=64; rNIcor=51; rNsEucl=23; rSSD=51; rNSW=35; rank_mean=47.286; match_rank=37 a 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 c 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 g 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0
MA0258.2_shift6 (ESR2)		0.907	0.477	7.708	0.476	0.931	0.963	0.952	26	101	52	79	26	31	28	49.000	41	; positions_6nt_m1 versus MA0258.2 (ESR2); m=6/9; ncol2=15; w=10; offset=4; strand=D; shift=6; score= 49; ------rGGTCAsmstGaCC ; cor=0.907; Ncor=0.477; logoDP=7.708; NIcor=0.476; NsEucl=0.931; SSD=0.963; NSW=0.952; rcor=26; rNcor=101; rlogoDP=52; rNIcor=79; rNsEucl=26; rSSD=31; rNSW=28; rank_mean=49.000; match_rank=41 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278
MA0160.1_shift5 (NR4A2)		0.904	0.517	7.972	0.518	0.912	0.998	0.938	28	74	47	55	80	32	44	51.429	45	; positions_6nt_m1 versus MA0160.1 (NR4A2); m=7/9; ncol2=8; w=8; offset=3; strand=D; shift=5; score=51.4286; -----aAGGTCAc------- ; cor=0.904; Ncor=0.517; logoDP=7.972; NIcor=0.518; NsEucl=0.912; SSD=0.998; NSW=0.938; rcor=28; rNcor=74; rlogoDP=47; rNIcor=55; rNsEucl=80; rSSD=32; rNSW=44; rank_mean=51.429; match_rank=45 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0
MA0112.2_shift1 (ESR1)		0.821	0.574	4.608	0.557	0.929	1.952	0.930	87	47	108	41	28	115	53	68.429	60	; positions_6nt_m1 versus MA0112.2 (ESR1); m=8/9; ncol2=20; w=14; offset=-1; strand=D; shift=1; score=68.4286; -vkscmaGGtCAcccTGaCC ; cor=0.821; Ncor=0.574; logoDP=4.608; NIcor=0.557; NsEucl=0.929; SSD=1.952; NSW=0.930; rcor=87; rNcor=47; rlogoDP=108; rNIcor=41; rNsEucl=28; rSSD=115; rNSW=53; rank_mean=68.429; match_rank=60 a 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 c 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 g 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 t 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61
MA0258.1_shift4 (ESR2)		0.781	0.469	6.610	0.464	0.911	2.297	0.904	125	104	72	87	82	135	109	102.000	107	; positions_6nt_m1 versus MA0258.1 (ESR2); m=9/9; ncol2=18; w=12; offset=2; strand=D; shift=4; score= 102; ----cwrGGTCAsgkTGmCC ; cor=0.781; Ncor=0.469; logoDP=6.610; NIcor=0.464; NsEucl=0.911; SSD=2.297; NSW=0.904; rcor=125; rNcor=104; rlogoDP=72; rNIcor=87; rNsEucl=82; rSSD=135; rNSW=109; rank_mean=102.000; match_rank=107 a 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46 c 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289 g 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0 t 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 10 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_shift2 (positions_7nt_m1)																		; positions_7nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=21; --byCCAGGTCACCtkg---- ; Alignment reference a 0 0 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 0 0 c 0 0 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 0 0 g 0 0 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 0 0 t 0 0 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0 0 0
MA0112.1_shift4 (ESR1)		0.869	0.565	6.130	0.554	0.935	1.424	0.945	45	49	87	42	19	64	36	48.857	40	; positions_7nt_m1 versus MA0112.1 (ESR1); m=1/9; ncol2=18; w=13; offset=2; strand=D; shift=4; score=48.8571; ----ccAGGTCaCcrtGrCCy ; cor=0.869; Ncor=0.565; logoDP=6.130; NIcor=0.554; NsEucl=0.935; SSD=1.424; NSW=0.945; rcor=45; rNcor=49; rlogoDP=87; rNIcor=42; rNsEucl=19; rSSD=64; rNSW=36; rank_mean=48.857; match_rank=40 a 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 2 c 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 4 g 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 0 t 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0 3
MA0258.2_shift6 (ESR2)		0.887	0.513	6.109	0.504	0.935	1.036	0.953	37	75	89	64	21	34	25	49.286	42	; positions_7nt_m1 versus MA0258.2 (ESR2); m=2/9; ncol2=15; w=11; offset=4; strand=D; shift=6; score=49.2857; ------rGGTCAsmstGaCCy ; cor=0.887; Ncor=0.513; logoDP=6.109; NIcor=0.504; NsEucl=0.935; SSD=1.036; NSW=0.953; rcor=37; rNcor=75; rlogoDP=89; rNIcor=64; rNsEucl=21; rSSD=34; rNSW=25; rank_mean=49.286; match_rank=42 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 834 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 2708 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 606 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278 4095
MA0071.1_shift2 (RORA_1)		0.832	0.555	8.394	0.568	0.910	1.634	0.918	77	53	33	37	86	78	79	63.286	55	; positions_7nt_m1 versus MA0071.1 (RORA_1); m=3/9; ncol2=10; w=10; offset=0; strand=D; shift=2; score=63.2857; --wwcwAGGTCA--------- ; cor=0.832; Ncor=0.555; logoDP=8.394; NIcor=0.568; NsEucl=0.910; SSD=1.634; NSW=0.918; rcor=77; rNcor=53; rlogoDP=33; rNIcor=37; rNsEucl=86; rSSD=78; rNSW=79; rank_mean=63.286; match_rank=55 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0
MA0112.2_shift1 (ESR1)		0.819	0.614	3.822	0.578	0.935	1.909	0.936	88	32	112	35	20	112	46	63.571	56	; positions_7nt_m1 versus MA0112.2 (ESR1); m=4/9; ncol2=20; w=15; offset=-1; strand=D; shift=1; score=63.5714; -vkscmaGGtCAcccTGaCCy ; cor=0.819; Ncor=0.614; logoDP=3.822; NIcor=0.578; NsEucl=0.935; SSD=1.909; NSW=0.936; rcor=88; rNcor=32; rlogoDP=112; rNIcor=35; rNsEucl=20; rSSD=112; rNSW=46; rank_mean=63.571; match_rank=56 a 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 c 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 g 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 t 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262
MA0141.1_shift0 (Esrrb)		0.832	0.489	7.555	0.497	0.909	1.660	0.917	78	89	58	66	91	85	83	78.571	72	; positions_7nt_m1 versus MA0141.1 (Esrrb); m=5/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=78.5714; rgsyCAAGGTCA--------- ; cor=0.832; Ncor=0.489; logoDP=7.555; NIcor=0.497; NsEucl=0.909; SSD=1.660; NSW=0.917; rcor=78; rNcor=89; rlogoDP=58; rNIcor=66; rNsEucl=91; rSSD=85; rNSW=83; rank_mean=78.571; match_rank=72 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)		0.831	0.489	7.647	0.496	0.909	1.674	0.916	79	90	53	68	93	86	87	79.429	75	; positions_7nt_m1 versus MA0141.2 (Esrrb); m=6/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=79.4286; rgsyCAAGGTCA--------- ; cor=0.831; Ncor=0.489; logoDP=7.647; NIcor=0.496; NsEucl=0.909; SSD=1.674; NSW=0.916; rcor=79; rNcor=90; rlogoDP=53; rNIcor=68; rNsEucl=93; rSSD=86; rNSW=87; rank_mean=79.429; match_rank=75 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0 0
MA0592.1_shift3 (ESRRA)		0.801	0.587	8.096	0.582	0.904	2.221	0.899	101	42	40	31	110	132	119	82.143	77	; positions_7nt_m1 versus MA0592.1 (ESRRA); m=7/9; ncol2=11; w=11; offset=1; strand=D; shift=3; score=82.1429; ---yCAAGGTCAcm------- ; cor=0.801; Ncor=0.587; logoDP=8.096; NIcor=0.582; NsEucl=0.904; SSD=2.221; NSW=0.899; rcor=101; rNcor=42; rlogoDP=40; rNIcor=31; rNsEucl=110; rSSD=132; rNSW=119; rank_mean=82.143; match_rank=77 a 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 0 0 c 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 0 0 g 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 0 0 t 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0 0 0
MA0160.1_shift5 (NR4A2)		0.855	0.456	6.404	0.458	0.897	1.347	0.916	59	113	77	90	120	56	88	86.143	87	; positions_7nt_m1 versus MA0160.1 (NR4A2); m=8/9; ncol2=8; w=8; offset=3; strand=D; shift=5; score=86.1429; -----aAGGTCAc-------- ; cor=0.855; Ncor=0.456; logoDP=6.404; NIcor=0.458; NsEucl=0.897; SSD=1.347; NSW=0.916; rcor=59; rNcor=113; rlogoDP=77; rNIcor=90; rNsEucl=120; rSSD=56; rNSW=88; rank_mean=86.143; match_rank=87 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0 0
MA0159.1_shift6 (RXR::RAR_DR5)		0.780	0.409	5.308	0.406	0.911	1.901	0.914	126	144	101	111	81	111	94	109.714	122	; positions_7nt_m1 versus MA0159.1 (RXR::RAR_DR5); m=9/9; ncol2=17; w=11; offset=4; strand=D; shift=6; score=109.714; ------rGkTCAysgrsAGKT ; cor=0.780; Ncor=0.409; logoDP=5.308; NIcor=0.406; NsEucl=0.911; SSD=1.901; NSW=0.914; rcor=126; rNcor=144; rlogoDP=101; rNIcor=111; rNsEucl=81; rSSD=111; rNSW=94; rank_mean=109.714; match_rank=122 a 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 c 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 g 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 t 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift2 ; 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_7nt_m5_shift2 (positions_7nt_m5)																		; positions_7nt_m5; m=0 (reference); ncol1=14; shift=2; ncol=20; --kbCCAGGTCAAGgt---- ; Alignment reference a 0 0 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 0 0 0 c 0 0 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 0 0 0 g 0 0 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 0 0 0 t 0 0 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0 0 0 0
MA0071.1_shift2 (RORA_1)		0.848	0.606	8.439	0.618	0.914	1.466	0.927	63	34	32	22	68	66	61	49.429	43	; positions_7nt_m5 versus MA0071.1 (RORA_1); m=1/6; ncol2=10; w=10; offset=0; strand=D; shift=2; score=49.4286; --wwcwAGGTCA-------- ; cor=0.848; Ncor=0.606; logoDP=8.439; NIcor=0.618; NsEucl=0.914; SSD=1.466; NSW=0.927; rcor=63; rNcor=34; rlogoDP=32; rNIcor=22; rNsEucl=68; rSSD=66; rNSW=61; rank_mean=49.429; match_rank=43 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
MA0141.1_shift0 (Esrrb)		0.847	0.529	7.537	0.531	0.913	1.502	0.925	65	68	60	52	71	68	67	64.429	57	; positions_7nt_m5 versus MA0141.1 (Esrrb); m=2/6; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=64.4286; rgsyCAAGGTCA-------- ; cor=0.847; Ncor=0.529; logoDP=7.537; NIcor=0.531; NsEucl=0.913; SSD=1.502; NSW=0.925; rcor=65; rNcor=68; rlogoDP=60; rNIcor=52; rNsEucl=71; rSSD=68; rNSW=67; rank_mean=64.429; match_rank=57 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)		0.846	0.529	7.627	0.530	0.913	1.515	0.924	66	69	56	53	75	71	70	65.714	58	; positions_7nt_m5 versus MA0141.2 (Esrrb); m=3/6; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=65.7143; rgsyCAAGGTCA-------- ; cor=0.846; Ncor=0.529; logoDP=7.627; NIcor=0.530; NsEucl=0.913; SSD=1.515; NSW=0.924; rcor=66; rNcor=69; rlogoDP=56; rNIcor=53; rNsEucl=75; rSSD=71; rNSW=70; rank_mean=65.714; match_rank=58 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0
MA0258.2_shift6 (ESR2)		0.811	0.427	6.029	0.437	0.909	1.659	0.917	93	128	92	93	90	84	82	94.571	97	; positions_7nt_m5 versus MA0258.2 (ESR2); m=4/6; ncol2=15; w=10; offset=4; strand=D; shift=6; score=94.5714; ------rGGTCAsmstGaCC ; cor=0.811; Ncor=0.427; logoDP=6.029; NIcor=0.437; NsEucl=0.909; SSD=1.659; NSW=0.917; rcor=93; rNcor=128; rlogoDP=92; rNIcor=93; rNsEucl=90; rSSD=84; rNSW=82; rank_mean=94.571; match_rank=97 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278
MA0160.1_shift5 (NR4A2)		0.811	0.464	6.218	0.462	0.887	1.649	0.897	92	108	85	88	132	82	125	101.714	106	; positions_7nt_m5 versus MA0160.1 (NR4A2); m=5/6; ncol2=8; w=8; offset=3; strand=D; shift=5; score=101.714; -----aAGGTCAc------- ; cor=0.811; Ncor=0.464; logoDP=6.218; NIcor=0.462; NsEucl=0.887; SSD=1.649; NSW=0.897; rcor=92; rNcor=108; rlogoDP=85; rNIcor=88; rNsEucl=132; rSSD=82; rNSW=125; rank_mean=101.714; match_rank=106 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0
MA0258.1_shift4 (ESR2)		0.762	0.457	5.240	0.449	0.909	2.380	0.901	143	112	103	92	89	141	116	113.714	126	; positions_7nt_m5 versus MA0258.1 (ESR2); m=6/6; ncol2=18; w=12; offset=2; strand=D; shift=4; score=113.714; ----cwrGGTCAsgkTGmCC ; cor=0.762; Ncor=0.457; logoDP=5.240; NIcor=0.449; NsEucl=0.909; SSD=2.380; NSW=0.901; rcor=143; rNcor=112; rlogoDP=103; rNIcor=92; rNsEucl=89; rSSD=141; rNSW=116; rank_mean=113.714; match_rank=126 a 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46 c 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289 g 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0 t 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift2 ; 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
positions_7nt_m3_shift2 (positions_7nt_m3)																		; positions_7nt_m3; m=0 (reference); ncol1=15; shift=2; ncol=21; --smCCAGGTCATGcyg---- ; Alignment reference a 0 0 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 0 0 0 0 c 0 0 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 0 0 0 0 g 0 0 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 0 0 0 0 t 0 0 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46 0 0 0 0
MA0071.1_shift2 (RORA_1)		0.845	0.564	9.031	0.577	0.913	1.513	0.924	67	50	24	36	73	70	69	55.571	48	; positions_7nt_m3 versus MA0071.1 (RORA_1); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score=55.5714; --wwcwAGGTCA--------- ; cor=0.845; Ncor=0.564; logoDP=9.031; NIcor=0.577; NsEucl=0.913; SSD=1.513; NSW=0.924; rcor=67; rNcor=50; rlogoDP=24; rNIcor=36; rNsEucl=73; rSSD=70; rNSW=69; rank_mean=55.571; match_rank=48 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0
MA0141.1_shift0 (Esrrb)		0.837	0.492	7.951	0.497	0.910	1.621	0.919	72	87	48	65	85	77	77	73.000	65	; positions_7nt_m3 versus MA0141.1 (Esrrb); m=2/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 73; rgsyCAAGGTCA--------- ; cor=0.837; Ncor=0.492; logoDP=7.951; NIcor=0.497; NsEucl=0.910; SSD=1.621; NSW=0.919; rcor=72; rNcor=87; rlogoDP=48; rNIcor=65; rNsEucl=85; rSSD=77; rNSW=77; rank_mean=73.000; match_rank=65 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)		0.836	0.492	8.042	0.496	0.910	1.635	0.918	73	88	43	67	87	79	80	73.857	66	; positions_7nt_m3 versus MA0141.2 (Esrrb); m=3/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=73.8571; rgsyCAAGGTCA--------- ; cor=0.836; Ncor=0.492; logoDP=8.042; NIcor=0.496; NsEucl=0.910; SSD=1.635; NSW=0.918; rcor=73; rNcor=88; rlogoDP=43; rNIcor=67; rNsEucl=87; rSSD=79; rNSW=80; rank_mean=73.857; match_rank=66 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0 0
MA0258.2_shift6 (ESR2)		0.805	0.466	6.496	0.469	0.914	1.789	0.919	95	105	73	83	69	100	78	86.143	88	; positions_7nt_m3 versus MA0258.2 (ESR2); m=4/7; ncol2=15; w=11; offset=4; strand=D; shift=6; score=86.1429; ------rGGTCAsmstGaCCy ; cor=0.805; Ncor=0.466; logoDP=6.496; NIcor=0.469; NsEucl=0.914; SSD=1.789; NSW=0.919; rcor=95; rNcor=105; rlogoDP=73; rNIcor=83; rNsEucl=69; rSSD=100; rNSW=78; rank_mean=86.143; match_rank=88 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 834 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 2708 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 606 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278 4095
MA0159.1_shift6 (RXR::RAR_DR5)		0.793	0.416	5.868	0.419	0.913	1.832	0.917	106	139	97	99	74	104	85	100.571	104	; positions_7nt_m3 versus MA0159.1 (RXR::RAR_DR5); m=5/7; ncol2=17; w=11; offset=4; strand=D; shift=6; score=100.571; ------rGkTCAysgrsAGKT ; cor=0.793; Ncor=0.416; logoDP=5.868; NIcor=0.419; NsEucl=0.913; SSD=1.832; NSW=0.917; rcor=106; rNcor=139; rlogoDP=97; rNIcor=99; rNsEucl=74; rSSD=104; rNSW=85; rank_mean=100.571; match_rank=104 a 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 c 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 g 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 t 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17
MA0067.1_shift7 (Pax2)		0.776	0.414	3.256	0.415	0.885	1.695	0.894	132	140	118	105	136	89	131	121.571	140	; positions_7nt_m3 versus MA0067.1 (Pax2); m=6/7; ncol2=8; w=8; offset=5; strand=D; shift=7; score=121.571; -------wgTCAykb------ ; cor=0.776; Ncor=0.414; logoDP=3.256; NIcor=0.415; NsEucl=0.885; SSD=1.695; NSW=0.894; rcor=132; rNcor=140; rlogoDP=118; rNIcor=105; rNsEucl=136; rSSD=89; rNSW=131; rank_mean=121.571; match_rank=140 a 0 0 0 0 0 0 0 10 7 3 0 26 2 2 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 7 1 2 28 1 17 0 11 0 0 0 0 0 0 g 0 0 0 0 0 0 0 5 21 0 1 3 1 19 11 0 0 0 0 0 0 t 0 0 0 0 0 0 0 9 2 26 2 1 11 10 8 0 0 0 0 0 0
MA0160.1_shift5 (NR4A2)		0.759	0.405	6.620	0.425	0.869	2.186	0.863	146	149	71	95	146	128	147	126.000	145	; positions_7nt_m3 versus MA0160.1 (NR4A2); m=7/7; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 126; -----aAGGTCAc-------- ; cor=0.759; Ncor=0.405; logoDP=6.620; NIcor=0.425; NsEucl=0.869; SSD=2.186; NSW=0.863; rcor=146; rNcor=149; rlogoDP=71; rNIcor=95; rNsEucl=146; rSSD=128; rNSW=147; rank_mean=126.000; match_rank=145 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift6 ; 12 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_shift6 (positions_6nt_m2)																		; positions_6nt_m2; m=0 (reference); ncol1=14; shift=6; ncol=20; ------acCATGACCTGGbc ; Alignment reference a 0 0 0 0 0 0 74 45 17 145 0 0 205 0 1 0 11 18 45 42 c 0 0 0 0 0 0 34 61 153 32 0 0 0 204 204 2 1 17 53 61 g 0 0 0 0 0 0 51 50 19 14 0 205 0 0 0 0 163 156 55 51 t 0 0 0 0 0 0 46 49 16 14 205 0 0 1 0 203 30 14 52 51
MA0089.1_shift8 (NFE2L1::MafG)		0.948	0.406	6.304	0.400	0.928	0.371	0.969	13	147	80	114	30	7	14	57.857	51	; positions_6nt_m2 versus MA0089.1 (NFE2L1::MafG); m=1/11; ncol2=6; w=6; offset=2; strand=D; shift=8; score=57.8571; --------sATGAC------ ; cor=0.948; Ncor=0.406; logoDP=6.304; NIcor=0.400; NsEucl=0.928; SSD=0.371; NSW=0.969; rcor=13; rNcor=147; rlogoDP=80; rNIcor=114; rNsEucl=30; rSSD=7; rNSW=14; rank_mean=57.857; match_rank=51 a 0 0 0 0 0 0 0 0 7 29 0 1 34 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 11 2 0 0 0 26 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 10 3 0 32 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 0 34 1 0 6 0 0 0 0 0 0
MA0071.1_rc_shift10 (RORA_1_rc)		0.867	0.619	1.095	-0.085	0.918	1.343	0.933	46	29	132	137	56	55	49	72.000	63	; positions_6nt_m2 versus MA0071.1_rc (RORA_1_rc); m=2/11; ncol2=10; w=10; offset=4; strand=R; shift=10; score= 72; ----------TGACCTwgww ; cor=0.867; Ncor=0.619; logoDP=1.095; NIcor=-0.085; NsEucl=0.918; SSD=1.343; NSW=0.933; rcor=46; rNcor=29; rlogoDP=132; rNIcor=137; rNsEucl=56; rSSD=55; rNSW=49; rank_mean=72.000; match_rank=63 a 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 7 3 15 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 4 5 4 0 2 g 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 2 12 1 1 t 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 21 11 6 9 15
MA0141.1_rc_shift10 (Esrrb_rc)		0.863	0.539	1.344	0.045	0.916	1.401	0.930	52	62	128	124	62	60	55	77.571	71	; positions_6nt_m2 versus MA0141.1_rc (Esrrb_rc); m=3/11; ncol2=12; w=10; offset=4; strand=R; shift=10; score=77.5714; ----------TGACCTTGrs ; cor=0.863; Ncor=0.539; logoDP=1.344; NIcor=0.045; NsEucl=0.916; SSD=1.401; NSW=0.930; rcor=52; rNcor=62; rlogoDP=128; rNIcor=124; rNsEucl=62; rSSD=60; rNSW=55; rank_mean=77.571; match_rank=71 a 0 0 0 0 0 0 0 0 0 0 27 85 3175 17 31 27 50 52 1693 805 c 0 0 0 0 0 0 0 0 0 0 129 170 244 3602 3586 60 248 627 448 1209 g 0 0 0 0 0 0 0 0 0 0 20 3376 46 12 5 2 32 2664 1250 1211 t 0 0 0 0 0 0 0 0 0 0 3458 9 182 21 32 3567 3326 310 259 420
MA0141.2_rc_shift10 (Esrrb_rc)		0.862	0.539	1.334	0.042	0.916	1.412	0.929	53	63	129	125	63	62	57	78.857	73	; positions_6nt_m2 versus MA0141.2_rc (Esrrb_rc); m=4/11; ncol2=12; w=10; offset=4; strand=R; shift=10; score=78.8571; ----------TGACCTTGrs ; cor=0.862; Ncor=0.539; logoDP=1.334; NIcor=0.042; NsEucl=0.916; SSD=1.412; NSW=0.929; rcor=53; rNcor=63; rlogoDP=129; rNIcor=125; rNsEucl=63; rSSD=62; rNSW=57; rank_mean=78.857; match_rank=73 a 0 0 0 0 0 0 0 0 0 0 26 85 3192 16 29 6 27 51 1702 807 c 0 0 0 0 0 0 0 0 0 0 128 167 243 3622 3597 60 248 630 449 1212 g 0 0 0 0 0 0 0 0 0 0 21 3394 43 11 2 2 32 2653 1230 1212 t 0 0 0 0 0 0 0 0 0 0 3478 9 180 12 33 3590 3347 312 260 403
MA0258.2_rc_shift1 (ESR2_rc)		0.853	0.449	2.624	0.342	0.917	1.392	0.930	60	116	123	117	61	59	52	84.000	82	; positions_6nt_m2 versus MA0258.2_rc (ESR2_rc); m=5/11; ncol2=15; w=10; offset=-5; strand=R; shift=1; score= 84; -rGGtCasksTGACCy---- ; cor=0.853; Ncor=0.449; logoDP=2.624; NIcor=0.342; NsEucl=0.917; SSD=1.392; NSW=0.930; rcor=60; rNcor=116; rlogoDP=123; rNIcor=117; rNsEucl=61; rSSD=59; rNSW=52; rank_mean=84.000; match_rank=82 a 0 4095 1278 977 1518 66 5133 1752 1228 801 87 89 7033 41 644 174 0 0 0 0 c 0 606 0 363 1391 6658 533 2173 1688 2738 57 533 989 8143 7170 2563 0 0 0 0 g 0 2708 5854 6469 2056 398 975 2510 3235 4202 1 7621 147 0 0 96 0 0 0 0 t 0 834 1111 434 3278 1121 1602 1808 2092 502 8098 0 74 59 429 5410 0 0 0 0
MA0258.1_rc_shift0 (ESR2_rc)		0.807	0.484	1.124	-0.035	0.916	2.040	0.915	94	98	131	131	64	120	92	104.286	109	; positions_6nt_m2 versus MA0258.1_rc (ESR2_rc); m=6/11; ncol2=18; w=12; offset=-6; strand=R; shift=0; score=104.286; srGGkCAmcsTGACCywg-- ; cor=0.807; Ncor=0.484; logoDP=1.124; NIcor=-0.035; NsEucl=0.916; SSD=2.040; NSW=0.915; rcor=94; rNcor=98; rlogoDP=131; rNIcor=131; rNsEucl=64; rSSD=120; rNSW=92; rank_mean=104.286; match_rank=109 a 67 240 22 53 61 4 279 97 81 72 19 0 292 0 55 2 107 55 0 0 c 136 0 0 2 19 265 24 147 149 113 0 0 33 319 275 154 41 63 0 0 g 94 90 289 268 99 25 33 61 63 123 1 357 19 20 0 15 51 161 0 0 t 60 27 46 34 178 63 21 52 64 49 337 0 13 18 27 186 158 78 0 0
MA0112.2_rc_shift1 (ESR1_rc)		0.766	0.536	2.155	0.105	0.921	2.422	0.914	138	65	125	122	47	142	95	104.857	110	; positions_6nt_m2 versus MA0112.2_rc (ESR1_rc); m=7/11; ncol2=20; w=14; offset=-5; strand=R; shift=1; score=104.857; -rGGtCAgggTGaCCtkgsm ; cor=0.766; Ncor=0.536; logoDP=2.155; NIcor=0.105; NsEucl=0.921; SSD=2.422; NSW=0.914; rcor=138; rNcor=65; rlogoDP=125; rNIcor=122; rNsEucl=47; rSSD=142; rNSW=95; rank_mean=104.857; match_rank=110 a 0 262 61 17 33 6 416 56 83 60 37 24 310 18 43 48 57 93 82 117 c 0 22 2 12 31 426 8 97 53 107 27 53 91 420 387 89 47 65 149 164 g 0 165 353 436 106 22 19 258 276 250 13 394 41 18 8 28 232 229 173 80 t 0 26 59 10 305 21 32 64 63 58 398 4 33 19 36 308 134 83 64 107
MA0592.1_rc_shift8 (ESRRA_rc)		0.784	0.616	0.359	-0.172	0.900	2.432	0.889	122	30	145	146	116	143	135	119.571	137	; positions_6nt_m2 versus MA0592.1_rc (ESRRA_rc); m=8/11; ncol2=11; w=11; offset=2; strand=R; shift=8; score=119.571; --------kgTGACCTTGr- ; cor=0.784; Ncor=0.616; logoDP=0.359; NIcor=-0.172; NsEucl=0.900; SSD=2.432; NSW=0.889; rcor=122; rNcor=30; rlogoDP=145; rNIcor=146; rNsEucl=116; rSSD=143; rNSW=135; rank_mean=119.571; match_rank=137 a 0 0 0 0 0 0 0 0 44 33 0 0 180 1 5 0 0 1 62 0 c 0 0 0 0 0 0 0 0 40 44 10 3 22 207 203 10 6 15 11 0 g 0 0 0 0 0 0 0 0 54 108 1 205 0 0 0 0 2 174 118 0 t 0 0 0 0 0 0 0 0 70 23 197 0 6 0 0 198 200 18 17 0
MA0160.1_rc_shift9 (NR4A2_rc)		0.802	0.458	3.369	0.101	0.880	1.850	0.884	100	111	117	123	142	107	140	120.000	138	; positions_6nt_m2 versus MA0160.1_rc (NR4A2_rc); m=9/11; ncol2=8; w=8; offset=3; strand=R; shift=9; score= 120; ---------gTGACCTt--- ; cor=0.802; Ncor=0.458; logoDP=3.369; NIcor=0.101; NsEucl=0.880; SSD=1.850; NSW=0.884; rcor=100; rNcor=111; rlogoDP=117; rNIcor=123; rNsEucl=142; rSSD=107; rNSW=140; rank_mean=120.000; match_rank=138 a 0 0 0 0 0 0 0 0 0 0 0 1 10 0 1 0 1 0 0 0 c 0 0 0 0 0 0 0 0 0 2 0 0 0 11 13 1 3 0 0 0 g 0 0 0 0 0 0 0 0 0 8 0 13 2 0 0 0 1 0 0 0 t 0 0 0 0 0 0 0 0 0 3 14 0 2 3 0 13 8 0 0 0
MA0112.1_rc_shift0 (ESR1_rc)		0.765	0.459	1.844	0.000	0.908	2.452	0.898	139	110	126	130	97	144	121	123.857	142	; positions_6nt_m2 versus MA0112.1_rc (ESR1_rc); m=10/11; ncol2=18; w=12; offset=-6; strand=R; shift=0; score=123.857; krGGyCaygGtGACCTgg-- ; cor=0.765; Ncor=0.459; logoDP=1.844; NIcor=0.000; NsEucl=0.908; SSD=2.452; NSW=0.898; rcor=139; rNcor=110; rlogoDP=126; rNIcor=130; rNsEucl=97; rSSD=144; rNSW=121; rank_mean=123.857; match_rank=142 a 1 3 0 1 0 0 6 0 1 0 1 0 9 0 0 0 2 2 0 0 c 1 0 0 0 3 8 1 4 1 1 2 2 0 9 7 1 1 1 0 0 g 4 4 9 8 1 0 1 2 5 7 0 7 0 0 0 1 5 5 0 0 t 3 2 0 0 5 1 1 3 2 1 6 0 0 0 2 7 1 1 0 0
MA0067.1_rc_shift7 (Pax2_rc)		0.784	0.448	0.410	-0.148	0.885	1.692	0.894	123	118	144	143	135	88	129	125.714	144	; positions_6nt_m2 versus MA0067.1_rc (Pax2_rc); m=11/11; ncol2=8; w=8; offset=1; strand=R; shift=7; score=125.714; -------vmrTGAcw----- ; cor=0.784; Ncor=0.448; logoDP=0.410; NIcor=-0.148; NsEucl=0.885; SSD=1.692; NSW=0.894; rcor=123; rNcor=118; rlogoDP=144; rNIcor=143; rNsEucl=135; rSSD=88; rNSW=129; rank_mean=125.714; match_rank=144 a 0 0 0 0 0 0 0 8 10 11 1 2 26 2 9 0 0 0 0 0 c 0 0 0 0 0 0 0 11 19 1 3 1 0 21 5 0 0 0 0 0 g 0 0 0 0 0 0 0 11 0 17 1 28 2 1 7 0 0 0 0 0 t 0 0 0 0 0 0 0 1 2 2 26 0 3 7 10 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m5_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_m5_shift0 (positions_6nt_m5)																		; positions_6nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; wwAATGTCATGwy ; Alignment reference a 127 136 335 387 8 9 13 10 395 18 45 135 102 c 66 70 28 7 1 3 7 384 6 14 27 66 111 g 80 60 27 9 8 402 2 11 7 14 319 75 73 t 144 151 27 14 400 3 395 12 9 371 26 141 131
MA0089.1_rc_shift5 (NFE2L1::MafG_rc)		0.948	0.437	0.234	-0.132	0.930	0.355	0.970	12	120	148	142	27	6	12	66.714	59	; positions_6nt_m5 versus MA0089.1_rc (NFE2L1::MafG_rc); m=1/2; ncol2=6; w=6; offset=5; strand=R; shift=5; score=66.7143; -----GTCATs-- ; cor=0.948; Ncor=0.437; logoDP=0.234; NIcor=-0.132; NsEucl=0.930; SSD=0.355; NSW=0.970; rcor=12; rNcor=120; rlogoDP=148; rNIcor=142; rNsEucl=27; rSSD=6; rNSW=12; rank_mean=66.714; match_rank=59 a 0 0 0 0 0 6 0 1 34 0 6 0 0 c 0 0 0 0 0 2 0 32 0 3 10 0 0 g 0 0 0 0 0 26 0 0 0 2 11 0 0 t 0 0 0 0 0 0 34 1 0 29 7 0 0
MA0067.1_shift4 (Pax2)		0.789	0.486	3.014	0.484	0.889	1.586	0.901	112	93	119	76	129	75	115	102.714	108	; positions_6nt_m5 versus MA0067.1 (Pax2); m=2/2; ncol2=8; w=8; offset=4; strand=D; shift=4; score=102.714; ----wgTCAykb- ; cor=0.789; Ncor=0.486; logoDP=3.014; NIcor=0.484; NsEucl=0.889; SSD=1.586; NSW=0.901; rcor=112; rNcor=93; rlogoDP=119; rNIcor=76; rNsEucl=129; rSSD=75; rNSW=115; rank_mean=102.714; match_rank=108 a 0 0 0 0 10 7 3 0 26 2 2 1 0 c 0 0 0 0 7 1 2 28 1 17 0 11 0 g 0 0 0 0 5 21 0 1 3 1 19 11 0 t 0 0 0 0 9 2 26 2 1 11 10 8 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift2 ; 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
positions_7nt_m4_shift2 (positions_7nt_m4)																		; positions_7nt_m4; m=0 (reference); ncol1=15; shift=2; ncol=21; --ssCCAGGTCAGGgcr---- ; Alignment reference a 0 0 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 0 0 c 0 0 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 0 0 g 0 0 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 0 0 t 0 0 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0 0 0
MA0071.1_shift2 (RORA_1)		0.825	0.550	8.532	0.567	0.908	1.696	0.915	80	54	31	38	96	91	90	68.571	61	; positions_7nt_m4 versus MA0071.1 (RORA_1); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score=68.5714; --wwcwAGGTCA--------- ; cor=0.825; Ncor=0.550; logoDP=8.532; NIcor=0.567; NsEucl=0.908; SSD=1.696; NSW=0.915; rcor=80; rNcor=54; rlogoDP=31; rNIcor=38; rNsEucl=96; rSSD=91; rNSW=90; rank_mean=68.571; match_rank=61 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0
MA0258.2_shift6 (ESR2)		0.816	0.473	6.236	0.465	0.917	1.681	0.924	89	102	84	86	60	87	71	82.714	78	; positions_7nt_m4 versus MA0258.2 (ESR2); m=2/7; ncol2=15; w=11; offset=4; strand=D; shift=6; score=82.7143; ------rGGTCAsmstGaCCy ; cor=0.816; Ncor=0.473; logoDP=6.236; NIcor=0.465; NsEucl=0.917; SSD=1.681; NSW=0.924; rcor=89; rNcor=102; rlogoDP=84; rNIcor=86; rNsEucl=60; rSSD=87; rNSW=71; rank_mean=82.714; match_rank=78 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 834 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 2708 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 606 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278 4095
MA0141.1_shift0 (Esrrb)		0.824	0.485	7.555	0.491	0.907	1.724	0.914	81	96	59	69	99	93	93	84.286	83	; positions_7nt_m4 versus MA0141.1 (Esrrb); m=3/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=84.2857; rgsyCAAGGTCA--------- ; cor=0.824; Ncor=0.485; logoDP=7.555; NIcor=0.491; NsEucl=0.907; SSD=1.724; NSW=0.914; rcor=81; rNcor=96; rlogoDP=59; rNIcor=69; rNsEucl=99; rSSD=93; rNSW=93; rank_mean=84.286; match_rank=83 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)		0.824	0.484	7.643	0.490	0.907	1.738	0.913	82	99	54	71	101	96	97	85.714	85	; positions_7nt_m4 versus MA0141.2 (Esrrb); m=4/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=85.7143; rgsyCAAGGTCA--------- ; cor=0.824; Ncor=0.484; logoDP=7.643; NIcor=0.490; NsEucl=0.907; SSD=1.738; NSW=0.913; rcor=82; rNcor=99; rlogoDP=54; rNIcor=71; rNsEucl=101; rSSD=96; rNSW=97; rank_mean=85.714; match_rank=85 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0 0
MA0159.1_shift6 (RXR::RAR_DR5)		0.794	0.416	5.433	0.412	0.913	1.817	0.917	105	138	99	106	70	103	81	100.286	102	; positions_7nt_m4 versus MA0159.1 (RXR::RAR_DR5); m=5/7; ncol2=17; w=11; offset=4; strand=D; shift=6; score=100.286; ------rGkTCAysgrsAGKT ; cor=0.794; Ncor=0.416; logoDP=5.433; NIcor=0.412; NsEucl=0.913; SSD=1.817; NSW=0.917; rcor=105; rNcor=138; rlogoDP=99; rNIcor=106; rNsEucl=70; rSSD=103; rNSW=81; rank_mean=100.286; match_rank=102 a 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 c 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 g 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 t 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17
MA0160.1_shift5 (NR4A2)		0.765	0.408	6.432	0.409	0.871	2.139	0.866	140	145	75	109	145	127	146	126.714	146	; positions_7nt_m4 versus MA0160.1 (NR4A2); m=6/7; ncol2=8; w=8; offset=3; strand=D; shift=5; score=126.714; -----aAGGTCAc-------- ; cor=0.765; Ncor=0.408; logoDP=6.432; NIcor=0.409; NsEucl=0.871; SSD=2.139; NSW=0.866; rcor=140; rNcor=145; rlogoDP=75; rNIcor=109; rNsEucl=145; rSSD=127; rNSW=146; rank_mean=126.714; match_rank=146 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0 0
MA0103.2_rc_shift5 (ZEB1_rc)		0.776	0.466	2.348	0.018	0.881	2.305	0.872	130	106	124	127	141	137	143	129.714	149	; positions_7nt_m4 versus MA0103.2_rc (ZEB1_rc); m=7/7; ncol2=9; w=9; offset=3; strand=R; shift=5; score=129.714; -----CAGGTGwGg------- ; cor=0.776; Ncor=0.466; logoDP=2.348; NIcor=0.018; NsEucl=0.881; SSD=2.305; NSW=0.872; rcor=130; rNcor=106; rlogoDP=124; rNIcor=127; rNsEucl=141; rSSD=137; rNSW=143; rank_mean=129.714; match_rank=149 a 0 0 0 0 0 0 3555 0 0 0 385 1594 564 414 0 0 0 0 0 0 0 c 0 0 0 0 0 3555 0 0 0 0 0 431 0 830 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 3555 3555 0 3170 333 2991 1455 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 3555 0 1197 0 856 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_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_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)																		; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=2; ncol=18; --waATGTCAkw------ ; Alignment reference a 0 0 562 707 1681 0 0 0 0 1681 394 446 0 0 0 0 0 0 c 0 0 356 407 0 0 0 0 1681 0 401 410 0 0 0 0 0 0 g 0 0 311 290 0 0 1681 0 0 0 434 392 0 0 0 0 0 0 t 0 0 452 277 0 1681 0 1681 0 0 452 433 0 0 0 0 0 0
MA0089.1_rc_shift6 (NFE2L1::MafG_rc)		0.904	0.543	0.059	-0.127	0.911	0.575	0.952	29	59	151	140	83	16	27	72.143	64	; oligos_6nt_mkv4_m1 versus MA0089.1_rc (NFE2L1::MafG_rc); m=1/4; ncol2=6; w=6; offset=4; strand=R; shift=6; score=72.1429; ------GTCATs------ ; cor=0.904; Ncor=0.543; logoDP=0.059; NIcor=-0.127; NsEucl=0.911; SSD=0.575; NSW=0.952; rcor=29; rNcor=59; rlogoDP=151; rNIcor=140; rNsEucl=83; rSSD=16; rNSW=27; rank_mean=72.143; match_rank=64 a 0 0 0 0 0 0 6 0 1 34 0 6 0 0 0 0 0 0 c 0 0 0 0 0 0 2 0 32 0 3 10 0 0 0 0 0 0 g 0 0 0 0 0 0 26 0 0 0 2 11 0 0 0 0 0 0 t 0 0 0 0 0 0 0 34 1 0 29 7 0 0 0 0 0 0
MA0067.1_shift5 (Pax2)		0.798	0.508	3.634	0.506	0.882	1.368	0.902	103	78	114	62	139	58	113	95.286	98	; oligos_6nt_mkv4_m1 versus MA0067.1 (Pax2); m=2/4; ncol2=8; w=7; offset=3; strand=D; shift=5; score=95.2857; -----wgTCAykb----- ; cor=0.798; Ncor=0.508; logoDP=3.634; NIcor=0.506; NsEucl=0.882; SSD=1.368; NSW=0.902; rcor=103; rNcor=78; rlogoDP=114; rNIcor=62; rNsEucl=139; rSSD=58; rNSW=113; rank_mean=95.286; match_rank=98 a 0 0 0 0 0 10 7 3 0 26 2 2 1 0 0 0 0 0 c 0 0 0 0 0 7 1 2 28 1 17 0 11 0 0 0 0 0 g 0 0 0 0 0 5 21 0 1 3 1 19 11 0 0 0 0 0 t 0 0 0 0 0 9 2 26 2 1 11 10 8 0 0 0 0 0
MA0071.1_shift0 (RORA_1)		0.754	0.503	8.794	0.515	0.869	2.196	0.863	148	83	28	58	147	129	148	105.857	113	; oligos_6nt_mkv4_m1 versus MA0071.1 (RORA_1); m=3/4; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=105.857; wwcwAGGTCA-------- ; cor=0.754; Ncor=0.503; logoDP=8.794; NIcor=0.515; NsEucl=0.869; SSD=2.196; NSW=0.863; rcor=148; rNcor=83; rlogoDP=28; rNIcor=58; rNsEucl=147; rSSD=129; rNSW=148; rank_mean=105.857; match_rank=113 a 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 c 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 g 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 t 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
MA0258.1_shift2 (ESR2)		0.754	0.419	5.998	0.417	0.900	1.992	0.900	149	131	93	102	115	116	117	117.571	134	; oligos_6nt_mkv4_m1 versus MA0258.1 (ESR2); m=4/4; ncol2=18; w=10; offset=0; strand=D; shift=2; score=117.571; --cwrGGTCAsgkTGmCC ; cor=0.754; Ncor=0.419; logoDP=5.998; NIcor=0.417; NsEucl=0.900; SSD=1.992; NSW=0.900; rcor=149; rNcor=131; rlogoDP=93; rNIcor=102; rNsEucl=115; rSSD=116; rNSW=117; rank_mean=117.571; match_rank=134 a 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46 c 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289 g 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0 t 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 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
dyads_m2_shift0 (dyads_m2)																		; dyads_m2; m=0 (reference); ncol1=15; shift=0; ncol=18; wrCAAATATTTACwt--- ; Alignment reference a 135 121 19 289 293 299 0 299 3 1 5 274 23 88 77 0 0 0 c 38 35 257 10 6 2 6 0 2 1 2 2 230 64 76 0 0 0 g 54 88 7 0 3 3 4 9 4 2 11 18 10 20 69 0 0 0 t 82 65 26 10 7 5 299 1 300 305 291 15 46 137 87 0 0 0
MA0047.2_shift6 (Foxa2)		0.860	0.430	6.826	0.417	0.913	1.223	0.932	54	125	69	101	72	47	51	74.143	67	; dyads_m2 versus MA0047.2 (Foxa2); m=1/6; ncol2=12; w=9; offset=6; strand=D; shift=6; score=74.1429; ------TRTTTACwywgg ; cor=0.860; Ncor=0.430; logoDP=6.826; NIcor=0.417; NsEucl=0.913; SSD=1.223; NSW=0.932; rcor=54; rNcor=125; rlogoDP=69; rNIcor=101; rNsEucl=72; rSSD=47; rNSW=51; rank_mean=74.143; match_rank=67 a 0 0 0 0 0 0 1 221 1 1 1 736 2 338 50 417 131 129 c 0 0 0 0 0 0 1 3 1 3 1 4 725 77 265 6 53 195 g 0 0 0 0 0 0 1 582 1 36 175 67 2 3 58 24 482 290 t 0 0 0 0 0 0 805 3 806 769 634 3 81 391 436 360 140 189
MA0047.1_shift3 (Foxa2)		0.791	0.633	6.095	0.599	0.909	2.373	0.901	109	22	91	27	88	140	114	84.429	84	; dyads_m2 versus MA0047.1 (Foxa2); m=2/6; ncol2=12; w=12; offset=3; strand=D; shift=3; score=84.4286; ---mawTrTTkryTY--- ; cor=0.791; Ncor=0.633; logoDP=6.095; NIcor=0.599; NsEucl=0.909; SSD=2.373; NSW=0.901; rcor=109; rNcor=22; rlogoDP=91; rNIcor=27; rNsEucl=88; rSSD=140; rNSW=114; rank_mean=84.429; match_rank=84 a 0 0 0 6 11 8 0 11 0 0 0 9 0 1 0 0 0 0 c 0 0 0 7 3 3 1 0 1 1 0 0 9 1 5 0 0 0 g 0 0 0 3 1 1 0 6 0 0 6 8 0 1 0 0 0 0 t 0 0 0 1 2 5 16 0 16 16 11 0 8 14 12 0 0 0
MA0148.1_shift6 (FOXA1)		0.787	0.416	6.254	0.400	0.893	1.847	0.897	118	135	83	112	125	106	123	114.571	129	; dyads_m2 versus MA0148.1 (FOXA1); m=3/6; ncol2=11; w=9; offset=6; strand=D; shift=6; score=114.571; ------TGTTTrCwywg- ; cor=0.787; Ncor=0.416; logoDP=6.254; NIcor=0.400; NsEucl=0.893; SSD=1.847; NSW=0.897; rcor=118; rNcor=135; rlogoDP=83; rNIcor=112; rNsEucl=125; rSSD=106; rNSW=123; rank_mean=114.571; match_rank=129 a 0 0 0 0 0 0 13 108 1 5 6 476 6 291 45 378 90 0 c 0 0 0 0 0 0 2 7 7 7 3 12 807 106 368 9 125 0 g 0 0 0 0 0 0 2 770 5 24 78 368 5 5 69 24 466 0 t 0 0 0 0 0 0 875 8 882 860 809 40 79 495 414 482 211 0
MA0148.2_shift6 (FOXA1)		0.787	0.416	6.296	0.400	0.893	1.851	0.897	119	136	81	113	126	108	124	115.286	130	; dyads_m2 versus MA0148.2 (FOXA1); m=4/6; ncol2=11; w=9; offset=6; strand=D; shift=6; score=115.286; ------TGTTTrCwywg- ; cor=0.787; Ncor=0.416; logoDP=6.296; NIcor=0.400; NsEucl=0.893; SSD=1.851; NSW=0.897; rcor=119; rNcor=136; rlogoDP=81; rNIcor=113; rNsEucl=126; rSSD=108; rNSW=124; rank_mean=115.286; match_rank=130 a 0 0 0 0 0 0 13 108 1 4 6 478 4 289 42 379 89 0 c 0 0 0 0 0 0 1 7 7 7 3 12 808 106 369 7 125 0 g 0 0 0 0 0 0 2 772 4 24 77 368 5 5 69 24 467 0 t 0 0 0 0 0 0 876 7 885 862 811 38 79 496 414 482 211 0
MA0031.1_rc_shift5 (FOXD1_rc)		0.780	0.416	4.283	0.132	0.871	2.116	0.868	127	137	110	120	144	125	145	129.714	148	; dyads_m2 versus MA0031.1_rc (FOXD1_rc); m=5/6; ncol2=8; w=8; offset=5; strand=R; shift=5; score=129.714; -----wTGTTTAC----- ; cor=0.780; Ncor=0.416; logoDP=4.283; NIcor=0.132; NsEucl=0.871; SSD=2.116; NSW=0.868; rcor=127; rNcor=137; rlogoDP=110; rNIcor=120; rNsEucl=144; rSSD=125; rNSW=145; rank_mean=129.714; match_rank=148 a 0 0 0 0 0 8 0 1 0 0 0 20 1 0 0 0 0 0 c 0 0 0 0 0 3 0 0 1 0 0 0 17 0 0 0 0 0 g 0 0 0 0 0 2 0 18 1 0 1 0 1 0 0 0 0 0 t 0 0 0 0 0 7 20 1 18 20 19 0 1 0 0 0 0 0
MA0157.1_rc_shift6 (FOXO3_rc)		0.761	0.406	2.783	0.129	0.873	2.063	0.871	144	148	120	121	143	122	144	134.571	151	; dyads_m2 versus MA0157.1_rc (FOXO3_rc); m=6/6; ncol2=8; w=8; offset=6; strand=R; shift=6; score=134.571; ------TGTTTACm---- ; cor=0.761; Ncor=0.406; logoDP=2.783; NIcor=0.129; NsEucl=0.873; SSD=2.063; NSW=0.871; rcor=144; rNcor=148; rlogoDP=120; rNIcor=121; rNsEucl=143; rSSD=122; rNSW=144; rank_mean=134.571; match_rank=151 a 0 0 0 0 0 0 1 1 0 0 0 9 0 8 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 10 5 0 0 0 0 g 0 0 0 0 0 0 0 12 0 1 0 0 2 0 0 0 0 0 t 0 0 0 0 0 0 12 0 13 12 13 3 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift7 ; 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_6nt_m4_shift7 (positions_6nt_m4)																		; positions_6nt_m4; m=0 (reference); ncol1=17; shift=7; ncol=24; -------styaaCCTGACCTGgsy ; Alignment reference a 0 0 0 0 0 0 0 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 0 0 0 0 0 0 0 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 0 0 0 0 0 0 0 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 0 0 0 0 0 0 0 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47
MA0071.1_rc_shift14 (RORA_1_rc)		0.857	0.504	1.382	-0.043	0.916	1.418	0.929	57	81	127	133	66	63	58	83.571	80	; positions_6nt_m4 versus MA0071.1_rc (RORA_1_rc); m=1/6; ncol2=10; w=10; offset=7; strand=R; shift=14; score=83.5714; --------------TGACCTwgww ; cor=0.857; Ncor=0.504; logoDP=1.382; NIcor=-0.043; NsEucl=0.916; SSD=1.418; NSW=0.929; rcor=57; rNcor=81; rlogoDP=127; rNIcor=133; rNsEucl=66; rSSD=63; rNSW=58; rank_mean=83.571; match_rank=80 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 7 3 15 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 4 5 4 0 2 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 2 12 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 21 11 6 9 15
MA0258.2_rc_shift5 (ESR2_rc)		0.803	0.550	2.699	0.311	0.923	1.998	0.923	98	55	122	118	42	117	72	89.143	91	; positions_6nt_m4 versus MA0258.2_rc (ESR2_rc); m=2/6; ncol2=15; w=13; offset=-2; strand=R; shift=5; score=89.1429; -----rGGtCasksTGACCy---- ; cor=0.803; Ncor=0.550; logoDP=2.699; NIcor=0.311; NsEucl=0.923; SSD=1.998; NSW=0.923; rcor=98; rNcor=55; rlogoDP=122; rNIcor=118; rNsEucl=42; rSSD=117; rNSW=72; rank_mean=89.143; match_rank=91 a 0 0 0 0 0 4095 1278 977 1518 66 5133 1752 1228 801 87 89 7033 41 644 174 0 0 0 0 c 0 0 0 0 0 606 0 363 1391 6658 533 2173 1688 2738 57 533 989 8143 7170 2563 0 0 0 0 g 0 0 0 0 0 2708 5854 6469 2056 398 975 2510 3235 4202 1 7621 147 0 0 96 0 0 0 0 t 0 0 0 0 0 834 1111 434 3278 1121 1602 1808 2092 502 8098 0 74 59 429 5410 0 0 0 0
MA0141.1_rc_shift14 (Esrrb_rc)		0.822	0.432	0.956	0.009	0.905	1.792	0.910	83	122	134	128	106	101	102	110.857	123	; positions_6nt_m4 versus MA0141.1_rc (Esrrb_rc); m=3/6; ncol2=12; w=10; offset=7; strand=R; shift=14; score=110.857; --------------TGACCTTGrs ; cor=0.822; Ncor=0.432; logoDP=0.956; NIcor=0.009; NsEucl=0.905; SSD=1.792; NSW=0.910; rcor=83; rNcor=122; rlogoDP=134; rNIcor=128; rNsEucl=106; rSSD=101; rNSW=102; rank_mean=110.857; match_rank=123 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 85 3175 17 31 27 50 52 1693 805 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 129 170 244 3602 3586 60 248 627 448 1209 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 3376 46 12 5 2 32 2664 1250 1211 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3458 9 182 21 32 3567 3326 310 259 420
MA0112.2_shift0 (ESR1)		0.772	0.418	4.953	0.390	0.917	2.301	0.912	134	132	105	115	57	136	100	111.286	124	; positions_6nt_m4 versus MA0112.2 (ESR1); m=4/6; ncol2=20; w=13; offset=-7; strand=D; shift=0; score=111.286; vkscmaGGtCAcccTGaCCy---- ; cor=0.772; Ncor=0.418; logoDP=4.953; NIcor=0.390; NsEucl=0.917; SSD=2.301; NSW=0.912; rcor=134; rNcor=132; rlogoDP=105; rNIcor=115; rNsEucl=57; rSSD=136; rNSW=100; rank_mean=111.286; match_rank=124 a 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 0 0 0 0 c 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 0 0 0 0 g 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 0 0 0 0 t 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262 0 0 0 0
MA0141.2_rc_shift14 (Esrrb_rc)		0.821	0.432	0.945	0.007	0.905	1.804	0.910	85	123	135	129	107	102	104	112.143	125	; positions_6nt_m4 versus MA0141.2_rc (Esrrb_rc); m=5/6; ncol2=12; w=10; offset=7; strand=R; shift=14; score=112.143; --------------TGACCTTGrs ; cor=0.821; Ncor=0.432; logoDP=0.945; NIcor=0.007; NsEucl=0.905; SSD=1.804; NSW=0.910; rcor=85; rNcor=123; rlogoDP=135; rNIcor=129; rNsEucl=107; rSSD=102; rNSW=104; rank_mean=112.143; match_rank=125 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 85 3192 16 29 6 27 51 1702 807 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 128 167 243 3622 3597 60 248 630 449 1212 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 3394 43 11 2 2 32 2653 1230 1212 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3478 9 180 12 33 3590 3347 312 260 403
MA0103.2_shift7 (ZEB1)		0.788	0.417	5.458	0.416	0.892	1.892	0.895	114	133	98	104	127	110	127	116.143	131	; positions_6nt_m4 versus MA0103.2 (ZEB1); m=6/6; ncol2=9; w=9; offset=0; strand=D; shift=7; score=116.143; -------cCwCACCTG-------- ; cor=0.788; Ncor=0.417; logoDP=5.458; NIcor=0.416; NsEucl=0.892; SSD=1.892; NSW=0.895; rcor=114; rNcor=133; rlogoDP=98; rNIcor=104; rNsEucl=127; rSSD=110; rNSW=127; rank_mean=116.143; match_rank=131 a 0 0 0 0 0 0 0 856 0 1197 0 3555 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1455 2991 333 3170 0 3555 3555 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 830 0 431 0 0 0 0 0 3555 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 414 564 1594 385 0 0 0 3555 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift4 ; 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_m2_shift4 (oligos_6nt_mkv4_m2)																		; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ssCGCCCGss ; Alignment reference a 0 0 0 0 86 94 4 2 17 25 0 3 75 91 c 0 0 0 0 348 238 731 1 644 536 700 15 338 254 g 0 0 0 0 217 359 11 742 66 168 47 726 253 319 t 0 0 0 0 97 57 2 3 21 19 1 4 82 84
MA0024.2_rc_shift1 (E2F1_rc)		0.840	0.517	1.305	-0.042	0.905	1.143	0.929	69	73	130	132	105	42	59	87.143	89	; oligos_6nt_mkv4_m2 versus MA0024.2_rc (E2F1_rc); m=1/3; ncol2=11; w=8; offset=-3; strand=R; shift=1; score=87.1429; -byTSSCGCscs-- ; cor=0.840; Ncor=0.517; logoDP=1.305; NIcor=-0.042; NsEucl=0.905; SSD=1.143; NSW=0.929; rcor=69; rNcor=73; rlogoDP=130; rNIcor=132; rNsEucl=105; rSSD=42; rNSW=59; rank_mean=87.143; match_rank=89 a 0 0 0 0 0 0 0 0 0 0 213 203 0 0 c 0 485 551 0 773 722 1059 0 1059 641 628 280 0 0 g 0 269 0 0 286 337 0 1059 0 274 0 317 0 0 t 0 305 508 1059 0 0 0 0 0 144 218 259 0 0
MA0470.1_rc_shift0 (E2F4_rc)		0.833	0.417	0.340	-0.096	0.891	1.165	0.917	75	134	146	138	128	43	84	106.857	116	; oligos_6nt_mkv4_m2 versus MA0470.1_rc (E2F4_rc); m=2/3; ncol2=11; w=7; offset=-4; strand=R; shift=0; score=106.857; yyyTCCCGCsc--- ; cor=0.833; Ncor=0.417; logoDP=0.340; NIcor=-0.096; NsEucl=0.891; SSD=1.165; NSW=0.917; rcor=75; rNcor=134; rlogoDP=146; rNIcor=138; rNsEucl=128; rSSD=43; rNSW=84; rank_mean=106.857; match_rank=116 a 366 97 0 0 0 0 0 0 0 0 388 0 0 0 c 616 720 625 75 1822 1633 1878 0 1867 1213 848 0 0 0 g 393 349 0 0 41 218 0 1878 11 510 370 0 0 0 t 503 712 1253 1803 15 27 0 0 0 155 272 0 0 0
MA0003.1_shift7 (TFAP2A)		0.769	0.448	3.531	0.410	0.885	1.295	0.908	136	117	115	108	134	50	107	109.571	121	; oligos_6nt_mkv4_m2 versus MA0003.1 (TFAP2A); m=3/3; ncol2=9; w=7; offset=3; strand=D; shift=7; score=109.571; -------GCCcbrr ; cor=0.769; Ncor=0.448; logoDP=3.531; NIcor=0.410; NsEucl=0.885; SSD=1.295; NSW=0.908; rcor=136; rNcor=117; rlogoDP=115; rNIcor=108; rNsEucl=134; rSSD=50; rNSW=107; rank_mean=109.571; match_rank=121 a 0 0 0 0 0 0 0 0 0 0 22 19 55 53 c 0 0 0 0 0 0 0 0 185 185 71 57 44 30 g 0 0 0 0 0 0 0 185 0 0 46 61 67 91 t 0 0 0 0 0 0 0 0 0 0 46 48 19 11

One-to-n matrix alignment; reference matrix: dyads_m1_shift3 ; 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
dyads_m1_shift3 (dyads_m1)																		; dyads_m1; m=0 (reference); ncol1=16; shift=3; ncol=19; ---bwGTAAATATTTACwv ; Alignment reference a 0 0 0 22 58 13 6 99 104 105 1 102 0 0 4 90 6 30 27 c 0 0 0 30 2 1 9 3 2 0 3 0 1 0 0 1 86 16 27 g 0 0 0 27 16 86 1 0 0 1 0 3 0 2 3 9 1 2 30 t 0 0 0 27 30 6 90 4 0 0 102 1 105 104 99 6 13 58 22
MA0047.1_shift7 (Foxa2)		0.791	0.593	6.324	0.564	0.908	2.456	0.898	111	38	78	39	98	145	122	90.143	94	; dyads_m1 versus MA0047.1 (Foxa2); m=1/2; ncol2=12; w=12; offset=4; strand=D; shift=7; score=90.1429; -------mawTrTTkryTY ; cor=0.791; Ncor=0.593; logoDP=6.324; NIcor=0.564; NsEucl=0.908; SSD=2.456; NSW=0.898; rcor=111; rNcor=38; rlogoDP=78; rNIcor=39; rNsEucl=98; rSSD=145; rNSW=122; rank_mean=90.143; match_rank=94 a 0 0 0 0 0 0 0 6 11 8 0 11 0 0 0 9 0 1 0 c 0 0 0 0 0 0 0 7 3 3 1 0 1 1 0 0 9 1 5 g 0 0 0 0 0 0 0 3 1 1 0 6 0 0 6 8 0 1 0 t 0 0 0 0 0 0 0 1 2 5 16 0 16 16 11 0 8 14 12
MA0047.2_rc_shift0 (Foxa2_rc)		0.858	0.406	1.015	-0.082	0.912	1.255	0.930	56	146	133	136	79	49	54	93.286	96	; dyads_m1 versus MA0047.2_rc (Foxa2_rc); m=2/2; ncol2=12; w=9; offset=-3; strand=R; shift=0; score=93.2857; ccwrwGTAAAYA------- ; cor=0.858; Ncor=0.406; logoDP=1.015; NIcor=-0.082; NsEucl=0.912; SSD=1.255; NSW=0.930; rcor=56; rNcor=146; rlogoDP=133; rNIcor=136; rNsEucl=79; rSSD=49; rNSW=54; rank_mean=93.286; match_rank=96 a 189 140 360 436 391 81 3 634 769 806 3 805 0 0 0 0 0 0 0 c 290 482 24 58 3 2 67 175 36 1 582 1 0 0 0 0 0 0 0 g 195 53 6 265 77 725 4 1 3 1 3 1 0 0 0 0 0 0 0 t 129 131 417 50 338 2 736 1 1 1 221 1 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 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_m3_shift3 (oligos_7nt_mkv5_m3)																		; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=3; ncol=15; ---wtATTTTTAww- ; Alignment reference a 0 0 0 185 133 557 0 6 5 7 1 557 196 213 0 c 0 0 0 88 130 0 0 0 1 1 0 0 95 90 0 g 0 0 0 103 105 0 0 2 1 1 0 0 81 94 0 t 0 0 0 181 189 0 557 549 550 548 556 0 185 160 0
MA0465.1_rc_shift7 (CDX2_rc)		0.864	0.403	0.857	-0.052	0.895	1.083	0.923	48	150	136	134	123	36	74	100.143	101	; oligos_7nt_mkv5_m3 versus MA0465.1_rc (CDX2_rc); m=1/4; ncol2=11; w=7; offset=4; strand=R; shift=7; score=100.143; -------tTTTATkr ; cor=0.864; Ncor=0.403; logoDP=0.857; NIcor=-0.052; NsEucl=0.895; SSD=1.083; NSW=0.923; rcor=48; rNcor=150; rlogoDP=136; rNIcor=134; rNsEucl=123; rSSD=36; rNSW=74; rank_mean=100.143; match_rank=101 a 0 0 0 0 0 0 0 121 0 0 0 1597 0 68 549 c 0 0 0 0 0 0 0 313 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 150 0 0 0 0 0 832 1048 t 0 0 0 0 0 0 0 1013 1597 1597 1597 0 1597 697 0
MA0497.1_rc_shift1 (MEF2C_rc)		0.803	0.589	0.422	-0.185	0.909	2.017	0.908	99	41	143	147	92	118	106	106.571	115	; oligos_7nt_mkv5_m3 versus MA0497.1_rc (MEF2C_rc); m=2/4; ncol2=15; w=11; offset=-2; strand=R; shift=1; score=106.571; -wkCTATTTTTrgmh ; cor=0.803; Ncor=0.589; logoDP=0.422; NIcor=-0.185; NsEucl=0.909; SSD=2.017; NSW=0.908; rcor=99; rNcor=41; rlogoDP=143; rNIcor=147; rNsEucl=92; rSSD=118; rNSW=106; rank_mean=106.571; match_rank=115 a 0 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752 c 0 126 148 1671 32 0 4 2 87 241 74 0 78 822 573 g 0 450 836 120 0 62 0 0 0 32 256 985 1412 196 151 t 0 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733
MA0052.2_rc_shift0 (MEF2A_rc)		0.792	0.581	2.732	0.021	0.905	2.206	0.900	108	43	121	126	108	131	118	107.857	118	; oligos_7nt_mkv5_m3 versus MA0052.2_rc (MEF2A_rc); m=3/4; ncol2=15; w=11; offset=-3; strand=R; shift=0; score=107.857; rdkCTATTTTTrGmh ; cor=0.792; Ncor=0.581; logoDP=2.732; NIcor=0.021; NsEucl=0.905; SSD=2.206; NSW=0.900; rcor=108; rNcor=43; rlogoDP=121; rNIcor=126; rNsEucl=108; rSSD=131; rNSW=118; rank_mean=107.857; match_rank=118 a 476 424 142 33 1 1467 83 116 51 346 119 1000 146 530 465 c 203 110 112 1160 0 0 0 0 39 119 14 0 32 625 379 g 449 409 632 49 0 0 0 5 0 0 68 473 1179 149 148 t 345 530 587 231 1472 6 1390 1352 1383 1008 1272 0 116 169 481
MA0151.1_rc_shift8 (ARID3A_rc)		0.754	0.411	4.276	0.275	0.849	1.647	0.863	150	142	111	119	151	81	149	129.000	147	; oligos_7nt_mkv5_m3 versus MA0151.1_rc (ARID3A_rc); m=4/4; ncol2=6; w=6; offset=5; strand=R; shift=8; score= 129; --------TTTrAT- ; cor=0.754; Ncor=0.411; logoDP=4.276; NIcor=0.275; NsEucl=0.849; SSD=1.647; NSW=0.863; rcor=150; rNcor=142; rlogoDP=111; rNIcor=119; rNsEucl=151; rSSD=81; rNSW=149; rank_mean=129.000; match_rank=147 a 0 0 0 0 0 0 0 0 6 0 0 17 27 0 0 c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 t 0 0 0 0 0 0 0 0 20 27 27 1 0 27 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_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_m3_shift0 (oligos_6nt_mkv4_m3)																		; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wsAGACCAgm ; Alignment reference a 164 115 526 0 527 0 0 527 123 194 c 79 143 1 0 0 527 524 0 99 134 g 116 145 0 527 0 0 3 0 181 79 t 168 124 0 0 0 0 0 0 124 120
MA0095.1_shift4 (YY1)		0.751	0.451	5.399	0.419	0.855	1.509	0.874	151	114	100	98	150	69	142	117.714	135	; oligos_6nt_mkv4_m3 versus MA0095.1 (YY1); m=1/1; ncol2=6; w=6; offset=4; strand=D; shift=4; score=117.714; ----rCCATc ; cor=0.751; Ncor=0.451; logoDP=5.399; NIcor=0.419; NsEucl=0.855; SSD=1.509; NSW=0.874; rcor=151; rNcor=114; rlogoDP=100; rNIcor=98; rNsEucl=150; rSSD=69; rNSW=142; rank_mean=117.714; match_rank=135 a 0 0 0 0 6 0 0 17 0 3 c 0 0 0 0 1 16 17 0 0 8 g 0 0 0 0 7 0 0 0 0 3 t 0 0 0 0 3 1 0 0 17 3